[{"hash":"828157998935534305","title":"Gene Expression Regulation and DNA Maintenance in Development","description":"These proteins show strong enrichment for DNA-templated transcription, DNA replication, and DNA repair, indicating core nuclear activities. They also include terms tied to gene expression regulation and numerous development-related processes (multicellular organism development, skeletal system development, Wnt signaling modulation), suggesting a role in developmental gene regulation. Some terms reflect stress responses (cellular response to cadmium, neutrophil clearance), which may be peripheral to the main theme but reflect broader regulatory networks. Overall, the cluster seems centered on transcriptional control and genomic maintenance within developmental contexts.","confidence":"Medium","size":29,"edges":341,"triangles":2361,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":18},{"id":"GO:0006349","count":14},{"id":"GO:0045819","count":12},{"id":"GO:0090090","count":12},{"id":"GO:0097350","count":12}]},{"hash":"2072349399935995012","title":"Innate Immune NF-kappaB Signaling and Cytokine Production","description":"This cluster is dominated by innate immunity and antiviral defense terms, especially NF-kappaB signaling. It also includes responses to dsRNA, LPS, and cytokine production (IL-6, IFN-beta), consistent with a shared role in activating inflammatory responses to pathogens.","confidence":"High","size":29,"edges":299,"triangles":1586,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045087","count":8},{"id":"GO:0051092","count":8},{"id":"GO:0043123","count":8},{"id":"GO:0051607","count":7},{"id":"GO:0043330","count":7}]},{"hash":"660503305782782228","title":"Mitotic Cell Cycle Machinery","description":"The dominant GO terms are cell division and mitotic cell cycle, with additional related terms like protein heterooligomerization and steroid hormone receptor complex assembly that can be part of mitotic machinery. Although some plant- or immune-related terms appear, the strongest and most frequent signals point to components involved in cell division and mitosis, justifying a label focused on the cell cycle machinery.","confidence":"Medium","size":29,"edges":201,"triangles":300,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":22},{"id":"GO:0000278","count":18},{"id":"GO:0051291","count":15},{"id":"GO:0006463","count":14},{"id":"GO:1903071","count":14}]},{"hash":"467009388899640396","title":"Neural development and signaling integration","description":"This cluster shows strong enrichment for neural development terms (cerebellum development, cerebral cortex development, motor neuron axon guidance) alongside broad signaling pathway terms (insulin receptor signaling, T cell receptor signaling, B cell receptor signaling, integrin-mediated signaling) and DNA-templated transcription/replication, suggesting a module of proteins coordinating gene expression with signaling cues during neural development, with cross-talk to immune signaling.","confidence":"Medium","size":29,"edges":125,"triangles":166,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":12},{"id":"GO:0008286","count":10},{"id":"GO:0050852","count":10},{"id":"GO:0007229","count":10},{"id":"GO:0050853","count":10}]},{"hash":"1537385130715835176","title":"Developmental gene expression and stress-response cluster","description":"The cluster centers on gene expression regulation and development, with GO terms for DNA-templated transcription, mRNA splicing, regulation of gene expression, and multicellular development (including skeletal system development). It also features stress and defense signals (cadmium response, defense against Gram-positive bacteria) and signaling dynamics (positive regulation of GTPase activity) that can impact cell cycle and growth (mitotic cell cycle, invasive growth under nutrient limitation). Together, these terms suggest a cohesive theme around developmental transcriptional control coupled with cellular stress responses.","confidence":"Medium","size":29,"edges":76,"triangles":39,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0071276","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0007275","count":9},{"id":"GO:0001501","count":8}]},{"hash":"1530889551308836124","title":"Innate immune recognition and leukocyte trafficking","description":"The cluster is dominated by terms for phagocytosis recognition, lectin-mediated complement activation, and leukocyte tethering/rolling, plus C-type lectin receptor signaling, pointing to innate immune activation and recruitment of immune cells. Some development-related terms are present but secondary.","confidence":"High","size":29,"edges":46,"triangles":30,"max_degree":9,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006910","count":25},{"id":"GO:0001502","count":21},{"id":"GO:0001867","count":20},{"id":"GO:0072177","count":19},{"id":"GO:0072218","count":19}]},{"hash":"280386938344094108","title":"Innate Immune Signaling and Cytoskeletal Dynamics","description":"The cluster is dominated by innate immune signaling terms, notably NOD2 signaling and NF-kappaB regulation, and is strongly linked to cytoskeletal remodeling, with actin filament bundle assembly and cell migration as prominent terms, plus a cellular response to mechanical stimulus. While telomere maintenance terms appear, the core pattern connects immune signal transduction with cytoskeletal dynamics and motility.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0070431","count":7},{"id":"GO:0032088","count":7},{"id":"GO:0071260","count":7},{"id":"GO:2001275","count":6},{"id":"GO:0007205","count":6}]},{"hash":"93117537172408209","title":"Postsynaptic actin remodeling with mitochondrial localization","description":"This cluster is dominated by actin cytoskeleton dynamics terms, including Arp2/3-mediated actin nucleation, patch and filament bundle assembly, and postsynaptic actin cytoskeleton organization, indicating robust actin remodeling at synapses. The presence of mitochondrial localization and inheritance terms suggests coordination between cytoskeletal remodeling and mitochondrial positioning. Retina homeostasis points to a neural-retinal context, while phagocytosis and aging terms may reflect broader maintenance roles. Overall, the central theme is actin-driven synaptic structural dynamics linked to organelle localization.","confidence":"High","size":29,"edges":406,"triangles":3654,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0001895","count":29},{"id":"GO:0000147","count":29},{"id":"GO:0051017","count":29},{"id":"GO:0098974","count":29},{"id":"GO:0002121","count":29}]},{"hash":"1953350304638633842","title":"Gene Expression and Cell Cycle Regulation","description":"These proteins cluster around processes tied to gene expression control and cell cycle dynamics, including transcription regulation during G1/S, translation, circadian regulation of gene expression, and general cell cycle processes. While some terms touch on differentiation and development (fat cell differentiation, ureteric bud morphogenesis, pregnancy), the common thread appears to be regulation of gene expression and proliferation. The absence of edges suggests a broad or functionally diverse set, but the shared GO themes justify a cohesive label focused on expression regulation and cell cycle.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006412","count":2}]},{"hash":"1039357995167258303","title":"Brain and craniofacial organogenesis","description":"The cluster is enriched for embryonic development terms spanning neural crest\u2013driven craniofacial formation (neural crest migration, palate development, tooth/dentin formation) and brain region development (hypothalamus, habenula), plus broader organogenesis like pancreas and digestive tract morphogenesis, indicating a cohesive theme of embryonic morphogenesis across neural crest derivatives and brain/craniofacial structures.","confidence":"High","size":29,"edges":406,"triangles":3654,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001755","count":22},{"id":"GO:0090190","count":22},{"id":"GO:0000122","count":22},{"id":"GO:0031018","count":22},{"id":"GO:0048557","count":22}]},{"hash":"113500867323368561","title":"Embryonic development and organ morphogenesis","description":"The cluster is dominated by GO terms related to early development and tissue formation, including mesoderm development, inner cell mass proliferation, embryonic organ development, stem cell maintenance, multicellular growth, and organ morphogenesis, pointing to a cohesive theme of embryogenesis and organ formation. A few terms about DNA repair/division are present but less central to the core theme.","confidence":"High","size":29,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0032957","count":2},{"id":"GO:0019827","count":2},{"id":"GO:0001833","count":2},{"id":"GO:0009887","count":2}]},{"hash":"126025945480868341","title":"Hormonal and Chemical Stress Response","description":"The top GO terms are dominated by responses to chemical and external stimuli (xenobiotic stimulus, lipopolysaccharide, ethanol, corticosterone), indicating a primary theme of chemical stress response. Additional terms point to metabolic and endocrine ties (thiamine biosynthesis, dopamine catabolic process, pituitary gland development), suggesting the cluster integrates hormonal signaling with stress/metabolic regulation. ","confidence":"Medium","size":29,"edges":46,"triangles":36,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0009228","count":6},{"id":"GO:0042493","count":5},{"id":"GO:0032496","count":5},{"id":"GO:0051573","count":5}]},{"hash":"830281737120825442","title":"Ubiquitin-Proteasome Regulation of Signaling","description":"The cluster is enriched for ubiquitin-proteasome\u2013related terms (SCF-dependent ubiquitin-protein catabolic process and ubiquitin-dependent protein catabolic process) alongside intracellular signal transduction and transcription regulation. Additional terms like fat cell differentiation and regulation of circadian rhythm suggest links to metabolism and temporal control of signaling. Together, these points indicate proteins that regulate signaling and transcription through ubiquitin-mediated degradation rather than a single linear pathway.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":9},{"id":"GO:0031146","count":8},{"id":"GO:0070431","count":7},{"id":"GO:0045444","count":7},{"id":"GO:0035556","count":7}]},{"hash":"1883413915474789055","title":"Neurodevelopment and synaptic signaling","description":"In this cluster, the strongest themes are neural development and synaptic function: axonogenesis, Schwann cell development, excitatory postsynaptic potentials, and long-term potentiation, along with visual perception. These point to a cohort of proteins involved in neuronal growth, differentiation, and synaptic plasticity. The presence of cell cycle terms (G2/M transition, mitotic cell cycle) and apoptotic regulation likely reflects roles during neural/Glial development or shared signaling components in developmental contexts, rather than a single non-neural pathway. Overall, the cluster centers on neurodevelopmental and synaptic processes with some ancillary cell-cycle signals.","confidence":"Medium","size":29,"edges":85,"triangles":205,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":28},{"id":"GO:0060079","count":28},{"id":"GO:0000086","count":28},{"id":"GO:0014044","count":28},{"id":"GO:0007409","count":28}]},{"hash":"1437234937848908951","title":"Rho-regulated actin and synaptic signaling","description":"Enriched terms point to coordination between Rho-driven actin remodeling and synaptic signaling in neurons, with proteins localizing to synapses and participating in guanylyl cyclase pathways. Behavioral GO terms (grooming/exploration) hint at neural function. Together these terms suggest a cluster of neuronal cytoskeletal regulators and synaptic signaling components.","confidence":"High","size":29,"edges":365,"triangles":2731,"max_degree":28,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0035023","count":21},{"id":"GO:0030036","count":21},{"id":"GO:0007605","count":21},{"id":"GO:0006470","count":21},{"id":"GO:0090630","count":21}]},{"hash":"1462265106498253473","title":"Bacterial LPS and O-antigen biosynthesis","description":"The cluster is enriched for lipopolysaccharide biosynthetic processes, including core and O-antigen-related steps, plus sugar-nucleotide biosynthesis (dTDP-rhamnose, UDP-N-acetylglucosamine) and PHB biosynthesis, pointing to bacterial envelope polysaccharide assembly and related pathways.","confidence":"High","size":29,"edges":187,"triangles":530,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0006541","count":10},{"id":"GO:0009103","count":8},{"id":"GO:0042619","count":8},{"id":"GO:0009244","count":7}]},{"hash":"1173907963346276039","title":"Embryonic development and organogenesis","description":"These terms indicate a developmental/organogenesis theme, spanning placental lineage, skeletal/cartilaginous morphogenesis, left-right patterning, and heart-associated EMT; a few generic transcription terms are present but do not outweigh the developmental signal.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060806","count":5},{"id":"GO:0060972","count":5},{"id":"GO:0035270","count":5}]},{"hash":"1546765208906714481","title":"Endothelial Lipid Transport and Activation","description":"The cluster\u2019s top GO terms are dominated by endothelial processes (endothelial cell activation) and lipid handling (lipoprotein metabolic process and lipid transport), with multiple transmembrane transport terms for various metabolites. This points to a cohesive function in lipid transport/metabolism within endothelial cells, possibly linked to activation states. The combination suggests a role in vascular lipid handling and endothelial signaling.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042118","count":7},{"id":"GO:0042157","count":7},{"id":"GO:0006869","count":7},{"id":"GO:0010917","count":2},{"id":"GO:0030974","count":2}]},{"hash":"2071586130557748546","title":"Brain Development and Cell Adhesion","description":"This cluster is anchored by brain morphogenesis and pyramidal neuron development terms, alongside cell adhesion and epithelial integrity processes, suggesting proteins involved in neural development with roles in tissue adhesion and barrier maintenance. The boron-related and symbiont-entry terms appear as less central outliers. ","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0048854","count":6},{"id":"GO:0034113","count":5},{"id":"GO:0046718","count":5},{"id":"GO:0035160","count":5},{"id":"GO:0034446","count":5}]},{"hash":"111892228562400247","title":"Unknown","description":"The terms span olfactory development, immune defense, signaling, synapse formation, adhesion, and bone maturation, with no single cohesive biological theme tying the cluster together. This heterogeneity makes a meaningful, specific label unreliable.","confidence":"","size":29,"edges":17,"triangles":1,"max_degree":4,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0021628","count":9},{"id":"GO:0071699","count":9},{"id":"GO:0042742","count":9},{"id":"GO:0051965","count":8},{"id":"GO:0070374","count":8}]},{"hash":"2161490745103043351","title":"Neural axon guidance and complement activation","description":"This cluster prominently features neuron development terms (axon guidance, sympathetic and branchiomotor neuron projection guidance, trigeminal nerve organization, semaphorin-plexin signaling) along with immune-related terms (proteolysis, complement activation via lectin and classical pathways). The combination suggests a theme around developmental remodeling where innate immune processes participate in neural patterning and axon pathfinding, which aligns with emerging roles of complement in synaptic pruning and neural circuit refinement. While some terms relate to broader development, the neural guidance terms anchor the cluster around nervous system development with immune signaling as a contributing facet.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":5},{"id":"GO:0001867","count":4},{"id":"GO:0006958","count":4},{"id":"GO:0014068","count":4},{"id":"GO:0001501","count":4}]},{"hash":"1859197174387754916","title":"Immune\u2013Endothelial Signaling Cluster","description":"The top terms are mainly immune-related (immunoglobulin production, plasma cell differentiation, defense response to virus) and endothelial/vascular (endothelial morphogenesis, regulation of endothelial proliferation), suggesting a cluster of proteins linking immune activity to vascular biology. Some terms (spermatid development, neuron projection regulation) seem less connected and may be outliers, but the core theme points to immune function with vascular context.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002377","count":3},{"id":"GO:0007286","count":3},{"id":"GO:0051607","count":2},{"id":"GO:0007585","count":2},{"id":"GO:0002317","count":2}]},{"hash":"1606318195172402859","title":"Innate immune signaling and actin remodeling","description":"This cluster centers on innate immune functions (defense response to bacterium, innate immune response, regulation of macrophage and NK/T cell activities) and cytoskeletal/cell\u2013adhesion processes (actin cytoskeleton organization, cell\u2013cell adhesion, synapse assembly). The co-occurrence of immune signaling terms with cytoskeletal remodeling suggests proteins that coordinate immune cell activation with cytoskeletal rearrangements during immune synapse formation and pathogen response.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0001501","count":11},{"id":"GO:0042742","count":11},{"id":"GO:0045087","count":11},{"id":"GO:0051963","count":8},{"id":"GO:0043031","count":8}]},{"hash":"376260850654177104","title":"Ion and nutrient transmembrane transporters","description":"Most top GO terms describe transmembrane transport activities for ions (Na+, K+, phosphate, nitrate) and various substrates (galactose, fucose, vitamins) as well as related metabolic processes. This pattern suggests a cluster of membrane transporter proteins specialized in moving diverse nutrients and ions across membranes, hence the name Ion and nutrient transmembrane transporters.","confidence":"High","size":29,"edges":274,"triangles":1409,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":29},{"id":"GO:0071805","count":29},{"id":"GO:0035435","count":27},{"id":"GO:1900754","count":27},{"id":"GO:0015757","count":27}]},{"hash":"99805199373532694","title":"Cardiac Electrical Activity and Ion Transport","description":"This cluster is dominated by GO terms tied to cardiac electrophysiology: atrial membrane repolarization, cardiac action potentials involved in contraction, potassium ion transport/import, and regulation of heart rate via cardiac conduction, along with regulation of resting membrane potential and calcium signaling. A mechanosensation term appears but is secondary; overall the annotations point to ion channels/transport and signaling that govern cardiac excitability and rhythm. Therefore, the label Cardiac Electrical Activity and Ion Transport best captures the core function of these proteins.","confidence":"High","size":29,"edges":44,"triangles":73,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098914","count":28},{"id":"GO:1990573","count":26},{"id":"GO:0086002","count":26},{"id":"GO:0086091","count":26},{"id":"GO:0050976","count":25}]},{"hash":"1533452957267772917","title":"Neuroimmune\u2013dopaminergic signaling","description":"This cluster blends immune-regulatory terms (negative regulation of inflammatory response, immune response, eosinophil chemotaxis, xenobiotic response) with neural/glial and dopaminergic terms (astrocyte chemotaxis, glial-derived neurotrophic factor production, dopamine transport, dopamine metabolism, PLC-activating dopamine receptor signaling). The combination points to a cohesive theme of neuroimmune interactions modulating dopaminergic signaling in the CNS.","confidence":"High","size":29,"edges":144,"triangles":270,"max_degree":19,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":29},{"id":"GO:0042493","count":29},{"id":"GO:2000458","count":29},{"id":"GO:1900168","count":29},{"id":"GO:0048245","count":29}]},{"hash":"1379513297064463752","title":"Neuroimmune modulation of dopamine signaling","description":"The top GO terms point to immune/inflammatory regulation, astrocyte/glial biology, and dopaminergic processes (dopamine transport, dopamine metabolism, phospholipase C\u2011activating dopamine receptor signaling). This suggests a functional theme where neuroimmune interactions influence dopamine signaling and glial function, rather than a single enzymatic pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":29},{"id":"GO:0042493","count":29},{"id":"GO:2000458","count":29},{"id":"GO:1900168","count":29},{"id":"GO:0048245","count":29}]},{"hash":"779559473935029637","title":"Dopaminergic neuroimmune signaling","description":"The top GO terms point to dopamine transport and signaling (dopamine transport, regulation of dopamine metabolism, phospholipase C-activating dopamine receptor signaling) together with immune and glial/neural context (immune response, negative regulation of inflammatory response, astrocyte chemotaxis, glial-derived neurotrophic factor production). This suggests a coherent theme where dopaminergic signaling interfaces with neuroimmune/glial regulation, including astrocyte activity.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":29},{"id":"GO:0042493","count":29},{"id":"GO:2000458","count":29},{"id":"GO:1900168","count":29},{"id":"GO:0048245","count":29}]},{"hash":"927575487628095647","title":"Ribosome biogenesis and translation regulation in mitosis","description":"The GO terms point strongly to ribosome biogenesis, formation of translation preinitiation complex, translation reinitiation, and related translation processes, coupled with mitotic cell cycle and APC-dependent catabolic activity. This suggests a cohesive theme around the protein synthesis machinery and its coordination with cell division. Additional terms like ER to Golgi transport and peptidyl-serine dephosphorylation hint at broader regulatory layers in dividing cells but do not outweigh the core translation-centric signal. Some outliers (skeletal development, cadmium response) exist but are not defining for the cluster. ","confidence":"Medium","size":28,"edges":345,"triangles":2554,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070262","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0008283","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0000278","count":6}]},{"hash":"35905802689190263","title":"Wnt-driven neural development and cytoskeletal dynamics","description":"Based on the dominant GO terms, the cluster centers on neural development and synaptic function (substantia nigra development; canonical Wnt signaling; regulation of synaptic vesicle exocytosis). Additional terms point to cell polarity and barrier establishment and to actin cytoskeleton remodeling, implying an integrated role of signaling, polarity, and trafficking in neural and related tissues.","confidence":"Medium","size":28,"edges":341,"triangles":2454,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061028","count":28},{"id":"GO:0060070","count":28},{"id":"GO:2000300","count":28},{"id":"GO:0021762","count":28},{"id":"GO:0090162","count":28}]},{"hash":"1407348646915404211","title":"Organogenesis and tissue morphogenesis","description":"The top GO terms cluster around development across multiple tissues\u2014motor neuron axon guidance, heart and face development, placenta and maternal placenta development, and metanephric renal vesicle morphogenesis\u2014supported by cell-matrix adhesion. A few immune-related terms appear, but the dominant theme is organogenesis and tissue morphogenesis across nervous, cardiovascular, craniofacial, placental, and renal contexts. This suggests the proteins collectively participate in broad developmental morphogenesis rather than a single pathway.","confidence":"High","size":28,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008045","count":8},{"id":"GO:0007507","count":8},{"id":"GO:0060324","count":7},{"id":"GO:0001890","count":7},{"id":"GO:0071222","count":7}]},{"hash":"896187404124250887","title":"Meiosis and Germline Development","description":"These proteins cluster around meiotic chromosome dynamics and germline development, with terms like homologous chromosome pairing at meiosis, spindle assembly and localization, pronuclear fusion, oogenesis, telomere localization, and chromosome localization to the nuclear envelope during segregation. Although rhabdomere development appears, the predominant signal is meiotic chromosome behavior and germ cell formation, suggesting the cluster reflects meiosis-associated processes and germline development.","confidence":"High","size":28,"edges":57,"triangles":49,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042052","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0034397","count":2},{"id":"GO:0090220","count":2}]},{"hash":"676140384852826724","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000472","count":15},{"id":"GO:0000462","count":15},{"id":"GO:0000480","count":15},{"id":"GO:0000463","count":14},{"id":"GO:0000466","count":14}]},{"hash":"1980025759838400329","title":"Developmental transcription and RNA processing","description":"This cluster centers on core gene expression regulation, with strong signals for DNA-templated transcription and mRNA splicing, plus ubiquitin-proteasome\u2013mediated protein turnover. In addition, several terms point to developmental processes (neural tube closure, forebrain development, skeletal system development), suggesting proteins involved in regulating transcription/splicing during development. Confidence: Medium","confidence":"","size":28,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":12},{"id":"GO:0000398","count":10},{"id":"GO:0031146","count":10},{"id":"GO:0001843","count":10},{"id":"GO:0030900","count":10}]},{"hash":"335986059881400087","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by ribosome biogenesis, ribosomal subunit export from the nucleus, cytoplasmic translation, and tRNA modification, indicating a shared function in ribosome assembly and protein synthesis. Cell cycle and cell division terms are also present, suggesting potential coordination with growth, but the core signal remains ribosome-related.","confidence":"High","size":28,"edges":110,"triangles":200,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":13},{"id":"GO:0007049","count":10},{"id":"GO:0090529","count":8},{"id":"GO:0000055","count":8},{"id":"GO:1901001","count":8}]},{"hash":"337975536368333752","title":"ESCRT-MVB Sorting and Viral Budding","description":"The cluster is dominated by GO terms tied to ESCRT-dependent vesicle trafficking, including multivesicular body assembly, ubiquitin-mediated sorting via the MVB pathway, and viral budding and life cycle, suggesting a cohesive module of host vesicle trafficking components co-opted by viruses, with additional links to Golgi retention and ER targeting.","confidence":"High","size":28,"edges":322,"triangles":2211,"max_degree":27,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:1904669","count":9},{"id":"GO:1902188","count":9},{"id":"GO:0036258","count":9},{"id":"GO:0043162","count":9}]},{"hash":"297240941409839012","title":"Embryonic organogenesis and placental/heart development","description":"The GO terms cluster around early development and organ formation, including placenta differentiation, heart development, cartilage and limb morphogenesis, and other embryonic patterning processes. This suggests the proteins function in embryogenesis and organogenesis, with notable emphasis on placental and cardiac development.","confidence":"High","size":28,"edges":6,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":8},{"id":"GO:0060536","count":8},{"id":"GO:0060972","count":8},{"id":"GO:0035270","count":8},{"id":"GO:0003323","count":8}]},{"hash":"558855091825537642","title":"Ubiquitin-Dependent Proteostasis and Antiviral Autophagy","description":"The top GO terms cluster around ubiquitination (protein autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent protein catabolic process, actin ubiquitination), autophagy, and antiviral/immune responses (defense response to virus, regulation of signaling pathways related to LPS). This suggests a cohesive theme of ubiquitin-driven protein turnover and autophagic processes contributing to antiviral defense and regulation of cellular transport during infection.","confidence":"High","size":28,"edges":9,"triangles":4,"max_degree":5,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":23},{"id":"GO:1901253","count":23},{"id":"GO:1903762","count":23},{"id":"GO:0051607","count":21},{"id":"GO:0070534","count":21}]},{"hash":"1646570979628668306","title":"Developmental morphogenesis and GTPase signaling","description":"This cluster includes proteins tied to diverse organogenesis processes (eye eyelid, face, cerebellum, heart structures) and prominently features GTPase-related signaling (Rap and Rho pathways, GTPase activation, serine phosphorylation). The shared theme appears to be regulators of developmental morphogenesis operating through small GTPase signaling. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0061029","count":6},{"id":"GO:0090630","count":5},{"id":"GO:0060324","count":5},{"id":"GO:0032486","count":4},{"id":"GO:0033138","count":4}]},{"hash":"985893997412920169","title":"Developmental transcriptional regulation and ER-stress signaling","description":"This cluster is dominated by RNA Pol II\u2013dependent transcription terms, plus several development-related processes (placenta, ring gland, salivary gland development; osteoblast differentiation). The inclusion of an intrinsic apoptotic pathway in response to ER stress further points to a theme of transcriptional control during development coupled with cellular stress responses. Some immune-related/obsolete terms are present but do not define the core pattern. ","confidence":"Medium","size":28,"edges":170,"triangles":622,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":16},{"id":"GO:0071353","count":13},{"id":"GO:0001892","count":12},{"id":"GO:0035271","count":12},{"id":"GO:0070059","count":12}]},{"hash":"1098698212122688233","title":"Cardiovascular and adipocyte differentiation","description":"The proteins in this cluster are enriched for heart development and fat cell differentiation, suggesting a developmental program spanning cardiovascular and adipose lineages. Supporting terms for cell migration, cell cycle, and intracellular signaling indicate broader regulatory roles in differentiation and tissue remodeling, with ubiquitination reflecting common post-translational control.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":7},{"id":"GO:0045444","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0010745","count":6},{"id":"GO:0016477","count":5}]},{"hash":"98763785364363346","title":"Neuronal Synaptic Signaling and Plasticity","description":"This cluster centers on neuronal communication and plasticity, with strong signals for regulation of synaptic vesicle exocytosis, long-term potentiation, brain development, and dopamine secretion. The presence of calcium- and GTPase/Rho-signaling regulation further ties these proteins to synaptic transmission and activity-dependent plasticity, suggesting a coherent theme of neural signaling and development.","confidence":"High","size":28,"edges":73,"triangles":22,"max_degree":21,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0010796","count":23},{"id":"GO:0031384","count":23},{"id":"GO:2000300","count":22},{"id":"GO:0060291","count":21},{"id":"GO:0035023","count":21}]},{"hash":"635241932854725839","title":"Stress-Responsive mRNA Stability and Translation Regulation","description":"This cluster appears to group proteins involved in post-transcriptional control: regulation of mRNA stability in response to stress, mRNA stabilization, regulation of translational initiation, formation of translation preinitiation complexes, translation reinitiation, and miRNA- and ncRNA-mediated gene silencing. The co-occurrence of these terms points to a shared theme of controlling gene expression at the RNA level under stress, coordinating RNA processing with translation control. Overall, the dominant signal is RNA stability and translational regulation in stress.","confidence":"High","size":28,"edges":374,"triangles":3176,"max_degree":27,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":28},{"id":"GO:0048255","count":17},{"id":"GO:0001825","count":17},{"id":"GO:0006446","count":17},{"id":"GO:1900363","count":17}]},{"hash":"33934834262903559","title":"Rho- and integrin-mediated cytoskeletal remodeling in development","description":"This cluster centers on Rho signaling, integrin activation, and actin dynamics, including filopodium assembly, indicating coordinated cytoskeletal remodeling and cell adhesion during development. The neural and odontogenesis terms suggest broader morphogenetic roles beyond a single tissue.","confidence":"High","size":28,"edges":18,"triangles":5,"max_degree":6,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0035023","count":8},{"id":"GO:0033622","count":6},{"id":"GO:0045792","count":6},{"id":"GO:0031532","count":6},{"id":"GO:0033623","count":6}]},{"hash":"1318793374368899661","title":"Embryonic Development and Morphogenesis","description":"The top GO terms cluster around embryogenesis and tissue morphogenesis (trophoblast giant cell differentiation, cartilage morphogenesis, left/right pattern formation, endocrine system development, pancreatic cell development, and placental-related differentiation), suggesting these proteins function in developmental patterning and organ formation; a few RNA-processing terms appear but are secondary to the main developmental theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":9},{"id":"GO:0060536","count":9},{"id":"GO:0060972","count":9},{"id":"GO:0035270","count":9},{"id":"GO:0003323","count":9}]},{"hash":"1203143334183904662","title":"Auditory and vestibular sensory transduction","description":"The top GO terms cluster around calcium ion transmembrane transport and sensory functions related to hearing and balance, including detection of mechanical stimuli in sound, auditory receptor cell development, and vestibular reflex. While there are some terms related to cell junctions and immune signaling, the dominant theme is inner-ear sensory transduction and calcium-dependent signaling essential for hearing and balance. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070588","count":3},{"id":"GO:0032060","count":3},{"id":"GO:2001199","count":3},{"id":"GO:0038095","count":3},{"id":"GO:0070830","count":3}]},{"hash":"1808566196886007174","title":"Embryogenesis and organ formation","description":"The cluster is dominated by GO terms for developmental processes across multiple tissues\u2014placental/trophoblast differentiation, cartilage morphogenesis, left-right patterning, endocrine system development, and EMT-related heart formation\u2014indicating a common theme of embryogenesis and organogenesis rather than a specific pathway.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060972","count":5},{"id":"GO:0035270","count":5},{"id":"GO:0003323","count":5}]},{"hash":"1133096924078673944","title":"Neural development and ER remodeling","description":"The cluster shows clear emphasis on neural development processes (axonal fasciculation, radial glia-guided migration, cortical development) together with substantial ER organization/remodeling signals (ER tubular network formation/organization), plus related cellular processes like nuclear pore assembly. This combination suggests proteins coordinating neural development with ER dynamics as a common theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060317","count":3},{"id":"GO:0032581","count":3},{"id":"GO:0006694","count":3},{"id":"GO:0007413","count":3},{"id":"GO:1990809","count":3}]},{"hash":"1877847345811753527","title":"Embryonic development and tissue morphogenesis","description":"The GO terms cluster around developmental processes across multiple tissues: placental differentiation, cartilage morphogenesis, left-right patterning, endocrine and pancreatic development, and EMT in cardiac cushion formation. While one term relates to photoreceptor membrane potential, the overall signal is a suite of embryonic development and tissue patterning functions, suggesting proteins involved in broad developmental differentiation rather than a single pathway. Confidence: Medium","confidence":"","size":28,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016058","count":1},{"id":"GO:0060707","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0035270","count":1}]},{"hash":"2133023759565126799","title":"Placental and embryonic morphogenesis","description":"The dominant GO terms cluster around placental development (trophoblast giant cell differentiation) and broad embryonic morphogenesis (left-right patterning, palate, heart cushion formation, cartilage), with additional endocrine and pancreatic development and transcriptional regulation terms, suggesting these proteins participate in embryogenesis with a focus on placental formation and tissue patterning.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":25},{"id":"GO:0060536","count":25},{"id":"GO:0060806","count":25},{"id":"GO:0060972","count":25},{"id":"GO:0035270","count":25}]},{"hash":"1479218828953105889","title":"Neural signaling and membrane-domain organization","description":"These proteins appear to cluster around neural function (myelination, sensory perception of sound, regulation of synaptic plasticity) with components related to barrier integrity (tight junctions, endothelial barrier). The presence of membrane-domain terms (eisosome assembly, membrane raft polarization) suggests a shared role in organizing membranes, which is important for neural signaling and barrier properties. The mix of signaling regulation terms (PKC, extrinsic apoptotic signaling) supports a theme of signaling control in neural and barrier contexts. Overall, the cluster seems best described as neural signaling linked to membrane-domain organization and barrier function.","confidence":"Medium","size":28,"edges":134,"triangles":263,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0042552","count":11},{"id":"GO:0070830","count":10},{"id":"GO:0061028","count":8},{"id":"GO:0007605","count":8},{"id":"GO:0050861","count":8}]},{"hash":"106400658572525395","title":"Innate Immune Response and Coagulation Signaling","description":"This cluster is dominated by GO terms related to innate immune activation and inflammation, including complement activation (classical pathway), Toll signaling, LPS response, and IL-1\u03b2 production, as well as coagulation-related processes such as Factor XII activation. These themes suggest a functional grouping around innate immune defense and coagulation cross-talk, with some additional broad signaling terms (Wnt, GPCR-PLC) that are less central. Overall, a cohesive interpretation centers on immune and coagulation signaling, hence this name. ","confidence":"Medium","size":28,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":28},{"id":"GO:0003050","count":28},{"id":"GO:0042127","count":27},{"id":"GO:1900738","count":27},{"id":"GO:0002542","count":27}]},{"hash":"870532843884505113","title":"Neuroimmune regulation and dopamine signaling","description":"The cluster combines immune-related terms (immune response, negative regulation of inflammatory response, eosinophil and xenobiotic responses) with neural/glial terms (astrocyte chemotaxis, glial-derived neurotrophic factor production) and clear dopamine-related terms (dopamine transport, metabolism, and receptor signaling), suggesting a cohesive theme of neuroimmune interactions modulated through dopaminergic pathways.","confidence":"High","size":28,"edges":10,"triangles":3,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":28},{"id":"GO:0042493","count":28},{"id":"GO:2000458","count":28},{"id":"GO:1900168","count":28},{"id":"GO:0048245","count":28}]},{"hash":"1481889194638575966","title":"Dopaminergic signaling and neuroimmune regulation","description":"This cluster centers on dopamine-related processes (dopamine transport, regulation of dopamine metabolism, and a phospholipase C-activating dopamine receptor signaling pathway) alongside immune and glial-related functions (immune response, negative regulation of inflammatory response, astrocyte/glial cell chemotaxis, and glial-derived neurotrophic factor production). The co-occurrence of neural signaling with glial/immune regulatory terms suggests a cohesive theme of neuroimmune modulation involving dopamine pathways. The xenobiotic response term further supports a broader neural-immune stress response context. Confidence: High","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":28},{"id":"GO:0042493","count":28},{"id":"GO:2000458","count":28},{"id":"GO:1900168","count":28},{"id":"GO:0048245","count":28}]},{"hash":"1815924293666827058","title":"Dopaminergic Neuroimmune Regulation","description":"The cluster\u2019s GO terms converge on glial-immune functions (astrocyte chemotaxis, glial-derived neurotrophic factor production, immune response, negative regulation of inflammatory response) and dopaminergic signaling (dopamine transport, dopamine metabolism, dopamine receptor signaling), plus xenobiotic response. This suggests a coherent module where neuroimmune modulation in the brain interfaces with dopamine pathways, pointing to a neuroimmune-dopaminergic regulatory role.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":27},{"id":"GO:0042493","count":27},{"id":"GO:2000458","count":27},{"id":"GO:1900168","count":27},{"id":"GO:0048245","count":27}]},{"hash":"1276161028658132167","title":"Glial Immunomodulation and Dopamine Signaling","description":"The cluster shows strong alignment between glial/immune functions and dopaminergic signaling (immune response, astrocyte chemotaxis, dopamine transport and signaling), indicating a neuroimmune-dopamine functional module.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":28},{"id":"GO:0042493","count":28},{"id":"GO:2000458","count":28},{"id":"GO:1900168","count":28},{"id":"GO:0048245","count":28}]},{"hash":"1554406196108908137","title":"Glutamatergic Synaptic Plasticity and Memory Signaling","description":"This cluster centers on glutamatergic synaptic transmission and plasticity, including short-term memory and long-term regulation of synaptic strength, with receptor internalization as part of synaptic modulation and additional neuronal signaling responses such as ethanol effects.","confidence":"High","size":27,"edges":96,"triangles":200,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031623","count":7},{"id":"GO:0048169","count":7},{"id":"GO:0007614","count":7},{"id":"GO:0051966","count":7},{"id":"GO:0007626","count":6}]},{"hash":"1251907220368455386","title":"Chromatin remodeling and transcription regulation","description":"This cluster concentrates on chromatin remodeling, histone modification (e.g., H3K27 trimethylation), nucleosome assembly, and transcription by RNA Polymerase II, with additional signals for centrosome cycle and spermatid nucleus differentiation\u2014indicating coordinated chromatin-based control of gene expression and cell division.","confidence":"High","size":27,"edges":190,"triangles":781,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0043044","count":9},{"id":"GO:0051225","count":7},{"id":"GO:0098532","count":6},{"id":"GO:0007098","count":6}]},{"hash":"261574780192886167","title":"Chromatin dynamics and transcriptional regulation during differentiation","description":"This cluster centers on chromatin organization and remodeling (nucleosome assembly, chromatin remodeling, heterochromatin formation) and transcriptional control (negative regulation of RNA Pol II), with differentiation-related processes such as spermatid nucleus differentiation and granulocyte differentiation, plus cell-division context (spindle assembly, centrosome cycle). The common theme is chromatin dynamics guiding differentiation and gamete-related development.","confidence":"High","size":27,"edges":348,"triangles":2853,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051225","count":9},{"id":"GO:0006334","count":8},{"id":"GO:0000122","count":8},{"id":"GO:0043044","count":7},{"id":"GO:0000183","count":7}]},{"hash":"1149600132396236042","title":"Ciliogenesis and centriole biogenesis in multiciliated cells","description":"This cluster is dominated by GO terms related to centriole replication, de novo centriole assembly, and multiciliated epithelial cell differentiation, indicating a coherent centriole/centrosome\u2013mediated ciliogenesis program in multiciliated cells. Other terms such as B cell activation and CD40 signaling are less connected to the main theme, suggesting secondary or off-target associations.","confidence":"High","size":27,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007099","count":5},{"id":"GO:1903251","count":4},{"id":"GO:0098535","count":4},{"id":"GO:0000132","count":2},{"id":"GO:0030500","count":2}]},{"hash":"945349090274316134","title":"Rho-driven cytoskeletal remodeling in synapses and development","description":"The top GO terms cluster around Rho signaling and actin cytoskeleton remodeling, with links to receptor clustering, synaptic localization, and dendritic spine morphogenesis, plus heart development, indicating a theme of Rho-mediated cytoskeletal dynamics shaping synaptic structure and developmental processes.","confidence":"High","size":27,"edges":79,"triangles":87,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007266","count":18},{"id":"GO:0000278","count":17},{"id":"GO:0031532","count":17},{"id":"GO:0035023","count":17},{"id":"GO:0043113","count":16}]},{"hash":"618262928607307427","title":"Neuronal Development and Synaptic Regulation","description":"Top GO terms indicate neural development and synaptic function as the core theme (axonogenesis, substantia nigra development, Wnt signaling, Rab-mediated trafficking, synaptic vesicle exocytosis), with a secondary tie to neurovascular aspects via endothelial barrier establishment. This combination points to brain development and synaptic activity as the defining cluster function.","confidence":"Medium","size":27,"edges":221,"triangles":927,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050771","count":24},{"id":"GO:0032482","count":24},{"id":"GO:0061028","count":22},{"id":"GO:0060070","count":22},{"id":"GO:2000300","count":22}]},{"hash":"1895130800471082850","title":"Innate immune response and xenophagy","description":"This cluster is driven by GO terms related to host defense, including innate immune response, LPS signaling, dsRNA response, and positive regulation of xenophagy, with apoptosis also represented. These points together suggest coordination of pathogen recognition, immune signaling, and selective autophagy of microbes. Additional terms hint at related cellular activities such as cytoskeletal changes and regulatory signaling, but the dominant theme remains innate immunity and microbial clearance.","confidence":"Medium","size":27,"edges":73,"triangles":60,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0032092","count":5},{"id":"GO:0031663","count":4},{"id":"GO:1904417","count":4},{"id":"GO:0006915","count":4}]},{"hash":"434095648563441778","title":"Ribosome biogenesis and cell-cycle regulation","description":"The cluster is enriched for ribosome biogenesis and cell cycle-related terms (ribosome biogenesis; mitotic cell cycle; cell division) and also includes positive regulation of cytoplasmic translation, plus RNA processing via spliceosome-related terms. This points to a cohesive theme around RNA processing and protein synthesis machinery linked to cell proliferation. Other terms are less central, but do not overwhelm the core theme.","confidence":"High","size":27,"edges":68,"triangles":44,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0014070","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0051301","count":3},{"id":"GO:2000767","count":3}]},{"hash":"1212825404178149239","title":"Epithelial immune signaling and ciliogenesis","description":"Top terms indicate innate immune pathways (NOD2 signaling), regulation of inflammatory signaling (NF-\u03baB/STAT), and cytoskeletal remodeling associated with multiciliated epithelial differentiation and cell migration. This combination suggests a coherent theme where immune signaling interfaces with ciliogenesis and epithelial remodeling, justifying a label focused on epithelial immune signaling and ciliogenesis.","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":2},{"id":"GO:0042518","count":2},{"id":"GO:0032088","count":2},{"id":"GO:1903251","count":2},{"id":"GO:0050728","count":1}]},{"hash":"328923555773378687","title":"Post-transcriptional mRNA processing and translation control","description":"The top GO terms cluster around mRNA maturation processes (polyadenylation, splicing, stability, and regulation of mRNA polyadenylation) and translation initiation/ regulation (formation of the preinitiation complex, initiation, and reinitiation), plus stress-related mRNA stability. This points to a coherent group of proteins involved in post-transcriptional expression control rather than transcriptional regulation.","confidence":"High","size":27,"edges":320,"triangles":2263,"max_degree":26,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":21},{"id":"GO:0006378","count":20},{"id":"GO:0048255","count":19},{"id":"GO:0001825","count":19},{"id":"GO:0010610","count":19}]},{"hash":"966187791594056681","title":"Developmental Morphogenesis and Cell Cycle Regulation","description":"This cluster is dominated by GO terms related to development (forebrain development, skeletal system development and morphogenesis, gastrulation) alongside cell cycle processes (mitotic cell cycle). The presence of RNA processing and ERAD-related terms suggests broader cellular roles, but the strongest signal is coordination of tissue morphogenesis with cell division, so the label captures the main theme.","confidence":"Medium","size":27,"edges":233,"triangles":1107,"max_degree":25,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":23},{"id":"GO:0030433","count":23},{"id":"GO:0030900","count":23},{"id":"GO:0001501","count":22},{"id":"GO:0048705","count":22}]},{"hash":"2197942520435611479","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by translation-related GO terms, notably translation (GO:0006412) with 24 hits. It also features several ribosome biogenesis terms (GO:0000027; GO:0042273; GO:0042254), pointing to assembly and production of ribosomal subunits. While there are additional terms related to transcription termination and some stress or immune responses, the strongest signal centers on the components and regulation of protein synthesis. Thus the cluster most likely represents ribosome assembly and translation machinery.","confidence":"High","size":27,"edges":344,"triangles":2756,"max_degree":26,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":24},{"id":"GO:0000027","count":8},{"id":"GO:0042273","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0031564","count":4}]},{"hash":"1630080569897797510","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":301,"triangles":1964,"max_degree":26,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0031118","count":4},{"id":"GO:0000495","count":4},{"id":"GO:1990481","count":4},{"id":"GO:0031120","count":4}]},{"hash":"363330488630484685","title":"Cardiac muscle contraction and sarcomere organization","description":"This cluster is dominated by GO terms for cardiac muscle contraction, sarcomere organization, ventricular morphogenesis, and calcium-dependent muscle function (including actin crosslinking and calcium detection). Thyroid hormone metabolism and regulation of protein kinase activity align with signaling that modulates heart contraction and development; occasional axonogenesis signals may reflect developmental cross-talk, but the core theme is heart muscle structure and function.","confidence":"High","size":27,"edges":36,"triangles":16,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060048","count":6},{"id":"GO:0045214","count":5},{"id":"GO:0014883","count":4},{"id":"GO:0055010","count":4},{"id":"GO:0032972","count":4}]},{"hash":"1499951885000178564","title":"Muscle and neural development","description":"This cluster is dominated by muscle development signals (sarcomere organization, myoblast fusion) and neural development signals (nervous system development, neuron development), with supporting terms related to cell adhesion and transcription. Immune-related terms are present but less defining, so the core theme appears to be developmental programs shaping muscle and nervous tissue.","confidence":"Medium","size":27,"edges":23,"triangles":0,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045214","count":4},{"id":"GO:0007520","count":4},{"id":"GO:0071397","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0050853","count":3}]},{"hash":"1673174899535606086","title":"Nuclear-import and cell-cycle/apoptosis regulators","description":"This cluster combines proteins involved in nuclear import (NLS-bearing proteins), regulation of cell cycle and apoptosis, and modulation of key signaling pathways (Wnt, MAPK). The mix of terms pointing to apoptosis promotion, proliferation inhibition, and signaling regulation suggests a module coordinating nuclear trafficking with growth control and cell fate decisions, with additional hints from GTPase activity and cytoskeletal localization. ","confidence":"Medium","size":27,"edges":47,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0043065","count":4},{"id":"GO:0072699","count":4}]},{"hash":"1323868906089913534","title":"Ubiquitination-Driven Immune Signaling","description":"This cluster centers on ubiquitination processes (autoubiquitination, K6- and K63-linked ubiquitination, actin ubiquitination) and links to immune pathways, including NF-\u03baB signaling, antiviral defense, and components of adaptive immunity (V(D)J recombination). The convergence of ubiquitin modifications with defense against viruses and regulation of immune signaling (LPS pathways, intracellular viral transport) suggests proteins functioning together in ubiquitin-mediated immune regulation.","confidence":"High","size":27,"edges":35,"triangles":3,"max_degree":10,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":24},{"id":"GO:0043123","count":24},{"id":"GO:0051607","count":23},{"id":"GO:0033151","count":23},{"id":"GO:0085020","count":23}]},{"hash":"1718766376622439934","title":"Rho-regulated cytoskeletal dynamics","description":"The top GO terms center on Rho signaling, lamellipodium assembly, microtubule anchoring, and neutrophil chemotaxis, indicating a cohesive theme of cytoskeletal remodeling and cell movement driven by signaling. Additional terms touching on general signal transduction and growth, plus neuronal-related terms, suggest broader roles but still point to cytoskeletal dynamics as the core function of this cluster.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0030032","count":4},{"id":"GO:0007165","count":3},{"id":"GO:1900087","count":3},{"id":"GO:0007621","count":3}]},{"hash":"1373599761311273766","title":"Innate immune signaling and vascular regulation","description":"The cluster centers on innate immune activity, with strong enrichment for complement activation (classical and lectin pathways), Toll signaling, and leukocyte migration, which points to inflammatory responses. It also includes vascular and renal context terms like regulation of blood pressure by ANP and renal sodium excretion, along with angiogenesis and Wnt signaling, suggesting broader vascular remodeling and signaling interactions. Together, these features support a cohesive theme of innate immune signaling coupled with vascular and renal regulation.","confidence":"Medium","size":27,"edges":32,"triangles":14,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":13},{"id":"GO:0003050","count":13},{"id":"GO:0045766","count":13},{"id":"GO:0016055","count":12},{"id":"GO:0045752","count":10}]},{"hash":"1236624716701629267","title":"RNA and Histone Methylation","description":"This cluster is dominated by methylation-related GO terms across RNA species (tRNA, rRNA, mRNA capping, guanine-N7 methylation) and histone methylation, along with ribosome maturation and related growth/senescence processes. The common thread is methyltransferase activity driving RNA processing and chromatin modification, with some connections to cobalamin biosynthesis. Hence, a label centered on RNA and histone methylation best captures the shared function of these proteins.","confidence":"High","size":27,"edges":172,"triangles":518,"max_degree":23,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030488","count":9},{"id":"GO:0019919","count":7},{"id":"GO:0009236","count":7},{"id":"GO:0043985","count":6},{"id":"GO:0016049","count":6}]},{"hash":"982910846477812744","title":"Cerebral cortex development and cytoskeletal migration","description":"This cluster centers on cerebral cortex development and neural progenitor behavior, with strong signals for cell migration and cytoskeletal dynamics (lamellipodium assembly, interkinetic nuclear migration, astral and spindle organization, Rho signaling) and mitotic progression, suggesting roles in cortex formation involving coordinated division and migration.","confidence":"High","size":27,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":4},{"id":"GO:0007091","count":4},{"id":"GO:0035046","count":4},{"id":"GO:0030953","count":4},{"id":"GO:0007279","count":4}]},{"hash":"136544552071658135","title":"Innate Immune Response and Wound Healing","description":"The top GO terms are dominated by innate immune and wound-response processes: complement activation (alternative pathway), regulation of granulocyte differentiation, interleukin-13 production, and general response to wounding. While there are miscellaneous terms like translation and xenobiotic response, the core theme points to immune activation and tissue injury response. The low connectivity suggests a heterogeneous cluster with a moderate level of confidence in this label.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0090116","count":2},{"id":"GO:0042493","count":1},{"id":"GO:0006469","count":1},{"id":"GO:2000667","count":1}]},{"hash":"171142840319987087","title":"Neural and craniofacial development signaling","description":"This cluster is dominated by GO terms related to developmental signaling and morphogenesis, particularly neural development (transmission of nerve impulse, synapse organization, trigeminal nerve development), craniofacial and ocular morphogenesis (embryonic cranial skeleton morphogenesis, lens fiber cell differentiation), and signaling pathways (regulation of Rho protein signal transduction, positive regulation of BMP signaling). Together these terms suggest a cohesive theme of coordinated neural and craniofacial tissue development governed by BMP and cytoskeletal signaling, rather than a single isolated process. ","confidence":"Medium","size":27,"edges":8,"triangles":0,"max_degree":6,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0030513","count":5},{"id":"GO:0019226","count":5},{"id":"GO:0070306","count":5}]},{"hash":"1801934840270752192","title":"Adhesion-ECM signaling in vascular development","description":"The dominant terms are heterophilic and cell-matrix adhesion, both high, indicating proteins involved in cell\u2013ECM interactions. Supporting this, BMP signaling and positive regulation of Smoothened signaling point to developmental pathways, while coron\u00adary artery morphogenesis and hyaluronan biosynthesis regulation align with vascular remodeling and extracellular matrix dynamics. Although a couple of terms (thyroid hormone generation, complement activation) are less directly tied to adhesion, the core cluster centers on adhesion and ECM signaling that drive vascular development.","confidence":"High","size":27,"edges":77,"triangles":73,"max_degree":22,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0007157","count":26},{"id":"GO:0007160","count":26},{"id":"GO:0001867","count":26},{"id":"GO:0006590","count":25},{"id":"GO:0060982","count":24}]},{"hash":"869234494719405217","title":"Neural development and auditory perception","description":"This cluster is dominated by GO terms for nervous system development, synapse assembly, and sensory perception of sound, including inner ear development. While a few terms reference collagen/ossification, the strongest signals point to neural development and auditory/sensory functions as the shared theme of the proteins in this cluster.","confidence":"High","size":27,"edges":3,"triangles":1,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051965","count":11},{"id":"GO:0007399","count":7},{"id":"GO:0030199","count":6},{"id":"GO:0014068","count":6},{"id":"GO:0043931","count":6}]},{"hash":"2136297990809257693","title":"Vertebrate Embryonic Development Regulators","description":"These proteins appear linked by broad vertebrate development processes spanning brain regions (forebrain, midbrain), cranial skeleton, inner ear, thyroid, and other organs (spleen, hematopoiesis). The presence of transcriptional-regulation GO terms, including negative regulation of RNA Pol II and circadian regulation of gene expression, suggests a role as transcriptional regulators coordinating embryonic development rather than a single tissue-specific function. This supports labeling the cluster as vertebrate embryonic development regulators.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008542","count":4},{"id":"GO:0030900","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0032922","count":3},{"id":"GO:0000122","count":3}]},{"hash":"2025139276979591956","title":"Ocular and cardiovascular morphogenesis","description":"The top GO terms strongly point to developmental processes in the eye (visual perception, lens morphogenesis) and in the cardiovascular system (heart development, branching morphogenesis of blood vessels). While there are hints of neural development (substantia nigra) and immune signaling terms, the most represented and coherent theme across the cluster is eye and vascular morphogenesis, making this an intuitive, specific label. ","confidence":"High","size":27,"edges":10,"triangles":7,"max_degree":5,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0007601","count":10},{"id":"GO:0007507","count":10},{"id":"GO:0001569","count":8},{"id":"GO:0006919","count":7},{"id":"GO:0000122","count":7}]},{"hash":"970624543136627012","title":"Neuromuscular calcium signaling and vesicle trafficking","description":"The terms converge on neuromuscular signaling, calcium homeostasis (ER Ca2+ concentration, transmembrane Ca2+ transport), cytoskeletal organization of neurons, and vesicle trafficking (endocytosis, Golgi vesicle budding), together suggesting a cohesive role in neuromuscular function and calcium-dependent vesicle dynamics.","confidence":"Medium","size":27,"edges":250,"triangles":1216,"max_degree":26,"top_function":"establishment or maintenance of cell polarity","top_go_terms":[{"id":"GO:0050884","count":6},{"id":"GO:0010248","count":5},{"id":"GO:0060052","count":5},{"id":"GO:0006897","count":5},{"id":"GO:0031448","count":4}]},{"hash":"1706713873452656032","title":"Mitochondrial glycerophospholipid synthesis and remodeling","description":"The top GO terms point to lipid biosynthesis and remodeling, especially glycerophospholipids and ether lipids (phosphatidylcholine remodeling, CDP-diacylglycerol biosynthesis, cardiolipin remodeling, platelet activating factor biosynthesis) and triglyceride biosynthesis, all tied to mitochondrial ATP production. This suggests a coherent cluster around lipid metabolism with a strong link to mitochondrial membrane lipid dynamics, with a couple of developmental terms that are less central to the core function. ","confidence":"High","size":27,"edges":241,"triangles":1129,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":23},{"id":"GO:2001246","count":15},{"id":"GO:0036151","count":15},{"id":"GO:0042775","count":14},{"id":"GO:0008611","count":14}]},{"hash":"1919781581235367132","title":"Transcriptional Regulation and Development","description":"The top GO terms cluster around regulation of transcription by RNA polymerase II (negative regulation and regulatory region binding), epigenetic control (DNA methylation), and RNA processing (splicing). Additional terms point to developmental programs (cartilage morphogenesis, left-right patterning, endocrine system development) and even replication initiation, suggesting a set of proteins that coordinate gene expression and chromatin state during development.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0090116","count":2},{"id":"GO:0060707","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000398","count":1}]},{"hash":"692778319049080606","title":"RNA Pol II Transcription Regulation","description":"Most top GO terms are related to transcription by RNA polymerase II, including DNA-templated transcription and negative regulation of transcription by RNA Pol II. The presence of a few developmental terms at lower counts suggests these proteins also participate in differentiation pathways, but the dominant signal centers on transcription regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007576","count":11},{"id":"GO:0006351","count":11},{"id":"GO:0010729","count":11},{"id":"GO:0070895","count":11},{"id":"GO:0046022","count":11}]},{"hash":"833152777824173015","title":"Ion and Metabolite Transmembrane Transporters","description":"The proteins show enrichment for transmembrane transport of diverse substrates (Na+, K+, phosphate, nitrate, galactose, sialic acid, vitamins, xenobiotics), indicating a common role as solute transporters.","confidence":"High","size":27,"edges":13,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":9},{"id":"GO:0071805","count":9},{"id":"GO:0006855","count":9},{"id":"GO:0015739","count":8},{"id":"GO:0035435","count":7}]},{"hash":"478264587542807876","title":"Neuronal GPCR signaling and axon guidance with vascular regulation","description":"This cluster centers on GPCR-mediated signaling (PLC- and AC-activating pathways) linked to neuronal development (axonal fasciculation, synapse assembly) and concurrent vascular signaling (angiogenesis, VEGF, blood pressure), suggesting a module where GPCRs coordinate neuronal connectivity with vascular regulation; energy metabolism terms may reflect general cellular context.","confidence":"Medium","size":27,"edges":10,"triangles":2,"max_degree":4,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0016525","count":26},{"id":"GO:0007413","count":26},{"id":"GO:0035025","count":26},{"id":"GO:0007200","count":26},{"id":"GO:0022900","count":26}]},{"hash":"2196996203581304136","title":"Unknown","description":"The GO terms span behavioral processes (locomotory behavior; regulation of sensory perception of pain), signaling (GPCR-PLC pathways; negative regulation of adenylate cyclase), immune responses (defense response to bacterium; cytolysis), energy metabolism (electron transport chain), and microbial processes (peptidoglycan and cell wall catabolic processes) as well as viral release from host cells. There isn\u2019t a single coherent biological function that links these diverse processes, suggesting a heterogeneous or non-specific cluster. ","confidence":"","size":27,"edges":102,"triangles":112,"max_degree":14,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007626","count":27},{"id":"GO:0051482","count":27},{"id":"GO:0051930","count":27},{"id":"GO:0019076","count":27},{"id":"GO:0022900","count":27}]},{"hash":"1845463783696821768","title":"Membrane Transporters and Immune Functions","description":"This cluster is dominated by transmembrane transport terms for various ions and small molecules (nitrite, sodium, iron, manganese, L-arginine), suggesting a core theme of membrane transport. Immune-related terms (MHC class II biosynthesis and T cell cytokine production) appear alongside, indicating potential immune roles of the same membrane proteins. Some developmental and sensory terms are present but do not override the transport-focused signal. Confidence: Medium","confidence":"","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0035725","count":6},{"id":"GO:0050960","count":6},{"id":"GO:0072205","count":6}]},{"hash":"435421459337531441","title":"Amino acid transport and osmotic homeostasis","description":"This cluster is dominated by GO terms for import of multiple amino acids (arginine, methionine, lysine) across the plasma membrane, plus related transport activities (polyamines, ammonium) and osmotic/volume regulation (cell volume homeostasis, hypotonic salinity response). The common theme is membrane-mediated amino acid transport coupled to cellular osmoregulation, with arginine metabolism linking to nitric oxide production. ","confidence":"High","size":27,"edges":159,"triangles":501,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0098713","count":25},{"id":"GO:0006884","count":25},{"id":"GO:0006527","count":25},{"id":"GO:0071477","count":25},{"id":"GO:1902269","count":25}]},{"hash":"2117192155078257461","title":"Neuroimmune Dopamine Signaling","description":"This cluster combines immune/inflammatory terms with dopaminergic processes and astrocyte-related activity, suggesting a cohesive theme of neuroimmune modulation via dopamine in glial contexts.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":23},{"id":"GO:0042493","count":23},{"id":"GO:2000458","count":23},{"id":"GO:1900168","count":23},{"id":"GO:0048245","count":23}]},{"hash":"247813014234119378","title":"Skin, nail, and enamel development","description":"This cluster is enriched for GO terms related to ectodermal derivatives and enamel formation, including skin and nail development as well as amelogenesis. Integrin-mediated signaling and cell-matrix adhesion point to epithelial\u2013mesenchymal interactions driving tissue differentiation, with mesodermal differentiation as a broader developmental context. The combination of skin/nail and enamel-related terms makes this a cohesive developmental module focused on ectodermal appendages and tooth enamel.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007160","count":6},{"id":"GO:0043588","count":5},{"id":"GO:0007229","count":5},{"id":"GO:0072001","count":5},{"id":"GO:0015867","count":4}]},{"hash":"152654806763650888","title":"Cell Stress Signaling and Apoptosis Regulation","description":"Most terms describe signaling pathways that govern cell survival and stress responses (MAPK/stress-activated cascades, JAK-STAT, PI3K/AKT) and apoptosis regulation. Some terms also point to xenobiotic or retinoic acid signaling and general metabolic stress responses (methylglyoxal). Taken together, the cluster seems to reflect cell stress signaling and apoptosis control rather than a single metabolic reaction, hence the label.","confidence":"Medium","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":27},{"id":"GO:0042843","count":27},{"id":"GO:0031098","count":27},{"id":"GO:0046427","count":27},{"id":"GO:0043066","count":27}]},{"hash":"767650428002026159","title":"Neuroimmune-Dopaminergic Signaling","description":"This cluster combines GO terms tied to immune and inflammatory regulation in neural/glial contexts (e.g., negative regulation of inflammatory response, astrocyte chemotaxis, glial-derived neurotrophic factor production) with dopaminergic processes (dopamine transport, dopamine metabolism, and PLC-activating dopamine receptor signaling). The co-occurrence suggests a cohesive theme of neuroimmune interactions modulated by dopamine signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":27},{"id":"GO:0042493","count":27},{"id":"GO:2000458","count":27},{"id":"GO:1900168","count":27},{"id":"GO:0048245","count":27}]},{"hash":"398613429531095215","title":"Neuroimmune Modulation and Dopaminergic Signaling","description":"This cluster's GO terms include immune and inflammatory processes (negative regulation of inflammatory response, immune response, eosinophil chemotaxis) together with neural-dopaminergic signals (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling) and astrocyte/glial-related activities. The common thread appears to be neuroimmune interactions in the CNS coupled with dopamine signaling, suggesting proteins here partake in coordinated immune modulation and dopaminergic pathways.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":27},{"id":"GO:0042493","count":27},{"id":"GO:2000458","count":27},{"id":"GO:1900168","count":27},{"id":"GO:0048245","count":27}]},{"hash":"1030504342781299894","title":"Neuroimmune Dopaminergic Signaling","description":"The cluster includes immune/inflammatory regulation terms (negative regulation of inflammatory response, immune response, eosinophil chemotaxis) alongside dopaminergic processes (dopamine transport, dopamine metabolic regulation, dopamine receptor signaling, phospholipase C-activating dopamine pathway) and glial-associated terms, suggesting a theme of interactions between neural (dopaminergic/glial) and immune signaling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":27},{"id":"GO:0042493","count":27},{"id":"GO:2000458","count":27},{"id":"GO:1900168","count":27},{"id":"GO:0048245","count":27}]},{"hash":"198872977345226818","title":"Neural development and synaptic signaling","description":"Top terms cluster around neural differentiation and function (axonogenesis, Schwann cell development, visual perception, excitatory postsynaptic potential) with supporting signaling via protein phosphorylation. Although cell cycle and heart development terms appear, the dominant theme is neural development and synaptic signaling, making this label representative. ","confidence":"Medium","size":26,"edges":73,"triangles":101,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":16},{"id":"GO:0000086","count":15},{"id":"GO:0006468","count":15},{"id":"GO:0007409","count":15},{"id":"GO:0043065","count":14}]},{"hash":"2095308237406933681","title":"Meiotic homologous recombination and telomere maintenance","description":"This cluster is dominated by terms linked to meiosis and DNA repair, such as reciprocal meiotic recombination, synthesis-dependent strand annealing repair of double-strand breaks, and meiotic recombinase assembly. Heteroduplex formation and telomere maintenance via recombination (including t-circle formation) point to recombination-driven telomere dynamics typical of meiosis. Spermatid development further supports a male-gametogenesis context. A xenobiotic stress response term is present but appears secondary to the core meiotic/recombination signal.","confidence":"High","size":26,"edges":204,"triangles":950,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007131","count":11},{"id":"GO:0045003","count":11},{"id":"GO:0000722","count":11},{"id":"GO:0030491","count":11},{"id":"GO:0006268","count":11}]},{"hash":"1909978481590000437","title":"Ubiquitin-Dependent Protein Turnover and RNA Processing","description":"The top GO terms cluster around ubiquitin-related processes (monoubiquitinated protein deubiquitination; ubiquitin-dependent protein catabolic process) and RNA metabolism (DNA-templated transcription, mRNA processing, RNA repair), with additional links to cell-cycle events (centrosome duplication, mitotic cell cycle). A minority of terms touch on innate immune defense, but the strongest cohesive theme is ubiquitin-regulated proteostasis together with RNA processing and gene expression. This makes the proposed label a concise, representative description of the cluster's functional core.","confidence":"Medium","size":26,"edges":48,"triangles":26,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0035520","count":4},{"id":"GO:1903070","count":4},{"id":"GO:0006511","count":4},{"id":"GO:0006397","count":4}]},{"hash":"479701620278148048","title":"Ribosome biogenesis, rRNA modification, and translation","description":"This cluster combines ribosome biogenesis and maturation (LSU preribosome formation, rRNA processing) with translation steps (initiation, reinitiation) and RNA modification (pseudouridine synthesis), plus stress-related mRNA stability regulation, indicating a cohesive module for ribosome production and translation control.","confidence":"High","size":26,"edges":325,"triangles":2600,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":11},{"id":"GO:0006412","count":8},{"id":"GO:0048025","count":6},{"id":"GO:0000463","count":5},{"id":"GO:1902626","count":4}]},{"hash":"1931790654043397210","title":"Cardiac and Skeletal Muscle Signaling and Differentiation","description":"This cluster centers on heart development and skeletal muscle differentiation, with shared signaling themes such as GPCR signaling, Rap-mediated pathways, thrombin receptor signaling, PKC signaling, and regulation of serine phosphorylation. While insulin secretion and fat cell differentiation appear, the dominant pattern is muscle/heart development intertwined with diverse signaling cascades, suggesting a coherent muscle- and heart-related signaling module.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0035914","count":4},{"id":"GO:0008277","count":4},{"id":"GO:0032486","count":4},{"id":"GO:0070493","count":4}]},{"hash":"304684866025323915","title":"Histone modification and transcription regulation","description":"This cluster centers on chromatin modification and transcriptional control. The top GO terms indicate histone modifications (H3/H4 acetylation and methylation, including H3-K27 and H4 acetylation at several lysines) and negative regulation of transcription by RNA polymerase II, pointing to epigenetic regulation of gene expression. Additional terms for mRNA splicing and spindle assembly suggest links to RNA processing and cell cycle, with a developmental angle such as placenta morphogenesis. Overall, the proteins seem to function in chromatin-based regulation of transcription, potentially coordinated with cell division and development.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":4},{"id":"GO:0080182","count":3},{"id":"GO:0060669","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0043984","count":2}]},{"hash":"2113091314139892737","title":"Skeletal muscle development and sarcomere organization","description":"Dominant GO terms center on skeletal muscle fiber development, skeletal muscle tissue development, and sarcomere organization, indicating a cohesive muscle-development and sarcomere-assembly theme. Additional terms touch on circadian regulation and immune or proteolytic processes, which may reflect broader cellular roles or cross-species annotations, but the core cluster appears to be muscle structure and development.","confidence":"Medium","size":26,"edges":39,"triangles":37,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":17},{"id":"GO:0048741","count":17},{"id":"GO:0042752","count":17},{"id":"GO:0045214","count":17},{"id":"GO:0050853","count":17}]},{"hash":"1280262106985916476","title":"Epigenetic Regulation and Lineage Differentiation","description":"This cluster centers on developmental differentiation across multiple lineages (macrophage, angioblast, mammary epithelium, mesoderm) and on epigenetic control of gene expression (CpG island methylation, miRNA transcription), plus stem cell maintenance and immune signaling, suggesting a cohesive theme of epigenetically guided development.","confidence":"Medium","size":26,"edges":196,"triangles":765,"max_degree":24,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0044027","count":20},{"id":"GO:0097011","count":20},{"id":"GO:0035779","count":19},{"id":"GO:0061614","count":19},{"id":"GO:0035019","count":19}]},{"hash":"1313221933361629342","title":"Lysosome-related organelle trafficking","description":"This cluster's terms cluster around lysosomal and secretory granule biology: lysosome localization; endosome to lysosome transport; melanosome localization; platelet alpha granule organization and degranulation. These point to trafficking and maturation of lysosome-related organelles and secretory granules in platelets and pigment cells. A few items (bone differentiation, redox, tRNA modification, glucose transport) are less connected and may reflect broader cellular processes or annotation noise. Overall the dominant pattern supports lysosome-related organelle trafficking as the defining theme.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045669","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0002143","count":1},{"id":"GO:0032418","count":1},{"id":"GO:0070889","count":1}]},{"hash":"451709221324607288","title":"Embryonic organogenesis and neural crest development","description":"The proteins cluster around embryonic morphogenesis across tissues (neural crest migration, pancreas, inner ear, cerebellum, habenula, etc.), indicating a shared role in early development and organ formation, with transcription regulation as a common supporting process.","confidence":"High","size":26,"edges":313,"triangles":2337,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":21},{"id":"GO:0090190","count":19},{"id":"GO:0001755","count":18},{"id":"GO:0031018","count":18},{"id":"GO:0048557","count":18}]},{"hash":"1947395564957832718","title":"Coagulation and ECM remodeling with inflammation","description":"This cluster centers on blood coagulation and fibrinolysis, collagen fibril organization, and acute-phase inflammatory responses, with additional hints toward kidney development and pregnancy. The shared themes point to vascular remodeling, hemostasis, and ECM dynamics during inflammatory and reproductive contexts.","confidence":"Medium","size":26,"edges":38,"triangles":7,"max_degree":9,"top_function":"protein maturation","top_go_terms":[{"id":"GO:0014068","count":14},{"id":"GO:0014912","count":13},{"id":"GO:0030199","count":13},{"id":"GO:0042270","count":13},{"id":"GO:0010951","count":13}]},{"hash":"774271257450627957","title":"Rho GTPase-driven multi-tissue development","description":"This cluster centers on GO terms for Rho GTPase signaling (activation and regulation) plus broad developmental processes across tissues (heart, nervous system, angiogenesis, multicellular development). The presence of immune signaling (B cell receptor pathway) and paranode localization hints at diverse, pleiotropic roles, but the common thread appears to be signaling pathways, particularly Rho GTPase\u2013mediated regulation that influences developmental outcomes in multiple tissues. The lack of edges may reflect dispersed annotations rather than a single cohesive interaction network.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0007507","count":4},{"id":"GO:0002175","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006355","count":3}]},{"hash":"2124558384256957458","title":"Membrane-domain signaling and adhesion regulation","description":"The GO terms point to processes involving membrane organization (eisosomes, membrane raft polarization) and signaling regulation (PKC, B cell receptor signaling, extrinsic apoptotic signaling), plus effects on cell adhesion and barrier integrity (endothelial barrier establishment, regulation of cell\u2013cell adhesion). This suggests a cohesive theme around membrane-associated signaling and intercellular interactions across multiple cell types, despite some neural or sensory terms appearing as secondary associations.","confidence":"Medium","size":26,"edges":123,"triangles":212,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0061028","count":4},{"id":"GO:0007605","count":4},{"id":"GO:0050861","count":4},{"id":"GO:0090038","count":4},{"id":"GO:0048169","count":4}]},{"hash":"690991668239249252","title":"Neuronal development and cytoskeletal endosomal transport","description":"Dominant signals point to neuronal development with cytoskeletal remodeling and endosomal transport: neuron formation, filopodium assembly, myelin-related processes, and Rho signaling are complemented by lipid metabolism and signaling pathways (PI5P, TGF-beta, prostaglandin) that regulate membrane dynamics and trafficking.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048666","count":3},{"id":"GO:0051262","count":3},{"id":"GO:0032288","count":3},{"id":"GO:1904562","count":3},{"id":"GO:0007179","count":3}]},{"hash":"1524629026336816702","title":"Neural development and signaling with cell adhesion","description":"The top terms are dominated by nervous system processes: peripheral nervous system development, transmission of nerve impulse, and AV node/His bundle cell adhesion involved in cell communication, plus heterophilic cell\u2013cell adhesion. While several immune-regulatory terms appear (negative regulation of macrophage activation, NK and T cell cytotoxicity), the strongest cohesive theme is neural development and neural signaling coupled with cell adhesion. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043031","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0019226","count":5},{"id":"GO:0007422","count":4},{"id":"GO:0000187","count":4}]},{"hash":"124408957154831569","title":"Lipid metabolism and innate immune signaling","description":"The cluster prominently features lipid-related processes (positive regulation of cholesterol efflux, reverse cholesterol transport, phospholipid and surfactant homeostasis) together with innate immune/inflammatory responses (acute-phase response, IL-8 production, LPS signaling). This combination suggests proteins linked to lipid handling at mucosal interfaces, accompanied by inflammatory signaling and barrier-related ion transport, pointing to a coordinated lipid-immune functional theme. ","confidence":"High","size":26,"edges":207,"triangles":745,"max_degree":22,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0010875","count":5},{"id":"GO:0006953","count":4},{"id":"GO:0055091","count":4},{"id":"GO:0032757","count":4},{"id":"GO:0043691","count":3}]},{"hash":"1188806508258115899","title":"Cholinergic Signaling and Neuronal Excitability","description":"This cluster is dominated by GO terms tied to acetylcholine receptor signaling, nicotine response, and action potential, with supporting terms on chloride transport regulation that influence neuronal excitability. The inclusion of circadian regulation and reflex/respiratory nervous system processes also points to a cohesive neuronal signaling theme centered on cholinergic control of excitability and related physiological rhythms.","confidence":"High","size":26,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:1902476","count":25},{"id":"GO:0032226","count":24},{"id":"GO:0045188","count":24},{"id":"GO:0060013","count":24},{"id":"GO:0002087","count":24}]},{"hash":"1577841557869247918","title":"Cellular stress response and detoxification","description":"The cluster centers on stress-responsive and detoxification processes, with enrichment in starvation response, toxin and oxidant detoxification (glutathione metabolism, toxin catabolic), and DNA repair, indicating a coordinated cellular defense and metabolic adaptation to challenging conditions. Calcium-related signaling in muscle contraction terms appears auxiliary, but the core theme remains stress response and maintenance. ","confidence":"High","size":26,"edges":325,"triangles":2600,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":26},{"id":"GO:0042594","count":26},{"id":"GO:0009072","count":26},{"id":"GO:0098869","count":26},{"id":"GO:0006289","count":26}]},{"hash":"3684400491912671","title":"Embryogenesis and tissue morphogenesis","description":"This cluster is dominated by GO terms tied to embryonic development and morphogenesis across multiple tissues (left-right patterning, cartilage and hair follicle development, placental and pancreatic cell development, EMT processes), with supporting transcriptional regulation terms. The coherence of development-focused processes suggests the proteins function together in embryogenesis and tissue formation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":6},{"id":"GO:0060806","count":6},{"id":"GO:0060972","count":6},{"id":"GO:0060536","count":6},{"id":"GO:0003323","count":6}]},{"hash":"1757804983488915487","title":"Glycosylation and glycosphingolipid metabolism","description":"The cluster is strongly enriched for GO terms tied to glycan processing and glycosphingolipid biosynthesis, including N-acetylneuraminate metabolism, various forms of N-linked and oligosaccharide metabolism, glycosylceramide, and ganglioside biosynthesis. A few terms related to pollen development and olfactory system formation likely reflect broader roles of glycosylation in cell signaling and membrane biology. Overall, the common theme is glycosylation and glycosphingolipid metabolism across diverse biological contexts.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006054","count":5},{"id":"GO:0006491","count":5},{"id":"GO:0009860","count":5},{"id":"GO:0009846","count":5},{"id":"GO:0021628","count":5}]},{"hash":"1792303103670407093","title":"Adaptive immune activation and germinal center regulation","description":"The cluster is dominated by terms related to B and T cell costimulation, proliferation, B cell homeostasis, and germinal center formation, pointing to a shared function in adaptive immune activation and germinal center dynamics. Some terms are less directly immune-related, but the strongest signal centers on lymphocyte activation and germinal center processes.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042998","count":2},{"id":"GO:0030216","count":1},{"id":"GO:0018149","count":1},{"id":"GO:0031296","count":1},{"id":"GO:0002636","count":1}]},{"hash":"1156277096647913326","title":"ECM Remodeling and Angiogenesis Control","description":"Based on the top GO terms, the proteins are enriched for extracellular matrix processes (collagen fibril organization, cell adhesion, regulation of fibrinolysis) and vascular remodeling (positive and negative regulation of angiogenesis). These themes point to a cluster of ECM-associated factors involved in coordinating blood vessel formation and matrix organization, rather than a single specific pathway. The other terms (mast cell immunity, chondrocyte differentiation regulation, kidney development) may reflect broader tissue contexts or secondary roles but do not override the dominant ECM/angiogenesis pattern.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0016525","count":6},{"id":"GO:0030199","count":5},{"id":"GO:0032331","count":5},{"id":"GO:0006958","count":5},{"id":"GO:0007155","count":5}]},{"hash":"983707391382184116","title":"Neuroimmune regulation and dopaminergic signaling","description":"This cluster is characterized by GO terms reflecting both brain immune/inflammatory processes (negative regulation of inflammatory response, immune response, eosinophil chemotaxis, response to xenobiotic stimulus) and glia-related functions (astrocyte chemotaxis, GDNF production), together with dopaminergic biology (dopamine transport, regulation of dopamine metabolism, phospholipase C-activating dopamine receptor signaling). The convergence of neuroimmune modulation and dopamine signaling suggests a cohesive theme around neuroimmune regulation of dopaminergic signaling in the brain.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":26},{"id":"GO:0042493","count":26},{"id":"GO:2000458","count":26},{"id":"GO:1900168","count":26},{"id":"GO:0048245","count":26}]},{"hash":"414024187130820928","title":"DNA replication and genome maintenance","description":"These proteins cluster around DNA replication, DNA repair, and chromatin/transcription regulation. The top GO terms include DNA replication, break-induced replication, telomere maintenance via recombination, and regulation of transcription, along with ubiquitin-dependent protein catabolic processes that modulate replication machinery. The combination of replication initiation, repair, telomere maintenance, and chromatin silencing points to a module dedicated to genome integrity during cell proliferation and transcriptional control.","confidence":"High","size":25,"edges":288,"triangles":2044,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006511","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0000727","count":4},{"id":"GO:0030466","count":4}]},{"hash":"302875602024613008","title":"DNA Repair and Genome Maintenance","description":"This cluster is characterized by multiple GO terms directly tied to DNA repair and genome integrity, including base-excision repair, DNA recombination, and DNA catabolic processes. Additional terms reflect cellular responses to stress, xenobiotic stimuli, and redox balance, which often intersect with DNA damage repair pathways. A nearby RNA processing term (poly(A) tail shortening) likely reflects broader stress-related RNA regulation but does not change the core theme toward genome maintenance.","confidence":"High","size":25,"edges":147,"triangles":435,"max_degree":19,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042493","count":7},{"id":"GO:0007568","count":7},{"id":"GO:0006284","count":7},{"id":"GO:0006310","count":6},{"id":"GO:0000289","count":6}]},{"hash":"1668488674093467641","title":"Neural and Cardiac Development Transcription Regulators","description":"The top GO terms cluster around DNA-templated transcription and regulatory processes, with strong hints of neural development (hippocampus and cerebellar cortex development) and cardiac/mesoderm formation (heart development, axial mesoderm formation), plus neuronal axon fasciculation. This pattern suggests proteins that regulate transcription during neural and cardiac developmental programs, rather than a single specialized pathway. Confidence: High","confidence":"","size":25,"edges":35,"triangles":7,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":23},{"id":"GO:0033138","count":23},{"id":"GO:0021766","count":23},{"id":"GO:2000811","count":23},{"id":"GO:0007507","count":23}]},{"hash":"2261193006829827365","title":"Developmental transcription and morphogenesis","description":"The cluster is enriched for transcription by RNA polymerase II and a broad set of developmental and morphogenetic processes, including cell adhesion, tissue differentiation, and organ formation (e.g., cardioblast migration, Malpighian tubule differentiation, vestibular nucleus development, circadian regulation of heart rate). This pattern suggests proteins that coordinate transcriptional control with developmental programs.","confidence":"High","size":25,"edges":238,"triangles":1212,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":24},{"id":"GO:0033627","count":16},{"id":"GO:0021750","count":16},{"id":"GO:0003259","count":16},{"id":"GO:0061382","count":16}]},{"hash":"1242090409306841970","title":"Mitotic and neural development signaling","description":"Based on the top GO terms, this cluster shows enrichment in mitotic cell cycle and cell division, nervous system development including dendritic spine development, and small GTPase\u2013mediated signal transduction. This suggests a theme of cell proliferation linked with neural development and signaling pathways that regulate cytoskeletal dynamics and trafficking, rather than a single tight pathway. Some terms are general or obsolete, but the dominant themes point to mitotic activity and neural development processes.","confidence":"Medium","size":25,"edges":212,"triangles":972,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000186","count":17},{"id":"GO:0051301","count":15},{"id":"GO:0007399","count":15},{"id":"GO:0000278","count":14},{"id":"GO:0007264","count":14}]},{"hash":"989455998351732092","title":"Ribosome Biogenesis and RNA Processing","description":"The cluster shows strong enrichment for ribosome biogenesis and rRNA maturation terms (large subunit biogenesis, maturation of LSU/SSU rRNA) along with general RNA processing activities (mRNA splicing, exon ligation, spliceosome dynamics). This points to a cohesive role in ribosome assembly and RNA maturation, with some apparent stress-related terms (SOS response, stress granule localization) that may reflect cellular stress states rather than defining function. Overall, the dominant theme is ribosome assembly and RNA processing.","confidence":"Medium","size":25,"edges":299,"triangles":2277,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":21},{"id":"GO:0009432","count":21},{"id":"GO:0006260","count":21},{"id":"GO:0000390","count":20},{"id":"GO:0000378","count":20}]},{"hash":"1807092309560830135","title":"Neurodevelopmental signaling and actin dynamics","description":"The cluster\u2019s frequent terms point to nervous system development (hippocampus, cerebellar cortex, nervous system development) and signaling processes (ERK cascade, regulation of phosphorylation) together with cytoskeletal organization (actin cytoskeleton). This pattern suggests proteins involved in neurodevelopmental signaling and cytoskeletal remodeling, with a secondary note of broader signaling functions such as B cell receptor signaling. Overall, the theme is cohesive around neural development and associated signaling.","confidence":"Medium","size":25,"edges":18,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070374","count":2},{"id":"GO:0030866","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0033138","count":2}]},{"hash":"365645578776612353","title":"Cytokine Regulation and NF-\u03baB Innate Immunity","description":"The top GO terms cluster around regulation of cytokines (IL-6, IL-8), innate defense responses to bacteria, and signaling pathways like LPS and NF-\u03baB, suggesting a cohesive immune/inflammatory signaling module with modulatory control over cytokine production.","confidence":"Medium","size":25,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045416","count":3},{"id":"GO:0032715","count":3},{"id":"GO:0032755","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0031663","count":3}]},{"hash":"404159058474322510","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":53,"triangles":41,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000472","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0000447","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0001843","count":3}]},{"hash":"194693186102560288","title":"RNA processing and translation machinery","description":"The top GO terms cluster around transcription, translation initiation/reinitiation, and mRNA splicing, pointing to core gene-expression machinery. Developmental and stress-related terms appear less central, suggesting the main theme is RNA processing and protein synthesis regulation.","confidence":"Medium","size":25,"edges":34,"triangles":20,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0002188","count":8},{"id":"GO:0043547","count":8},{"id":"GO:0001843","count":8}]},{"hash":"1966683546319034120","title":"CNS Neuron Development and Synaptic Localization","description":"The cluster is dominated by terms for neuron development (neuron projection development, axon extension, dendrite morphogenesis, CNS neuron development) and memory, with supporting terms on synaptic protein localization and mitochondrial distribution. This points to a cohesive theme of neural development and synaptic organization, spanning axon/dendrite formation and synapse targeting.","confidence":"High","size":25,"edges":8,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031175","count":7},{"id":"GO:0045773","count":6},{"id":"GO:0007613","count":6},{"id":"GO:0048813","count":6},{"id":"GO:0021954","count":6}]},{"hash":"1647017016352929253","title":"mRNA Splicing and Translation Regulation","description":"Most GO terms point to spliceosome-mediated mRNA splicing and regulation of alternative splicing, plus facets of mRNA stability, polyadenylation, and translational initiation (including IRES-dependent initiation). The cluster thus reflects post-transcriptional processing and control of translation, with a developmental term (blastocyst formation) that may reflect expression context. Confidence: High","confidence":"","size":25,"edges":279,"triangles":1909,"max_degree":24,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":14},{"id":"GO:0006378","count":13},{"id":"GO:0000381","count":12},{"id":"GO:0075522","count":12},{"id":"GO:0048255","count":11}]},{"hash":"2079763698803302057","title":"Proteasome-Linked Antigen Processing and Innate Immunity","description":"These proteins cluster around two main themes: proteolysis and antigen processing, and innate immune signaling. The prominent GO terms include proteasomal ubiquitin-independent protein catabolic process, APC/C-dependent catabolic process, and antigen processing/presentation via MHC class I (TAP-dependent), which tie peptide generation to antigen presentation. Additional terms point to innate signaling pathways such as stimulatory C-type lectin receptor signaling and non-canonical NF-kappaB signaling. While a few terms (e.g., plant hypersensitive response, hypoxia-regulated transcription, and Wnt regulation) add diversity, the core signal is proteolysis linked to immune processing and signaling. Confidence: Medium","confidence":"","size":25,"edges":275,"triangles":1941,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0010499","count":18},{"id":"GO:0061418","count":18},{"id":"GO:0010363","count":18},{"id":"GO:0010950","count":18},{"id":"GO:0002479","count":18}]},{"hash":"992491285970401193","title":"Chromosome maintenance and RNA processing","description":"The cluster\u2019s top GO terms emphasize chromatin assembly during DNA replication and meiotic sister chromatid cohesion, pointing to chromosome maintenance. Additional terms highlight RNA processing regulation (rRNA, tRNA) and protein ubiquitination, suggesting supporting roles in post-translational modification and RNA maturation. While a couple terms are less directly connected (signaling or reproduction-related), the dominant theme is genome integrity through chromatin organization and RNA processing.","confidence":"Medium","size":25,"edges":96,"triangles":192,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0042921","count":3},{"id":"GO:0006335","count":3},{"id":"GO:0051754","count":3},{"id":"GO:0035037","count":2},{"id":"GO:0019089","count":2}]},{"hash":"1097419710051454031","title":"Cell Division and Developmental Regulation","description":"The top terms cluster around mitotic cell cycle and cell division, with additional signals for brain development and regulation of vesicle exocytosis, apoptosis, and growth processes. This points to a set of proteins involved in fundamental cell-cycle control plus broader developmental and regulatory roles, including neuronal context. Given the mix of processes (cell division, development, and regulatory pathways), the label highlights the core theme without overfitting to a single pathway.","confidence":"Medium","size":25,"edges":202,"triangles":860,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0051301","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0031274","count":4},{"id":"GO:0006378","count":4}]},{"hash":"225358255867497549","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":19,"triangles":11,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048024","count":4},{"id":"GO:0002091","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000380","count":3}]},{"hash":"2289639838355113860","title":"RNA Translation and Folate Metabolism","description":"The top GO terms show a strong emphasis on translation and cytoplasmic translation, initiation and preinitiation complex formation, and transcription-related processes, indicating a core set of proteins involved in protein synthesis. Secondary terms point to folate/one-carbon metabolism (tetrahydrofolate interconversion, folic acid biosynthesis/catabolism, formate metabolism) and RNA turnover (miRNA catabolic process). Together, they suggest a cluster centered on translation machinery with linked folate metabolism pathways. ","confidence":"Medium","size":25,"edges":134,"triangles":309,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0035999","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3}]},{"hash":"1794491612864173183","title":"Immune organ development and T cell homeostasis","description":"The top GO terms cluster around immune system development and regulation: thymus and lymph node development, T cell homeostasis, and negative regulation of NF-kappaB signaling and extrinsic apoptotic pathways, pointing to proteins involved in shaping immune organs and modulating immune signaling. A few terms about skeletal and lens differentiation appear as minor associations, but the dominant theme is immune development and regulation.","confidence":"Medium","size":25,"edges":20,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043124","count":2},{"id":"GO:1902042","count":2},{"id":"GO:2000617","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0048538","count":2}]},{"hash":"2002197550957472677","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0007026","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0050896","count":1},{"id":"GO:1900186","count":1}]},{"hash":"1788003122766271232","title":"Embryonic tissue differentiation and morphogenesis","description":"The top GO terms indicate broad embryonic development across multiple tissues (placenta/trophoblast, cartilage, pancreas, left-right patterning, EMT-related processes) and endocrine development, with supporting cytoskeletal and vesicle trafficking terms (actin depolymerization, exocytosis, slow endocytic recycling) pointing to cellular morphogenesis. This suggests a cluster of proteins involved in embryonic tissue differentiation and morphogenesis rather than a single pathway.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":7},{"id":"GO:0060536","count":7},{"id":"GO:0060972","count":7},{"id":"GO:0035270","count":7},{"id":"GO:0003323","count":7}]},{"hash":"1413595451893540485","title":"Ubiquitin-Driven Cell Cycle and DNA Replication Regulation","description":"The top GO terms are dominated by ubiquitination processes (protein polyubiquitination, ubiquitin-dependent protein catabolic process, and positive regulation of protein polyubiquitination) and by regulation of DNA replication initiation and G1/S transition, pointing to a theme of ubiquitin-mediated control of the cell cycle and DNA replication. Some terms on circadian rhythm and stress responses (cadmium/methylmercury) likely reflect proteostasis and stress signaling intertwined with ubiquitin pathways. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000083","count":20},{"id":"GO:0042787","count":18},{"id":"GO:0060386","count":17},{"id":"GO:0042752","count":16},{"id":"GO:0071276","count":16}]},{"hash":"496973986776704282","title":"Ubiquitin-Proteasome Mediated Degradation","description":"The top terms cluster around ubiquitination (K48, K63, K11, K6 linkages), autoubiquitination, neddylation, and SCF-dependent proteasomal degradation, plus ubiquitin-dependent protein catabolic processes. Peroxisome matrix protein import also ties into ubiquitin signaling for targeting proteins for degradation. Collectively, these terms point to the ubiquitin-proteasome system governing protein turnover, including regulation of E3 ligases and degradation via the proteasome. ","confidence":"High","size":25,"edges":241,"triangles":1198,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":16},{"id":"GO:0085020","count":15},{"id":"GO:0070936","count":15},{"id":"GO:0051865","count":15},{"id":"GO:0016558","count":14}]},{"hash":"2093721410570727617","title":"Actin cytoskeleton remodeling regulators","description":"The top GO terms point to actin filament dynamics\u2014nucleation, bundling, and depolymerization\u2014and related signaling responses (EGF, HGF, BMP), indicating the proteins coordinate actin cytoskeleton remodeling and associated signaling pathways.","confidence":"High","size":25,"edges":66,"triangles":65,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0071364","count":2},{"id":"GO:0030836","count":2}]},{"hash":"359269122910749240","title":"Neuronal glutamatergic synapse regulation and spine morphogenesis","description":"The cluster is dominated by terms related to excitatory synaptic signaling and dendritic spine remodeling: AMPA receptor activity, NMDA receptor clustering, positive regulation of excitatory postsynaptic potential, and dendritic spine morphogenesis. It also includes Rho/Rac GTPase pathway regulation, which governs cytoskeletal changes important for spine structure. Although apoptotic processes appear, the prevailing theme is synaptic regulation and spine morphogenesis in neurons (with social behavior reflecting neuronal circuit implications). ","confidence":"High","size":25,"edges":19,"triangles":11,"max_degree":9,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006915","count":13},{"id":"GO:0035021","count":12},{"id":"GO:0043547","count":12},{"id":"GO:0035176","count":12},{"id":"GO:0035023","count":12}]},{"hash":"830136374115462576","title":"Adaptive immune signaling and lymphocyte regulation","description":"The top GO terms point to adaptive immunity and lymphocyte signaling, including B cell receptor signaling, Fc-epsilon receptor signaling, adaptive immune response, and IL-2 production, alongside regulatory effects on macrophages and NK cell activity. This suggests a cohesive module centered on activation and modulation of adaptive immune responses, with supporting roles in leukocyte communication and regulation.","confidence":"High","size":25,"edges":10,"triangles":2,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0010765","count":19},{"id":"GO:0038095","count":17},{"id":"GO:0050853","count":17},{"id":"GO:0002250","count":17},{"id":"GO:1900042","count":17}]},{"hash":"144147838147581258","title":"ER Quality Control and Stress Response","description":"Top GO terms indicate chaperone-assisted refolding, ER-associated degradation, regulation of translation initiation in response to ER stress, post-translational targeting to membranes, and ER protein quality control processes. Together they point to a cohesive function: maintaining protein folding homeostasis and coordinating degradation and translation under ER stress. Some entries are obsolete or broader (DNA replication, signaling regulation), but the predominant theme is ER quality control.","confidence":"High","size":25,"edges":261,"triangles":1600,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":23},{"id":"GO:0070389","count":23},{"id":"GO:1900035","count":23},{"id":"GO:0031204","count":23},{"id":"GO:0006260","count":23}]},{"hash":"1435133939960037868","title":"Cytoskeletal Remodeling and Mechanotransduction","description":"This set is dominated by terms for actin filament organization, response to mechanical stimuli, and cell migration/polarity, all pointing to cytoskeletal dynamics and mechanosensing. Ubiquitination may regulate these processes, while a few telomere-related terms seem incidental. Confidence: High","confidence":"","size":25,"edges":95,"triangles":111,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":4},{"id":"GO:0050966","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0071260","count":4},{"id":"GO:2001275","count":3}]},{"hash":"899867867017157283","title":"Cell Signaling and Differentiation","description":"These proteins appear linked to multiple signaling pathways (NF-kappaB regulation, GPCR/PKC signaling, Wnt) and a differentiation process (fat cell differentiation), plus regulatory activities like proteasome assembly and telomere maintenance. While the terms are diverse and some are obsolete, the unifying theme is involvement in signal transduction and regulation of cellular fate rather than a single metabolic or structural function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:2001275","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0045444","count":3},{"id":"GO:0050968","count":3}]},{"hash":"497886343616124686","title":"Immune signaling and cytokine regulation","description":"The cluster's terms cluster around immune and inflammatory processes\u2014type II interferon production, chemokine and IL-6 regulation, monocyte aggregation, and NF-kappaB signaling\u2014suggesting proteins that modulate inflammatory responses. While a couple terms (like rRNA methylation and heat response) are broader, the dominant theme is cytokine signaling and immune regulation. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":2},{"id":"GO:0042095","count":1},{"id":"GO:0045080","count":1},{"id":"GO:0070487","count":1},{"id":"GO:0045410","count":1}]},{"hash":"1791044000203441330","title":"Telomere maintenance and telomeric regulation","description":"This cluster is dominated by GO terms related to telomere maintenance, including telomere capping, localization to the telomeric region, telomeric DNA binding, and regulation of telomere lengthening, indicating a cohesive telomere-focused function. Additional terms like Wnt signaling and cell migration appear but are secondary to the core telomere-associated activities.","confidence":"High","size":25,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0032212","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0016477","count":4},{"id":"GO:1904743","count":4}]},{"hash":"1811809850808583005","title":"Developmental Signaling and Differentiation","description":"These proteins cluster around developmental processes across tissues (kidney, CNS, placenta) and around regulation of signaling pathways (BMP signaling, tyrosine phosphorylation) and receptor organization. The combination suggests a group of proteins involved in coordinating differentiation and tissue development via signaling modulation, rather than a single specific function.","confidence":"Medium","size":25,"edges":16,"triangles":4,"max_degree":3,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0007596","count":8},{"id":"GO:0001822","count":8},{"id":"GO:0048671","count":8},{"id":"GO:0043113","count":7},{"id":"GO:0007417","count":6}]},{"hash":"1478395682942506380","title":"Pollen exine formation and glycosylation","description":"The cluster is enriched for GO terms related to N-linked glycosylation and pollen wall development (pollen exine formation) as well as anther dehiscence, suggesting a plant-specific module involved in glycoprotein processing during pollen wall formation. Some nucleotide catabolic processes are present, but the strongest theme ties to pollen development and protein glycosylation.","confidence":"Medium","size":25,"edges":142,"triangles":505,"max_degree":21,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0006487","count":7},{"id":"GO:0071405","count":7},{"id":"GO:0046032","count":7},{"id":"GO:0006256","count":7},{"id":"GO:0046712","count":7}]},{"hash":"1584541242807407681","title":"Mammalian reproduction and lactation","description":"The top GO terms center on mammary gland development, lactose biosynthesis, and sperm\u2013egg interaction (acrosome reaction, sperm binding and zona pellucida penetration) with some epithelial wound-healing terms; together these point to reproductive biology and milk production, despite a few outlier neural terms.","confidence":"Medium","size":25,"edges":194,"triangles":730,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":19},{"id":"GO:0060046","count":19},{"id":"GO:0060054","count":19},{"id":"GO:0005989","count":19},{"id":"GO:0060058","count":19}]},{"hash":"553247845742427470","title":"Organ Development and Post-Translational Modifications","description":"This cluster\u2019s top GO terms cluster around organ development processes (liver regeneration, heart development, Purkinje cell differentiation) and PTMs (protein ubiquitination, deglutamylation). The combination suggests a theme of developmental regulation coordinated with protein modification/remodeling. Some terms touch blood pressure regulation and stress responses, but the dominant signal is developmental programs coupled with post-translational modification processes, justifying a focused label rather than a single narrowly defined function. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":4},{"id":"GO:0021702","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0035611","count":3}]},{"hash":"894209875809644600","title":"Neural signaling and brain development regulators","description":"The cluster's top GO terms focus on neuronal signaling and brain development, including regulation of synaptic vesicle exocytosis, cellular calcium response, and pathways like Wnt and VEGF signaling, plus insulin secretion. This points to proteins that modulate signaling events relevant to neural function and development; a few terms (ABA signaling, TNF regulation) are broader, but the dominant theme is signaling control in neural/developmental contexts.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":3},{"id":"GO:0071277","count":3},{"id":"GO:0036324","count":3},{"id":"GO:0035773","count":3},{"id":"GO:0009738","count":3}]},{"hash":"1748693630840921221","title":"Vertebrate craniofacial and sensory organ development","description":"The top GO terms point to embryonic development in vertebrates, especially craniofacial formation (roof of mouth development, neural crest migration), sensory system development (retina development, visual perception), and related organogenesis (proepicardium, ureteric bud branching). While some terms are general (transcription and RNA processing), the overall theme centers on vertebrate organ and tissue patterning, particularly in facial and sensory structures.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006378","count":6},{"id":"GO:0045292","count":6},{"id":"GO:0060021","count":6},{"id":"GO:0003342","count":6},{"id":"GO:0007601","count":5}]},{"hash":"1917917373768992282","title":"Development and Differentiation","description":"The Top Terms include multiple development-related processes across tissues (bone development, fat cell differentiation, retinal rod cell development) along with general gene-expression activities (mRNA processing, DNA-templated transcription) and cytoskeletal organization (actin filament bundle assembly). This suggests a broad theme centered on developmental processes and gene regulation, rather than a single, cohesive pathway. Hence, a general label of Development and Differentiation captures the cluster\u2019s overarching function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031322","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060348","count":2}]},{"hash":"569604294537545483","title":"Chromatin acetylation and mitotic cohesion","description":"This cluster is dominated by GO terms for acetylation of histones and other proteins (peptidyl-lysine N6-acetylation; obsolete histone H4 acetylation) and for chromosomal cohesion during mitosis, plus acetylation of polyamines (putrescine, spermidine, spermine). Together these point to chromatin modification and chromosome segregation as the core theme. Angiogenesis and melatonin biosynthesis appear less central and may reflect broader metabolic connections. ","confidence":"High","size":25,"edges":105,"triangles":185,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":9},{"id":"GO:0006044","count":9},{"id":"GO:0019491","count":8},{"id":"GO:0032920","count":8},{"id":"GO:0030187","count":8}]},{"hash":"1520723234069746917","title":"p53-dependent intrinsic apoptosis and DNA damage response","description":"The proteins in this cluster are annotated mainly with apoptosis- and DNA-damage-related GO terms (intrinsic/mitochondrial apoptotic signaling, p53-mediated response to DNA damage, and cellular response to ionizing radiation). This suggests a cohesive theme of programmed cell death triggered by genomic stress.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001056","count":1},{"id":"GO:1900740","count":1},{"id":"GO:0001844","count":1},{"id":"GO:0043525","count":1},{"id":"GO:0042771","count":1}]},{"hash":"2016763314638017133","title":"Unknown","description":"The top terms show a mix of transport and metabolic processes (glucose, cystine, amino acids; amino acid homeostasis; glycosylation), plus some organismal traits (grooming behavior, lens development) and oxidative stress-related terms. There is no single cohesive function or pathway linking these terms across the cluster, so there isn\u2019t a clear, representative label. ","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071447","count":1},{"id":"GO:1903204","count":1},{"id":"GO:1902083","count":1},{"id":"GO:1904659","count":1},{"id":"GO:0007625","count":1}]},{"hash":"1415938943038925618","title":"Chromatin and RNA methylation","description":"The top GO terms cluster around methylation processes (peptidyl-lysine methylation and dimethylation; rRNA methylation) and rDNA heterochromatin formation, suggesting an epigenetic regulation theme through chromatin modification. Dephosphorylation and apoptosis-related hints, plus some bone development terms, may be peripheral noise, but the core signal is chromatin-associated methylation.","confidence":"Medium","size":25,"edges":11,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0019509","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0001958","count":2},{"id":"GO:0035630","count":2}]},{"hash":"1387542276940948659","title":"Neural ECM Remodeling and Regeneration","description":"The cluster includes GO terms for collagen fibril organization, cell-matrix and neuron adhesion, synapse assembly, and peripheral nerve axon regeneration, along with angiogenesis and innate immune response. This combination points to a program coordinating extracellular matrix remodeling to support neural growth and regeneration, with angiogenic and immune-modulatory components. The presence of both positive and negative regulation terms (e.g., negative regulation of angiogenesis/axon extension) suggests a balanced regenerative process rather than a single pathway.","confidence":"Medium","size":25,"edges":68,"triangles":30,"max_degree":10,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030199","count":6},{"id":"GO:0051965","count":6},{"id":"GO:0001525","count":5},{"id":"GO:0007158","count":5},{"id":"GO:0007160","count":5}]},{"hash":"319955724611260820","title":"Neuronal Synaptic Signaling and Circadian Regulation","description":"The terms point to neural communication (glutamatergic and GABAergic synaptic transmission, neuropeptide signaling, action potential modulation) together with circadian wakefulness regulation, suggesting a cluster of proteins involved in brain signaling and circadian rhythm control.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904240","count":1},{"id":"GO:1903070","count":1},{"id":"GO:1904153","count":1},{"id":"GO:1903061","count":1},{"id":"GO:0010841","count":1}]},{"hash":"1877687485968546729","title":"Cytokinesis and Actin Cytoskeleton Dynamics","description":"Proteins here map to mitosis-related processes (spindle organization, contractile ring assembly, membrane addition at cytokinesis) and actin-based transport, with supporting signals for organelle inheritance. The unified theme is mitosis and actin cytoskeleton remodeling during cytokinesis.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045033","count":1},{"id":"GO:0007118","count":1},{"id":"GO:0021678","count":1},{"id":"GO:0030050","count":1},{"id":"GO:0000001","count":1}]},{"hash":"348558881397841030","title":"Unknown","description":"The terms span diverse areas: transcriptional regulation, lipid and small-molecule metabolism, vitamin biosynthesis, and developmental morphogenesis, with no single dominant function tying the proteins together. This suggests no cohesive cluster function can be assigned.","confidence":"","size":25,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045892","count":6},{"id":"GO:0019433","count":6},{"id":"GO:0006469","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0009820","count":5}]},{"hash":"300454770933901685","title":"Cardiac muscle contraction and sarcomere organization","description":"The cluster is dominated by GO terms related to sarcomere organization and cardiac function (positive regulation of sarcomere organization, sarcomere organization, and cardiac muscle contraction) as well as heart-rate regulation by epinephrine and vascular smooth muscle regulation, all pointing to a muscle-contraction/heart physiology theme. Some non-muscle terms appear (phototransduction, nervous system development), but they are less representative of the core set. This supports a cohesive label centered on heart muscle structure and function.","confidence":"High","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0060298","count":25},{"id":"GO:1904706","count":25},{"id":"GO:0034609","count":25},{"id":"GO:0003065","count":25},{"id":"GO:1904753","count":25}]},{"hash":"1531089542999017621","title":"Neural development and endocytic signaling","description":"This cluster centers on neural development and glial-axon interactions, with strong signals for microglia development, paranodal junction assembly, Notch signaling, and receptor internalization/endosomal transport. The mix of VEGF signaling and visual perception terms fits neural/retinal development and communication, while endosome-to-melanosome transport reinforces the endocytic trafficking theme. Overall, a cohesive theme around neural development and endocytic signaling.","confidence":"Medium","size":25,"edges":290,"triangles":2093,"max_degree":24,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0014005","count":21},{"id":"GO:0030913","count":21},{"id":"GO:2000145","count":21},{"id":"GO:1900746","count":21},{"id":"GO:0035646","count":21}]},{"hash":"40881506636622870","title":"Embryonic development and morphogenesis","description":"The GO terms point to broad embryonic tissue and organ formation processes\u2014placental/trophoblast differentiation, mesoderm development, and various morphogenesis events (cartilage, hair follicle, roof of the mouth), along with patterning and EMT related to heart development. Together these terms describe a cohesive theme of developmental biology and tissue morphogenesis in the embryo.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":25},{"id":"GO:0007498","count":25},{"id":"GO:0060536","count":25},{"id":"GO:0060806","count":25},{"id":"GO:0031069","count":25}]},{"hash":"612300694763279747","title":"Cytochrome P450 steroid and xenobiotic metabolism","description":"This cluster is heavily enriched for GO terms tied to steroid hormone production (androgen metabolic process, testosterone biosynthetic process) and mammary/gonad development, but also shows strong association with P450-related detoxification pathways (omega-hydroxylase P450 pathway, fatty acid omega-oxidation, retinoic acid catabolic process, insecticide and alkaloid metabolism). The common thread appears to be cytochrome P450\u2013driven metabolism affecting both endogenous steroids and xenobiotics, so a single cohesive label referencing P450-mediated steroid and xenobiotic metabolism is appropriate.","confidence":"High","size":25,"edges":4,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":25},{"id":"GO:0061370","count":25},{"id":"GO:0030879","count":24},{"id":"GO:0010193","count":24},{"id":"GO:0008585","count":24}]},{"hash":"537906445680606620","title":"Embryonic vascular and hematopoietic development","description":"This cluster centers on GO terms tied to hematopoietic stem cell proliferation, leukocyte trafficking, endothelial proliferation, and angiogenesis, all within an embryonic development context (somite and roof of mouth development). The combination suggests a broader developmental program coordinating blood/immune system formation with vascular development, rather than a single tight pathway, which fits a labeled theme of embryonic vascular and hematopoietic development.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071425","count":5},{"id":"GO:0050901","count":4},{"id":"GO:0001935","count":4},{"id":"GO:0045766","count":4},{"id":"GO:0061053","count":3}]},{"hash":"9033978950784297","title":"Paranodal adhesion and axon guidance proteins","description":"This cluster is dominated by GO terms about localizing and assembling components at paranode/juxtaparanode regions of axons, along with heterophilic cell\u2013cell adhesion and general axon guidance. The strongest signals are about paranode localization and axon pathfinding, suggesting a cohesive function in organizing neural cell contacts and guidance cues, despite a few less-specific terms (angiogenesis, ossification) present among the top terms.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0071205","count":10},{"id":"GO:0007155","count":10},{"id":"GO:0001525","count":10},{"id":"GO:0030913","count":10},{"id":"GO:0043931","count":10}]},{"hash":"426950693518207266","title":"Neuroimmune Regulation of Dopaminergic Signaling","description":"The GO terms show a strong mix of neuroimmune features (immune response, negative regulation of inflammatory response, eosinophil chemotaxis, astrocyte chemotaxis) and glial signaling with dopaminergic processes (dopamine transport, dopamine metabolism, phospholipase C-activating dopamine receptor signaling), suggesting a theme where neuroinflammation and glial activity modulate dopamine pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":25},{"id":"GO:0042493","count":25},{"id":"GO:2000458","count":25},{"id":"GO:1900168","count":25},{"id":"GO:0048245","count":25}]},{"hash":"2114247681368850147","title":"Dopaminergic signaling and neuroimmune regulation","description":"This cluster combines dopamine transport/signaling with CNS neuroimmune functions (astrocyte/glial activity and immune response). The top GO terms include dopamine transport, phospholipase C-activating dopamine receptor signaling, astrocyte chemotaxis, regulation of glial-derived neurotrophic factor production, immune response, and response to xenobiotic stimulus, suggesting proteins that couple dopaminergic signaling to glial/immune processes in the brain.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":25},{"id":"GO:0042493","count":25},{"id":"GO:2000458","count":25},{"id":"GO:1900168","count":25},{"id":"GO:0048245","count":25}]},{"hash":"1952400431654177783","title":"Integrin signaling and actin cytoskeleton remodeling","description":"These proteins show strong enrichment for integrin-mediated signaling, regulation of the actin cytoskeleton (including cortical actin and stress fibers), and cell adhesion via integrins, pointing to a core role in adhesion-driven cytoskeletal remodeling. Additional terms related to bone mineralization, cell polarity, and signal complex assembly align with coordinated cell\u2013matrix signaling and cytoskeletal dynamics. ","confidence":"High","size":24,"edges":46,"triangles":57,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032092","count":7},{"id":"GO:0030500","count":7},{"id":"GO:0051492","count":7},{"id":"GO:0007229","count":7},{"id":"GO:0008285","count":7}]},{"hash":"1987522011963852040","title":"Translation and ribosome biogenesis","description":"The top GO terms cluster around protein synthesis and ribosome assembly (translation, translational initiation, ribosome biogenesis) and transcription by RNA Pol III, indicating a core theme of the gene expression machinery. Some other terms (innate immune response, antibiotic response, organ identity maintenance) are broader cellular processes that appear as secondary annotations but do not redefine the primary function of the group.","confidence":"Medium","size":24,"edges":152,"triangles":513,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006359","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0045947","count":2}]},{"hash":"224523213489515469","title":"DNA Repair and Cellular Stress Response","description":"Based on the prominent GO terms, this cluster centers on maintaining genome integrity (base-excision repair, DNA recombination, DNA catabolic processes) and mounting cellular defenses against stress (response to xenobiotic stimulus, redox homeostasis). The inclusion of signaling-related terms such as phosphatidylinositol dephosphorylation suggests coordination with cellular signaling. Taken together, proteins in this cluster appear linked to DNA maintenance and broader stress-response pathways.","confidence":"Medium","size":24,"edges":120,"triangles":276,"max_degree":19,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006284","count":14},{"id":"GO:0046856","count":14},{"id":"GO:0006308","count":13},{"id":"GO:2000327","count":13},{"id":"GO:0042493","count":13}]},{"hash":"654976482504094081","title":"Ubiquitin-regulated TNF/NF-\u03baB signaling and apoptosis","description":"The top GO terms point to ubiquitin-dependent protein modification (K6-linked ubiquitination, autoubiquitination), regulation of TNF-mediated signaling and I-kappaB phosphorylation (NF-\u03baB pathway), and control of apoptotic processes, with additional links to antiviral transport and V(D)J recombination. This suggests a cohesive theme of ubiquitin-driven signaling in immune responses and cell survival, justifying a label centered on ubiquitin-mediated regulation of immune signaling. ","confidence":"High","size":24,"edges":42,"triangles":14,"max_degree":8,"top_function":"autophagy","top_go_terms":[{"id":"GO:1903265","count":10},{"id":"GO:0042787","count":10},{"id":"GO:0042981","count":9},{"id":"GO:1901253","count":9},{"id":"GO:0033151","count":9}]},{"hash":"1180446458828967422","title":"Cardiac and vascular morphogenesis with calcium signaling","description":"The cluster is driven by terms related to heart development, ventricular muscle morphogenesis, calcium signaling regulation (calcium channel activity and import), and branching morphogenesis of vessels and lungs, with supporting ECM remodeling (collagen catabolic process). Some outliers exist (short-term memory, amyloid fibril formation), but the core theme aligns with cardiac/vascular development and calcium control.","confidence":"Medium","size":24,"edges":37,"triangles":12,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007614","count":9},{"id":"GO:0043129","count":7},{"id":"GO:1990000","count":7},{"id":"GO:0055010","count":6},{"id":"GO:0060315","count":6}]},{"hash":"127783740768439103","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":92,"triangles":127,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033129","count":8},{"id":"GO:0070935","count":8},{"id":"GO:0098586","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0051965","count":7}]},{"hash":"282313801431685194","title":"Neuronal signaling and pain processing","description":"The top GO terms are dominated by neural-related functions: locomotory behavior, regulation of sensory perception of pain, prepulse inhibition, and modulation of glutamatergic synaptic transmission, along with responses like amphetamine exposure. Electron transport chain terms suggest mitochondrial activity typical in neurons, supporting neural signaling. A few items (viral release, cytolysis, cell wall catabolic process) are less directly related and may reflect broader cellular roles or annotation noise, but the core pattern points to neural signaling and sensory/pain processing.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":8},{"id":"GO:0007626","count":8},{"id":"GO:0051482","count":8},{"id":"GO:0001975","count":8},{"id":"GO:0051967","count":8}]},{"hash":"383010285454550908","title":"Chloroplast Energy Metabolism and Transport","description":"The top GO terms center on proton transmembrane transport, vacuolar acidification, photosynthesis, and nonphotochemical quenching, all of which point to chloroplast- and vacuole-associated energy capture and proton-driven processes. Translation is also listed, which can reflect chloroplast gene expression, while several catabolic terms (toluene/carbazole) seem peripheral and may reflect broader metabolic capabilities rather than core function of this cluster. Overall, the dominant theme is chloroplast-related energy production and membrane transport.","confidence":"Medium","size":24,"edges":170,"triangles":701,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":5},{"id":"GO:0006412","count":3},{"id":"GO:0015991","count":3},{"id":"GO:0007035","count":3},{"id":"GO:0055114","count":2}]},{"hash":"126451715262173721","title":"Embryonic development and organogenesis","description":"The top GO terms cluster around diverse developmental and morphogenetic processes across multiple organs (placenta/trophoblast, cartilage, left-right patterning, endocrine development, pancreatic cell development, heart cushion formation via EMT, acrosome reaction, cochlea development) and related differentiation. While varied, they collectively point to embryonic development and tissue morphogenesis rather than a single, narrow function, justifying the label of broad developmental organogenesis.","confidence":"Medium","size":24,"edges":8,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060972","count":5},{"id":"GO:0035270","count":5},{"id":"GO:0003323","count":5}]},{"hash":"65867819824407865","title":"Actin-driven endothelial migration and angiogenesis","description":"The shared terms point to dynamic actin cytoskeleton remodeling (lamellipodium and filopodium assembly, actin organization) driving cell spreading and movement. VEGF response and GTPase activation support migratory/angiogenic signaling in vascular contexts, while the vascular remodeling terms tie the cluster to endothelial behavior. Overall, this cluster seems focused on cytoskeleton-mediated endothelial cell migration and angiogenesis.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0060313","count":7},{"id":"GO:0043314","count":7},{"id":"GO:0030032","count":6},{"id":"GO:1900026","count":6},{"id":"GO:0046847","count":6}]},{"hash":"2092560561922659302","title":"Cilium-related mitosis and visual perception","description":"The cluster is dominated by mitotic cell cycle and cell division terms, suggesting a core link to cell proliferation. At the same time, several terms point to cilium assembly and visual perception, aligning with ciliary functions required for photoreceptor signaling and intracellular transport (Ran signaling, GTPase regulation, endosome dynamics). This combination implies proteins involved in ciliary biology that intersects with cell cycle processes and intracellular trafficking. ","confidence":"Medium","size":24,"edges":89,"triangles":45,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":19},{"id":"GO:0051301","count":18},{"id":"GO:0007601","count":11},{"id":"GO:0031291","count":10},{"id":"GO:0002098","count":10}]},{"hash":"470390759843297688","title":"RNA Processing and Innate Antiviral Defense","description":"The cluster centers on RNA processing (mRNA, miRNA, siRNA) and includes antiviral/innate immunity terms (innate immune response, regulation of viral transcription and replication) plus translational control via eIF2\u03b1 phosphorylation, suggesting a shared function in RNA metabolism linked to host antiviral defense and stress-related protein synthesis regulation.","confidence":"High","size":24,"edges":158,"triangles":493,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":5},{"id":"GO:0035196","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0010998","count":3}]},{"hash":"1046235980420546230","title":"Innate Immune Signaling and Cytokine Regulation","description":"This cluster is strongly enriched for innate immune and cytokine-related terms: innate immune response, defense against viruses and Gram-negative bacteria, macrophage activation, dendritic cell cytokine production regulation, and Toll-like receptor 2 signaling. While a few terms touch on mechanotransduction or bone remodeling, the dominant theme is pathogen recognition and cytokine-mediated immune signaling, justifying a label centered on innate immunity and cytokine control.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":7},{"id":"GO:0051607","count":6},{"id":"GO:0071260","count":5},{"id":"GO:0034134","count":5},{"id":"GO:1900155","count":5}]},{"hash":"673265322600366370","title":"Developmental signaling and synaptic vesicle trafficking","description":"This cluster centers on signaling pathways (Rho regulation; GPCR-related signaling), and synaptic vesicle processes (priming, budding), with neural (sound perception) and broader developmental terms (heart development, blood vessel remodeling, cell migration) suggesting a shared theme of developmental signaling intertwined with neuronal/synaptic function and vesicle dynamics. Hence the label focusing on developmental signaling and synaptic vesicle trafficking.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":8},{"id":"GO:0007205","count":7},{"id":"GO:0007605","count":7},{"id":"GO:0016477","count":7},{"id":"GO:0016082","count":7}]},{"hash":"551707239459146626","title":"Innate immune signaling and xenophagy","description":"The top GO terms cluster around innate immune responses and antiviral signaling, including response to dsRNA, innate immune response, interferon-beta production, and NF-kappaB regulation, as well as lipopolysaccharide signaling and xenophagy. This suggests a functionally cohesive group of proteins involved in initial pathogen sensing and inflammatory signaling, with autophagic targeting of microbes (xenophagy) being a key theme. Some terms like apoptotic process or mitotic cell cycle appear less central to the main theme but can be connected to broader stress responses.","confidence":"High","size":24,"edges":23,"triangles":5,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006915","count":9},{"id":"GO:0043330","count":8},{"id":"GO:0045087","count":8},{"id":"GO:0045359","count":8},{"id":"GO:0031663","count":8}]},{"hash":"2241801283947175246","title":"Nuclear pore transport and ribosome export","description":"The cluster is strongly enriched for nuclear transport-related GO terms, including nuclear pore complex assembly and ribosomal subunit export from the nucleus, with some related transcription regulation and GTPase activity terms that appear peripheral. This points to a cohesive theme around nuclear trafficking and ribosome biogenesis rather than a single alternative process.","confidence":"Medium","size":24,"edges":270,"triangles":1896,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0051292","count":9},{"id":"GO:0060188","count":8},{"id":"GO:0042176","count":8}]},{"hash":"1442954764873498370","title":"Mitotic progression and ubiquitin-mediated proteolysis","description":"Most of the top GO terms point to mitosis and protein turnover: mitotic cell cycle, metaphase/anaphase transition, APC-dependent catabolic process, and ubiquitin-dependent protein degradation including K11-linked ubiquitination. Other terms about cadmium response, interferon signaling, and steroid receptor assembly appear less central to the core theme. Overall, the cluster seems to group proteins involved in cell-cycle control coupled with ubiquitin-mediated proteolysis.","confidence":"High","size":24,"edges":6,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0070979","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0042787","count":5}]},{"hash":"797973065216798443","title":"Post-transcriptional mRNA processing and translation control","description":"This cluster centers on post-transcriptional regulation: spliceosome-mediated mRNA processing, mRNA stability, and regulation of translation initiation and miRNA-mediated silencing. The prominence of splicing, stability, and translation-related GO terms indicates a unified theme of mRNA maturation and usage rather than a single enzyme pathway.","confidence":"High","size":24,"edges":190,"triangles":1021,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048025","count":15},{"id":"GO:0048255","count":14},{"id":"GO:0001825","count":14},{"id":"GO:0010610","count":14},{"id":"GO:0006446","count":14}]},{"hash":"1095718636279785724","title":"Germ cell differentiation and chromatin regulation","description":"This cluster centers on spermatid nucleus differentiation, with multiple terms pointing to transcriptional and epigenetic control (negative regulation of transcription by RNA polymerase II, DNA methylation and histone modifications), plus spindle assembly and Wnt signaling related to developmental processes. The combination suggests a theme of germ cell development coordinated by chromatin remodeling and transcriptional regulation, despite some historical/obsolete terms.","confidence":"High","size":24,"edges":11,"triangles":1,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007289","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0051225","count":4},{"id":"GO:0016055","count":3},{"id":"GO:0090308","count":3}]},{"hash":"1137576804397143592","title":"Developmental gene regulation","description":"Most enriched GO terms point to DNA-templated transcription and regulation of gene expression during development (neural tube closure, multicellular organism development, skeletal system development), with some involvement in cell cycle processes (mitotic cell cycle, sister chromatid cohesion). This pattern suggests a cohesive theme of transcriptional control in developmental contexts, despite a few terms related to stress or immune responses. ","confidence":"Medium","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0001843","count":4},{"id":"GO:0007064","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0006349","count":3}]},{"hash":"2098367325937588151","title":"Neuronal development and signaling cluster","description":"The top GO terms focus on neural development and signaling processes, e.g., axial mesoderm formation and fasciculation of sensory neuron axons, along with neural function readouts like visual learning and receptor clustering. Regulatory and catabolic processes (JNK pathway regulation and proteasomal degradation) support dynamic signaling and protein turnover in neurons. Some terms touch metabolism and immunity, but the strongest pattern is neural development and signaling, making this a reasonable label despite breadth. ","confidence":"Medium","size":24,"edges":124,"triangles":289,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":23},{"id":"GO:0048320","count":23},{"id":"GO:0097155","count":23},{"id":"GO:0032092","count":23},{"id":"GO:0008542","count":23}]},{"hash":"558162934521373832","title":"Neuronal differentiation and microtubule regulation","description":"The dominant GO terms cluster around neuron development and dentate gyrus development, paired with \u03b1-tubulin acetylation and regulation of the microtubule cytoskeleton. This points to a shared role in neuronal differentiation controlled by microtubule dynamics. Some terms (e.g., angiogenesis, thigmotaxis, NLRP3 inflammasome regulation) are more peripheral, and an outlier entry (ectoine biosynthetic process) may reflect annotation noise, but the core theme remains neural development intertwined with cytoskeletal regulation.","confidence":"Medium","size":24,"edges":95,"triangles":233,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":7},{"id":"GO:0048666","count":4},{"id":"GO:0021542","count":4},{"id":"GO:1900227","count":4},{"id":"GO:0071929","count":4}]},{"hash":"766658710548672224","title":"Developmental signaling and neurodevelopment","description":"The cluster shows strong representation of signaling pathways central to development and neural patterning (Wnt signaling, ephrin receptor signaling, CNS and blastocyst development). Additional terms like neurotransmitter secretion and mammary gland involution reflect broader developmental remodeling, while translation is a general cellular process co-occurring with these pathways. Overall, these terms converge on embryonic development and neural differentiation, suggesting a cohesive but not perfect signature.","confidence":"Medium","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:0006412","count":3},{"id":"GO:2000271","count":2},{"id":"GO:0060056","count":2},{"id":"GO:0007269","count":2}]},{"hash":"655335156170260109","title":"Unknown","description":"The GO terms span insect reproductive development, skeletal muscle development, immune signaling, circadian rhythm, gravitropism, and renal physiology, showing no single cohesive function or pathway for the cluster. This diversity suggests no clear common theme, so a generic Unknown label is appropriate.","confidence":"","size":24,"edges":44,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045497","count":6},{"id":"GO:0048741","count":6},{"id":"GO:2000176","count":6},{"id":"GO:0045496","count":6},{"id":"GO:0042748","count":6}]},{"hash":"2016180262076793982","title":"Neuronal development and axon guidance","description":"These proteins are tied to neuronal wiring and synaptic maturation, evidenced by go terms for retinal ganglion cell axon guidance, CNS projection neuron axonogenesis, dendritic spine morphogenesis, ephrin signaling, and integrin-mediated adhesion. Additional terms related to neurodevelopment and general cell regulation support a cohesive theme around neural development rather than other pathways. ","confidence":"High","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0048320","count":2},{"id":"GO:0031290","count":2}]},{"hash":"762512447042823772","title":"Cerebellar development and excitatory synaptic signaling","description":"The cluster is dominated by brain-related development terms, especially cerebellum and ventricle development, along with excitatory synaptic activity (excitatory postsynaptic potential) and related neural functions like visual learning. Some terms are broader or peripheral (apoptosis, nuclear export), but the prevailing theme is neural development and synaptic signaling, justifying this label.","confidence":"Medium","size":24,"edges":64,"triangles":39,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021678","count":9},{"id":"GO:0021592","count":9},{"id":"GO:0008542","count":9},{"id":"GO:0060079","count":9},{"id":"GO:0006349","count":9}]},{"hash":"1484341438546266515","title":"Neuro-immune inflammation and pain signaling","description":"The cluster is enriched for innate immune and inflammatory responses (innate immune response, cellular response to LPS, response to dsRNA, interferon-beta production, defense against Gram-positive bacteria) alongside neural/pain-related terms (behavioral response to formalin-induced pain, cellular response to dopamine, corpus callosum development), suggesting a group of proteins involved in neuro-immune communication and pain signaling.","confidence":"Medium","size":24,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":5},{"id":"GO:0022038","count":4},{"id":"GO:0061368","count":4},{"id":"GO:0043330","count":4},{"id":"GO:1903351","count":4}]},{"hash":"1740576327021765469","title":"Cytoskeletal remodeling during cell migration","description":"The proteins map to processes that govern cell movement and cytoskeletal dynamics, notably lamellipodium assembly and Rho signaling, along with GPCR, thrombin receptor, and prostaglandin signaling pathways that regulate actin remodeling. Immune-related cytokine responses (IL-7, IL-4) accompany these signals, suggesting roles in immune cell migration and signaling, with heart development as a broader contextual hint. Overall, the cluster centers on cytoskeletal remodeling driving cell migration.","confidence":"High","size":24,"edges":90,"triangles":80,"max_degree":15,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007507","count":10},{"id":"GO:0007205","count":10},{"id":"GO:0016477","count":9},{"id":"GO:0030032","count":8},{"id":"GO:0098761","count":8}]},{"hash":"13122792397590014","title":"Motor neuron development and axon guidance","description":"Dominated by neural development terms, especially spinal cord motor neuron cell fate specification and motor neuron axon guidance, along with general neuron development and nervous system development. This suggests the cluster centers on motor neuron formation and pathfinding, with ancillary signals like cell growth and cell-matrix adhesion.","confidence":"High","size":24,"edges":268,"triangles":1869,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060766","count":6},{"id":"GO:0021520","count":6},{"id":"GO:0008045","count":5},{"id":"GO:0048666","count":5},{"id":"GO:0016049","count":4}]},{"hash":"1157789159652555715","title":"GPCR-Rho Signaling and Cell Migration","description":"The top GO terms cluster around GPCR signaling (GO:0007205), regulation of Rho signaling (GO:0035023), and cell migration (GO:0016477), implying a functional group centered on GPCR-driven signal transduction that modulates cytoskeletal dynamics to promote movement. While other terms touch on telomere regulation, LPS signaling, or protein tetramerization, these appear as secondary associations rather than core themes. Overall, the dominant pattern is GPCR-mediated signaling guiding cell migration.","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007205","count":13},{"id":"GO:2001275","count":10},{"id":"GO:0016477","count":10},{"id":"GO:0007605","count":9},{"id":"GO:0051262","count":9}]},{"hash":"1416396246957933550","title":"Neuroimmune signaling and axon guidance","description":"The proteins show a blend of immune-related terms (complement activation, innate immunity) and neuronal development terms (axon extension, neuron projection guidance, regeneration), suggesting a cluster involved in neuroimmune signaling and neural remodeling or neuroinflammation. Additional terms about STAT phosphorylation and monocyte chemotactic factors point toward signaling cross-talk between immune and neural pathways.","confidence":"Medium","size":24,"edges":125,"triangles":294,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0014068","count":4},{"id":"GO:0001867","count":4},{"id":"GO:0048691","count":3},{"id":"GO:0042523","count":3},{"id":"GO:0006958","count":3}]},{"hash":"690942671466145071","title":"Cartilage development and ECM remodeling","description":"This cluster centers on cartilage-related development (growth plate chondrocyte morphogenesis; endodermal differentiation) and dynamic extracellular matrix (ECM) remodeling (negative regulation of ECM assembly; positive regulation of metallopeptidase activity; cell-matrix adhesion and migration). The heterotrimerization term suggests collagen/trimer formation, consistent with cartilage ECM, together indicating a functional theme of cartilage formation coupled with ECM remodeling. Although complement activation and coagulation appear, they are likely secondary context within tissue remodeling or inflammation and do not negate the core cartilage/ECM theme.","confidence":"High","size":24,"edges":102,"triangles":193,"max_degree":21,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0070208","count":9},{"id":"GO:0035987","count":9},{"id":"GO:0003429","count":9},{"id":"GO:1901202","count":9},{"id":"GO:0034113","count":9}]},{"hash":"1289761955797714612","title":"Amino acid metabolism and cofactor biosynthesis","description":"The top GO terms cluster around biosynthetic pathways for cofactors (biotin biosynthesis, protoporphyrinogen IX biosynthesis) and several amino acid biosynthesis/catabolism routes (lysine, tyrosine, alanine, threonine, kynurenine). There are also a couple of signaling pathways (Notch signaling, salicylic acid\u2013mediated defense), suggesting the proteins form a metabolic module with broader regulatory roles. This combination points to a cohesive theme of metabolism with linked signaling, rather than a single dedicated pathway, hence the label.","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009102","count":16},{"id":"GO:0006782","count":16},{"id":"GO:0019878","count":16},{"id":"GO:0007219","count":13},{"id":"GO:0097053","count":13}]},{"hash":"1017048450083181637","title":"Unknown","description":"This set mixes developmental/organ physiology terms (ureteric bud morphogenesis, renal sodium absorption, respiratory system process) with cellular organization and regulatory processes (secretory granule localization, centrosome maintenance, GTPase activity regulation) and even immune and viral-host terms. There is no clear unifying function across the proteins, so a specific functional label cannot be supported.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0032252","count":2},{"id":"GO:0051661","count":2},{"id":"GO:0032922","count":2},{"id":"GO:0007565","count":2}]},{"hash":"1213695201766736910","title":"Sphingolipid metabolism and phospholipid remodeling","description":"This cluster is dominated by GO terms tied to lipid biology: sphingosine and sphinganine-1-phosphate metabolic processes, regulation of sphingolipid\u2013mediated signaling, phospholipid catabolic and dephosphorylation activities, and phosphatidylglycerol biosynthesis. While there is a hint of carbohydrate transport and oxidant detoxification, the strongest and most cohesive signal is coordinated sphingolipid and phospholipid metabolism/remodeling, suggesting a lipid-centric functional theme for the protein set.","confidence":"High","size":24,"edges":245,"triangles":1451,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0015760","count":4},{"id":"GO:0009395","count":4},{"id":"GO:0044328","count":4},{"id":"GO:0046839","count":4},{"id":"GO:0006670","count":4}]},{"hash":"747605188907092540","title":"Osteochondral Differentiation and Ossification","description":"This cluster is dominated by GO terms for BMP signaling and differentiation of bone and cartilage lineages (chondrocytes/chondroblasts, osteoblasts) and endochondral ossification, plus ERK signaling involvement. Together these points indicate a cohesive module focused on skeletal development, specifically osteogenesis and chondrogenesis, with a secondary note of related BMP-driven development such as heart valve morphogenesis. ","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"wound healing","top_go_terms":[{"id":"GO:0030513","count":22},{"id":"GO:0003181","count":22},{"id":"GO:0060591","count":22},{"id":"GO:0060710","count":22},{"id":"GO:0045669","count":22}]},{"hash":"779259742514038351","title":"Innate immune response and complement activation","description":"The cluster's top GO terms are dominated by innate immunity and complement activation (classical pathway), with supporting terms like neutrophil homeostasis and immunoglobulin transcytosis, indicating an immune-defense theme. A few terms relate to unrelated processes, possibly due to annotation breadth or dual-function proteins, but the primary signal is innate immune function.","confidence":"High","size":24,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006958","count":8},{"id":"GO:0045087","count":8},{"id":"GO:1902414","count":5},{"id":"GO:0070352","count":5},{"id":"GO:0002415","count":5}]},{"hash":"2104888888257532989","title":"DNA damage response and apoptosis","description":"The top GO terms cluster around programmed cell death and DNA-related processes (apoptotic process, DNA catabolic process, DNA recombination). Additional terms indicate broader stress responses to xenobiotics, hormone signaling, and redox/homeostatic regulation, including cAMP signaling. This combination points to a module primarily involving DNA damage response and apoptosis, with supporting stress-response pathways. ","confidence":"High","size":24,"edges":186,"triangles":791,"max_degree":22,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006915","count":17},{"id":"GO:0006308","count":16},{"id":"GO:2000327","count":16},{"id":"GO:0042493","count":16},{"id":"GO:0071375","count":16}]},{"hash":"1317511144653679803","title":"Neural development and synaptic signaling","description":"The cluster is dominated by terms related to nervous system development, brain development, and neural plate axis specification, plus synaptic transmission (glutamatergic) and cell\u2013cell adhesion (homophilic/heterophilic). These point to roles in brain development and neuronal connectivity, with adhesion molecules facilitating synapse formation and signaling. Ossification appears only as a minor theme, making the neural development/synaptic signaling interpretation the most coherent overall.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":3},{"id":"GO:0007156","count":3},{"id":"GO:0007157","count":3},{"id":"GO:0010447","count":3},{"id":"GO:0045087","count":3}]},{"hash":"1817966974194074099","title":"Placental and embryonic morphogenesis","description":"The top GO terms cluster around embryonic development with a clear focus on placental lineage and morphogenesis (placental development, trophoblast differentiation, mesoderm development, left/right patterning, EMT in heart/endocardial cushion), supported by related endocrine and organ development terms. This suggests a cohesive theme of early developmental differentiation and tissue formation, especially in placenta-related contexts.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":6},{"id":"GO:0060806","count":6},{"id":"GO:0060972","count":6},{"id":"GO:0060536","count":6},{"id":"GO:0003323","count":6}]},{"hash":"2147474494721045889","title":"Unknown","description":"The GO terms are highly mixed, spanning apoptosis, RNA silencing pathways (regulatory ncRNA, piRNA processing), germline development (spermatid development), ubiquitination regulation, and cardiac electrophysiology, with no single unifying function. The lack of edges/triangles further suggests this cluster does not reflect a cohesive module, so a precise label isn\u2019t defensible.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":1},{"id":"GO:0008625","count":1},{"id":"GO:0010596","count":1},{"id":"GO:0031397","count":1},{"id":"GO:0031047","count":1}]},{"hash":"666121178456453131","title":"Fatty acid and secondary metabolite biosynthesis","description":"The GO terms are dominated by biosynthetic processes: fatty acid elongation and very long-chain fatty acid synthesis, alongside biosynthesis of antibiotics, phylloquinone, poly-hydroxybutyrate, and cofactor tetrahydrobiopterin, plus glucocorticoid biosynthesis. This points to a cluster of proteins involved in lipid and other metabolite biosynthesis, with ancillary regulatory aspects. ","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030497","count":24},{"id":"GO:0006704","count":24},{"id":"GO:0042376","count":24},{"id":"GO:0042619","count":24},{"id":"GO:0055114","count":24}]},{"hash":"849671494308122658","title":"Potassium transport and membrane potential in heart and neurons","description":"The top GO terms cluster around potassium ion transport and regulation of resting membrane potential, including cardiac action potentials and heart-rate regulation, indicating a shared role in excitability of heart and neural tissues. While a few terms touch mechanosensation and vestibular development, the dominant theme is potassium-driven membrane potential control in excitable cells.","confidence":"High","size":24,"edges":94,"triangles":144,"max_degree":18,"top_function":"nervous system process","top_go_terms":[{"id":"GO:0060075","count":24},{"id":"GO:0098914","count":24},{"id":"GO:1990573","count":23},{"id":"GO:0086002","count":23},{"id":"GO:0086091","count":23}]},{"hash":"1813548461807667231","title":"Glycan processing and glycosphingolipid biosynthesis","description":"The top GO terms converge on glycan metabolism and glycosphingolipid biosynthesis: N-acetylneuraminate metabolism, N-glycan processing, oligosaccharide metabolism, glycosylceramide metabolism, and ganglioside biosynthesis, with a note on an obsolete N-linked glycosylation term. This suggests a cohesive cluster centered on protein and lipid glycosylation pathways that influence membrane composition and signaling, even though a few pollen/olfactory-related terms appear sparsely in the set. Overall, the common theme is glycan processing and glycosphingolipid production.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006054","count":4},{"id":"GO:0006491","count":4},{"id":"GO:0009860","count":4},{"id":"GO:0009846","count":4},{"id":"GO:0021628","count":4}]},{"hash":"1196688092555945010","title":"Unknown","description":"The GO terms are highly diverse (development, immune response, neural signaling, osmoregulation) and there are no edges connecting the proteins. There isn't a single cohesive function that ties the 24 proteins together; only a subset relates to ion transport or osmotic stress, while many terms point to unrelated biological processes.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040018","count":3},{"id":"GO:0032094","count":3},{"id":"GO:2000311","count":2},{"id":"GO:0051023","count":2},{"id":"GO:0070977","count":2}]},{"hash":"2140785786125253743","title":"Spermatogenesis and piRNA silencing","description":"The cluster centers on germline-related processes: spermatid development and piRNA processing with regulatory ncRNA-mediated gene silencing, plus a transposon regulation term. These together suggest a theme of germ cell development coupled with piRNA-powered genome defense against transposable elements. A few terms related to mitochondrial assembly and signaling may reflect ancillary metabolic or signaling aspects in developing germ cells, but the dominant signal is spermatogenesis linked to piRNA-mediated silencing.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":2},{"id":"GO:0033617","count":2},{"id":"GO:1901625","count":1},{"id":"GO:0032148","count":1},{"id":"GO:0010738","count":1}]},{"hash":"1365809099541587504","title":"Diverse substrate transmembrane transport","description":"This cluster is enriched for GO terms describing transport across membranes for a variety of substrates (xenobiotics, sugars, nitrate/nitrite, sialic acid, and neurotransmitter loading into vesicles), indicating a cohesive theme of membrane transporter activity with broad substrate specificity rather than a single substrate or pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0006855","count":6},{"id":"GO:0035435","count":6},{"id":"GO:0098700","count":6},{"id":"GO:1900754","count":6},{"id":"GO:0042128","count":6}]},{"hash":"1110937459728364812","title":"Muscle Ion Transport and Excitation","description":"These proteins cluster around ion transport across membranes (Ca2+, Na+, K+, Zn/Cd) and electrochemical gradient maintenance, with a note on regulation of fast-twitch skeletal muscle contraction, suggesting involvement in skeletal muscle excitation\u2013contraction coupling.","confidence":"High","size":24,"edges":160,"triangles":779,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0031448","count":21},{"id":"GO:0099132","count":21},{"id":"GO:0010248","count":21},{"id":"GO:0070588","count":21},{"id":"GO:0002028","count":21}]},{"hash":"2074376792034653687","title":"Cell adhesion and immune regulation","description":"This cluster is enriched for GO terms tying cell adhesion (heterophilic adhesion, general cell adhesion) to immune cell functions (neutrophil extravasation, macrophage activation regulation, NK and CTL activity regulation) and actin cytoskeleton dynamics linked to adhesion, suggesting a theme of adhesion-mediated immune signaling and cell trafficking.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2000391","count":13},{"id":"GO:0051963","count":12},{"id":"GO:0043031","count":12},{"id":"GO:0046718","count":12},{"id":"GO:0002859","count":12}]},{"hash":"1304580242966756318","title":"Membrane Transport of Cofactors and Metabolites","description":"This cluster is dominated by GO terms for transmembrane transport of small molecules and cofactors (thiamine pyrophosphate, phosphate, CoA, PLP, glycine, malate-aspartate shuttle) and mitochondrial ATP transport, indicating a cohesive theme around membrane transport of metabolites and cofactors, with mitochondrial involvement. A single term about necroptosis regulation is less related but does not override the prevalent transport signal.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0030974","count":24},{"id":"GO:0035435","count":24},{"id":"GO:0035349","count":24},{"id":"GO:0036233","count":24},{"id":"GO:0043490","count":24}]},{"hash":"1985422642576882268","title":"Neuroimmune Regulation of Dopamine Signaling","description":"The cluster shows strong enrichment for immune/inflammatory terms alongside dopaminergic neural terms, and includes glial-associated processes. This combination points to a cohesive theme of neuroimmune interactions affecting dopamine transport/metabolism and glial modulation of neural signaling.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":23},{"id":"GO:0042493","count":23},{"id":"GO:2000458","count":23},{"id":"GO:1900168","count":23},{"id":"GO:0048245","count":23}]},{"hash":"592840885212325508","title":"Glial-Immune Regulation of Dopamine Signaling","description":"The cluster shows enrichment for immune-related terms (immune response; negative regulation of inflammatory response; eosinophil chemotaxis), astrocyte/glial-related terms (regulation of astrocyte chemotaxis; glial cell-derived neurotrophic factor production), xenobiotic response, and dopaminergic processes (dopamine transport; regulation of dopamine metabolic process; phospholipase C-activating dopamine receptor signaling). This pattern suggests coordinated glial involvement in neuroinflammation and modulation of dopamine signaling, potentially in response to xenobiotics, providing a cohesive theme of glial-immune interactions with dopamine pathways.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":24},{"id":"GO:0042493","count":24},{"id":"GO:2000458","count":24},{"id":"GO:1900168","count":24},{"id":"GO:0048245","count":24}]},{"hash":"1922848125403366389","title":"Cell cycle, centrosome function, and telomere maintenance","description":"This cluster centers on centrosome cycle, DNA replication, telomere maintenance via telomerase, and mitotic DNA damage checkpoints, pointing to a module of cell-cycle control and genome stability. Some developmental terms appear but likely reflect broader roles in proliferative/regulatory contexts rather than a primary developmental theme.","confidence":"Medium","size":23,"edges":83,"triangles":142,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0051973","count":4},{"id":"GO:0001890","count":4}]},{"hash":"1808580512168099488","title":"Chromatin Regulation and Proteostasis","description":"The cluster centers on DNA-templated transcription and chromatin modification (histone marks, deacetylation) and includes proteostasis-related processes (aggresome formation, misfolded protein transport, chaperone-mediated assembly) as well as mitophagy and oxidative stress\u2013related cell death, suggesting a functional module tying transcriptional control to protein quality control and stress responses.","confidence":"Medium","size":23,"edges":135,"triangles":374,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006355","count":7},{"id":"GO:0051568","count":3},{"id":"GO:0010870","count":3},{"id":"GO:0034983","count":3}]},{"hash":"1937663824067295002","title":"Synaptic vesicle trafficking and endocytosis","description":"The top GO terms cluster around vesicle transport and recycling in neurons\u2014anterograde/retrograde synaptic vesicle movement, endocytosis, synaptic vesicle budding, and ER-Golgi trafficking\u2014along with a neuronal development hint from Purkinje cell layer maturation, pointing to neuronal synaptic vesicle cycling and intracellular trafficking as the shared function.","confidence":"High","size":23,"edges":181,"triangles":777,"max_degree":22,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0048490","count":13},{"id":"GO:0006890","count":13},{"id":"GO:0035646","count":13},{"id":"GO:0006888","count":13},{"id":"GO:0006886","count":12}]},{"hash":"1387116789348341037","title":"Rho GTPase signaling and cytoskeletal remodeling in development","description":"The top GO terms center on positive regulation of GTPase activity and Rho-mediated signaling, along with actin cytoskeleton organization and microtubule-based movement, indicating roles in cytoskeletal dynamics and cell movement. Development-related terms such as spinal cord development and multicellular organism development, plus IGF receptor signaling, suggest these proteins participate in growth and morphogenesis signaling networks. Together, these points support a theme of Rho GTPase\u2013driven cytoskeletal remodeling during development.","confidence":"High","size":23,"edges":45,"triangles":21,"max_degree":10,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043547","count":11},{"id":"GO:0035023","count":7},{"id":"GO:0021510","count":7},{"id":"GO:0048009","count":7},{"id":"GO:0007264","count":7}]},{"hash":"952889176081602254","title":"Ribosome biogenesis and translation","description":"This cluster centers on ribosome biogenesis and translation: rRNA maturation and pseudouridine synthesis, large subunit assembly, and cytoplasmic translation, with additional RNA processing links such as spliceosome-related regulation.","confidence":"High","size":23,"edges":246,"triangles":1634,"max_degree":22,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:0042254","count":6},{"id":"GO:0000027","count":4},{"id":"GO:0031118","count":3},{"id":"GO:0031120","count":3}]},{"hash":"1281342854999877696","title":"Neural development and synapse formation","description":"The cluster shows strong representation of nervous system development, cell adhesion at synapses (homophilic and heterophilic), and chemical synaptic transmission, along with corticospinal tract morphogenesis and regulation of oligodendrocyte progenitor proliferation. These terms together point to neural connectivity, axon tract formation, and subsequent myelination, with additional supportive processes like angiogenesis and phagocytosis that aid neurodevelopment and synapse remodeling. Overall, the theme is neural development focused on synapse formation and maturation.","confidence":"High","size":23,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007156","count":7},{"id":"GO:0007157","count":7},{"id":"GO:0043931","count":6},{"id":"GO:0007268","count":5},{"id":"GO:0021957","count":5}]},{"hash":"640273593466582345","title":"Gametogenesis and Heterochromatin Regulation","description":"The top GO terms are dominated by heterochromatin formation across several genomic contexts (rDNA, pericentric, subtelomeric) and related transcriptional repression, along with sex-chromosome dosage compensation. In addition, germline development terms (oogenesis, spermatogenesis, vitellogenesis) suggest a link between gamete formation and chromatin regulation. A few outliers (plasmid partitioning, Rho signaling) are likely incidental to the cluster. ","confidence":"Medium","size":23,"edges":249,"triangles":1693,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0048477","count":21},{"id":"GO:0030543","count":20},{"id":"GO:0035023","count":20},{"id":"GO:0031509","count":20},{"id":"GO:0007296","count":20}]},{"hash":"2131428201620779009","title":"Spindle assembly and centrosome cycle regulation","description":"The top GO terms point to mitotic spindle assembly, centrosome cycle, and microtubule-related regulation (tubulin deacetylation) with accompanying ubiquitin-dependent proteolysis, all hinting at cell-cycle and spindle dynamics. Other terms (autophagy, histone acetylation, viral transcription, foam cell differentiation) appear less central, but do not override the primary microtubule/mitosis theme.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0006990","count":3},{"id":"GO:0043969","count":3},{"id":"GO:1901097","count":3}]},{"hash":"794759014858336317","title":"Clathrin-mediated endocytosis and actin remodeling","description":"This cluster is dominated by vesicle trafficking and endocytosis terms, especially clathrin-mediated endocytosis, clathrin coat assembly, and actin cytoskeleton remodeling (including Arp2/3 regulation) along with Golgi-to-endosome transport. The inclusion of PDGFR-beta signaling and iron import hints at endocytic regulation of signaling and nutrient uptake, supporting a cohesive endocytic/trafficking module centered on clathrin-mediated pathways.","confidence":"High","size":23,"edges":252,"triangles":1750,"max_degree":22,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006895","count":18},{"id":"GO:2000369","count":17},{"id":"GO:0000147","count":16},{"id":"GO:0006915","count":16},{"id":"GO:0098711","count":15}]},{"hash":"176949298162817649","title":"Chemical Stress Response and Redox Signaling","description":"The cluster centers on GO terms related to responses to chemical stimuli (estradiol, ethanol, nitrophenol) and redox/oxidative processes (oxidation-reduction, nitric oxide biosynthesis), with additional hints of apoptosis regulation, aging, and memory. Taken together, these points suggest a theme of cellular responses to chemical stress and associated redox signaling, rather than a single, cohesive pathway. Some terms are obsolete, indicating potential annotation noise. ","confidence":"Medium","size":23,"edges":23,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0032355","count":4},{"id":"GO:0045471","count":4},{"id":"GO:0055114","count":4}]},{"hash":"30242791899584529","title":"Developmental signaling and differentiation","description":"The top GO terms point to developmental and differentiation programs, including spinal cord development, striated muscle cell differentiation, and regulation of Notch signaling, with supporting chromatin modification roles (histone acetylation/methylation) and signaling pathways (Rho). While there are also general cellular processes (protein transport, rRNA maturation), these can accompany differentiation and development, suggesting a cohesive theme around developmentally regulated signaling and cell fate changes. ","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":2},{"id":"GO:0043001","count":2},{"id":"GO:2000617","count":2},{"id":"GO:0051146","count":2},{"id":"GO:0007605","count":2}]},{"hash":"2227220296547345534","title":"Organelle inheritance and spindle organization","description":"The GO terms point to intracellular partitioning: mitochondrion and peroxisome inheritance, spindle organization, and vesicle transport along actin\u2014key aspects of organelle inheritance and chromosome segregation during cell division. Additional terms for transcription, DNA repair, and protein complex assembly may reflect general maintenance of cellular machinery, but the dominant theme is inheritance and cytoskeletal coordination during division. Some terms (like cobalamin biosynthesis) are less clearly connected, but they do not override the main signal from the inheritance and spindle-related terms.","confidence":"Medium","size":23,"edges":8,"triangles":0,"max_degree":3,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0006461","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0045033","count":1}]},{"hash":"130395750860276689","title":"Rho-Driven Actin Remodeling and Cell Migration","description":"The cluster is dominated by GO terms tied to actin cytoskeleton dynamics and movement: regulation of Rho signaling, lamellipodium and microspike assembly, actin filament bundle assembly, and cell migration, with supporting pathways such as thrombin receptor signaling and Wnt signaling that influence cytoskeletal remodeling. These collectively point to a cohesive role in actin-driven motility and structural rearrangements, even if a few terms (like mitotic spindle assembly) are tangentially related.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0030032","count":5},{"id":"GO:0070493","count":5},{"id":"GO:2001275","count":4},{"id":"GO:0016477","count":4}]},{"hash":"853717084685364295","title":"B cell receptor signaling and actin remodeling","description":"This cluster centers on signals that activate B cells while reorganizing the actin cytoskeleton. Key terms include regulation of Rho-mediated signaling and actin filament organization, alongside B cell receptor signaling and follicular B cell differentiation, all pointing to cytoskeletal reorganization during B cell activation. Although a few terms touch on translation initiation or broader signaling like Wnt, the dominant theme is B cell\u2013associated signaling coupled with actin dynamics.","confidence":"Medium","size":23,"edges":27,"triangles":17,"max_degree":13,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0050853","count":5},{"id":"GO:1903679","count":5},{"id":"GO:0000147","count":5},{"id":"GO:2000251","count":5}]},{"hash":"597220242302438418","title":"Redox Homeostasis and Oxidative Stress Response","description":"This cluster is dominated by GO terms for maintaining redox balance and detoxifying oxidants (cell redox homeostasis, cellular oxidant detoxification, cellular response to oxidative stress) and includes redox-related protein modifications like deglutathionylation. There are also transcription-related terms that may reflect redox-regulated transcription. Overall, the core theme is redox balance and oxidative stress response with some link to transcriptional regulation.","confidence":"High","size":23,"edges":129,"triangles":374,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":15},{"id":"GO:0098869","count":11},{"id":"GO:1903026","count":10},{"id":"GO:0055114","count":10},{"id":"GO:0018401","count":10}]},{"hash":"1413912924413198778","title":"Ras/Rho/Ral GTPase Signaling Regulators","description":"The dominant GO terms point to regulation and activation of small GTPases (Ras, Rho, Ral) and GTPase activity, suggesting a shared role in modulating GTPase signaling. Some terms also relate to neural development and insulin signaling, but the core signal is GTPase regulation, supporting a label focused on Ras/Rho/Ral pathways.","confidence":"Medium","size":23,"edges":15,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032485","count":2},{"id":"GO:0035023","count":2},{"id":"GO:1904693","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0046580","count":2}]},{"hash":"1790742284377880389","title":"Wnt signaling regulation and transcription in development","description":"The dominant themes are transcriptional regulation and Wnt pathway control, with supporting signals for pancreatic and brain development, cell cycle control, and insulin signaling, hinting at coordinated developmental gene expression programs.","confidence":"High","size":23,"edges":93,"triangles":177,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090090","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0071285","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0031018","count":2}]},{"hash":"1993533124998035504","title":"Rab-regulated ER-Golgi and endosome trafficking","description":"This cluster centers on COPII-coated vesicle cargo loading, Rab protein signaling, and transport steps linking the plasma membrane, endosomes, and Golgi, including retrograde transport and endosome-to-Golgi routes. The convergence on Rab signaling and vesicle trafficking across secretory and endocytic compartments supports labeling the cluster as Rab-regulated vesicle trafficking in the secretory pathway.","confidence":"High","size":23,"edges":49,"triangles":32,"max_degree":18,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0090110","count":4},{"id":"GO:0032486","count":4},{"id":"GO:0048227","count":4},{"id":"GO:0032483","count":4},{"id":"GO:0034499","count":4}]},{"hash":"668368072340285664","title":"Developmental epigenetic regulation","description":"The terms cluster around chromatin modification and transcriptional control (histone methylation, heterochromatin formation, negative regulation of transcription), alongside developmental processes (placental morphogenesis, uterine gland development) and growth/division signals (insulin signaling, spindle assembly) and immune development (negative thymic T cell selection). This pattern suggests a module of development governed by epigenetic regulation, rather than a single pathway, hence the label. ","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":7},{"id":"GO:0051225","count":6},{"id":"GO:0000122","count":6},{"id":"GO:2000584","count":6},{"id":"GO:0097676","count":6}]},{"hash":"1053942248219909851","title":"Mammary gland development and proliferation","description":"The top GO terms point to mammary gland biology\u2014mammary gland epithelial cell proliferation, lactation, multicellular organism growth, and cell division\u2014coupled with cell cycle regulation and TGF-beta signaling, suggesting a cohesive module of mammary gland development and functional expansion. Forebrain development and DNA-templated transcription appear, but the dominant themes are mammary growth and lactation-related processes.","confidence":"High","size":23,"edges":46,"triangles":32,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045737","count":6},{"id":"GO:0035264","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0007595","count":4}]},{"hash":"1878931926750457322","title":"Developmental morphogenesis and transcriptional regulation","description":"The leading GO terms point to embryonic organogenesis and tissue morphogenesis across diverse lineages (endocrine pancreas development, neural crest cell migration, ureteric bud branching, digestive tract morphogenesis, peripheral nervous system development), together with gene-expression regulation (negative regulation of transcription by RNA polymerase II, chromatin remodeling, positive regulation of DNA binding). This pattern suggests a cohesive set of proteins that coordinate developmental programs by regulating transcription and chromatin state, rather than a single tissue-specific function.","confidence":"High","size":23,"edges":51,"triangles":31,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":10},{"id":"GO:0031018","count":10},{"id":"GO:0043044","count":7},{"id":"GO:0001755","count":7},{"id":"GO:0090190","count":7}]},{"hash":"628546810376809297","title":"Viral life cycle: entry, budding, assembly, and integration","description":"Most top GO terms describe stages of viral infection and propagation: entry into host cells (symbiont entry into host), virion assembly, ESCRT-mediated budding, viral release, and DNA integration into the host genome (proviral latency). While a couple of terms relate to host chromatin modification, the dominant theme is viral life cycle processes, so this label is representative of the cluster.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007289","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0051096","count":2},{"id":"GO:0030260","count":2},{"id":"GO:0019076","count":2}]},{"hash":"806100386933943350","title":"Inflammation-Linked Apoptotic Signaling","description":"The cluster is dominated by inflammatory and stress-responsive GO terms (response to lipopolysaccharide; NF-kappaB and JNK signaling) and extrinsic apoptotic pathways, with additional links to development-related signaling (heart development, neurotrophin signaling). This suggests a cohesive theme of inflammation-driven apoptosis and stress signaling rather than a single specialized function. ","confidence":"Medium","size":23,"edges":115,"triangles":257,"max_degree":18,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051092","count":13},{"id":"GO:0097192","count":12},{"id":"GO:0035234","count":10},{"id":"GO:0071260","count":10},{"id":"GO:0032496","count":10}]},{"hash":"993953492308997140","title":"TLR2-driven Innate Immune Signaling in Macrophages","description":"This cluster centers on innate immune sensing and macrophage activation: TLR2 signaling, diacyl lipopeptide detection, defense against virus, macrophage activation, and IL-6 production, with accompanying regulation of signaling pathways (NF-kB, protein kinase activity). Some GO terms are less relevant (bone trabecula formation, lysosomal pH), but the dominant theme is TLR2-driven innate immunity.","confidence":"High","size":23,"edges":9,"triangles":1,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045410","count":5},{"id":"GO:0006469","count":5},{"id":"GO:0042346","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0034134","count":5}]},{"hash":"933505290432122842","title":"TLR2-driven innate immune signaling","description":"The cluster is dominated by GO terms tied to toll-like receptor 2 signaling, detection of diacyl lipopeptides, macrophage activation, defense against viruses, and interleukin-6 production, all pointing to innate immune recognition and inflammatory NF-kappaB signaling. A few developmental terms (hair follicle maturation, lymph vessel morphogenesis, bone trabecula regulation) are present but appear peripheral to the core immune theme, suggesting the primary function of this cluster is TLR2-mediated immune response.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0048820","count":4},{"id":"GO:0045410","count":4},{"id":"GO:0006469","count":4},{"id":"GO:0042346","count":4},{"id":"GO:0051607","count":4}]},{"hash":"1291450234572383882","title":"Transcriptional Regulation in Vertebrate Development","description":"This cluster is dominated by GO terms related to transcription control (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) and various developmental processes (endocrine system development, left-right pattern formation, cartilage morphogenesis). The combination suggests a set of transcriptional regulators coordinating vertebrate development, despite some obsolete terms in the list.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":23},{"id":"GO:0006351","count":21},{"id":"GO:0035270","count":20},{"id":"GO:0046022","count":20},{"id":"GO:0060806","count":20}]},{"hash":"1048692530574784888","title":"Vesicle trafficking and cytoskeletal dynamics","description":"The terms cluster around endomembrane processes (intralumenal vesicle formation, membrane/Golgi trafficking, plasma membrane repair, ER/polarization) and cytoskeletal regulation (GTPase activity, actin cortical patches, microtubule depolymerization). This suggests a protein set coordinating membrane trafficking with cytoskeletal dynamics, even though a few terms (neural axis specification, leading strand elongation) are less clearly connected and may reflect multifunctionality or annotation noise. ","confidence":"Medium","size":23,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":4},{"id":"GO:0070676","count":3},{"id":"GO:0051666","count":3},{"id":"GO:0021997","count":3},{"id":"GO:0001778","count":2}]},{"hash":"225913753597090327","title":"UV-induced DNA repair and transcription regulation","description":"The terms show a clear emphasis on UV response (UV-B, UV-C), nucleotide-excision repair (NER and transcription-coupled repair), and transcriptional control by RNA polymerase II, with supporting signals of keratinization and cell cycle regulation that fit a DNA-damage\u2013response context in epidermal tissues; some development terms (eye morphogenesis) may reflect tissue-specific roles but don't negate the core UV/repair theme.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":5},{"id":"GO:0010224","count":3},{"id":"GO:0010225","count":3},{"id":"GO:0000720","count":3},{"id":"GO:0048597","count":3}]},{"hash":"2164805529544195723","title":"RNA stability and translation control","description":"The top GO terms cluster tightly around post-transcriptional regulation: mRNA stabilization and stability under stress, regulation of translational initiation, preinitiation complex formation, translation reinitiation, and ncRNA-mediated gene silencing affecting translation. This suggests the proteins function together in controlling the mRNA life cycle and translation rather than transcription, reflecting RNA processing and translational control mechanisms.","confidence":"High","size":23,"edges":22,"triangles":3,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":6},{"id":"GO:0001825","count":6},{"id":"GO:0010610","count":6},{"id":"GO:0006446","count":6},{"id":"GO:1900363","count":6}]},{"hash":"1118280443540225880","title":"Adipogenesis and Innate Immune Signaling","description":"The top terms are centered on fat cell differentiation and innate immune pathways (TLR9 signaling and NF-kappaB regulation), with related macrophage foam cell differentiation. This pattern suggests a cohesive theme of adipocyte development intertwined with innate immune signaling, despite additional developmental terms that are broader. ","confidence":"High","size":23,"edges":19,"triangles":20,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001275","count":9},{"id":"GO:0045444","count":9},{"id":"GO:0010745","count":9},{"id":"GO:0035902","count":9},{"id":"GO:0006351","count":8}]},{"hash":"1514372554961893305","title":"Neural development and axon guidance","description":"The terms cluster around nervous system formation and axon pathfinding (axial mesoderm formation and sensory neuron axon fasciculation), plus related signaling activities (receptor clustering, proteasomal regulation), suggesting a neural development/axon guidance theme despite some broader terms.","confidence":"Medium","size":23,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":23},{"id":"GO:0048320","count":23},{"id":"GO:0097155","count":23},{"id":"GO:0032092","count":23},{"id":"GO:0008542","count":23}]},{"hash":"1693606293745851469","title":"Unknown","description":"The proteins are annotated with highly diverse GO terms including DNA repair, dephosphorylation, viral process, brush border assembly, equilibrioception, cell-cycle regulation, and various metabolic biosynthetic pathways (CoA catabolism, folic acid, IPP/FPP). This broad mix suggests no single cohesive function or pathway defining the cluster, and the lack of edges supports a non-specific grouping.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":4},{"id":"GO:0016311","count":2},{"id":"GO:0016032","count":2},{"id":"GO:1904970","count":2},{"id":"GO:0050957","count":2}]},{"hash":"2047191710445303805","title":"Mitochondrial protein import and proton transport","description":"Top terms point to mitochondrial membrane processes: protein import into the matrix, insertion into the inner membrane, and proton transmembrane transport. The inclusion of vacuolar acidification reinforces a membrane-transport theme. A few older or unrelated terms (chromatin remodeling, budding) are likely background noise in this cluster, but do not override the main mitochondrial localization/transport signal.","confidence":"Medium","size":23,"edges":6,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:0045039","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0031116","count":1}]},{"hash":"1260434398883526872","title":"Glycolysis and Carbohydrate Metabolism","description":"The top GO terms cluster around glycolysis, glycogen catabolic process, fructose-6-phosphate metabolism, pentose phosphate shunt, and broader carbohydrate metabolic processes. This indicates a cohesive group of enzymes involved in central carbohydrate metabolism, including energy-producing pathways and related biosynthetic steps, supporting a glycolysis/carbohydrate metabolism theme.","confidence":"High","size":23,"edges":216,"triangles":1163,"max_degree":22,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0046835","count":9},{"id":"GO:0061621","count":6},{"id":"GO:0006002","count":6},{"id":"GO:0093001","count":5},{"id":"GO:0005980","count":5}]},{"hash":"171045966652884050","title":"Cardiac development and embryonic organogenesis","description":"The cluster\u2019s prominent GO terms center on embryonic development and tissue formation, especially heart-related processes (heart development, left/right pattern formation, endocardial cushion EMT), along with morphogenesis and transcriptional regulation (cartilage morphogenesis, DNA-templated transcription). While a B cell receptor signaling term and endocrine development appear, the strongest signal is cardiac/embryonic organogenesis, suggesting proteins involved in developmental differentiation and heart formation. Confidence reflects the cohesive theme around cardiac and embryonic tissue development.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0050853","count":4},{"id":"GO:0060707","count":4},{"id":"GO:0060536","count":4},{"id":"GO:0060972","count":4}]},{"hash":"1921929216481348161","title":"Immune Defense and Host Cell Adhesion","description":"The cluster is enriched for innate and adaptive immune terms (innate immune response, complement activation, defense against bacteria, B cell receptor signaling) and adhesion terms (heterophilic/homophilic cell-cell adhesion), suggesting a set of proteins involved in immune defense and immune cell interactions with host tissues. Some ancillary terms (proteolysis, symbiont entry) also fit within host-microbe interactions, reinforcing the immune-focused theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0007157","count":4},{"id":"GO:0006508","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0042742","count":3}]},{"hash":"347690103907414435","title":"Fatty acid oxidation and BCAA catabolism","description":"The top GO terms cluster around fatty acid breakdown (beta-oxidation, acyl-CoA biosynthesis, carnitine metabolism) and branched-chain amino acid catabolism (valine, leucine), with supporting signals in gluconeogenesis regulation. A cardiac muscle differentiation term appears but the dominant theme is energy metabolism through lipid and BCAA pathways.","confidence":"High","size":23,"edges":229,"triangles":1374,"max_degree":22,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006574","count":17},{"id":"GO:0006552","count":15},{"id":"GO:0018896","count":14},{"id":"GO:0046949","count":14},{"id":"GO:0055007","count":14}]},{"hash":"1553399648172539213","title":"Toll-like receptor signaling and innate immunity","description":"The top GO terms are dominated by Toll-like receptor signaling pathways (TLR2, TLR3, TLR9) with MyD88-dependent and independent branches, NF-\u03baB activation (I-kappaB phosphorylation), and defense responses to Gram-negative bacteria/LPS, indicating a cohesive theme of TLR-mediated innate immune sensing and response.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0034134","count":2},{"id":"GO:0002755","count":2},{"id":"GO:0050829","count":2}]},{"hash":"9437494230565345","title":"Mitochondrial biogenesis and mitophagy","description":"The set strongly centers on mitochondrial processes: assembly of respiratory chain complexes (e.g., complex IV), cristae formation, and mitophagy, along with protein import and insertion into mitochondrial membranes and matrices. These terms indicate a cohesive theme of mitochondrial biogenesis, maintenance, and turnover. A few outliers (like chloroplast import and obsolete terms) exist, but they do not outweigh the core mitochondrial signal.","confidence":"High","size":23,"edges":218,"triangles":1183,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0042407","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0010259","count":2},{"id":"GO:0043457","count":2}]},{"hash":"2300081615698523651","title":"Cardiac muscle development and contraction","description":"This cluster is dominated by GO terms related to heart development and function, including ventricular morphogenesis, cardiac muscle contraction, and regulation of calcium-release channel activity, suggesting a core theme of cardiac muscle development and excitation-contraction coupling. Some terms about retina, Schwann cell, and metanephric development appear as broader developmental processes, but the strongest signal centers on cardiac muscle biology.","confidence":"Medium","size":23,"edges":29,"triangles":8,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055010","count":8},{"id":"GO:0061179","count":7},{"id":"GO:0060315","count":7},{"id":"GO:0060048","count":6},{"id":"GO:0097274","count":6}]},{"hash":"1475721994016529135","title":"TLR4-MyD88 innate signaling with muscle development","description":"The cluster centers on MyD88-dependent Toll-like receptor 4 signaling, indicating innate immune response activity, and also includes terms tied to muscle and heart development, cytoskeletal remodeling (lamellipodium assembly, cell migration), and signaling pathways (Rho/Ras) that connect immune signaling to developmental and motility processes.","confidence":"Medium","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035660","count":14},{"id":"GO:0007527","count":14},{"id":"GO:0006355","count":14},{"id":"GO:0035023","count":9},{"id":"GO:0046580","count":8}]},{"hash":"653449946325710795","title":"Embryogenesis and Organogenesis","description":"The cluster is dominated by GO terms related to embryonic development and tissue morphogenesis across multiple lineages\u2014placental/trophoblast differentiation, endocrine and pancreatic cell development, left-right patterning, EMT in heart development, cartilage morphogenesis, and skeletal muscle development\u2014suggesting a common theme of early development and organogenesis. The inclusion of signaling pathways like the p38MAPK cascade further supports coordinated developmental signaling. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0060707","count":6},{"id":"GO:0060536","count":6},{"id":"GO:0060972","count":6},{"id":"GO:0035270","count":6},{"id":"GO:0003323","count":6}]},{"hash":"1458183405646942119","title":"Developmental morphogenesis and differentiation","description":"GO terms in this cluster cluster around embryonic digit morphogenesis, neural crest formation, osteoblast development, and spermatogenesis, indicating a broad developmental and morphogenetic focus across lineages. Additional terms on membrane targeting and receptor-mediated endocytosis may reflect cellular processes that support development and tissue formation. Overall, the cluster appears best described by developmental morphogenesis/differentiation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090118","count":2},{"id":"GO:0051205","count":2},{"id":"GO:0001580","count":2},{"id":"GO:0006612","count":2},{"id":"GO:0007626","count":2}]},{"hash":"927286197451189932","title":"Glycosaminoglycan proteoglycan biosynthesis and metabolism","description":"The cluster is dominated by GO terms for glycosaminoglycan and proteoglycan biosynthesis/metabolism (heparan sulfate, chondroitin/dermatan sulfate, sulfation-related processes) and related sugar metabolism, indicating a cohesive theme around proteoglycan GAG biosynthesis and modification. Additional metabolic terms align with broader cellular metabolism but do not override the proteoglycan-focused signal. ","confidence":"High","size":23,"edges":116,"triangles":293,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0015015","count":12},{"id":"GO:0030206","count":12},{"id":"GO:0000103","count":10},{"id":"GO:0006044","count":10},{"id":"GO:0002002","count":10}]},{"hash":"1644310741991249404","title":"Inflammatory and immune signaling","description":"The top GO terms cluster around immune and inflammatory pathways: NF-kappaB signaling (I-kappaB phosphorylation and regulation of non-canonical NF-kappaB), regulation of stress-activated MAPK cascades, prostaglandin biosynthesis, hydrogen peroxide response, NK cell\u2013mediated cytotoxicity, and osteoclast differentiation. These together point to inflammatory signaling and immune modulation as the core function of the cluster, with a few terms on reproduction or general transcription regulation likely reflecting pleiotropy or annotation noise. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":4},{"id":"GO:0042345","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0001516","count":3},{"id":"GO:0007252","count":3}]},{"hash":"34347998152775933","title":"Embryonic development and tissue morphogenesis","description":"This cluster is dominated by GO terms related to embryonic development across multiple tissues and organs, including placenta (trophoblast giant cell differentiation, placental development), mesoderm formation, cartilage and hair follicle morphogenesis, palate development, and left-right patterning, with mention of epithelial-to-mesenchymal transition in cardiac structures. The common theme is broad developmental processes shaping tissues and organs during embryogenesis.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":18},{"id":"GO:0060536","count":18},{"id":"GO:0060806","count":18},{"id":"GO:0060972","count":18},{"id":"GO:0035270","count":18}]},{"hash":"1849845190838705018","title":"Glycosylation and cell-surface polarity in follicle epithelium","description":"The top GO terms cluster around carbohydrate modification (glycosylation, glycosphingolipid biosynthesis) and cell-surface organization/polarity, including follicle cell adhesion and epithelial polarity maintenance, suggesting a module focused on glycosylation-dependent cell-surface architecture in the follicular epithelium.","confidence":"Medium","size":23,"edges":245,"triangles":1615,"max_degree":22,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":8},{"id":"GO:0006688","count":7},{"id":"GO:0075015","count":7},{"id":"GO:0030259","count":5},{"id":"GO:0033580","count":5}]},{"hash":"159736805507903353","title":"Actin-driven cell migration and cytokinesis","description":"The cluster\u2019s GO terms cluster around actin-based processes: negative regulation of cell migration, vesicle transport along actin, membrane addition at cytokinesis, dorsal closure and leading edge differentiation, and myosin thick filament assembly, indicating actin\u2013myosin cytoskeletal remodeling during movement and division. Some terms touch on tissue-specific development (ventricular cardiac muscle development, third ventricle development) but still reflect cytoskeletal dynamics in morphogenesis; peroxisome inheritance also aligns with organelle partitioning linked to cytoskeletal transport. Overall, the theme is actin-driven cytoskeletal dynamics governing cell movement, division, and intracellular trafficking.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030336","count":2},{"id":"GO:0045033","count":1},{"id":"GO:0007118","count":1},{"id":"GO:0021678","count":1},{"id":"GO:0030241","count":1}]},{"hash":"1332603157487055588","title":"Embryonic Organogenesis and Tissue Differentiation","description":"This cluster has GO terms centered on embryonic development and organ morphogenesis across multiple tissues (pancreas, placenta, cartilage, palate, hair follicles, heart/endocardial cushions) and processes like epithelial-to-mesenchymal transition, left-right patterning, and endocrine system development, suggesting a shared role in developmental differentiation rather than a single molecular function.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0003323","count":16},{"id":"GO:0060707","count":16},{"id":"GO:0060536","count":16},{"id":"GO:0060806","count":16},{"id":"GO:0060972","count":16}]},{"hash":"460135872630893109","title":"Developmental Morphogenesis and Inflammation","description":"The cluster centers on developmental processes: collagen fibril organization, skeletal system development, axon guidance, neuron migration, and branching morphogenesis, indicating tissue morphogenesis and ECM remodeling. The accompanying inflammatory terms (complement activation, inflammatory response, chemokine production) suggest concurrent immune signaling within these developmental contexts, making the combined theme a developmental morphogenesis with inflammation.","confidence":"Medium","size":23,"edges":13,"triangles":1,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006958","count":4},{"id":"GO:0030199","count":4},{"id":"GO:0035987","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0090197","count":3}]},{"hash":"838735576052396649","title":"Nervous system development and signaling","description":"This label fits because the most represented terms point to neural development and signaling pathways (Roundabout/Slit-Robo, Smoothened/Hedgehog, BMP signaling, myelination, PNS development, and myoblast differentiation). The inclusion of cell adhesion and STAT signaling suggests coordination of neural patterning and intercellular communication, making nervous system development the best overarching theme for the cluster.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":7},{"id":"GO:0035385","count":6},{"id":"GO:0042552","count":6},{"id":"GO:0007422","count":5},{"id":"GO:0030513","count":5}]},{"hash":"2004375980043168446","title":"Embryogenesis and organ morphogenesis","description":"Top GO terms point to embryonic development across multiple tissues, including trophoblast differentiation, pancreatic and cartilage development, and left-right patterning, with EMT in heart cushion formation and broader endocrine development. This suggests a cohesive theme of developmental differentiation and morphogenesis, although some terms reflect general cellular processes (splicing, ribosome export, microtubule regulation) that are shared across proteins. Confidence: Medium","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":3},{"id":"GO:0003323","count":2},{"id":"GO:0060536","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0060972","count":2}]},{"hash":"1372913342885364615","title":"ER\u2013mitochondrial calcium signaling and apoptosis","description":"This cluster centers on calcium dynamics between the ER and mitochondria (positive/negative regulation of mitochondrial and ER calcium) and on mitochondrial apoptotic processes (cytochrome c release, mitochondrial depolarization) as well as extrinsic apoptotic signaling, indicating a cohesive theme of calcium-regulated apoptosis. A secondary term on ER-to-Golgi transport suggests broader organelle crosstalk but does not override the core apoptosis/calcium pattern.","confidence":"Medium","size":23,"edges":131,"triangles":329,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0051561","count":3},{"id":"GO:0032471","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0048538","count":2},{"id":"GO:0030890","count":2}]},{"hash":"2275423957799537801","title":"Cardiac development and electrophysiology","description":"This cluster centers on heart-related developmental and functional processes: mitral valve development, atrioventricular junction remodeling, and regulation of ventricular muscle cell membrane depolarization, pointing to cardiac structure and electrical activity. Other terms like chemical synaptic transmission and transmembrane transport are common in many tissues and do not override the cardiac focus, though sensory perception terms present are less informative for the core theme. Overall, the dominant signal is cardiac development and function.","confidence":"Medium","size":23,"edges":208,"triangles":1043,"max_degree":22,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0007605","count":10},{"id":"GO:0060373","count":9},{"id":"GO:0003174","count":9},{"id":"GO:0003294","count":9},{"id":"GO:0007268","count":9}]},{"hash":"724031295444669672","title":"Endothelial Angiogenesis and Migration","description":"The cluster is dominated by GO terms related to vascular development and endothelial behavior, including endothelial cell chemotaxis, sprouting angiogenesis, blood vessel endothelial cell migration, and positive regulation of angiogenesis, with supporting signaling like ERK and phospholipase activity; this points to a cohesive function in angiogenesis and endothelial cell movement during vessel formation and remodeling, potentially relevant to heart development contexts.","confidence":"High","size":23,"edges":211,"triangles":1109,"max_degree":22,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0035767","count":17},{"id":"GO:0070374","count":14},{"id":"GO:0071230","count":13},{"id":"GO:0007596","count":13},{"id":"GO:0002040","count":13}]},{"hash":"781010222845091449","title":"Developmental morphogenesis and EMT","description":"These terms cluster around tissue and organ formation, including skeletal morphogenesis, chondrocyte development, and pancreas development, as well as epithelial-to-mesenchymal transition and general cell differentiation. The actin filament bundle organization term points to cytoskeletal remodeling common in morphogenesis. The presence of several obsolete or broad terms suggests a broad developmental theme rather than a single pathway, supporting a label focused on development and morphogenesis rather than a specific signaling axis.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048705","count":1},{"id":"GO:0061572","count":1},{"id":"GO:1900158","count":1},{"id":"GO:0061182","count":1},{"id":"GO:0001837","count":1}]},{"hash":"1029380692408169036","title":"Neuronal adhesion, axon guidance, and synapse assembly","description":"The cluster centers on neuronal connections and pathfinding: multiple GO terms for cell adhesion (heterophilic/homophilic), axon guidance (ROBO signaling, axon guidance, chemorepulsion), and neuron migration, plus a clear signal for synapse assembly. The presence of paranode localization supports axon structure involvement, while complement activation may reflect roles in CNS remodeling. Overall, it points to neuronal adhesion-guided connectivity and synapse formation.","confidence":"High","size":23,"edges":12,"triangles":3,"max_degree":4,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":10},{"id":"GO:0007156","count":9},{"id":"GO:0006958","count":8},{"id":"GO:0007155","count":7},{"id":"GO:0002175","count":7}]},{"hash":"2237647117554254621","title":"Neural development and synaptic adhesion","description":"This cluster is dominated by GO terms related to nervous system development, brain development, neuron cell-cell adhesion, and regulation of synapse assembly, indicating a primary role in neural development and synaptic connectivity. A few terms reference non-neural organogenesis (nephron development, ossification), suggesting broader developmental roles for adhesion processes, but the core signal remains neural development. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":12},{"id":"GO:0043931","count":12},{"id":"GO:0007157","count":12},{"id":"GO:0051965","count":12},{"id":"GO:0007156","count":11}]},{"hash":"2074731744660415387","title":"Glycans and carbohydrate metabolism","description":"Top GO terms are dominated by carbohydrate metabolism and various catabolic/biosynthetic processes (maltose, glycogen, trehalose, sucrose, alpha-glucan) and even keratan sulfate proteoglycan turnover. This points to a functional cluster of proteins involved in glycan metabolism and energy storage/turnover. The neuromuscular process annotation is present but appears ancillary, not defining the core theme. Overall, the cluster is best described as glycan and carbohydrate metabolism.","confidence":"High","size":23,"edges":16,"triangles":5,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000023","count":6},{"id":"GO:0042340","count":5},{"id":"GO:0050884","count":4},{"id":"GO:0051692","count":4},{"id":"GO:0005980","count":4}]},{"hash":"561291352870858160","title":"Neuroimmune Modulation and Dopamine Signaling","description":"These proteins cluster around immune regulation and neural signaling, especially glial/astrocyte\u2013mediated regulation, neurotrophic factor production, and dopaminergic pathways (dopamine transport and receptor signaling). The GO terms suggest a cohesive theme of neuroimmune interaction with dopaminergic signaling, anchored by glial involvement in inflammation and neural modulation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":23},{"id":"GO:0042493","count":23},{"id":"GO:2000458","count":23},{"id":"GO:1900168","count":23},{"id":"GO:0048245","count":23}]},{"hash":"1898040684171602685","title":"Neuroimmune modulation of dopamine signaling","description":"Explanation: The cluster shows a cohesive theme linking immune/inflammatory processes (immune response, negative regulation of inflammatory response, eosinophil and astrocyte chemotaxis) with dopaminergic signaling (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling) and glial/neurotrophic aspects (astrocyte chemotaxis, GDNF production) in response to xenobiotic stimuli, suggesting neuroimmune crosstalk that modulates dopamine pathways.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":23},{"id":"GO:0042493","count":23},{"id":"GO:2000458","count":23},{"id":"GO:1900168","count":23},{"id":"GO:0048245","count":23}]},{"hash":"1812687163868592122","title":"Ubiquitin/SUMO-mediated protein regulation","description":"The cluster is dominated by GO terms related to post-translational modification and protein quality control, including ubiquitin-dependent ERAD, K63-linked deubiquitination, and sumoylation. These indicate a cohesive focus on regulating protein stability and function. Other terms hint at cell cycle and pheromone signaling, which frequently intersect with proteostasis and stress responses, while tRNA modification and iron-sulfur cluster assembly suggest broader metabolic coordination that can influence protein production and maturation. Overall, the strongest signal is regulatory control of proteins via ubiquitin/SUMO pathways, with ancillary links to metabolism and signaling.","confidence":"Medium","size":22,"edges":175,"triangles":723,"max_degree":21,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0002098","count":4},{"id":"GO:0045226","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0016226","count":4},{"id":"GO:0030433","count":4}]},{"hash":"1600567561126235721","title":"Immune Activation via Complement and T Cells","description":"The cluster is driven by terms tied to both innate and adaptive immunity: classical complement activation, immunoglobulin production, T cell costimulation and proliferation, and innate immune responses. These point to a cohesive module of immune activation involving antibody-mediated and T cell\u2013mediated processes, with some supporting roles in cell adhesion and signaling (e.g., NF-kappaB activity). ","confidence":"High","size":22,"edges":16,"triangles":4,"max_degree":9,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":10},{"id":"GO:0002377","count":9},{"id":"GO:0031295","count":9},{"id":"GO:0042102","count":9},{"id":"GO:0006508","count":8}]},{"hash":"1862545545854907441","title":"Chromatin remodeling and heterochromatin formation","description":"This cluster is dominated by GO terms tying proteins to heterochromatin formation and chromatin remodeling (e.g., rDNA heterochromatin formation, transcription initiation-coupled chromatin remodeling, chromatin assembly). Additional terms related to developmental processes (brain development, vitellogenesis, sex-chromosome dosage compensation) and even plasmid partitioning suggest a role for chromatin state in regulating gene expression across development and cellular contexts. Overall, the proteins likely function as a chromatin-modifying/regulatory module coordinating transcription during development.","confidence":"High","size":22,"edges":189,"triangles":1001,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":18},{"id":"GO:0006335","count":18},{"id":"GO:0051290","count":18},{"id":"GO:0045815","count":18},{"id":"GO:0007420","count":17}]},{"hash":"243998349058013174","title":"Developmental signaling and cytoskeletal regulation","description":"These proteins cluster around developmental processes and cytoskeletal control: axial mesoderm formation and keratinocyte proliferation suggest growth and differentiation; retinal ganglion cell axon guidance and fasciculation of sensory neurons point to neural pathfinding; and negative regulation of Rac/Rho signaling alongside cell cycle regulation aligns with cytoskeletal dynamics and proliferation. While there are outliers related to immune costimulation and lipid biosynthesis, the core theme is developmentally oriented signaling coupled with cytoskeletal regulation. ","confidence":"Medium","size":22,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000525","count":4},{"id":"GO:1905373","count":4},{"id":"GO:0043616","count":4},{"id":"GO:0048320","count":4},{"id":"GO:0031290","count":4}]},{"hash":"1048500926841733182","title":"Retroviral entry, integration, and latency","description":"Based on the top GO terms, this cluster is strongly linked to steps of a retroviral life cycle: entry into the host cell, penetration into the host nucleus, integration of proviral DNA, and establishment of proviral latency, along with RNA-templated DNA synthesis and DNA replication/recombination. The presence of negative regulation of siRNA processing also aligns with viral strategies to suppress host RNA silencing. Together, these terms point to proteins involved in retroviral genome integration and latency rather than generic cellular DNA processes. ","confidence":"High","size":22,"edges":223,"triangles":1398,"max_degree":21,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":20},{"id":"GO:0006260","count":20},{"id":"GO:0046718","count":19},{"id":"GO:0075732","count":19},{"id":"GO:0075713","count":19}]},{"hash":"1630033124051129219","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":135,"triangles":419,"max_degree":21,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016310","count":14},{"id":"GO:2000821","count":12},{"id":"GO:0035418","count":12},{"id":"GO:0048541","count":12},{"id":"GO:1903753","count":12}]},{"hash":"674876037267754423","title":"Rap GTPase\u2013driven endosome trafficking and actin remodeling","description":"The cluster is dominated by terms tied to Rap GTPase signaling, endosome organization/transport, and actin cytoskeleton remodeling, suggesting a core function in Rap-mediated vesicle trafficking and cytoskeletal dynamics. While TOR and NFAT-related terms are present, the strongest, most coherent theme centers on GTPase-regulated endosomal processes and cytoskeletal changes.","confidence":"High","size":22,"edges":10,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0032007","count":4},{"id":"GO:0019933","count":3},{"id":"GO:0032486","count":3},{"id":"GO:0007032","count":3}]},{"hash":"215489499292642278","title":"Photoreception and touch signaling","description":"The cluster is dominated by GO terms for sensory perception and signaling, especially photoreception (detection of light) and somatosensory perception (touch). The presence of receptor guanylyl cyclase signaling and intracellular signal transduction supports a theme of sensory signal transduction in sensory cells, such as photoreceptors and mechanosensory pathways. Some terms appear peripheral (cell wall organization, pons maturation, obsolete cAMP term), but the core pattern points to visual and tactile sensory signaling.","confidence":"High","size":22,"edges":63,"triangles":86,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":8},{"id":"GO:0021586","count":8},{"id":"GO:0007168","count":8},{"id":"GO:0035556","count":8},{"id":"GO:1900194","count":8}]},{"hash":"1368800354773766150","title":"Mitotic progression and cell cycle control","description":"The cluster is dominated by GO terms describing mitosis and cell cycle processes (mitotic cell cycle, cell division, cell cycle) and the anaphase-promoting complex\u2013dependent catabolic process, pointing to regulation of progression through mitosis. A secondary signal is a cellular response to cadmium, but the strongest and most frequent terms center on mitotic progression and cycle control, justifying this name.","confidence":"High","size":22,"edges":173,"triangles":785,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045842","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":4}]},{"hash":"636747489711883716","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":230,"triangles":1520,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0042273","count":9},{"id":"GO:0048026","count":8},{"id":"GO:0031047","count":8},{"id":"GO:0000463","count":6},{"id":"GO:0000472","count":6}]},{"hash":"2231480326951343819","title":"Chromatin regulation and signaling","description":"The top GO terms point to chromatin-related regulation (historical notes on methylation and chromatin organization) alongside several signaling pathways (Wnt, insulin receptor) and differentiation-related processes (spermatid nucleus differentiation). The mix suggests a broad regulatory cluster where chromatin state influences or interfaces with signaling to control cell division and differentiation, though the presence of obsolete terms and diverse pathways reduces cohesion. Confidence is Medium.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051225","count":5},{"id":"GO:0061087","count":4},{"id":"GO:1903758","count":4},{"id":"GO:0010216","count":4},{"id":"GO:0048549","count":4}]},{"hash":"2177128207633492335","title":"Membrane Lipid Biosynthesis and Maintenance","description":"Top GO terms in this cluster are heavily skewed toward lipid metabolism and membrane composition, including regulation of ergosterol biosynthesis, unsaturated fatty acid biosynthesis, and sphingolipid metabolism (mannosyl-inositol phosphorylceramide). Additionally, terms such as CNS myelin maintenance and sebaceous gland differentiation point to lipid-rich membranes and lipid-associated pathways. Other terms like nitrate assimilation and nitric oxide biosynthesis are more peripheral, and mitochondrial inheritance adds variance. Overall, the dominant theme centers on lipid production and membrane biogenesis, with some outliers.","confidence":"Medium","size":22,"edges":81,"triangles":169,"max_degree":15,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0001949","count":5},{"id":"GO:0032286","count":5},{"id":"GO:0006675","count":5},{"id":"GO:0055114","count":4}]},{"hash":"1265666512971781654","title":"Gene expression regulation and proteostasis","description":"This cluster shows a cohesive set of terms spanning transcriptional control (negative regulation of transcription by RNA Pol II), transcription-coupled DNA repair, regulation of translation initiation and preinitiation complex formation, and proteasome assembly/ubiquitin-dependent degradation, with ties to cell cycle control and stem cell differentiation. Together, these indicate a network coordinating gene expression, protein turnover, and developmental decisions, rather than a single isolated function.","confidence":"High","size":22,"edges":100,"triangles":178,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006283","count":5},{"id":"GO:0048863","count":5},{"id":"GO:0010972","count":5},{"id":"GO:0043248","count":4},{"id":"GO:0006446","count":4}]},{"hash":"1176262650584051357","title":"Post-transcriptional mRNA regulation and translation control","description":"The top GO terms center on mRNA splicing regulation, stability, polyadenylation, splice-site recognition, and translation initiation/reinitiation, plus miRNA-mediated translational repression. This points to a cohesive cluster whose proteins function in post-transcriptional processing and control of gene expression, with blastocyst formation reflecting developmental regulation via mRNA regulation.","confidence":"High","size":22,"edges":228,"triangles":1482,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":22},{"id":"GO:0048025","count":16},{"id":"GO:0048255","count":15},{"id":"GO:0001825","count":15},{"id":"GO:0006446","count":15}]},{"hash":"2218903398320372383","title":"Stress-Responsive Transcription and Signaling in Development","description":"The cluster centers on transcriptional regulation (DNA-templated transcription) and modulation of DNA repair, with strong signals for cellular responses to heavy metal stress (arsenite, cadmium), cytokine/growth factor signaling (GM-CSF, insulin receptor, ephrin receptor pathways), cell cycle progression, hypoxia response, and cranial skeletal morphogenesis, suggesting a coordinated program of gene expression and signaling during development under stress and growth cues.","confidence":"Medium","size":22,"edges":134,"triangles":378,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:2001033","count":9},{"id":"GO:1903936","count":9},{"id":"GO:0071276","count":9},{"id":"GO:0097011","count":8}]},{"hash":"840915031170987712","title":"Leukocyte adhesion and transmigration signaling","description":"Based on the top GO terms, this cluster is enriched for integrin-mediated signaling, cell\u2013cell adhesion, substrate-dependent cell migration, and cellular extravasation, which together describe how leukocytes adhere to endothelium and migrate through tissues. The T cell activation term also supports an immune-signaling context. Some ubiquitin-proteasome related terms likely reflect general protein turnover. Overall, the dominant theme is adhesion and migration in immune contexts, justifying this label.","confidence":"Medium","size":22,"edges":97,"triangles":211,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":10},{"id":"GO:0035987","count":8},{"id":"GO:0034113","count":8},{"id":"GO:0006929","count":8},{"id":"GO:0045123","count":8}]},{"hash":"1648438380916755183","title":"Cytoskeletal remodeling and growth-factor signaling","description":"This cluster is dominated by GO terms for actin cytoskeleton organization and regulation of Rho/small GTPase signaling, with related growth factor receptor pathways (growth hormone receptor and IGF signaling). The combination points to coordinated cytoskeletal dynamics and signal transduction driven by growth-factor signals, including effects on cell migration and vascular permeability, despite some coupling to Golgi localization terms. ","confidence":"High","size":22,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":5},{"id":"GO:0060396","count":5},{"id":"GO:0051683","count":5},{"id":"GO:0051497","count":4},{"id":"GO:0090334","count":4}]},{"hash":"175511645607614690","title":"Mitochondrial translation and energy metabolism","description":"The cluster is dominated by terms related to mitochondrial protein synthesis (translation and aminoacylation of glutamyl- and glutaminyl-tRNA, plus tRNA modification) and core mitochondrial energy pathways (TCA cycle, fatty acid beta-oxidation via acyl-CoA oxidase, and carnitine metabolism). This suggests a coherent theme around mitochondrial function combining protein synthesis with energy metabolism, despite a few older or broader terms that are less specific. ","confidence":"High","size":22,"edges":106,"triangles":191,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006424","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0019254","count":2}]},{"hash":"4864629430759558","title":"Carbohydrate Metabolism and Developmental Processes","description":"This cluster shows strong enrichment for carbohydrate-related metabolic terms (fructose metabolism, gluconeogenesis, carbohydrate phosphorylation, L-serine biosynthesis) and energy-related regulation (dephosphorylation), with additional developmental terms (brain development, intestinal epithelial cell development). While there are a few outliers (cobalt ion response, respiration), the dominant signal ties metabolism to developmental processes, supporting the label.","confidence":"Medium","size":22,"edges":185,"triangles":876,"max_degree":20,"top_function":"autophagy","top_go_terms":[{"id":"GO:0016311","count":13},{"id":"GO:0007585","count":12},{"id":"GO:0006564","count":12},{"id":"GO:0033133","count":12},{"id":"GO:0046835","count":12}]},{"hash":"2277684130837096036","title":"Renal and endocrine organ development","description":"The terms show kidney-specific development (ureteric bud branching; renal sodium absorption) and endocrine pancreas development, plus related organogenesis processes (respiratory system development; female pregnancy) and regulatory controls (Notch signaling, circadian gene expression). This points to a cluster of proteins involved in organ development with a renal/endocrine emphasis rather than a single, narrow pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090190","count":3},{"id":"GO:0071284","count":2},{"id":"GO:0031018","count":2},{"id":"GO:0032922","count":2},{"id":"GO:0007565","count":2}]},{"hash":"692510556589714060","title":"Growth signaling and gene expression regulation","description":"These proteins cluster around regulation of signaling and growth-related processes: GTPase activity regulation, mitotic cell cycle, and cell proliferation, together with transcription and translation initiation/reinitiation. While some terms touch on stress and immune signaling (cadmium response, NK cell degranulation), the predominant pattern points to growth signaling and control of gene expression. ","confidence":"Medium","size":22,"edges":8,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1108302198080431476","title":"Quinone biosynthesis and fatty acid catabolism","description":"The terms show strong presence of menaquinone and phylloquinone biosynthesis, indicating a quinone-based electron transport theme, paired with fatty acid beta-oxidation and related catabolic processes (phenylacetate, valine). This points to a bacterial metabolic module centered on energy production via quinones and lipid-derived substrates; a few outliers (neuromuscular regulation, buoyancy) appear peripheral to the core function.","confidence":"High","size":22,"edges":91,"triangles":135,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0006635","count":4},{"id":"GO:0010124","count":4},{"id":"GO:0042372","count":4}]},{"hash":"980021538688822890","title":"mRNA processing and translation regulation","description":"The cluster is enriched for mRNA stabilization, regulation of translational initiation, stress-responsive mRNA stability, splicing-related processes, and formation/reinitiation of the translation preinitiation complex, indicating a coherent group focused on post-transcriptional gene expression control and translation initiation. This combination suggests proteins involved in mRNA maturation, turnover, and the initiation of translation, including components of the small-subunit processome and related regulatory mechanisms.","confidence":"High","size":22,"edges":75,"triangles":155,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":5},{"id":"GO:0001825","count":5},{"id":"GO:0006446","count":5},{"id":"GO:0010610","count":5},{"id":"GO:1900363","count":5}]},{"hash":"1581125891705234880","title":"Embryonic organ development and tissue differentiation","description":"This cluster shows a strong enrichment for developmental and morphogenesis processes across multiple lineages and organs (heart, cartilage, pancreas, fat), as well as lineage specification and patterning (left/right, epithelial-to-mesenchymal transition). The common theme is embryonic organogenesis and differentiation programs, rather than a single tissue-specific function.","confidence":"High","size":22,"edges":76,"triangles":81,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0060707","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060806","count":5}]},{"hash":"1966046835162239348","title":"Mitochondrial respiration and stress response","description":"The top GO terms center on mitochondrial electron transport and respiratory chain assembly, plus autophagy and cellular senescence, pointing to a core theme of mitochondrial energy production and stress-related quality control that can influence aging. Other terms like transcription and methylation reflect broader regulatory connections but do not override the dominant mitochondrial/ stress signal. ","confidence":"Medium","size":22,"edges":49,"triangles":22,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0019919","count":2}]},{"hash":"670540774196404871","title":"Embryonic Development and Tissue Morphogenesis","description":"This cluster centers on developmental and morphogenetic processes across multiple tissues and organ systems, including spinal interneuron specification, cochlea morphogenesis, cartilage morphogenesis, left-right patterning, and endocrine and pancreatic development, indicating a cohesive theme of embryonic development and tissue formation rather than a single pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000055","count":3},{"id":"GO:0021521","count":3},{"id":"GO:0090103","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0060707","count":2}]},{"hash":"154757277246211065","title":"Mitochondrial translation and import","description":"This cluster is dominated by GO terms for mitochondrial protein synthesis and assembly, including mitochondrial translation and its elongation/termination, protein import into the mitochondrial matrix, and assembly of respiratory chain complex I, all tied to proton-motive force\u2013driven ATP production. These points together strongly indicate a mitochondrial biogenesis/program of gene expression and energy production.","confidence":"High","size":22,"edges":205,"triangles":1245,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0032981","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0070126","count":2}]},{"hash":"1526827191856988986","title":"Kidney development and circadian regulation","description":"The top GO terms cluster around kidney-related processes (renal sodium ion absorption; ureteric bud morphogenesis) and circadian regulation of gene expression, suggesting a functional group tied to kidney development with time-dependent transcription. Additional terms span broader organ system processes and some RNA modification/DNA repair activities, but the strongest coherence is kidney morphogenesis with circadian gene regulation, hence the label.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0032922","count":3},{"id":"GO:0007565","count":3},{"id":"GO:0070294","count":3},{"id":"GO:0090190","count":3},{"id":"GO:0003016","count":3}]},{"hash":"1042019577132705730","title":"Cardiac development and heart-function signaling","description":"The main GO terms cluster around ventricular cardiac muscle cell development and heart contraction, with related signaling pathways (Notch regulation, PI3K/AKT, neurotrophin signaling) and stress/apoptosis processes (ER-stress\u2013induced intrinsic apoptosis), plus transcriptional regulation. This points to a set of proteins involved in heart development and associated signaling/stress responses.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0055015","count":2},{"id":"GO:0032298","count":2},{"id":"GO:0051897","count":2}]},{"hash":"975343198440324220","title":"Multitissue development and morphogenesis","description":"The cluster\u2019s top terms span nervous system development, mesoderm and cartilage morphogenesis, hair follicle morphogenesis, and trophoblast differentiation, plus miscellaneous developmental and cellular-process terms. This pattern suggests proteins involved in broad developmental and morphogenetic roles across tissues rather than a single pathway, justifying a general label of multitissue development and morphogenesis.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048712","count":2},{"id":"GO:2001038","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0060707","count":2}]},{"hash":"253416536411747943","title":"Neural development and cytoskeletal dynamics","description":"The top GO terms point to neural development (neural tube closure; spinal cord motor neuron fate specification) and cytoskeletal remodeling (lamellipodium assembly; cell morphogenesis; GTPase activity). These together suggest a cluster centered on neurodevelopment and actin-driven cell movement, even though some terms are broader signaling processes that may be shared. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0032922","count":2},{"id":"GO:0070294","count":2},{"id":"GO:0043547","count":2}]},{"hash":"482072174325574358","title":"Synaptic transmission and plasticity regulation","description":"The cluster is dominated by GO terms linked to neuronal signaling and synaptic function: neurotransmitter secretion, long-term synaptic potentiation, and regulation of synaptic vesicle exocytosis, along with calcium- and phosphatidylinositol-mediated signaling and Rho/GTPase regulation that supports cytoskeletal changes during synaptic remodeling. While a few terms are broader, the central theme is neuronal communication and plasticity.","confidence":"High","size":22,"edges":48,"triangles":52,"max_degree":12,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":18},{"id":"GO:0043065","count":16},{"id":"GO:0071277","count":16},{"id":"GO:0048015","count":16},{"id":"GO:0007269","count":16}]},{"hash":"761816199026146926","title":"Nuclear transcription regulation and cell cycle control","description":"The top terms center on DNA-templated transcription, G2/M transition, and regulation of nuclear export, indicating a core role in controlling nuclear activities and cell cycle progression, with additional links to phosphorylation and metabolism as supportive functions.","confidence":"Medium","size":22,"edges":150,"triangles":489,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019346","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0000086","count":8},{"id":"GO:0046827","count":8},{"id":"GO:0033138","count":7}]},{"hash":"475462731979907394","title":"Unknown","description":"The Top Terms show a broad mix: embryonic axis formation, neural development (axon fasciculation, visual learning), signaling/modulation (JNK cascade, IL-7 response), protein turnover (proteasomal ubiquitin-dependent degradation), receptor clustering, and metabolism regulation (glycogen biosynthesis, insulin-related glucose import). This lack of a dominant shared function suggests no single, coherent biological role for the cluster; therefore the safe label is Unknown.","confidence":"","size":22,"edges":36,"triangles":7,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":21},{"id":"GO:0048320","count":21},{"id":"GO:0097155","count":21},{"id":"GO:0032092","count":21},{"id":"GO:0008542","count":21}]},{"hash":"1154826283215204505","title":"Nuclear transcription and RNA processing factors","description":"This cluster center on nuclear gene expression machinery: multiple terms point to DNA-templated transcription, RNA polymerase II regulation, and mRNA splicing, plus ribosomal large subunit export from the nucleus. A few developmental terms (left-right pattern formation, cartilage morphogenesis, trophoblast differentiation) suggest regulatory roles in development that can be tied to transcriptional control. The innate immune response term seems less connected to the core theme. Overall, the shared theme appears to be nuclear transcription and RNA processing components with some developmental associations.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0000398","count":3},{"id":"GO:1903026","count":3},{"id":"GO:0032298","count":3}]},{"hash":"1362112266505425504","title":"Amino Acid Biosynthesis and Metabolism","description":"The majority of top terms are amino acid biosynthetic and catabolic processes (alanine, serine, lysine, threonine) and related metabolite synthesis (pyruvate, biotin, protoporphyrinogen IX), grouping proteins around amino acid metabolism and cofactor biosynthesis. Notch signaling appears as an outlier rather than the core function of this cluster.","confidence":"Medium","size":22,"edges":189,"triangles":960,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":12},{"id":"GO:0097053","count":12},{"id":"GO:0042853","count":12},{"id":"GO:0042866","count":10},{"id":"GO:0009102","count":9}]},{"hash":"15595782506040603","title":"Cardiac conduction and calcium signaling","description":"Most top GO terms cluster around heart function and calcium handling: regulation of SA node action potential, Purkinje signaling, outflow tract morphogenesis, and calcium release from the sarcoplasmic reticulum in cardiac muscle. Vitamin D\u2013related response and caffeine response tie into signaling and calcium regulation, while skin development and immune-related terms are more peripheral. Overall, the dominant signal points to cardiac conduction and calcium signaling. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033280","count":14},{"id":"GO:0098907","count":14},{"id":"GO:0043588","count":13},{"id":"GO:0014808","count":13},{"id":"GO:0086029","count":13}]},{"hash":"2077073021716105672","title":"Synaptic development and Rho-mediated signaling in neurons","description":"The dominant terms describe synapse formation and localization (receptor clustering, protein localization to synapse, dendritic spine morphogenesis) and Rho-family signaling (Rho and regulation of Rho signaling), which together drive actin remodeling during synaptic development. Behavioral terms (grooming, exploration) and sensory term (sound perception) suggest involvement of neural circuits that regulate behavior and auditory processing, reinforcing a neuronal synapse-focused theme.","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043113","count":22},{"id":"GO:0035418","count":22},{"id":"GO:0008285","count":22},{"id":"GO:0007266","count":22},{"id":"GO:0060997","count":22}]},{"hash":"621925112324637413","title":"Vertebrate organogenesis and neural crest development","description":"Based on the top GO terms, the proteins are enriched for multiple developmental processes across vertebrate organs, including heart development, brain and inner ear development, neural crest cell migration, organ induction, and branching morphogenesis. Although one term reflects a general transcription process, the overall pattern points to a coordinated developmental program rather than a single pathway, justifying a label focused on organogenesis and neural crest\u2013related development.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":7},{"id":"GO:0007626","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0048839","count":6},{"id":"GO:0007420","count":6}]},{"hash":"2244296354267749991","title":"Neural development and cell adhesion","description":"This cluster is driven by cell adhesion terms (heterophilic/homophilic adhesion) and neural connectivity processes (synapse assembly, interneuron migration, axon localization), suggesting proteins involved in nervous system development and cell\u2013cell interactions. The presence of broader development signals (skeletal development, angiogenesis regulation, inflammation) indicates a general developmental context but with a strong emphasis on neural wiring.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007157","count":13},{"id":"GO:0051965","count":13},{"id":"GO:0021836","count":11},{"id":"GO:0043931","count":11},{"id":"GO:0007156","count":11}]},{"hash":"1423217171720114512","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"The cluster\u2019s top GO terms cluster around actin-driven protrusion and rearrangement (lamellipodium/filopodium assembly, actin cytoskeleton organization), adhesion-dependent spreading, and fibroblast migration, indicating a cohesive module governing actin remodeling and cell motility. Some signals (EGF response) and secretion terms may provide upstream or auxiliary context, but the dominant theme is actin dynamics governing movement and adhesion. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0030032","count":5},{"id":"GO:0051489","count":5},{"id":"GO:0010763","count":5},{"id":"GO:0030036","count":5},{"id":"GO:1900026","count":5}]},{"hash":"748927731896537281","title":"Multitissue development and differentiation","description":"The top GO terms point to morphogenesis and development across multiple tissues (digestive tract morphogenesis, thymus development, spermatogenesis, melanocyte differentiation) with supporting neural and cellular regulation (neuron apoptotic regulation, synaptic vesicle exocytosis). This pattern suggests the proteins collectively participate in broad developmental and differentiation programs rather than a single, narrow pathway.","confidence":"Medium","size":22,"edges":152,"triangles":552,"max_degree":20,"top_function":"cytokinesis","top_go_terms":[{"id":"GO:0001844","count":5},{"id":"GO:0071230","count":4},{"id":"GO:0030279","count":4},{"id":"GO:0010248","count":4},{"id":"GO:2000302","count":4}]},{"hash":"1375480153588015724","title":"Membrane Transport and Ion Homeostasis","description":"This cluster is dominated by transmembrane transport terms (chloride, borate, vitamin, fluid transport) and regulation of ionic/acid-base balance (pH, blood pressure), suggesting a shared role in membrane transport and homeostasis. Immune response and neuron development terms appear as incidental links rather than core functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006955","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0030194","count":2},{"id":"GO:0042044","count":2},{"id":"GO:0021860","count":2}]},{"hash":"395275156658455203","title":"Placental Branching Morphogenesis","description":"Two GO terms explicitly describe placental branching morphogenesis (labyrinthine layer morphogenesis and epithelial morphogenesis involved in placental branching), which strongly suggests a cluster centered on placental epithelial branching and development. While there are other terms related to broader development and signaling, they do not redefine the core theme. ","confidence":"Medium","size":22,"edges":5,"triangles":1,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045742","count":8},{"id":"GO:0090200","count":8},{"id":"GO:0042730","count":8},{"id":"GO:0043388","count":8},{"id":"GO:2001268","count":8}]},{"hash":"1761350140569375316","title":"Embryonic organogenesis and ECM remodeling","description":"The cluster centers on diverse developmental processes across organs (limb, adrenal gland, male gonad, ureteric bud, chorionic trophoblast) and extracellular matrix organization, with related regulation of TGF-beta signaling and cytoskeletal dynamics, suggesting a unifying theme of embryonic tissue morphogenesis and ECM remodeling.","confidence":"Medium","size":22,"edges":90,"triangles":186,"max_degree":14,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0007596","count":7},{"id":"GO:0060718","count":6},{"id":"GO:0030325","count":6},{"id":"GO:0051497","count":6},{"id":"GO:0008584","count":6}]},{"hash":"1317659911372870034","title":"Energy metabolism: photosynthesis and mitochondrial respiration","description":"The cluster is dominated by GO terms related to energy production, including proton transmembrane transport, photosynthesis (light reactions) and photosynthesis in general, as well as mitochondrial electron transport steps (ubiquinol to cytochrome c, NADH to ubiquinone) and ATP synthesis linked to electron transport. This combination indicates proteins that function in capturing and converting energy in both chloroplasts (photosynthesis) and mitochondria (respiratory ETC/ATP synthesis). Therefore, a concise label emphasizing overall energy metabolism across photosynthetic and respiratory pathways is appropriate.","confidence":"High","size":22,"edges":215,"triangles":1266,"max_degree":21,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1902600","count":7},{"id":"GO:0019684","count":6},{"id":"GO:0006122","count":6},{"id":"GO:0042773","count":5},{"id":"GO:0006810","count":5}]},{"hash":"2233946150437023267","title":"Circadian Lipid Metabolism and Immune Signaling","description":"Genes in this cluster repeatedly show triglyceride mobilization/catabolism and lipid remodeling, along with regulation of circadian rhythm and defense/virus-related immune responses. While transcription and ubiquitin-mediated degradation terms appear, the strongest cohesive themes are lipid metabolic processes aligned with circadian and immune signaling, suggesting a coordinated metabolic-immune-circadian module.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0042092","count":2},{"id":"GO:0042752","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0051607","count":2}]},{"hash":"429386320563947439","title":"Embryonic Organogenesis and Patterning","description":"These proteins are linked to multiple developmental processes: endocrine system development, placental differentiation, left-right pattern formation, cartilage morphogenesis, pancreatic islet cell development, epithelial-to-mesenchymal transition in heart structures, and hair follicle morphogenesis. Together these GO terms point to a cohesive theme of embryonic organogenesis and tissue patterning. A few terms about general transcription and ribosome export are present but do not overshadow the developmental signal. Overall, the cluster appears to reflect embryonic organogenesis and patterning mechanisms.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":7},{"id":"GO:0060806","count":7},{"id":"GO:0060972","count":7},{"id":"GO:0060536","count":7},{"id":"GO:0003323","count":7}]},{"hash":"1738713702727576676","title":"Inflammation-Associated Apoptosis and Lipid Homeostasis","description":"This cluster is enriched for apoptotic process, acute-phase response, and interleukin signaling (cellular response to interleukin-1, positive regulation of interleukin-8 production), along with phospholipid homeostasis. Together, these terms suggest a core theme of inflammation-linked cell death and membrane lipid regulation. Some development-related terms and chitin catabolic processes may be incidental or species-specific annotations, but the dominant pattern centers on inflammation, apoptosis, and lipid homeostasis.","confidence":"Medium","size":22,"edges":51,"triangles":49,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0055091","count":4},{"id":"GO:0071347","count":4},{"id":"GO:0032757","count":3},{"id":"GO:0045721","count":3}]},{"hash":"873964919662864724","title":"LPS-triggered inflammatory signaling and cytokine production","description":"The cluster\u2019s top GO terms center on lipopolysaccharide response, inflammatory signaling, and cytokine production (notably IL-6 and IL-23), as well as TNF-related responses and B cell apoptotic processes. This points to a cohesive immune/inflammatory module driven by endotoxin sensing and cytokine regulation, with some peripheral terms (urine volume regulation, PI3K signaling) that are less central. Overall, the theme is immune activation and cytokine-mediated inflammation with associated apoptosis in B cells.","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":3},{"id":"GO:0032747","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0001783","count":3},{"id":"GO:2000778","count":3}]},{"hash":"864386874285265532","title":"Erythroid and bone development","description":"The dominant terms point to red blood cell development (heme biosynthesis and erythrocyte differentiation) and skeletal formation (bone morphogenesis and bone mineralization), suggesting a cluster centered on hematopoietic and skeletal development. Additional terms reflect immune responses and trafficking but do not override these primary themes.","confidence":"Medium","size":22,"edges":49,"triangles":30,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006783","count":3},{"id":"GO:0030218","count":2},{"id":"GO:0035455","count":2},{"id":"GO:0009607","count":2},{"id":"GO:0035456","count":2}]},{"hash":"2133275919865287832","title":"Vacuolar amino acid transport","description":"Most terms describe transmembrane transport of amino acids (arginine, lysine, serine, histidine, asparagine) across the vacuolar membrane, with a few related terms on ion transport and stress response. The consistent theme is amino acid flux into/out of vacuoles, supporting a vacuolar amino acid transport function for the cluster.","confidence":"High","size":22,"edges":37,"triangles":15,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006867","count":8},{"id":"GO:1990818","count":8},{"id":"GO:0090517","count":8},{"id":"GO:0089707","count":8},{"id":"GO:0051365","count":8}]},{"hash":"497488572257378484","title":"Developmental Transcription and Morphogenesis","description":"The cluster shows strong enrichment for transcription by RNA polymerase II (22 genes), plus a mix of development and morphogenesis terms across various tissues (integrin-mediated adhesion, cardioblast migration, Malpighian tubule differentiation, circadian regulation of heart rate, seminal vesicle morphogenesis, etc). This points to a cohesive theme: proteins involved in regulating gene expression to drive development and tissue morphogenesis across multiple organ systems.","confidence":"High","size":22,"edges":42,"triangles":24,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":22},{"id":"GO:0033627","count":20},{"id":"GO:0021750","count":20},{"id":"GO:0003259","count":20},{"id":"GO:0061382","count":20}]},{"hash":"2129120256122244160","title":"Unknown","description":"The top GO terms cover a broad mix of processes including cell division and spindle organization, zygote asymmetric division, neural signaling and plasticity, visual perception, organ development (lung, heart), muscle contraction, and leukocyte chemotaxis, with no clear, single shared function tying the cluster together. This heterogeneity makes a cohesive, specific label inappropriate, so the cluster is best described as Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007051","count":5},{"id":"GO:0010070","count":5},{"id":"GO:0031914","count":5},{"id":"GO:0043407","count":5},{"id":"GO:0060487","count":4}]},{"hash":"1664609285414642368","title":"Glycosylation and glycosphingolipid biosynthesis","description":"The top GO terms cluster around N-linked glycosylation, oligosaccharide metabolism, and glycosphingolipid/ganglioside biosynthesis (including N-acetylneuraminate metabolism and glycosylceramide metabolism). This points to glycan processing and sphingolipid biosynthesis pathways as the core theme. Some pollen-related terms (pollen tube growth and pollen germination) can be linked to membrane and signaling roles of glycosphingolipids in plant reproduction, supporting a cohesive interpretation rather than unrelated annotations.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006054","count":3},{"id":"GO:0006491","count":3},{"id":"GO:0009860","count":3},{"id":"GO:0009846","count":3},{"id":"GO:0021628","count":3}]},{"hash":"2281282506815779623","title":"UV-induced DNA Damage Response and NER","description":"The dominant signals are responses to UV-B and UV-C and two nucleotide-excision repair terms (pyrimidine dimer repair and transcription-coupled NER), indicating a focus on UV-triggered DNA damage recognition and repair. Additional terms about transcription regulation and cell cycle control align with processes that accompany DNA repair, while eye morphogenesis may reflect broader developmental roles of some related factors. Overall, the cluster appears driven by UV-induced DNA damage response and repair pathways.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010224","count":2},{"id":"GO:0010225","count":2},{"id":"GO:0000720","count":2},{"id":"GO:0048597","count":2},{"id":"GO:0045944","count":2}]},{"hash":"1596676575794475334","title":"Multi-tissue differentiation and signaling","description":"Top terms point to differentiation in adipose and skin, immune signaling, calcium signaling, and ER protein folding. Together they suggest proteins involved in differentiation and broad signal transduction across tissues, with a shared emphasis on secretory pathway maturation rather than a single pathway.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":3},{"id":"GO:0051209","count":3},{"id":"GO:0043031","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0030216","count":3}]},{"hash":"400273447784837221","title":"Neural development and synaptic signaling","description":"The top GO terms point to nervous system development, synapse assembly, and axon guidance (including serotonergic axon guidance) as well as glutamatergic synaptic transmission and sensory perception, indicating a cohesive role in neural differentiation, network formation, and synaptic connectivity. Some PCP-related terms reflect planar polarity components that can influence neural wiring, reinforcing the neural-development/synaptic-theme interpretation.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":5},{"id":"GO:0051965","count":5},{"id":"GO:0007605","count":4},{"id":"GO:0060489","count":4},{"id":"GO:1904938","count":4}]},{"hash":"1458514118067124779","title":"Complement Activation and Leukocyte Adhesion","description":"This cluster centers on immune system processes: multiple terms for complement activation (classical and alternative), regulation of complement, and membrane attack complex activity, along with leukocyte adhesion/rolling, and IL-10 production. The co-occurrence of T cell death signaling and extrinsic apoptotic pathways further supports a theme of immune regulation and cell interactions during inflammatory responses.","confidence":"High","size":22,"edges":35,"triangles":17,"max_degree":7,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0007157","count":9},{"id":"GO:0006958","count":7},{"id":"GO:0006924","count":5},{"id":"GO:0045959","count":5},{"id":"GO:0032613","count":5}]},{"hash":"1551124755861743808","title":"ER Stress, Redox Homeostasis, and NF-\u03baB Signaling","description":"The cluster shows enrichment for ER unfolded protein response, redox/homeostasis functions (including removal of superoxide), and regulation of canonical NF-\u03baB signaling, with additional signals related to innate immunity (RIG-I) and lipopolysaccharide response, suggesting a cohesive stress-response/immune signaling theme rather than a single, narrow function.","confidence":"Medium","size":22,"edges":33,"triangles":10,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0034101","count":2},{"id":"GO:0030968","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0019430","count":2}]},{"hash":"1423406953023776539","title":"Complement and coagulation with vascular remodeling","description":"Proteins in this cluster show strong enrichment for complement activation (classical and lectin pathways), coagulation, fibrinolysis, and plasminogen activation, indicating a core immune-hemostasis signal. They also include acute-phase response and extracellular matrix disassembly with angiogenesis, pointing to vascular tissue remodeling. The ANP-mediated regulation of blood pressure ties the cluster to cardiovascular inflammatory processes. Overall, the terms converge on immune-driven coagulation and remodeling in the vascular context.","confidence":"High","size":22,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":9},{"id":"GO:0001867","count":7},{"id":"GO:0003050","count":6},{"id":"GO:0045766","count":6},{"id":"GO:0006953","count":5}]},{"hash":"1409158514550492204","title":"Immune and ECM remodeling with angiogenesis","description":"This cluster centers on immune-related processes (adaptive immune response, complement activation pathways, NK cell regulation) alongside extracellular matrix organization (collagen fibril organization) and cell adhesion, plus angiogenesis and signaling (ERK cascade). Together these terms point to a module where immune activity and ECM remodeling promote blood vessel formation and tissue remodeling, with some muscle development context suggested by myoblast differentiation and channel clustering. ","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0001525","count":7},{"id":"GO:0030199","count":7},{"id":"GO:0045162","count":7},{"id":"GO:0001867","count":6},{"id":"GO:0002250","count":6}]},{"hash":"1335408227716173508","title":"Tissue development and differentiation","description":"This cluster includes GO terms spanning epidermal differentiation (keratinization, hair follicle morphogenesis, keratinocyte migration), lens development, neural development/differentiation (PNS axon regeneration, Bergmann glial differentiation), heart development (ventricular cardiac muscle), and liver apoptosis, plus autophagy regulation. The common thread is broad developmental and differentiation programs across multiple tissues, rather than a single specific pathway, justifying a high-level label of tissue development and differentiation.","confidence":"Medium","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":22},{"id":"GO:0014012","count":22},{"id":"GO:0031069","count":22},{"id":"GO:1904714","count":22},{"id":"GO:0055015","count":22}]},{"hash":"1089526053429527383","title":"Embryonic vascular and skeletal development","description":"This cluster centers on developmental processes involving the formation of blood vessels and skeletal tissues, supported by terms like sprouting angiogenesis, blood coagulation, ossification, and collagen fibril organization. Additional terms (multicellular organism development, ventral spinal cord development, Wnt signaling, cell adhesion) point to broad embryonic morphogenesis and tissue organization, with extracellular matrix remodeling as a common thread. The overall theme fits vascular growth, bone formation, and tissue patterning during development.","confidence":"High","size":22,"edges":7,"triangles":1,"max_degree":3,"top_function":"wound healing","top_go_terms":[{"id":"GO:0007596","count":9},{"id":"GO:0044332","count":8},{"id":"GO:0021517","count":8},{"id":"GO:0046697","count":8},{"id":"GO:0030199","count":7}]},{"hash":"372075691821367934","title":"Calcium-Dependent Barrier Junctions","description":"The terms cluster around calcium ion transport and its regulation, coupled with junctional assembly (septate and tight junctions) and barrier formation (glial BBB, tracheal system structure). The inclusion of calcium-regulated signaling (calcineurin-NFAT) supports a theme where calcium signaling drives junctional integrity and barrier function across epithelial and neural contexts.","confidence":"High","size":22,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070588","count":4},{"id":"GO:0034765","count":3},{"id":"GO:0019991","count":3},{"id":"GO:0045671","count":3},{"id":"GO:0070296","count":3}]},{"hash":"1548078276842239709","title":"Innate and Adaptive Immune Activation","description":"The cluster is dominated by GO terms related to immune function, including complement activation via the classical pathway, phagocytosis recognition and engulfment, and the broader innate immune response, along with adaptive immunity signals such as B cell receptor signaling and positive regulation of B and T cell activity. Together these terms suggest a group of proteins coordinating both innate recognition/clearance (phagocytosis, complement) and adaptive signaling (B and T cell activation). A few terms (e.g., lens morphogenesis) may be incidental rather than indicative of this cluster\u2019s core function.","confidence":"High","size":22,"edges":42,"triangles":12,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":20},{"id":"GO:0006910","count":20},{"id":"GO:0045087","count":20},{"id":"GO:0006911","count":20},{"id":"GO:0050853","count":20}]},{"hash":"2171842054159631897","title":"Placental and Embryonic Morphogenesis","description":"This cluster is dominated by placental/embryonic development terms (trophoblast giant cell differentiation, embryonic placenta development, endocrine system development, left/right pattern formation, EMT in heart development) along with broader organ morphogenesis (cartilage morphogenesis) and transcription. The convergence on placental and early embryonic morphogenesis suggests proteins function together in placenta formation and overall embryonic development rather than a single tissue-specific process.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060972","count":22},{"id":"GO:0060707","count":22},{"id":"GO:0035270","count":22},{"id":"GO:0060806","count":22},{"id":"GO:0003323","count":22}]},{"hash":"103380644120616597","title":"Diverse membrane transporters","description":"This cluster is dominated by GO terms for transmembrane transport across a wide range of substrates, including xenobiotics, phosphate, sugars, nitrate/nitrite, and sialic acid, plus a vesicular neurotransmitter loading term. The common thread is membrane transporter activity with diverse substrate specificities, with one term indicating vesicular transport of neurotransmitters, supporting a cohesive label of diverse transmembrane transporters.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":11},{"id":"GO:0035435","count":11},{"id":"GO:0098700","count":11},{"id":"GO:1900754","count":11},{"id":"GO:0042128","count":11}]},{"hash":"324238591347796359","title":"Complement and Phagocytosis Immunity","description":"This cluster centers on immune functions: high representation of complement activation (classical pathway), B cell receptor signaling and positive regulation of B cell activation, innate immune response, and phagocytosis recognition/engulfment, indicating coordinated innate and adaptive immune activity with phagocytic processes. Some terms like retina homeostasis or xenobiotic response are present but do not override the dominant immune theme. Overall, the proteins appear to function in immune activation and phagocytosis pathways.","confidence":"High","size":22,"edges":173,"triangles":777,"max_degree":20,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":21},{"id":"GO:0050853","count":21},{"id":"GO:0045087","count":21},{"id":"GO:0006910","count":21},{"id":"GO:0050871","count":21}]},{"hash":"1642147941653169551","title":"Bacterial Secretion and Xenobiotic Transporters","description":"These proteins cluster around membrane transport and secretion functions, especially Type I secretion\u2013related protein export and bacteriocin transport, as well as transmembrane transport of amino acids and xenobiotics. The GO terms suggest roles in secreting proteins (Type I secretion system, bacteriocin transport) and in transporting ions and small molecules (chloride, amino acids, cadmium detoxification, xenobiotics), pointing to a cohesive theme of secretion and efflux/transport in bacteria. The sperm capacitation term is unusual for bacteria but may reflect broader ion/pH regulation by transport systems in this cluster.","confidence":"High","size":22,"edges":38,"triangles":47,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051454","count":14},{"id":"GO:1902476","count":14},{"id":"GO:0048240","count":14},{"id":"GO:0098849","count":9},{"id":"GO:0030253","count":9}]},{"hash":"1415908307875741804","title":"Epithelial immune defense and cell junctions","description":"This cluster centers on immune and barrier-related functions: complement activation (classical pathway), innate immune response, and immunoglobulin transcytosis via pIgR, together with protein localization to cell junction and cell adhesion terms. These collectively point to an epithelial barrier where immune defense and cell\u2013cell contacts are coordinated. Development-related terms are present but appear ancillary to the main theme. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":18},{"id":"GO:0007156","count":17},{"id":"GO:0007157","count":17},{"id":"GO:0006508","count":17},{"id":"GO:0045087","count":17}]},{"hash":"15647868920883805","title":"Notch signaling in embryonic development","description":"The top terms center on Notch signaling and broad developmental processes, including organogenesis and tissue differentiation (pancreas exocrine development, bone morphogenesis, pharyngeal and somite development, left/right symmetry). The presence of transcriptional regulation terms also supports a Notch-driven gene regulatory role during development. This suggests the cluster represents Notch-associated developmental regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007219","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0031017","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0007275","count":2}]},{"hash":"964936448085202242","title":"Axon Guidance and Neural Crest Migration","description":"The dominant GO terms center on axon guidance and neural crest\u2013related development (semaphorin-plexin signaling, branchiomotor neuron and trigeminal nerve guidance/organization, axonal fasciculation, sympathetic neuron projection guidance/extension). Additional terms for neural crest migration and related nerve projection support a cohesive theme of guiding neuronal connections during development. ","confidence":"High","size":22,"edges":5,"triangles":0,"max_degree":2,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0007157","count":8},{"id":"GO:1902287","count":5},{"id":"GO:0021785","count":5},{"id":"GO:0021637","count":5},{"id":"GO:0007413","count":5}]},{"hash":"89135929130083304","title":"Peripheral nerve development and ion channel clustering","description":"The cluster shows strong enrichment for clustering of voltage-gated sodium channels and peripheral nervous system development, suggesting a core theme of neural development and ion channel organization. Additional terms around cell adhesion and signaling indicate broader developmental processes but do not outweigh the neural/ion-channel focus.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045162","count":17},{"id":"GO:0007155","count":16},{"id":"GO:0048661","count":14},{"id":"GO:0006910","count":13},{"id":"GO:0007422","count":13}]},{"hash":"1047657300594784953","title":"Cartilage and bone morphogenesis signaling","description":"The top GO terms cluster around cartilage development (growth plate chondrocyte development) and endochondral bone morphogenesis, plus ECM/collagen signaling pathways, suggesting a cohesive role in skeletal development and extracellular matrix signaling rather than general immunity or lipid metabolism.","confidence":"High","size":22,"edges":42,"triangles":20,"max_degree":16,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":18},{"id":"GO:0071230","count":17},{"id":"GO:0070208","count":17},{"id":"GO:0060351","count":17},{"id":"GO:0038063","count":17}]},{"hash":"1767577629670658769","title":"Cell-Cell Adhesion and Immune Regulation","description":"The cluster is dominated by GO terms for cell adhesion (homophilic and heterophilic cell-cell adhesion, protein localization to cell junction) and immune modulation (negative regulation of macrophage activation, NK cell cytotoxicity, and CTL degranulation), suggesting proteins that function at cell\u2013cell interfaces to regulate immune signaling and tissue communication. While some terms like lens morphogenesis and symbiont entry are more context-specific, the common theme appears to be cell\u2013cell interactions influencing immune responses.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043031","count":17},{"id":"GO:0007157","count":17},{"id":"GO:0002859","count":16},{"id":"GO:0043318","count":16},{"id":"GO:0007156","count":16}]},{"hash":"687133899399403121","title":"Ovarian follicle development and ovulation","description":"Top GO terms cluster around reproductive cycle events (fertilization, ovulation) and signaling pathways (integrin adhesion, Notch processing, VEGF signaling) that drive follicle remodeling and angiogenesis. Together, these suggest proteins involved in ovarian follicle development, ovulation, and related signaling.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":20},{"id":"GO:0010042","count":19},{"id":"GO:0034612","count":19},{"id":"GO:0033631","count":19},{"id":"GO:1900748","count":19}]},{"hash":"2280469666834972910","title":"Vertebrate organogenesis and cartilage formation","description":"The terms cluster around broad multicellular development and organ morphogenesis (lung, face, ureteric bud branching) with a clear emphasis on cartilage-related processes (collagen fibril organization, chondrocyte proliferation/differentiation). Signaling pathways (BMP signaling upregulation, modulation of Wnt signaling) and angiogenesis support a cohesive developmental program driving organ formation, including skeletal/cartilage aspects. Therefore, labeling this cluster as vertebrate organogenesis with cartilage development is appropriate.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0030199","count":4},{"id":"GO:0030324","count":4},{"id":"GO:0045766","count":4},{"id":"GO:0060325","count":3}]},{"hash":"202378889120133359","title":"Hair Keratinization Proteins","description":"The top GO terms are keratinization and hair cycle, which strongly indicate a hair-specific set of proteins involved in keratin formation and hair follicle dynamics; the cluster likely contains keratins and related structural/regulatory factors.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":21},{"id":"GO:0042633","count":21}]},{"hash":"2146721147652538900","title":"Glial Neuroimmune Regulation and Dopamine Signaling","description":"This cluster shows strong enrichment for immune/glial-related GO terms (negative regulation of inflammatory response; immune response; regulation of astrocyte chemotaxis; glial-derived neurotrophic factor production; eosinophil chemotaxis) together with dopaminergic pathway terms (dopamine transport; regulation of dopamine metabolic process; phospholipase C-activating dopamine receptor signaling). The co-occurrence of astrocyte/glial regulation with dopamine-related processes points to CNS neuroimmune modulation involving glial cells and dopaminergic signaling.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":22},{"id":"GO:0042493","count":22},{"id":"GO:2000458","count":22},{"id":"GO:1900168","count":22},{"id":"GO:0048245","count":22}]},{"hash":"53199561669353905","title":"Ubiquitin-Proteasome\u2013Mediated Mitotic Regulation","description":"This cluster centers on mitosis and cell cycle control, with terms like mitotic cell cycle, cell division, and CENP-A chromatin assembly, plus DNA-templated transcription. It is dominated by ubiquitin-dependent processes (polyubiquitination, SCF-dependent proteasomal degradation) and degradation pathways (ERAD), indicating tight regulation of protein stability during division, alongside proteostasis-related trafficking (ER to Golgi). Together, these signals point to mitotic regulation governed by the ubiquitin-proteasome system.","confidence":"High","size":21,"edges":123,"triangles":390,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":12},{"id":"GO:0051301","count":11},{"id":"GO:0061641","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0051260","count":10}]},{"hash":"2109306668299542691","title":"Developmental transcription and ribosome biogenesis","description":"This cluster centers on foundational nuclear processes: DNA-templated transcription, chromatin regulation (histone acetylation), and ribosome biogenesis, along with cell division. The presence of retinal and skeletal development terms suggests that these proteins participate in developmental programs while maintaining basic gene-expression machinery. The combination fits a label emphasizing transcriptional control and ribosome assembly with a developmental context.","confidence":"Medium","size":21,"edges":201,"triangles":1183,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":10},{"id":"GO:0006351","count":10},{"id":"GO:0060041","count":9},{"id":"GO:0043966","count":9},{"id":"GO:0051301","count":9}]},{"hash":"183816817546433561","title":"Developmental Regulation and Ubiquitin-Proteasome Degradation","description":"Top terms show strong emphasis on organism development (face, hippocampus, melanocyte migration, multicellular development) and proteasome-ubiquitin pathways (K48-linked ubiquitination, proteasomal degradation). The connection suggests a cluster of regulators coordinating development with protein turnover.","confidence":"Medium","size":21,"edges":146,"triangles":702,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032436","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0032495","count":4},{"id":"GO:0070936","count":4},{"id":"GO:0060324","count":4}]},{"hash":"1262990669154945051","title":"Wnt-mediated adipogenesis and bone formation","description":"This cluster centers on Wnt signaling and differentiation, with multiple GO terms for fat cell differentiation, Wnt signaling, and intramembranous ossification, pointing to a developmental program governing adipogenesis and bone formation. Other terms reflect linked signaling and cellular dynamics (calcium signaling, GTPase activity, migration), but the core association is Wnt-driven lineage specification toward adipose and bone tissues.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0051209","count":3},{"id":"GO:0070294","count":3},{"id":"GO:0048549","count":3}]},{"hash":"337991037911337557","title":"Calcium-dependent actin remodeling and cell migration","description":"Based on the top GO terms, the cluster centers on calcium-responsive signaling (cellular response to calcium ion, calcineurin-NFAT pathway) promoting dynamic actin remodeling (lamellipodium/filopodium assembly, actin cytoskeleton organization) and adhesion-driven migration (fibroblast migration, substrate adhesion-dependent spreading). Developmental terms like heart development and motor neuron specification suggest broader roles in differentiation where actin dynamics and calcium signaling are pivotal. Together these indicate a cohesive theme of calcium-regulated actin remodeling underpinning cell movement and adhesion.","confidence":"High","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":6},{"id":"GO:0030032","count":5},{"id":"GO:0070886","count":5},{"id":"GO:0010801","count":5},{"id":"GO:0021520","count":5}]},{"hash":"946237775939476237","title":"Neuronal transcription and endosomal trafficking regulators","description":"These proteins show enrichment for DNA-templated transcription and signaling regulation, along with neuronal synaptic functions (glutamatergic transmission and regulation of synaptic plasticity) and intracellular trafficking (endosome transport, Rab signaling) plus ubiquitin-related processes (K11- and K48-linked deubiquitination). The combination suggests a theme where transcriptional control and endo-lysosomal trafficking/ubiquitination coordinate synaptic signaling and receptor turnover in neurons.","confidence":"Medium","size":21,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0051534","count":6},{"id":"GO:0034499","count":5},{"id":"GO:0045022","count":4},{"id":"GO:0035871","count":4}]},{"hash":"1288144957204158220","title":"Auditory Hair Cell Synapses and Cerebellar Development","description":"Top terms cluster around synapse organization, auditory perception, and stereocilium organization, with supporting signals for cerebellar Purkinje cell layer formation and dendrite development, suggesting proteins involved in auditory hair cell synapses and cerebellar neuron development. While a couple of terms (carnitine transport, morphine response) are more general neuronal processes, they do not outweigh the dominant auditory-synaptic theme.","confidence":"High","size":21,"edges":170,"triangles":759,"max_degree":20,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0043113","count":20},{"id":"GO:0015879","count":17},{"id":"GO:0051612","count":17},{"id":"GO:0050808","count":17},{"id":"GO:0007266","count":17}]},{"hash":"1701009831201734702","title":"Nuclear transport and chromatin assembly","description":"The cluster is enriched for GO terms related to import into the nucleus and chromatin assembly during DNA replication, as well as mRNA transport and transcription regulation by RNA polymerase III. This points to core nuclear processes coordinating genome organization and gene expression. Some terms about meiosis and apoptosis appear, but the dominant pattern centers on nuclear transport, chromatin dynamics, and transcription-related processes.","confidence":"Medium","size":21,"edges":78,"triangles":171,"max_degree":16,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0060188","count":6},{"id":"GO:0071230","count":6},{"id":"GO:1903538","count":6},{"id":"GO:2001241","count":6},{"id":"GO:0051028","count":6}]},{"hash":"1786423921386522946","title":"Cytoskeleton Remodeling and Cell Migration Regulation","description":"The top terms cluster around actin-based structures (lamellipodium, stress fibers, podosome) and Rho signaling, which govern cytoskeletal remodeling and cell movement, plus processes at the vascular/immune interface (extravasation, vascular permeability). A few terms like mitotic spindle assembly and vitellogenesis appear but broadly reflect cytoskeletal control and vascular interaction rather than unrelated functions. This supports labeling the cluster as cytoskeleton-driven migration and vascular remodeling regulation.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":4},{"id":"GO:0002692","count":4},{"id":"GO:0043314","count":4},{"id":"GO:0060313","count":4},{"id":"GO:0051496","count":3}]},{"hash":"2287198967672305959","title":"Embryonic neural crest and organ morphogenesis","description":"Based on the top GO terms, the proteins are enriched for neural crest cell migration and development of various organs (inner ear, pituitary, pancreas, hypothalamus, spinal cord interneurons) and general morphogenetic processes. This points to a coherent theme of embryonic organ morphogenesis and neural crest\u2013driven development.","confidence":"High","size":21,"edges":38,"triangles":22,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001755","count":6},{"id":"GO:0090190","count":6},{"id":"GO:0021983","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0048839","count":6}]},{"hash":"1309647118339531359","title":"Unknown","description":"The top GO terms span immune signaling, ubiquitin-dependent protein catabolism, circadian rhythm, muscle development, gravitropism, and sexual development, with no single dominant function tying the proteins together. This diversity suggests there is no cohesive, representative theme for the cluster.","confidence":"","size":21,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0045497","count":3},{"id":"GO:0048741","count":3},{"id":"GO:2000176","count":3},{"id":"GO:0045496","count":3}]},{"hash":"1756930505278829449","title":"Developmental transcriptional regulation and morphogenesis","description":"The terms cluster around RNA polymerase II\u2013mediated transcription and chromatin assembly, including both activation and negative regulation, alongside several embryonic development processes (palatal/roof of mouth development, endocardial cushion EMT for heart valve formation, hemangioblast differentiation, left-right patterning, endocrine system development, placenta formation). This pattern indicates proteins coordinating transcriptional programs during embryogenesis and organogenesis, particularly in cardiac and craniofacial morphogenesis.","confidence":"High","size":21,"edges":135,"triangles":444,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0060021","count":4},{"id":"GO:0003199","count":4},{"id":"GO:0060217","count":4}]},{"hash":"21053359546471051","title":"Embryonic development and morphogenesis","description":"The cluster shows a strong enrichment for developmental and morphogenesis terms, including trophoblast giant cell differentiation, cartilage morphogenesis, left-right pattern formation, endocrine system development, and pancreatic cell development, suggesting a shared theme in embryonic differentiation and organogenesis. While there are also general RNA processing terms, the developmental signals are the most representative link for the cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0000055","count":5},{"id":"GO:0032298","count":5},{"id":"GO:1903026","count":5},{"id":"GO:0060707","count":4}]},{"hash":"895506150379192249","title":"Chromatin regulation and mitotic spindle control","description":"The cluster shows a combination of chromatin-related processes (histone H3-K27 methylation, negative regulation of transcription by RNA polymerase II, chromatin silencing-related terms) together with cell division machinery (centrosome cycle, spindle assembly). This suggests a cohesive theme where chromatin state is coordinated with mitotic spindle and centrosome dynamics. Confidence: High","confidence":"","size":21,"edges":100,"triangles":169,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0007098","count":5},{"id":"GO:0051225","count":5},{"id":"GO:0098532","count":4},{"id":"GO:0061087","count":4}]},{"hash":"658827246681776669","title":"Lipid biosynthesis and ER-Golgi trafficking","description":"Enriched terms point to lipid metabolism (fatty acid elongation, very long-chain fatty acids, sphingolipid biosynthesis) and inflammatory lipid signaling (leukotriene and lipoxygenase pathways). The ER-to-Golgi transport term adds a vesicular trafficking/secretory dimension, fitting with membrane lipid production and mediator transport in inflammation.","confidence":"High","size":21,"edges":164,"triangles":726,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0030497","count":2},{"id":"GO:0030148","count":2},{"id":"GO:0042761","count":2},{"id":"GO:0019370","count":2}]},{"hash":"201074967750482204","title":"Unknown","description":"The GO terms are highly diverse, spanning hippocampus and skeletal muscle development, B cell receptor signaling, melanocyte migration, and various regulatory processes such as proteasomal degradation, transcription, DNA replication initiation, glycogen catabolism, and multiple signaling pathways. There is no clear, single biological function tying all proteins together, suggesting the cluster comprises proteins with varied regulatory roles rather than a cohesive pathway.","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032436","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0007519","count":3},{"id":"GO:0032298","count":3}]},{"hash":"602887822572105397","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":3},{"id":"GO:0000398","count":3},{"id":"GO:1903026","count":3},{"id":"GO:0032298","count":3},{"id":"GO:0000387","count":2}]},{"hash":"83904433096857173","title":"Cytoskeletal signaling in immunity and development","description":"The cluster highlights cytoskeletal dynamics (actin lamellipodium and cortical patch, microtubule localization) and signaling pathways (Rho regulation, PDGFR signaling) with developmental and immune contexts (heart, thymus, innate immune response), suggesting a cohesive theme of cytoskeleton-driven signaling across immunity and development.","confidence":"Medium","size":21,"edges":101,"triangles":250,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0035023","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0060291","count":4}]},{"hash":"67179323158062784","title":"APC/C-dependent mitotic proteolysis","description":"This cluster is driven by mitosis- and cell-cycle related GO terms, notably APC/C-dependent catabolic processes and mitotic cell cycle regulation, supported by ubiquitination (K11-linked) and GTPase activity modulation. Other terms (cadmium response, TORC1 signaling, lens differentiation) are peripheral to the main mitotic thread, suggesting a core theme of mitotic progression controlled by ubiquitin-mediated proteolysis.","confidence":"High","size":21,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0071276","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0043547","count":6},{"id":"GO:0061087","count":6}]},{"hash":"451633652219701702","title":"Spliceosome Assembly and mRNA Processing","description":"Top GO terms are dominated by splicing-related processes (mRNA cis splicing via spliceosome, spliceosomal complex and snRNP assembly) and mRNA metabolism/degradation (deadenylation-dependent decapping, P-body assembly, nuclear import). These signals point to a cluster of proteins functioning in RNA processing and surveillance, particularly splicing and mRNA turnover, with some chromatin-related terms noted as auxiliary connections. ","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":20},{"id":"GO:0000245","count":19},{"id":"GO:0000387","count":19},{"id":"GO:1990141","count":19},{"id":"GO:0009414","count":19}]},{"hash":"362625528849945331","title":"Epithelial polarity and EMT regulation","description":"Proteins in this cluster are centered on epithelial cell architecture and plasticity, including apical/basal polarity establishment, terminal web assembly, and cortical microtubule organization, as well as barrier formation like the endothelial barrier. The presence of epithelial-to-mesenchymal transition and its positive regulation reinforces a theme of remodeling epithelial cells, with signaling modulation reflected by p38MAPK and NOS activity terms. Overall, the cluster represents core epithelial polarity, cytoskeletal organization, and EMT-related remodeling functions.","confidence":"High","size":21,"edges":41,"triangles":68,"max_degree":10,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:1902896","count":18},{"id":"GO:0051000","count":18},{"id":"GO:0001837","count":18},{"id":"GO:0010718","count":18},{"id":"GO:0045198","count":18}]},{"hash":"1667198673993628403","title":"Mitochondrial Translation and Ribosome Biogenesis","description":"The cluster shows strong enrichment for mitochondrial translation, general translation, maturation of SSU-rRNA, and ribosomal large subunit assembly, along with mitochondrial ATP synthase complex assembly, indicating a cohesive mitochondrial protein synthesis and ribosome biogenesis program.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0032543","count":5},{"id":"GO:0000462","count":3},{"id":"GO:0006415","count":2},{"id":"GO:0031564","count":2}]},{"hash":"1112704638492146654","title":"RNA Splicing and Stress-Responsive Transcription with Apoptosis","description":"This cluster is driven by RNA processing and transcription regulation: splicing (including alternative splicing via spliceosome), RNA stabilization, and transcription initiation in response to stress, with supporting links to circadian rhythm and androgen receptor signaling, as well as apoptotic pathways. The convergence of splicing, transcriptional control, and apoptosis terms suggests a coherent module of gene expression regulation under stress that can influence cell fate.","confidence":"High","size":21,"edges":131,"triangles":465,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":4},{"id":"GO:0008380","count":4},{"id":"GO:0048255","count":3},{"id":"GO:0007623","count":3},{"id":"GO:2001244","count":3}]},{"hash":"1982892215659437663","title":"Neural development and axon guidance","description":"The dominant GO terms cluster around neuronal development and axon guidance, including pyramidal neuron development, branchiomotor neuron axon guidance, optic vesicle formation, and semaphorin-plexin signaling. Additional terms point to signaling and cytoskeletal regulation (regulation of GTPase activity, smoothened signaling) that influence neurite outgrowth, with broader roles in metabolism and post-transcriptional regulation supplementing but not dominating the theme.","confidence":"High","size":21,"edges":5,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0043087","count":5},{"id":"GO:0050873","count":4},{"id":"GO:0007224","count":4},{"id":"GO:0000288","count":3},{"id":"GO:2000637","count":3}]},{"hash":"2046757320668032144","title":"Rho-regulated actin remodeling and membrane dynamics","description":"Most frequent GO terms describe regulation of Rho protein signal transduction, actin filament organization, lamellipodium assembly, actin bundle assembly, and plasma membrane tubulation, indicating a cohesive role in actin cytoskeleton remodeling and membrane dynamics guided by Rho signaling. A few terms touch on signaling (tyrosine phosphorylation) and specific differentiation pathways (osteoblast fate) or metabolism (fatty acid oxidation), but the dominant theme is cytoskeletal remodeling and protrusive membrane structures.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":20},{"id":"GO:0007015","count":20},{"id":"GO:0097320","count":20},{"id":"GO:0000147","count":19},{"id":"GO:0050731","count":19}]},{"hash":"1660076513513480477","title":"Neuronal development and actin remodeling","description":"The top terms emphasize cerebral cortex development, excitatory synaptic signaling, and actin cytoskeleton dynamics (microspike assembly and actin reorganization), all pointing to neural development and synaptic remodeling driven by cytoskeletal changes. A B cell receptor signaling term appears but is not the dominant theme; overall the cluster aligns with neuronal growth, synaptic activity, and cytoskeletal regulation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050853","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0030035","count":3}]},{"hash":"1651866097652371946","title":"Muscle development and actin cytoskeleton","description":"The top GO terms cluster around heart and skeletal muscle development, actin crosslinking, and terminal web assembly, indicating a shared focus on muscle morphogenesis and cytoskeletal remodeling. Other terms touch circadian regulation and neuronal signaling, but they appear as secondary signals; the dominant theme is muscle development linked with cytoskeletal organization.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050966","count":3},{"id":"GO:0051764","count":3},{"id":"GO:0014898","count":3},{"id":"GO:1902896","count":3},{"id":"GO:0007507","count":3}]},{"hash":"2272446789645445205","title":"Cardiac mechanotransduction with immune signaling","description":"This cluster prominently features GO terms for cellular/muscle mechanical stimulus response and SA node\u2013related cardiac signaling (action potential regulation and SA node to atrial muscle communication), pointing to a cardiac mechanotransduction theme. Added immune and apoptotic terms (T cell death, IL-12 regulation, hepatocyte apoptosis, dendritic cell differentiation, miRNA transcription) suggest some cross-talk with immune pathways, but the dominant pattern is mechanosensitive cardiac signaling. Confidence: Medium","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006924","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0032088","count":2}]},{"hash":"2037114185261510756","title":"Cytoskeletal remodeling and endothelial signaling","description":"The top GO terms cluster around actin cytoskeleton dynamics (actin filament bundle assembly, response to muscle stretch) and membrane trafficking/signaling (pinocytosis, Wnt signaling, NF-kappaB-related regulation) with an endothelial context suggested by delamination. Telomere maintenance terms appear less coherent with the others, but the strongest shared theme points to cytoskeletal remodeling combined with signaling processes, particularly in vascular/endothelial contexts. The connections are somewhat loose (low density), so this label is a best-fit rather than a tight module.","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051017","count":10},{"id":"GO:0035994","count":10},{"id":"GO:0048549","count":10},{"id":"GO:0016055","count":10},{"id":"GO:2001275","count":9}]},{"hash":"1942415268543905775","title":"Spliceosome-driven mRNA processing and regulation","description":"The top GO terms cluster around spliceosome-mediated mRNA processing: regulation of alternative mRNA splicing, mRNA splicing via the spliceosome, splice site recognition, and mRNA stability/regulation of translation initiation. This points to a cohesive role in post-transcriptional control of gene expression, with some related but obsolete polyadenylation terms reflecting maturation processes. Overall, the proteins appear to participate in coordinated mRNA processing and stability mechanisms.","confidence":"High","size":21,"edges":199,"triangles":1146,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":18},{"id":"GO:1901407","count":18},{"id":"GO:0006378","count":18},{"id":"GO:0045292","count":18},{"id":"GO:0048255","count":17}]},{"hash":"1140814228114271002","title":"PI3K-AKT Growth Signaling and Proliferation","description":"The top terms point to a central theme of signal transduction via the PI3K/AKT pathway and control of cell growth and proliferation (positive regulation of G1/S transition, endothelial proliferation). Translation and other miscellaneous terms are present but appear secondary to the growth-signaling signal, making this a plausible overall label despite some heterogeneity.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0043491","count":2},{"id":"GO:0007165","count":1},{"id":"GO:1900087","count":1},{"id":"GO:0007621","count":1}]},{"hash":"648644783772846454","title":"Complement Activation and MAC Regulation","description":"Most top terms cluster around the complement system: activation via classical, lectin, and alternative pathways and positive regulation of membrane attack complex activation, indicating a set rich in complement components/regulators; other terms are more peripheral, suggesting pleiotropy rather than the main theme.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0001970","count":6},{"id":"GO:0006957","count":6},{"id":"GO:0006958","count":6},{"id":"GO:0034392","count":6},{"id":"GO:0001701","count":6}]},{"hash":"809472274054645968","title":"Developmental Signaling and Cytoskeletal Dynamics","description":"Most terms point to signaling pathways and developmental processes (heart development, spermatid development, KIT signaling, PI3K/NF-kB-related terms) and cytoskeletal remodeling (GTPase activation, filopodium assembly). The cluster likely comprises proteins coordinating growth signaling with actin dynamics across tissues, hence a developmental signaling and cytoskeletal theme.","confidence":"Medium","size":21,"edges":14,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0010765","count":3},{"id":"GO:0050860","count":3}]},{"hash":"1767672251418310860","title":"Immune cell signaling and cytoskeleton remodeling","description":"The top terms show lamellipodium and filopodium assembly, indicating actin cytoskeleton remodeling, driven by small GTPases (Rho, Rac, Ras) and their signaling regulation. The inclusion of immune-related processes such as B cell affinity maturation, NK T cell differentiation, and IL-4 production, along with IL-7\u2013mediated responses, suggests a cohesive module where cytoskeletal dynamics support immune cell migration, activation, and differentiation. This combination is best captured by a label emphasizing immune signaling linked to cytoskeletal remodeling.","confidence":"High","size":21,"edges":176,"triangles":820,"max_degree":20,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0030032","count":14},{"id":"GO:0046847","count":12},{"id":"GO:0098761","count":11},{"id":"GO:0007264","count":11},{"id":"GO:0035023","count":11}]},{"hash":"1200505523949226798","title":"Ubiquitination and Telomere Regulation in Metabolic Signaling","description":"The cluster highlights protein ubiquitination and telomere maintenance/capping as dominant themes, with supportive signals from metabolic pathways (response to vitamin D, fat cell differentiation, insulin-related regulation) and vascular signaling (endothelial delamination). This suggests a cohesive view of post-translational modification and genome stability intertwined with metabolic and vascular signaling. Confidence: Medium","confidence":"","size":21,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":12},{"id":"GO:0000083","count":10},{"id":"GO:0033280","count":9},{"id":"GO:0045444","count":9},{"id":"GO:2001275","count":8}]},{"hash":"228419620197187881","title":"Broad developmental transcription and morphogenesis","description":"This cluster features GO terms centered on transcription by RNA polymerase II and a range of development- and morphogenesis-related processes across diverse tissues (e.g., integrin-mediated adhesion, vestibular nucleus development, cardioblast migration, Malpighian tubule and seminal vesicle morphogenesis, pancreatic cell development). The overarching theme appears to be general developmental regulation and tissue morphogenesis rather than a single specific pathway, suggesting proteins involved in broad developmental roles. ","confidence":"Medium","size":21,"edges":73,"triangles":81,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":21},{"id":"GO:0033627","count":18},{"id":"GO:0021750","count":18},{"id":"GO:0003259","count":18},{"id":"GO:0061382","count":18}]},{"hash":"222710564600757602","title":"Organ development and patterning","description":"The top GO terms center on developmental processes across multiple organs (heart development, cartilage morphogenesis, left-right pattern formation, endocrine system development, and pancreatic beta-cell development), suggesting a cluster of proteins involved in organogenesis and body plan specification. A couple terms (gastric acid secretion, photoperiodism) appear less related, likely annotation noise.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030819","count":2},{"id":"GO:0009648","count":2},{"id":"GO:0045987","count":2},{"id":"GO:0001696","count":2},{"id":"GO:0007507","count":2}]},{"hash":"2160222569179822884","title":"Metabolic catabolism and biosynthesis","description":"This cluster is centered on metabolic transformation of small molecules, spanning amino acid and lipid catabolism as well as biosynthesis of quinones and antibiotics. The diverse GO terms imply a broad metabolic role rather than a single pathway, consistent with a protein group that handles multiple chemical transformations.","confidence":"Medium","size":21,"edges":76,"triangles":88,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006574","count":9},{"id":"GO:0010124","count":8},{"id":"GO:0006635","count":7},{"id":"GO:0009234","count":7},{"id":"GO:0042372","count":7}]},{"hash":"630348728273753384","title":"Mitochondrial Respiratory Chain and Translation","description":"Top GO terms point to mitochondrial energy production, including electron transport (NADH to ubiquinone, cytochrome c to oxygen) and assembly of respiratory chain complexes II and IV, plus mitochondrial translation. These indicate a coherent theme of mitochondrial respiration and protein synthesis, with some peripheral metabolic terms (retinoid and fatty acid-related processes) that are less central. Overall, the cluster centers on mitochondrial energy metabolism and ribosomal activity within mitochondria.","confidence":"High","size":21,"edges":190,"triangles":1051,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0006123","count":3},{"id":"GO:0034553","count":3},{"id":"GO:0006729","count":3}]},{"hash":"2144644932109111562","title":"Embryonic organogenesis","description":"The top GO terms cluster around developmental and morphogenetic processes across multiple organs (eye morphogenesis and retinal guidance, dentin/odontogenesis, pituitary development, ureteric bud elongation, lung branching, and broader transcriptional machinery), indicating a coordinated theme of embryonic organ development and patterning.","confidence":"High","size":21,"edges":57,"triangles":73,"max_degree":15,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":17},{"id":"GO:0043010","count":16},{"id":"GO:0060441","count":16},{"id":"GO:0048048","count":16},{"id":"GO:0021983","count":15}]},{"hash":"1242958103953412899","title":"Keratinization and skin appendage morphogenesis","description":"This cluster centers on epidermal differentiation and morphogenesis of keratinized tissues and ectodermal appendages: keratinization and keratinocyte proliferation, hair follicle morphogenesis, and salivary gland branching. The presence of isopeptide cross-linking in the cornified envelope (transglutaminase activity) and related calcium signaling supports epidermal/secretory epithelial function. A spleen development term appears less representative but does not override the dominant skin/appendage theme.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048536","count":4},{"id":"GO:0031424","count":3},{"id":"GO:0060662","count":3},{"id":"GO:0031069","count":3},{"id":"GO:0001974","count":3}]},{"hash":"92471372639054331","title":"Stress-Immune-Endocrine Regulation","description":"This cluster shows proteins linked to immobilization stress response, LPS- and systemic acquired resistance\u2013related immunity, RAAS-related processes (angiotensin maturation and blood volume regulation), digestion, proteolysis, and cAMP signaling. The common thread seems to be stress-induced endocrine signaling that interfaces with immune and digestive functions, rather than a single highly specific pathway. Hence the label reflects the broad, interconnected theme.","confidence":"Medium","size":21,"edges":6,"triangles":0,"max_degree":3,"top_function":"autophagy","top_go_terms":[{"id":"GO:0035902","count":11},{"id":"GO:0042756","count":10},{"id":"GO:0002016","count":10},{"id":"GO:0048469","count":10},{"id":"GO:0002003","count":10}]},{"hash":"757085007327361451","title":"Unknown","description":"The terms in this cluster cover a wide and disparate set of functions (lipid metabolism, signaling regulation, development, immune and stress responses, digestion, and tissue remodeling) with no clear single theme tying all proteins together. Because there isn\u2019t a coherent common function that uniquely represents the cluster, the appropriate label is Unknown.","confidence":"","size":21,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006685","count":4},{"id":"GO:0031953","count":4},{"id":"GO:0043588","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0007586","count":3}]},{"hash":"321684115661597144","title":"Fatty acid and sphingolipid biosynthesis","description":"The cluster is dominated by fatty acid\u2013related biosynthetic terms (very long-chain, unsaturated, elongation, long-chain acyl-CoA) and sphingolipid biosynthesis, indicating a lipid metabolism\u2013centric group. Some terms about pheromone metabolism and courtship behavior hint at lipid-derived signaling in reproduction, with swim bladder development and vesicle transport possibly reflecting fish-specific secretion pathways. Overall, the core theme is lipid biosynthesis with potential links to reproductive signaling.","confidence":"High","size":21,"edges":190,"triangles":1012,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0042761","count":9},{"id":"GO:0006636","count":8},{"id":"GO:0042810","count":7},{"id":"GO:0048794","count":7},{"id":"GO:0019367","count":7}]},{"hash":"906445766705992243","title":"Mitochondrial Cofactor and Metabolite Transport","description":"The terms show a clear emphasis on transmembrane transport of vitamins and cofactors (thiamine pyrophosphate, pyridoxal phosphate, CoA, glycine) and other metabolites, combined with mitochondrial energy-related processes (malate-aspartate shuttle, mitochondrial ATP transport). This points to a cohesive theme of mitochondrial metabolite transport and energy metabolism, with insulin secretion modulation as a downstream metabolic link.","confidence":"High","size":21,"edges":202,"triangles":1190,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":18},{"id":"GO:0030974","count":17},{"id":"GO:0035435","count":17},{"id":"GO:0035349","count":17},{"id":"GO:0036233","count":17}]},{"hash":"1135115102969066443","title":"Ciliary Hedgehog and BMP developmental signaling","description":"The top GO terms cluster around cilium assembly and signaling pathways such as Smoothened (Hedgehog) and BMP, alongside broader developmental processes (embryonic development, neural differentiation, intestinal stem cell homeostasis). This pattern suggests proteins operate in primary cilium\u2013mediated signaling to regulate development and neurogenesis, with some negative regulatory roles in differentiation and migration. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048642","count":2},{"id":"GO:0008101","count":2},{"id":"GO:0036335","count":2},{"id":"GO:0070236","count":2},{"id":"GO:0030336","count":2}]},{"hash":"1394308933864381171","title":"Neural and Ectodermal Embryonic Development","description":"The top GO terms are dominated by neural development and ectodermal formation (neuron differentiation, retinal ganglion axon guidance, metencephalon development) along with several embryonic organogenesis terms (ureteric bud, gonad/uterine development). This suggests a shared theme of embryonic development with emphasis on neural/ectodermal lineages, justifying the name.","confidence":"High","size":21,"edges":11,"triangles":1,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021526","count":15},{"id":"GO:0031290","count":15},{"id":"GO:0060677","count":15},{"id":"GO:0001705","count":15},{"id":"GO:0008585","count":15}]},{"hash":"1250650167099651459","title":"Mucosal innate antibacterial defense","description":"Top GO terms center on antibacterial humoral response and defense against both Gram-positive and Gram-negative bacteria, along with innate immune response in mucosa. This points to a cohesive function in frontline mucosal antibacterial defense mediated by innate immunity, despite a couple of obsolete signaling terms that can be disregarded for current interpretation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019731","count":1},{"id":"GO:0035584","count":1},{"id":"GO:0050830","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0019933","count":1}]},{"hash":"1039205665838444800","title":"Neural development and synapse assembly","description":"The cluster is enriched for nervous system development, positive regulation of synapse assembly, and cell\u2013cell adhesion, with additional signals of potassium channel clustering, pointing to neuronal development and synaptic organization. While a few terms touch on heart or bone development and immune processes, the strongest theme centers on neural development and synaptogenesis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":11},{"id":"GO:0007399","count":10},{"id":"GO:0006958","count":10},{"id":"GO:0043931","count":9},{"id":"GO:0007156","count":9}]},{"hash":"1224115766278929044","title":"Proteoglycan and Glycosaminoglycan Biosynthesis","description":"Based on the top GO terms, the cluster is strongly enriched for processes involved in building glycosaminoglycans and proteoglycans, including heparan sulfate, chondroitin sulfate, and dermatan sulfate biosynthesis, as well as related N-acetylglucosamine metabolism. This points to a cohesive module of enzymes and factors dedicated to proteoglycan/GAG production and modification, rather than unrelated metabolic pathways. Although some terms touch broader metabolism, the dominant signal is proteoglycan/GAG biosynthesis.","confidence":"High","size":21,"edges":175,"triangles":875,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0015015","count":15},{"id":"GO:0000103","count":15},{"id":"GO:0006044","count":15},{"id":"GO:0030206","count":15},{"id":"GO:0002002","count":15}]},{"hash":"1827472217148830101","title":"UV Response and NER in Skin and Eye Development","description":"The top GO terms cluster around UV-induced damage response and nucleotide-excision repair (UV-B/UV-C responses, pyrimidine dimer repair, transcription-coupled NER), coupled with keratinization and eye morphogenesis. This suggests a theme of UV-related DNA damage repair in ectoderm-derived tissues (skin) and developmental processes (eye), with some general transcription and cell-cycle regulation context. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":4},{"id":"GO:0010224","count":3},{"id":"GO:0010225","count":3},{"id":"GO:0000720","count":3},{"id":"GO:0048597","count":3}]},{"hash":"1430512817627574425","title":"Lipid signaling and secondary metabolism","description":"The top GO terms cluster around lipid-based signaling (regulation of endocannabinoid signaling) and lipid catabolism (triglyceride, prostaglandin), together with diverse secondary metabolism (alkaloids, antibiotic biosynthesis, PHB) and related pathways (beta-ketoadipate, uracil catabolic). This pattern points to a broad metabolic processing theme\u2014especially lipid signaling and secondary metabolite turnover\u2014rather than a single, unified function for all members.","confidence":"Medium","size":21,"edges":131,"triangles":450,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":20},{"id":"GO:0017000","count":20},{"id":"GO:0019433","count":20},{"id":"GO:0042952","count":19},{"id":"GO:0042619","count":19}]},{"hash":"1182865140158134985","title":"Neural development and synaptic adhesion proteins","description":"Predominant terms center on nervous system development, neuron-cell adhesion, and synapse assembly, supported by multiple GO terms for homophilic and heterophilic cell adhesion and positive regulation of synapse assembly. Additional terms involve collagen fibril organization and ossification, suggesting extracellular matrix and developmental context; some entries also relate to broader developmental processes like nephron development and locomotory behavior, and an immune component (complement activation) that may reflect shared signaling. Overall, the cluster appears to group proteins involved in neural development with adhesion-mediated cell interactions.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051965","count":10},{"id":"GO:0007157","count":10},{"id":"GO:0007399","count":9},{"id":"GO:0007158","count":9},{"id":"GO:0007156","count":9}]},{"hash":"631595693405461563","title":"Aromatic compound catabolism and secondary metabolism","description":"The top GO terms point to degradation and metabolism of aromatic and other small molecules (beta-ketoadipate pathway, 3-phenylpropionate, uracil catabolic, triglyceride catabolic) as well as secondary metabolism (alkaloid metabolism, antibiotic biosynthesis) and regulatory processes. This suggests a cluster of proteins involved in diverse catabolic and secondary metabolic pathways rather than a single unified function, justifying a label focused on aromatic compound catabolism and secondary metabolism.","confidence":"Medium","size":21,"edges":46,"triangles":49,"max_degree":10,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0042952","count":11},{"id":"GO:0019433","count":11},{"id":"GO:2000124","count":10},{"id":"GO:0010223","count":10},{"id":"GO:0055114","count":10}]},{"hash":"1706581140388063235","title":"Lens and Eye Morphogenesis","description":"Top terms cluster around visual system and lens biology, including visual perception, lens development, lens fiber cell differentiation/morphogenesis, and camera-type eye development. Some terms extend to epithelium morphogenesis and semicircular canal morphogenesis, indicating broader sensory organ formation. The dominant theme is lens/eye morphogenesis, with only minor relation to other sensory structures.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0021846","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0002088","count":2},{"id":"GO:0002009","count":2}]},{"hash":"2016432451185235215","title":"Skin immune defense and oxidative stress response","description":"The cluster is enriched for defense response, acute-phase response, cellular response to hydrogen peroxide, xenobiotic stimulus, and epidermis development, pointing to skin-associated immune defense and barrier-related oxidative stress responses. While eye development, endothelial regulation, and lipid metabolism terms appear, the dominant theme centers on epidermal defense and inflammatory/oxidative stress processes, with supplementary metabolic signals. Confidence: Medium","confidence":"","size":21,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006952","count":5},{"id":"GO:0008544","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006953","count":3},{"id":"GO:0006915","count":3}]},{"hash":"2082275661168251298","title":"Embryonic Development and Transcriptional Regulation","description":"The proteins cluster shows strong enrichment for developmental processes across embryogenesis and organogenesis (placenta, cartilage, roof of the mouth, left-right patterning, trophoblast differentiation, endocardial cushion formation) and for transcriptional control (negative regulation of transcription by RNA polymerase II, DNA-templated transcription). This combination suggests a cohesive module centered on developmental differentiation coupled with gene regulation.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":16},{"id":"GO:0035270","count":15},{"id":"GO:0060806","count":15},{"id":"GO:0060972","count":15},{"id":"GO:0060536","count":15}]},{"hash":"1904516745329488038","title":"Membrane Signaling in Neural and Immune Processes","description":"This cluster includes terms tied to neural functions (myelination, sensory perception of sound, synaptic plasticity) and immune signaling (B cell receptor signaling, B cell differentiation) as well as membrane biology (eisosomes, membrane raft polarization) and signaling regulation (PKC pathway, extrinsic apoptotic signaling). The common thread is membrane-associated signaling and cell communication across neural and immune contexts, rather than a single specialized function, suggesting a membrane-centric signaling theme that spans systems.","confidence":"Medium","size":21,"edges":134,"triangles":392,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0042552","count":10},{"id":"GO:0061028","count":9},{"id":"GO:0007605","count":9},{"id":"GO:0050861","count":9},{"id":"GO:0090038","count":9}]},{"hash":"814957610035287740","title":"Embryonic development and morphogenesis","description":"The top GO terms cluster around developmental processes and tissue morphogenesis: mesoderm development, cartilage morphogenesis, hair follicle morphogenesis, left-right pattern formation, roof of mouth development, and trophoblast giant cell differentiation. This suggests a common theme of embryonic development and organ/tissue patterning. Some terms (ribosomal export, mRNA splicing, complement activation) are more general or outliers, but the dominant signal points to development and morphogenesis.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":3},{"id":"GO:0060707","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0007498","count":2}]},{"hash":"673649514759695083","title":"Unknown","description":"The proteins have GO terms covering apoptosis regulation, GPI anchor biosynthesis, left-right asymmetry in the nervous system, intercellular and ion transport, protein hexamerization, defecation rhythm, anesthetic response, and cytokine production, with little overlap to suggest a single coherent pathway or function. This broad and mixed collection does not point to a specific common theme, so a unified label is not apparent.","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902230","count":2},{"id":"GO:0006506","count":2},{"id":"GO:0035545","count":1},{"id":"GO:0010496","count":1},{"id":"GO:0006811","count":1}]},{"hash":"834617705931212723","title":"Immune activation and T cell migration","description":"Reasoning: The top GO terms predominantly reflect adaptive immune function and cell movement, including immune response, helper T cell extravasation, eosinophil chemotaxis, IL-13 response, granzyme A production, and non-canonical NF-\u03baB signaling. Receptor internalization and regulation of the cell cycle suggest signaling and regulatory aspects that support immune cell activity. A couple of terms like neuron migration and negative regulation of angiogenesis are less directly tied to immunity but may reflect shared migratory or signaling pathways present in immune contexts.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"wound healing","top_go_terms":[{"id":"GO:0001764","count":21},{"id":"GO:0031623","count":21},{"id":"GO:0016525","count":21},{"id":"GO:0035962","count":20},{"id":"GO:0035684","count":20}]},{"hash":"1032361831323921606","title":"Zinc Transport and Homeostasis","description":"The cluster is dominated by terms related to zinc ion import across membranes, intracellular zinc ion homeostasis, and detoxification of zinc (and cadmium) ions, pointing to a cohesive role in zinc transport and metal ion regulation. A limb development term appears, but the prevailing signal is zinc handling, suggesting a functional group of zinc transporters and homeostasis proteins.","confidence":"High","size":21,"edges":123,"triangles":473,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":15},{"id":"GO:0010312","count":15},{"id":"GO:0006882","count":15},{"id":"GO:0060173","count":14},{"id":"GO:0034224","count":14}]},{"hash":"800714697075602470","title":"Sphingolipid and Phospholipid Metabolism","description":"This cluster centers on lipid metabolism, with multiple terms tied to sphingolipid pathways (sphingosine and sphinganine-1-phosphate metabolism, regulation of sphingolipid signaling) and phospholipid remodeling (phospholipid catabolic and dephosphorylation, phosphatidylglycerol biosynthesis). A glucose-6-phosphate transport and cellular oxidant detoxification are present but secondary. The convergence on sphingolipid/phospholipid metabolism and signaling suggests a coherent lipid metabolism cluster.","confidence":"High","size":21,"edges":17,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015760","count":4},{"id":"GO:0009395","count":4},{"id":"GO:0044328","count":4},{"id":"GO:0046839","count":4},{"id":"GO:0006670","count":4}]},{"hash":"1919366718559603578","title":"Developmental signaling and transcription regulation","description":"This cluster centers on regulatory processes, including signaling pathway modulation (STAT phosphorylation, smooth muscle proliferation, mast cell degranulation) and gene expression mechanisms (RNA Pol II regulation, mRNA splicing, ribosomal export), with several development-related terms (endocrine system development, left-right pattern formation, placenta development). Together, these suggest proteins that coordinate signaling and transcriptional control during development rather than a single isolated function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042523","count":4},{"id":"GO:0048661","count":4},{"id":"GO:0014068","count":4},{"id":"GO:0043303","count":4},{"id":"GO:0000055","count":3}]},{"hash":"1719032248536948398","title":"Immune response and immunoglobulin transport","description":"The top GO terms cluster around immune-related processes: immunoglobulin production and immunoglobulin transcytosis via pIgR, neutrophil homeostasis, regulation of NK T cell activation, cellular response to peptidoglycan, and CCR7 signaling. While a few terms (e.g., AV node action potential, lens morphogenesis) are less related, the immune-associated terms dominate, suggesting the cluster centers on immune recognition and antibody-related transport.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902414","count":4},{"id":"GO:0070352","count":4},{"id":"GO:0002415","count":4},{"id":"GO:0086016","count":4},{"id":"GO:0001780","count":4}]},{"hash":"1823363441449458205","title":"Embryonic Development and Organ Morphogenesis","description":"This cluster centers on broad developmental processes across multiple tissues, including placenta/trophoblast differentiation, mesoderm development, left/right patterning, epithelial-to-mesenchymal transitions, and various organ morphogenesis events (hair follicles, palate, endocrine and pancreatic development), suggesting a cohesive theme of embryogenesis and tissue formation.","confidence":"High","size":21,"edges":44,"triangles":53,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":18},{"id":"GO:0060536","count":18},{"id":"GO:0060972","count":18},{"id":"GO:0035270","count":18},{"id":"GO:0003323","count":18}]},{"hash":"270109742374094073","title":"Coagulation and complement activation with immune defense","description":"Cluster shows strong enrichment for blood coagulation, classical complement activation, and fibrinolysis, plus defense against Gram-positive bacteria and Factor XII activation. This points to a cohesive set of plasma proteases/regulators involved in hemostasis and innate immunity. A few terms like digestion or ANP-regulated blood pressure are peripheral but do not override the core coagulation/immune theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007596","count":7},{"id":"GO:0006958","count":7},{"id":"GO:0042730","count":6},{"id":"GO:0050830","count":6},{"id":"GO:0014068","count":6}]},{"hash":"1923179533119381602","title":"GPCR Signaling and Chemosensory Detection","description":"This cluster centers on G protein-coupled receptor (GPCR)\u2013mediated signal transduction and chemosensory responses. Top GO terms highlight sensory detection of sweet taste, catecholamine and glucagon signaling, receptor guanylyl cyclase pathways, and intracellular signal transduction in response to chemical stimuli, pointing to a cohesive theme of chemical-sense and hormone-related signaling. Some terms (hypoxia detection, trehalose response, oocyte maturation) are broader stress or developmental signals but still align with a general signaling/response framework.","confidence":"Medium","size":21,"edges":49,"triangles":26,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035556","count":5},{"id":"GO:0001582","count":4},{"id":"GO:0007195","count":4},{"id":"GO:0007168","count":4},{"id":"GO:0070483","count":4}]},{"hash":"746312228339472797","title":"Innate immune recognition and complement activation","description":"The cluster\u2019s top GO terms cluster around phagocytosis recognition, leukocyte tethering/rolling, C-type lectin receptor signaling, and lectin pathway complement activation, pointing to innate immune recognition and activation. While there are some developmental terms present, the dominant pattern is immune-related, suggesting these proteins function in lectin-mediated immune responses and phagocyte engagement.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006910","count":15},{"id":"GO:0072177","count":14},{"id":"GO:0001502","count":14},{"id":"GO:0072218","count":14},{"id":"GO:0060355","count":14}]},{"hash":"2078635441502488592","title":"Retina and visual system development with ERK signaling","description":"This cluster is dominated by GO terms for retina development and visual perception (e.g., retina development in camera-type eye and visual perception), along with signaling-related terms like positive regulation of the ERK cascade and related PI biosynthesis. Together, these suggest proteins involved in eye/retina development and associated signaling pathways, with ERK signaling as a central theme, complemented by glial/neuronal regulation and broader inflammatory/xenobiotic responses. Confidence: High","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0070374","count":19},{"id":"GO:0010513","count":15},{"id":"GO:0007626","count":15},{"id":"GO:0007601","count":15},{"id":"GO:0007507","count":15}]},{"hash":"2066452932808887462","title":"Taste perception and chemical sensing","description":"Based on the top GO terms, the cluster is dominated by sensory perception of taste and detection of chemical stimuli (including bitter taste), with related signaling pathways (GPCR signaling) and responses to chemical cues (pheromones, xenobiotics). While some terms are broader or metabolic, the shared theme centers on chemical sensing and taste perception, making this a coherent label that remains specific yet inclusive.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0001580","count":15},{"id":"GO:0050909","count":15},{"id":"GO:0019236","count":9},{"id":"GO:0007606","count":9},{"id":"GO:0022900","count":7}]},{"hash":"510224816010714835","title":"Dopamine-Linked Neuroimmune Signaling","description":"This cluster centers on dopamine transport and receptor signaling, paired with glial (astrocyte) regulation and glial-derived neurotrophic factor production, indicating a dopamine-glia axis. It also includes immune and xenobiotic response terms, suggesting a broader neuroimmune modulation by dopamine and chemical stimuli; the common thread appears to be dopamine-influenced neuroimmune and glial signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":21},{"id":"GO:0042493","count":21},{"id":"GO:2000458","count":21},{"id":"GO:1900168","count":21},{"id":"GO:0048245","count":21}]},{"hash":"383764222660060423","title":"Neuroimmune Signaling and Glial Modulation","description":"The cluster shows prominent terms related to immune/inflammatory regulation (negative regulation of inflammatory response, immune response, eosinophil chemotaxis) alongside neural/glial functions (astrocyte chemotaxis, regulation of glial cell-derived neurotrophic factor production, dopamine transport, and dopamine signaling/metabolism). This suggests a cohesive theme of neuroimmune interactions with glial modulation affecting dopaminergic pathways. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":21},{"id":"GO:0042493","count":21},{"id":"GO:2000458","count":21},{"id":"GO:1900168","count":21},{"id":"GO:0048245","count":21}]},{"hash":"1338742211196293237","title":"Dopaminergic signaling and glial immune regulation","description":"This cluster combines dopamine-related processes (dopamine transport, regulation of dopamine metabolism, and dopamine receptor signaling) with glial/immune functions (astrocyte chemotaxis, glial neurotrophic regulation, and immune response/xenobiotic-stimulated responses). The co-occurrence of neural dopamine pathways and glial/immune modulation suggests proteins here link dopaminergic signaling to neuroimmune interactions and detox-related responses.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":21},{"id":"GO:0042493","count":21},{"id":"GO:2000458","count":21},{"id":"GO:1900168","count":21},{"id":"GO:0048245","count":21}]},{"hash":"597933190519419724","title":"Embryonic Development and Transcriptional Regulation","description":"The cluster shows strong enrichment for DNA-templated transcription and key developmental processes (multicellular organism development, skeletal system development, neural tube closure), indicating proteins involved in embryogenesis and morphogenesis. Additional enrichments for growth hormone response and the mitotic cell cycle support proliferative, growth-related signaling during development, while cadmium response and defense against Gram-positive bacteria reflect broader cellular stress responses that can accompany development. Overall, the dominant theme is developmental transcriptional programs shaping vertebrate morphogenesis, making this label representative.","confidence":"High","size":20,"edges":80,"triangles":102,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":15},{"id":"GO:0006349","count":14},{"id":"GO:0007275","count":14},{"id":"GO:0001501","count":11},{"id":"GO:0071276","count":11}]},{"hash":"21247996517899470","title":"Mechanical signaling and adipocyte differentiation","description":"The cluster\u2019s top terms center on responses to mechanical stimuli (cellular/mechanical stimulus, muscle stretch) and fat cell differentiation, plus cell migration, suggesting a shared theme of how cells sense mechanical cues and drive adipogenic differentiation. Other terms like mRNA processing, ubiquitination, and telomere maintenance are present but seem less central to the core theme. ","confidence":"Medium","size":20,"edges":70,"triangles":69,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":7},{"id":"GO:0032212","count":7},{"id":"GO:0016477","count":7},{"id":"GO:0006397","count":7},{"id":"GO:0045444","count":7}]},{"hash":"166902918276706674","title":"Hypoxia-responsive heart and skeletal muscle development","description":"The strongest signals in this cluster are response to hypoxia, heart development, and slow-twitch skeletal muscle contraction, suggesting a cohesive theme around hypoxia-adapted cardiovascular and skeletal muscle growth and function. Other terms like receptor-mediated endocytosis and protein heterooligomerization appear peripheral but do not override the core muscle- and heart-related signals.","confidence":"High","size":20,"edges":103,"triangles":287,"max_degree":17,"top_function":"wound healing","top_go_terms":[{"id":"GO:0001666","count":15},{"id":"GO:0007507","count":11},{"id":"GO:0070293","count":9},{"id":"GO:0010764","count":9},{"id":"GO:0031444","count":9}]},{"hash":"1529932558670164787","title":"DNA replication and genome maintenance","description":"The top GO terms point to core genome stability processes: DNA replication, nucleotide-excision repair and general DNA repair, plus telomere maintenance. Other terms touch on transcription regulation and development, suggesting these proteins participate in DNA damage response and related cellular processes, with genome maintenance as the dominant theme. Confidence: High","confidence":"","size":20,"edges":82,"triangles":115,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0033683","count":4},{"id":"GO:0035315","count":4},{"id":"GO:0001666","count":4}]},{"hash":"669498485834219819","title":"DNA replication, repair, and chromatin assembly","description":"The top GO terms point to DNA metabolism (replication, repair, recombination) and chromatin-related processes (centromeric CENP-A assembly, histone modification, chromatin localization). Transcription-related terms are present but sit within the same nuclear context of genome maintenance and chromatin regulation, suggesting a cohesive module linking DNA processing with chromatin dynamics and transcription readiness.","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006281","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006352","count":5},{"id":"GO:0051123","count":5}]},{"hash":"1396982685464111269","title":"Vesicle trafficking and actin remodeling","description":"Proteins in this cluster are enriched for intracellular transport processes (Golgi-ER transport, ER-Golgi transport, endocytosis, vesicle exocytosis regulation) and for actin cytoskeleton dynamics (actin polymerization, stress fiber assembly, formin-nucleated actin assembly). The presence of endothelial barrier establishment and Wnt signaling hints at vascular context where signaling modulates cytoskeleton and trafficking. Overall, the common theme is vesicle trafficking coupled with actin remodeling.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":14},{"id":"GO:0090338","count":14},{"id":"GO:0030838","count":14},{"id":"GO:0051496","count":14},{"id":"GO:0006890","count":13}]},{"hash":"1418173230491911733","title":"Pro-inflammatory Cytokine and Chemokine Signaling","description":"The proteins in this cluster are enriched for GO terms such as positive regulation of interleukin-6 production, positive regulation of chemokine production, defense response to virus, and signaling cascades like NF-kappaB and JNK. The convergence on cytokine/chemokine production and neutrophil extravasation indicates a cohesive innate immune inflammatory program focused on antiviral defense and recruitment of immune cells.","confidence":"High","size":20,"edges":47,"triangles":32,"max_degree":10,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051092","count":11},{"id":"GO:0045410","count":9},{"id":"GO:0051607","count":9},{"id":"GO:0090197","count":9},{"id":"GO:0046330","count":9}]},{"hash":"466976378947124212","title":"Unknown","description":"The top GO terms span mitotic cell cycle, stress and immune responses, and various developmental and neural processes (cadmium response, innate immunity, axial mesoderm formation, axon fasciculation, receptor clustering, etc.), with no clear, single shared function or pathway tying them together. This suggests the cluster represents a mix of disparate, loosely related roles rather than a cohesive biological theme.","confidence":"","size":20,"edges":13,"triangles":4,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":20},{"id":"GO:0071276","count":20},{"id":"GO:0045087","count":20},{"id":"GO:2001275","count":19},{"id":"GO:0048320","count":19}]},{"hash":"1468710003729016581","title":"Post-transcriptional mRNA processing and translation control","description":"The top GO terms cluster around post-transcriptional regulation: splicing (spliceosome), mRNA export, stability, and regulatory processes like ncRNA-mediated gene silencing and regulation of translational initiation. This suggests a coherent module of proteins involved in mRNA maturation, processing, and control of translation, rather than transcription initiation or protein modification. The emphasis on splicing, export, and stability supports a post-transcriptional expression control theme.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006446","count":19},{"id":"GO:1900363","count":19},{"id":"GO:0031047","count":19},{"id":"GO:0048026","count":19},{"id":"GO:0006406","count":19}]},{"hash":"1756230621302263150","title":"Embryonic morphogenesis and organ development","description":"The top GO terms point to developmental processes involved in embryo formation and organogenesis, including ureteric bud morphogenesis (kidney), cartilage morphogenesis, left-right patterning, placental and trophoblast differentiation, and epithelial-to-mesenchymal transition in heart development. While there is a spliceosome-related term, the dominant signal is embryonic morphogenesis and organ development, which justifies a label focused on developmental morphogenesis rather than a single pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090190","count":3},{"id":"GO:0060707","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0060536","count":3},{"id":"GO:0060972","count":3}]},{"hash":"1136431981488947702","title":"Neural development and Rho/Rac signaling","description":"This cluster is enriched for terms tied to neural development and glial growth (perineurial glial growth; negative regulation of neuroblast proliferation) and to signaling via Rho and Rac GTPases (regulation of Rho/Rac signal transduction, GTPase activity). Deubiquitination common to signaling regulation supports a theme of protein-level control within developing neural cells, with a few terms pointing to broader stress or antiviral responses that sit within this regulatory network.","confidence":"Medium","size":20,"edges":19,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0016579","count":3},{"id":"GO:2000212","count":2}]},{"hash":"251411186693569006","title":"Golgi Vesicle Trafficking and Organization","description":"The top GO terms overwhelmingly describe vesicle transport involving the Golgi (ER-to-Golgi, intra-Golgi, Golgi-to-vacuole), Golgi ribbon formation, and regulation of Golgi organization, indicating a cohesive function in Golgi trafficking and organization with related secretory processes.","confidence":"High","size":20,"edges":113,"triangles":318,"max_degree":19,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0048280","count":16},{"id":"GO:0006891","count":13},{"id":"GO:0006896","count":13},{"id":"GO:0006888","count":13},{"id":"GO:0090161","count":13}]},{"hash":"228237945830812991","title":"Chromatin modification and cell cycle regulation","description":"The top GO terms point to histone methylation (H3-K27, H3-K4, H3-K79) together with mitotic DNA replication and cell division processes (Okazaki fragment processing in mitotic replication, centrosome cycle, DNA-templated transcription). This pattern suggests a cluster of proteins involved in epigenetic regulation of chromatin states that coordinate DNA replication and mitosis. A few terms related to growth hormone response and lens fiber differentiation are present but appear peripheral to the core theme of chromatin modification linked to cell cycle control.","confidence":"High","size":20,"edges":30,"triangles":22,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061087","count":4},{"id":"GO:0051301","count":3},{"id":"GO:1903461","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0060416","count":3}]},{"hash":"1795724595808501656","title":"Hypoxia-responsive translation initiation and ribosome biogenesis","description":"This cluster centers on translation initiation and ribosome biogenesis, with strong enrichment for cellular response to hypoxia and translation reinitiation. The alignment of preinitiation complex formation, ribosome biogenesis, and translational regulation suggests a coordinated adjustment of protein synthesis during hypoxic stress, with occasional notes on IRES-dependent initiation that can accompany stress responses.","confidence":"High","size":20,"edges":172,"triangles":866,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0071456","count":6},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0000070","count":4},{"id":"GO:0042273","count":4}]},{"hash":"674735499215019404","title":"Mammary Gland Development and Reproduction","description":"The strongest signals are mammary gland\u2013related: epithelial cell proliferation, lactation, and female pregnancy. Additional terms touch on broader developmental processes (ureteric bud branching, renal function) and circadian regulation, suggesting a general developmental/reproductive theme rather than a single pathway. Given the isolated nature of the cluster (no edges) and mixed tissue contexts, this label emphasizes the dominant mammary/reproductive signals while noting broader development.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0032922","count":4},{"id":"GO:0007565","count":4},{"id":"GO:0070294","count":4},{"id":"GO:0090190","count":4}]},{"hash":"1383432984102955788","title":"Spliceosome-driven mRNA processing and export","description":"This cluster centers on post-transcriptional RNA processing, especially mRNA splicing via the spliceosome, along with regulation of alternative splicing, mRNA export, and aspects of mRNA stability under stress. The presence of translation-related GO terms suggests integration of RNA maturation with protein synthesis in response to cellular conditions, forming a cohesive module of RNA processing and export. ","confidence":"High","size":20,"edges":165,"triangles":772,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006378","count":5},{"id":"GO:0010610","count":5},{"id":"GO:0048025","count":5},{"id":"GO:0000381","count":4}]},{"hash":"172410232999712729","title":"RISC Assembly and miRNA/siRNA Processing","description":"The GO terms cluster around RNA interference pathways: RISC complex assembly, miRNA and siRNA processing, and gene silencing by mRNA cleavage, with supporting pre-miRNA processing and general mRNA processing terms. This coherent set strongly indicates a cluster of proteins functioning in RNAi machinery rather than unrelated processes.","confidence":"High","size":20,"edges":88,"triangles":143,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0035087","count":3},{"id":"GO:0035280","count":3},{"id":"GO:0035196","count":3},{"id":"GO:0030423","count":3},{"id":"GO:0090502","count":3}]},{"hash":"168914005132074586","title":"ER stress and secretory trafficking in cell division","description":"The cluster\u2019s top GO terms point to ER quality control and secretory pathway activity (ER unfolded protein response, ubiquitin-dependent ERAD, COPII vesicle loading, retrograde transport), alongside mitotic and ciliogenesis-related processes (cell division, spindle pole localization, cilium assembly). This suggests a cohesive function linking ER stress response with vesicle trafficking and division-related regulation, justifying a label focused on ER stress and secretory trafficking in the context of cell division.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0045737","count":4},{"id":"GO:0030968","count":3},{"id":"GO:0032889","count":3}]},{"hash":"838013471027875478","title":"Wnt Signaling in Tissue Development","description":"This cluster centers on the Wnt signaling pathway with several development-related terms across multiple tissues (heart, fat cells, prostate epithelium, visual system, peripheral nerves), alongside related intracellular signaling and cytoskeletal/endocytic activities, suggesting a shared role in developmental signaling and cell differentiation.","confidence":"Medium","size":20,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0035556","count":3}]},{"hash":"923722598847385132","title":"Viral DNA Integration and Nuclear Transport","description":"The top GO terms cluster around proviral latency establishment, DNA integration, and intracellular transport of viral material toward the nucleus, with supporting roles for cytoskeletal regulation and microtubule movement, indicating a cohesive theme of viral genome integration and intracellular trafficking within the host.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0075521","count":2},{"id":"GO:0043087","count":2}]},{"hash":"1732894303407379394","title":"Ribosome and Translation Machinery","description":"Proteins cluster around core translation roles: 14 proteins annotated with translation (GO:0006412), plus terms for translational elongation and termination and ribosomal large subunit assembly, and a note on translational fidelity. The presence of a translational and ribosome-focused set explains a tight functional theme, with a few stress-related terms reflecting regulation of protein synthesis under stress (ionizing radiation, stringent response).","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0090305","count":2},{"id":"GO:0006259","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0032232","count":1}]},{"hash":"1863811240400292723","title":"Microtubule Dynamics and Cell Motility","description":"The strongest terms are microtubule polymerization, centrosome separation, and locomotion, pointing to cytoskeletal regulation of movement; additional terms show some noise, but the core theme is microtubule-based cytoskeletal dynamics driving cell movement and organization.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031987","count":3},{"id":"GO:0051299","count":3},{"id":"GO:0046785","count":3},{"id":"GO:0016578","count":2},{"id":"GO:0043569","count":2}]},{"hash":"288929749397031372","title":"Embryonic neural and craniofacial development","description":"The top GO terms point to broad embryonic organogenesis with emphasis on neural differentiation and cerebral regionalization, craniofacial structures (pituitary, palate), and limb/digital and heart morphogenesis, suggesting a cohesive theme of early developmental processes across multiple tissues.","confidence":"High","size":20,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0060021","count":7},{"id":"GO:0021524","count":6},{"id":"GO:0048706","count":6},{"id":"GO:0021902","count":6}]},{"hash":"420297771506378450","title":"Unknown","description":"The Top Terms span diverse processes across animals, plants, and viruses (circadian regulation and sleep, nervous system and muscle development, ubiquitin\u2011dependent proteolysis, plant brassinosteroid signaling and flower development, chromosome passenger complex localization during mitosis, synaptic vesicle endocytosis, and viral latency release), with no clear single functional theme tying all proteins together. Therefore a cohesive label is not evident.","confidence":"","size":20,"edges":24,"triangles":13,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042752","count":18},{"id":"GO:0042787","count":18},{"id":"GO:0007399","count":17},{"id":"GO:0019046","count":17},{"id":"GO:0009742","count":17}]},{"hash":"1345304039324800140","title":"Ciliary trafficking and neural development","description":"The terms cluster around cilium-localization, vesicle trafficking (COPII, synaptic vesicle budding), cytoskeletal/tubulin assembly, and neural development, suggesting proteins that coordinate ciliary transport and neural vesicle dynamics; some mitotic terms are present but do not override the primary ciliogenesis/neural theme.","confidence":"High","size":20,"edges":188,"triangles":1105,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097499","count":20},{"id":"GO:1990386","count":20},{"id":"GO:0006878","count":20},{"id":"GO:0007264","count":20},{"id":"GO:0003400","count":20}]},{"hash":"1330008070037846157","title":"GTPase-driven cell migration and actin dynamics","description":"The cluster is dominated by terms tied to cell migration (GO:0016477) and actin filament bundle assembly (GO:0051017), with additional emphasis on positive regulation of GTPase activity (GO:0043547) and intracellular signal transduction (GO:0035556). These points together suggest a cohesive theme of cytoskeletal remodeling and migration regulated by GTPase signaling pathways, with supporting signals from growth hormone receptor signaling and transcriptional regulation that can accompany migratory programs. Overall, the proteins appear aligned with cytoskeleton dynamics and cell movement.","confidence":"High","size":20,"edges":32,"triangles":6,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0032088","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0060396","count":4},{"id":"GO:0006351","count":4}]},{"hash":"785720152449065524","title":"Phytochrome signaling and plant circadian rhythm","description":"This cluster is best named for phytochrome-mediated light perception and the regulation of circadian rhythm in plants. The top GO terms include far-red light signaling pathway, red/far-red light phototransduction, and positive regulation of circadian rhythm, with supporting terms related to chlorophyll catabolic processes, all indicating a plant-specific light-sensing and circadian-control module. Other metabolic terms are variably related but do not override this primary theme.","confidence":"High","size":20,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010018","count":1},{"id":"GO:0042753","count":1},{"id":"GO:0009585","count":1},{"id":"GO:0006306","count":1},{"id":"GO:0019889","count":1}]},{"hash":"1595160179852774939","title":"Positive Regulation of Diverse Cellular Processes","description":"The top GO terms all describe positive regulation in various biological contexts, ranging from signaling (Rho regulation), immune responses (dsRNA response, antiviral defense, T cell chemotaxis), to cellular dynamics (mitochondrial fission, membrane targeting, protein oligomerization) and development (eye development). This suggests the cluster represents proteins that broadly modulate or upregulate multiple cellular processes rather than a single pathway. Confidence is Medium.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0071360","count":2},{"id":"GO:0090141","count":2},{"id":"GO:1901028","count":2},{"id":"GO:0043010","count":2}]},{"hash":"1843316860063980207","title":"Ubiquitin-regulated plant light signaling","description":"The cluster is dominated by ubiquitin-related terms (ubiquitin-dependent protein catabolic process, autoubiquitination, ubiquitin ligase activity regulation, K63-linked ubiquitination) and photomorphogenesis/blue light response terms (primary root development and photoreceptor-related signaling), indicating a cohesive theme of ubiquitin-mediated protein turnover shaping plant light signaling. The presence of JNK cascade regulation suggests cross-talk with MAPK signaling downstream of light responses. Taken together, these functions point to a role in coordinating ubiquitin-mediated regulation of photomorphogenesis and growth signaling in plants.","confidence":"High","size":20,"edges":8,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0080022","count":3},{"id":"GO:1904667","count":3},{"id":"GO:0010099","count":3},{"id":"GO:0055121","count":3}]},{"hash":"1635219322356070571","title":"Regulation of cell migration and vascular remodeling","description":"This cluster centers on GO terms related to negative regulation of cell extravasation and neutrophil degranulation, plus vascular remodeling and permeability, and includes cytoskeletal regulation (Rho signaling and lamellipodium assembly). The presence of morphogenesis terms suggests broader tissue remodeling as well, collectively pointing to controlled cell movement and blood vessel remodeling.","confidence":"Medium","size":20,"edges":103,"triangles":278,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0002692","count":6},{"id":"GO:0043314","count":6},{"id":"GO:0060313","count":6},{"id":"GO:0043114","count":5},{"id":"GO:0035023","count":5}]},{"hash":"2107935640175252110","title":"ECM remodeling during embryonic development","description":"This cluster is driven by collagen fibril organization and tissue morphogenesis terms (collagen fibril organization, cartilage morphogenesis, left-right pattern formation, trophoblast differentiation, endocrine and pancreatic development) pointing to extracellular matrix\u2013mediated development and organogenesis. Additional terms like sprouting angiogenesis and innate immune regulation align with development-associated tissue remodeling, supporting an ECM-development theme rather than a single immune pathway.","confidence":"Medium","size":20,"edges":20,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":4},{"id":"GO:2000483","count":3},{"id":"GO:0002040","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0032088","count":2}]},{"hash":"1741759931967428500","title":"Mitochondrial ATP Synthesis and Proton Transport","description":"The top GO terms strongly point to mitochondrial energy metabolism, with multiple entries for proton motive force\u2013driven ATP synthesis and proton transmembrane transport, plus a note about mitochondrial targeting. A few terms (angiogenesis, flagellar motility, transcription termination, proteasome granule assembly) appear as outliers, but the dominant signal is mitochondrial bioenergetics and membrane transport, justifying a mitochondria-focused energy-production label.","confidence":"Medium","size":20,"edges":163,"triangles":756,"max_degree":19,"top_function":"lipid metabolic process","top_go_terms":[{"id":"GO:0006626","count":6},{"id":"GO:0042777","count":6},{"id":"GO:0001525","count":5},{"id":"GO:0090463","count":5},{"id":"GO:0042776","count":5}]},{"hash":"1602537103476679142","title":"Embryonic organ morphogenesis","description":"Most of the top GO terms describe developmental and morphogenetic processes across multiple organs and tissues (heart development, placental development, embryonic eye morphogenesis, hindlimb morphogenesis, outflow tract morphogenesis, roof of the mouth, prostate gland development, habenula development). A secondary theme is regulation of tissue growth (myoblast proliferation). This pattern suggests a cluster enriched for proteins involved in embryonic organogenesis and general developmental morphogenesis rather than a tissue-specific function.","confidence":"High","size":20,"edges":9,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":11},{"id":"GO:0021986","count":11},{"id":"GO:2000288","count":10},{"id":"GO:0008584","count":10},{"id":"GO:0001890","count":10}]},{"hash":"3695322952265816","title":"Angiogenesis and developmental signaling","description":"The top GO terms cluster around blood vessel formation and growth-factor\u2013driven development, including angiogenesis, cellular response to VEGF, and forebrain/multicellular development, plus IGF receptor signaling. While there are immune and oxidative stress terms present, the dominant pattern ties to vascular development and growth signaling during organism development, suggesting the proteins collectively participate in angiogenic regulation and developmental growth pathways.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0035924","count":3},{"id":"GO:0071447","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0048009","count":3}]},{"hash":"153842156675565584","title":"ER Stress\u2013Induced Apoptosis and Innate Immunity","description":"This cluster centers on cellular stress responses that connect to innate immunity. The top GO terms include glutathione catabolic process and an intrinsic apoptotic pathway triggered by ER stress, plus negative regulation of Notch signaling. Additional terms point to innate immune regulation and inflammation, such as IL-17 and IL-15 production, IL-10 regulation, NK cell differentiation, neutrophil-mediated killing, and the broader inflammatory response. Taken together, the terms suggest a theme of stress-induced cell fate decisions intertwined with immune signaling and inflammatory control.","confidence":"Medium","size":20,"edges":15,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006751","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0045746","count":3},{"id":"GO:0032700","count":1},{"id":"GO:0001779","count":1}]},{"hash":"1231467531177996699","title":"Transcriptional Regulation and NF-kB Signaling","description":"Most terms point to control of gene expression (DNA-templated transcription and its regulation) and chromatin modification (histone acetylation), with a signal transduction angle via NF-kB. A few terms touch on cytoskeleton dynamics and vesicle transport, but the core theme remains transcriptional regulation and chromatin state. ","confidence":"Medium","size":20,"edges":20,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007026","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0044154","count":1},{"id":"GO:0043981","count":1}]},{"hash":"75817511182003180","title":"Neurodevelopmental and angiogenic signaling","description":"This cluster is enriched for nervous system development, angiogenesis, myelination, and synapse assembly, along with regulatory signaling in the ERK/MAPK axis and FGF receptor pathways, plus organ induction and endothelial chemotaxis to FGF. Together these terms point to a coordinated developmental signaling program governing neural and vascular development.","confidence":"High","size":20,"edges":35,"triangles":6,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0042552","count":4},{"id":"GO:0051965","count":4},{"id":"GO:0070352","count":4}]},{"hash":"183674521512746110","title":"Actin Cytoskeleton Remodeling and Rho Signaling","description":"The top GO terms cluster around actin filament organization and cortical assembly, plus regulation of Rho/GTPase signaling and membrane remodeling, tying together processes like cell spreading, phagocytosis, and synaptic/muscle tissue remodeling. This suggests a cohesive theme of actin cytoskeleton dynamics governed by Rho-family signaling across adhesion, membrane remodeling, and remodeling contexts.","confidence":"High","size":20,"edges":172,"triangles":864,"max_degree":19,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043652","count":12},{"id":"GO:0034446","count":12},{"id":"GO:0000147","count":11},{"id":"GO:0043547","count":11},{"id":"GO:0035023","count":11}]},{"hash":"314299291681789708","title":"Cytoskeletal Remodeling and Cell Migration","description":"This cluster centers on actin-based cytoskeleton dynamics\u2014filopodium and lamellipodium assembly, and regulation of Rho/Ral signaling\u2014which together drive cell migration and morphogenesis (including heart development). Some terms appear obsolete or peripheral, but the core theme remains cytoskeletal remodeling guiding movement.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0046847","count":5},{"id":"GO:0007205","count":5}]},{"hash":"1363257500224922922","title":"Developmental organogenesis","description":"The top GO terms indicate broad roles in organ formation and morphogenesis across many tissues (heart, pancreas, midbrain, uterus, dentin), plus organ induction and nodal signaling. This pattern points to a general developmental/organogenesis theme rather than a single tissue-specific function, hence the label Developmental organogenesis.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090190","count":4},{"id":"GO:0001759","count":3},{"id":"GO:0042475","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0038092","count":3}]},{"hash":"179816591232232334","title":"Golgi-ER trafficking and lysosome targeting","description":"The proteins cluster around intracellular protein sorting and trafficking, highlighted by GO terms for Golgi retention/organization, ER tubular network formation, and targeting to lysosomes, with an additional signal from aggrephagy. This points to a coherent module coordinating ER-to-Golgi transport and lysosomal targeting, possibly connected to autophagy and cytoskeletal dynamics. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0071787","count":2},{"id":"GO:0034145","count":2},{"id":"GO:0006622","count":2}]},{"hash":"1567504759829507870","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":28,"triangles":44,"max_degree":8,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":4},{"id":"GO:1904628","count":3},{"id":"GO:0071364","count":3},{"id":"GO:0031086","count":3}]},{"hash":"1347953195235739537","title":"ER Stress and Proteostasis Network","description":"The top terms point to protein quality control and folding within the ER and secretory pathway: oligomerization, ERAD, chaperone-assisted refolding, translation initiation during ER stress, and redox/homeostasis maintenance. Together, these suggest a cohesive proteostasis/ER stress response theme, with some annotations (e.g., mesoderm formation) likely reflecting pleiotropy or broader regulatory roles rather than a core function of the cluster.","confidence":"High","size":20,"edges":169,"triangles":836,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051259","count":20},{"id":"GO:0006469","count":20},{"id":"GO:1901621","count":20},{"id":"GO:0030433","count":20},{"id":"GO:0036494","count":20}]},{"hash":"2008068989814801816","title":"Neural development and cytoskeleton regulation","description":"This cluster prominently features terms tied to nervous system development and pathways governing cytoskeleton organization and microtubule-based transport. While a few terms touch on broader stress responses or viral transport, the dominant signals point to neural differentiation and cytoskeletal dynamics that govern intracellular trafficking. The name reflects the most representative theme without overstating viral-specific functions.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048712","count":2},{"id":"GO:0048147","count":2},{"id":"GO:0006950","count":1},{"id":"GO:0034605","count":1},{"id":"GO:0075521","count":1}]},{"hash":"2134567449001476327","title":"Mitochondrial Translation and Cristae Assembly","description":"This cluster is dominated by mitochondrial processes: translation and mitochondrial translation initiation, insertion of proteins into the mitochondrial membrane, cristae formation, and rRNA import into mitochondrion, with additional signals of Fe-S cluster assembly and related ion homeostasis, pointing to a mitochondrial biogenesis/maintenance module.","confidence":"High","size":20,"edges":188,"triangles":1105,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0051204","count":2},{"id":"GO:0042407","count":2},{"id":"GO:0070131","count":2},{"id":"GO:0030007","count":2}]},{"hash":"401126675356037985","title":"Transcription-driven organogenesis","description":"Top GO terms indicate a strong emphasis on transcription by RNA polymerase II and diverse organogenesis/differentiation processes across multiple tissues, with supportive roles for integrin-mediated adhesion in morphogenesis. This combination suggests a cluster of proteins that coordinate gene expression to drive organ development rather than a single tissue-specific function.","confidence":"High","size":20,"edges":144,"triangles":559,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":17},{"id":"GO:0033627","count":15},{"id":"GO:0021750","count":15},{"id":"GO:0003259","count":15},{"id":"GO:0061382","count":15}]},{"hash":"1680380285001299052","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms describing ubiquitination (protein ubiquitination, polyubiquitination, autoubiquitination) and proteasome/ERAD-related catabolic processes (SCF-dependent proteasomal ubiquitin-dependent protein catabolic process), indicating a shared function in tagging proteins for degradation via the ubiquitin-proteasome system. Some outliers like V(D)J recombination and dosage compensation appear incidental but do not disrupt the overall theme.","confidence":"High","size":20,"edges":6,"triangles":1,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":19},{"id":"GO:0030433","count":15},{"id":"GO:0051865","count":11},{"id":"GO:0016567","count":11},{"id":"GO:0000209","count":10}]},{"hash":"429796462648170395","title":"Apoptosis signaling and cell cycle arrest","description":"The cluster shows strong representation of apoptotic pathways (intrinsic and extrinsic, cytochrome c release, caspase activation) and regulation of the G1/S transition, plus hypoxia response, indicating a cohesive theme of programmed cell death and cell cycle control. Minor terms like spermatogenesis/gonad development may reflect tissue-specific contexts.","confidence":"High","size":20,"edges":13,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097202","count":4},{"id":"GO:0090200","count":4},{"id":"GO:0048147","count":3},{"id":"GO:0019076","count":3},{"id":"GO:0007283","count":3}]},{"hash":"1213797081090980755","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"Reason: The majority of top GO terms describe actin cytoskeleton organization, lamellipodium assembly, small GTPase signaling (Rho), and cell migration, indicating a shared function in cytoskeletal remodeling and movement. A couple of terms outside this theme (sound perception, insulin signaling) are peripheral noise and do not derail the main cluster.","confidence":"High","size":20,"edges":4,"triangles":0,"max_degree":2,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007605","count":11},{"id":"GO:0030036","count":11},{"id":"GO:0008286","count":11},{"id":"GO:0035023","count":10},{"id":"GO:0030032","count":10}]},{"hash":"1087243478911708048","title":"Vascular ECM remodeling and complement activation","description":"The dominant terms point to extracellular matrix organization (collagen fibril organization, elastic fiber assembly), vascular development (aorta development), and endothelial regulation, alongside immune activity via complement activation pathways. This suggests a cluster of proteins involved in maintaining vascular ECM and associated immune modulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2001027","count":7},{"id":"GO:0030199","count":7},{"id":"GO:0051965","count":7},{"id":"GO:0001970","count":7},{"id":"GO:0006958","count":7}]},{"hash":"1261610542407888611","title":"Developmental differentiation and cell adhesion","description":"The cluster\u2019s top GO terms cluster around developmental processes (endodermal differentiation, chondrocyte morphogenesis, stamen formation) and cell\u2013matrix/cell\u2013cell adhesion, along with cytoskeletal remodeling and ECM-related processes. This suggests proteins functioning in tissue development and structural organization, despite a few outlier terms such as chlorophyll biosynthetic process that may reflect cross-species annotations. Overall, the dominant theme is developmental differentiation coupled with adhesion and matrix remodeling.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":6},{"id":"GO:0070208","count":5},{"id":"GO:0007161","count":5},{"id":"GO:0031532","count":4},{"id":"GO:0015995","count":4}]},{"hash":"2192187340018282170","title":"Neuromuscular junction assembly and trafficking","description":"Top GO terms center on synaptic assembly at the neuromuscular junction and its regulation, complemented by intracellular trafficking (ER membrane fusion, Golgi organization) and cytoskeletal dynamics (microtubule depolymerization). Immune signaling terms (IFN-\u03b3 response, IL-1\u03b2 production, NLRP3 inflammasome) imply inflammatory regulation that can modulate NMJ activity, suggesting these proteins participate in NMJ formation/maintenance with linked trafficking and cytoskeletal remodeling, and possibly immune crosstalk.","confidence":"Medium","size":20,"edges":14,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071346","count":4},{"id":"GO:1900041","count":4},{"id":"GO:1900025","count":4},{"id":"GO:0008582","count":4},{"id":"GO:0007019","count":4}]},{"hash":"2166836973876554724","title":"Unknown","description":"The top GO terms are a mix of neuronal signaling/regulation (synaptic plasticity and ephrin signaling), cytoskeletal dynamics (microtubule polymerization), chromatin remodeling (nucleosome disassembly, histone acetylation), germ cell chromatin changes (sperm DNA decondensation), and general growth/division processes (budding growth, stem cell division). This diverse set does not point to a single coherent function or pathway, so a specific, intuitive cluster name cannot be confidently assigned beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900383","count":2},{"id":"GO:1901187","count":2},{"id":"GO:0031116","count":2},{"id":"GO:2000617","count":2},{"id":"GO:0007117","count":2}]},{"hash":"2002352055942730100","title":"Cardiac electrical activity and potassium homeostasis","description":"Most top GO terms cluster around cardiac electrophysiology and potassium handling: membrane repolarization during atrial cardiac muscle action potential, regulation of resting membrane potential, potassium ion transport and intracellular potassium ion homeostasis, stabilization of membrane potential, and regulation of heart rate by cardiac conduction, plus cardiac muscle action potential involved in contraction. A touch-detection term appears but is less central, and vestibular development is not core to this cluster. Overall, the dominant theme is potassium-dependent regulation of cardiac excitability and membrane potential.","confidence":"High","size":20,"edges":131,"triangles":535,"max_degree":17,"top_function":"nervous system process","top_go_terms":[{"id":"GO:0098914","count":20},{"id":"GO:0060075","count":17},{"id":"GO:1990573","count":14},{"id":"GO:0086091","count":14},{"id":"GO:0086002","count":14}]},{"hash":"105470380815527356","title":"Unknown","description":"The top GO terms are scattered across immunity (cellular response to type I interferon), lipid and lipid-like metabolism (lipopolysaccharide metabolic process; regulation of lipid biosynthetic process), development/hormone signaling (steroid hormone receptor complex assembly; male sex differentiation; cytokinin-activated signaling), and even an obsolete/less specific term, with no clear shared function linking the proteins. This suggests no coherent single theme for the cluster.","confidence":"","size":20,"edges":66,"triangles":134,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006490","count":3},{"id":"GO:0006463","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0008653","count":2}]},{"hash":"549223988360600496","title":"Complement activation and immune regulation","description":"The top GO terms point strongly to the complement system (classical and alternative pathways), MAC regulation, and immune cell interactions (IL-10 production, T cell death, leukocyte adhesion/rolling), suggesting a module focused on immune responses and complement control rather than other processes. Some terms like fertilization or vocalization seem incidental to the core immune-related signals.","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0032613","count":4},{"id":"GO:0006958","count":4},{"id":"GO:0007338","count":4},{"id":"GO:0007157","count":4},{"id":"GO:0006924","count":3}]},{"hash":"1320279075268466286","title":"Embryonic organogenesis","description":"The top terms indicate involvement in broad developmental processes across multiple tissues (habenula, palate, kidney, pancreas, muscle, ear, skull) along with core transcriptional regulation (DNA-templated transcription and RNA Pol II regulation), suggesting a cluster of proteins participating in embryonic organogenesis and tissue morphogenesis rather than a single tissue-specific function.","confidence":"High","size":20,"edges":133,"triangles":445,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021986","count":10},{"id":"GO:0090190","count":9},{"id":"GO:0060021","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0035914","count":7}]},{"hash":"1393842956815789969","title":"Organogenesis and morphogenesis","description":"The top GO terms cover development of various organs and tissues (palate, eye, heart, mesoderm, cartilage, hair follicles, left/right patterning, endocrine system, pancreatic cells), suggesting a broad developmental program rather than a single tissue-specific function. The label reflects a general theme of organogenesis and morphogenesis across lineages.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":8},{"id":"GO:0007601","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0060707","count":5},{"id":"GO:0007498","count":5}]},{"hash":"678513819395750435","title":"Hepatic peptide hormone processing and xenobiotic response","description":"This cluster is enriched for liver-related processes, including regulation of angiotensin and bradykinin catabolism, liver regeneration, and hepatocyte proliferation; plus insulin processing and proteolysis, indicating involvement in hepatic peptide hormone metabolism and xenobiotic response, with supporting protein processing modifications such as deglutamylation.","confidence":"High","size":20,"edges":48,"triangles":34,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0030070","count":4},{"id":"GO:0006508","count":3},{"id":"GO:0035611","count":3},{"id":"GO:0009408","count":3}]},{"hash":"236059952747182519","title":"Transcription Regulation by RNA Polymerase II","description":"The proteins in this cluster are dominated by GO terms describing DNA-templated transcription and modulation of RNA Pol II activity (e.g., transcription, negative regulation of transcription by RNA Pol II). Though a few terms relate to peroxisome inheritance or vesicle transport, the prevailing signal is transcriptional regulation by RNA Pol II, making the proposed label representative.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007576","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0010729","count":9},{"id":"GO:0070895","count":9},{"id":"GO:0046022","count":9}]},{"hash":"1374394301763185582","title":"Cartilage development and ECM organization","description":"Explanation: The prominent GO terms converge on cartilage formation and extracellular matrix remodeling\u2014chondrocyte proliferation, cartilage condensation, collagen fibril organization, and BMP signaling regulation\u2014consistent with skeletogenesis and an avascular cartilage phenotype; ancillary terms related to vascular regulation do not override the cartilage-centric theme.","confidence":"High","size":20,"edges":45,"triangles":33,"max_degree":9,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0007596","count":10},{"id":"GO:0001558","count":10},{"id":"GO:0010751","count":9},{"id":"GO:0035988","count":8},{"id":"GO:0016525","count":8}]},{"hash":"1054428504530456129","title":"Embryonic morphogenesis and neural differentiation","description":"This cluster is dominated by embryonic development signals: tissue morphogenesis (ectoderm formation, skeletal system morphogenesis, renal vesicle morphogenesis, placental differentiation) and neuronal differentiation/migration (lateral/medial motor column). The actin filament bundle assembly term supports morphogenesis, while a viral transcription term stands out as a less related outlier.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":3},{"id":"GO:0048704","count":2},{"id":"GO:0050434","count":2},{"id":"GO:0042308","count":2},{"id":"GO:0010735","count":1}]},{"hash":"2086872794035591922","title":"Sodium and Potassium Ion Transport and Membrane Potential","description":"This cluster\u2019s proteins are tied to ion movement across membranes and maintaining electrochemical gradients, particularly for sodium and potassium. GO terms such as potassium ion import across the plasma membrane, sodium ion export across the plasma membrane, regulation of sodium ion transport activity, establishment/maintenance of transmembrane electrochemical gradients, and transmembrane transport point to a core function in ion transport and membrane potential regulation, with a note of cardiac muscle-related membrane potential as context. Therefore, a label focused on ion transport and membrane potential best captures the cluster\u2019s common theme.","confidence":"High","size":20,"edges":36,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":1},{"id":"GO:0036376","count":1},{"id":"GO:2000649","count":1},{"id":"GO:0086036","count":1},{"id":"GO:1903278","count":1}]},{"hash":"288526725552774826","title":"Embryonic Development and Morphogenesis","description":"The GO terms point to overarching developmental and morphogenetic processes across multiple tissues (left/right patterning, mesoderm development, placenta-related differentiation, and organ morphogenesis such as cartilage, hair follicles, and oral structures) as well as endocrine system development, indicating a cohesive theme of embryogenesis and tissue formation rather than a single tissue-specific function.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060972","count":7},{"id":"GO:0035270","count":6},{"id":"GO:0060806","count":6},{"id":"GO:0060536","count":6},{"id":"GO:0003323","count":6}]},{"hash":"2238343970528138373","title":"Embryonic development and morphogenesis","description":"The GO terms cluster around embryogenesis, including placental, heart, cartilage, and pancreas development, as well as left-right patterning and EMT-related processes; together they point to coordinated tissue differentiation and morphogenesis during early development.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":4},{"id":"GO:0060536","count":4},{"id":"GO:0060972","count":4},{"id":"GO:0035270","count":4},{"id":"GO:0003323","count":4}]},{"hash":"187850001554385908","title":"Neuronal signaling and endosomal transport","description":"The main signals revolve around neuronal activity and membrane transport: calcium ion transmembrane movement, membrane hyperpolarization, neuronal action potential propagation, and trafficking of neurotransmitter receptors between endosomal compartments. A few terms (tight junction assembly, bone resorption) are less connected, but the dominant pattern ties to neural membrane signaling and endosomal trafficking.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070588","count":5},{"id":"GO:0070830","count":4},{"id":"GO:0032060","count":4},{"id":"GO:0060081","count":3},{"id":"GO:0045779","count":3}]},{"hash":"843704362090084791","title":"Neuronal GPCR Signaling and Receptor Trafficking","description":"The cluster centers on G protein-coupled receptor signaling (including dopamine receptor signaling and taste GPCR terms) and processes governing receptor trafficking and endocytosis (receptor recycling, endosome-to-postsynaptic transport, clathrin coat assembly), indicating a cohesive theme of GPCR signaling with receptor trafficking in neurons. The regulatory ncRNA-mediated gene silencing term appears less connected to the main theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050916","count":1},{"id":"GO:0050917","count":1},{"id":"GO:0015867","count":1},{"id":"GO:0050913","count":1},{"id":"GO:0048268","count":1}]},{"hash":"810139429444402308","title":"Carbohydrate and Xenobiotic Transport","description":"The top GO terms cluster strongly around membrane transport, especially for sugars (glucose, fructose, trehalose) and other solutes (organic anions/cations, xenobiotics). Terms like glucose import in response to insulin and cellular responses to glucose starvation support a transporter-focused role in nutrient uptake and metabolic regulation, with a possible link to intestinal epithelial structure maintenance. Together these suggest a cluster of proteins functioning mainly as carbohydrate and xenobiotic membrane transporters.","confidence":"High","size":20,"edges":185,"triangles":1060,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0043252","count":18},{"id":"GO:1904659","count":18},{"id":"GO:0070715","count":18},{"id":"GO:0060731","count":18},{"id":"GO:1990539","count":18}]},{"hash":"605646221740779168","title":"Diverse membrane transporters for nutrients and xenobiotics","description":"The top GO terms are dominated by transmembrane transport across a wide range of substrates (nitrate, phosphate, galactose, vitamins, sodium, xenobiotics) plus related metabolism (fucose). This points to a cluster of membrane transporter proteins specialized for uptake and efflux of diverse nutrients and xenobiotics, with some metabolic context. ","confidence":"High","size":20,"edges":54,"triangles":96,"max_degree":12,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0042128","count":13},{"id":"GO:0035435","count":12},{"id":"GO:1900754","count":12},{"id":"GO:0015757","count":12},{"id":"GO:0035461","count":12}]},{"hash":"1664448998502435458","title":"Developmental signaling and morphogenesis","description":"Top terms are dominated by developmental processes (heart trabecula formation, nervous system development, olfactory lobe development, endothelial morphogenesis) and signaling pathways (smoothened signaling, positive regulation of tyrosine phosphorylation of STAT), suggesting a cohesive theme of developmental signaling guiding tissue formation. Innate immune and host-symbiont interaction terms appear less central, so the label emphasizes development and morphogenesis with associated signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0060347","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0032930","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0007155","count":3}]},{"hash":"2218931387486432517","title":"Membrane Metal Ion Transport and Detoxification","description":"The top GO terms are heavily focused on transport of metal ions (cadmium, zinc, iron, cobalt) across the plasma membrane, plus detoxification and homeostasis of these ions, with calcium and amino acid transport also represented. This suggests a cohesive theme of membrane-associated ion export and metal detoxification, possibly involving metal efflux transporters and related proteins. The connection across multiple metals and detoxification processes supports a single functional cluster centered on metal ion transport and homeostasis.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":5},{"id":"GO:0032973","count":5},{"id":"GO:0070574","count":5},{"id":"GO:0071577","count":5},{"id":"GO:0098849","count":5}]},{"hash":"1051832634444374681","title":"Neuropeptide GPCR-cAMP stress and fear signaling","description":"Most represented term is neuropeptide signaling pathway, with several stress-related terms (cortisol secretion, startle and fear responses, immobilization stress) and GPCR/cAMP signaling terms. Together, these indicate a cluster of proteins involved in neuropeptide\u2013GPCR signaling that modulates stress and fear responses. Therefore the name fits.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007218","count":6},{"id":"GO:0010193","count":3},{"id":"GO:0010737","count":3},{"id":"GO:0019933","count":3},{"id":"GO:0007189","count":3}]},{"hash":"1192603686438849718","title":"Immune signaling with cardiac and bone remodeling","description":"Top GO terms point to immune activity (positive regulation of IL-6 production, defense against Gram-positive bacteria, T cell homeostasis) together with pathways linked to apoptosis (extrinsic apoptotic signaling and phospholipid scrambling). Several terms indicate control of tissue remodeling and function in the heart and bone (negative regulation of cardiac hypertrophy, relaxation of cardiac muscle, negative regulation of bone resorption). This combination suggests a cluster of proteins involved in immune signaling that also modulate cell death and tissue remodeling in cardiovascular and skeletal contexts, hence the label Immune signaling with cardiac and bone remodeling.","confidence":"Medium","size":20,"edges":96,"triangles":230,"max_degree":17,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0032755","count":8},{"id":"GO:0050830","count":8},{"id":"GO:0045332","count":8},{"id":"GO:0097191","count":7},{"id":"GO:0010614","count":7}]},{"hash":"177728692600669187","title":"ECM remodeling and immune signaling","description":"The top GO terms point to extracellular matrix organization and cell-matrix adhesion (collagen fibril organization, cell-matrix adhesion), prostaglandin biosynthesis, and components of innate immunity (blood coagulation, engulfment of apoptotic cells, activation of membrane attack complex). There are also signals of membrane receptor clustering and GPCR-mediated signaling, suggesting coordinated membrane organization and downstream immune/inflammatory responses. Altogether, the cluster seems centered on extracellular matrix remodeling coupled with immune and inflammatory signaling, with some membrane signaling context.","confidence":"Medium","size":20,"edges":30,"triangles":21,"max_degree":13,"top_function":"wound healing","top_go_terms":[{"id":"GO:0043113","count":9},{"id":"GO:0007566","count":9},{"id":"GO:0007213","count":9},{"id":"GO:0007596","count":8},{"id":"GO:0019800","count":8}]},{"hash":"452633415690023878","title":"Lens development and eye morphogenesis","description":"The top GO terms are dominated by lens-related processes (lens fiber cell differentiation, morphogenesis, development) and camera-type eye development, indicating proteins collectively function in lens and eye formation rather than other cellular roles. A few terms like visual perception appear but are secondary to the lens/eye development signal, supporting a cohesive theme of lens and eye morphogenesis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0002088","count":2},{"id":"GO:0002009","count":2},{"id":"GO:0070309","count":2}]},{"hash":"559440130801033394","title":"Glycinergic Synaptic Transmission and Glycine Transport","description":"This cluster is dominated by glycine-handling at synapses: glycinergic transmission, glycine import/export, and glycine secretion, indicating a core theme of glycine-based neurotransmission and its transport. Additional terms about serotonin uptake/secretion and dopamine catabolism flank this theme, suggesting broader neurotransmitter regulation in neural contexts, but glycine-related terms are the strongest signal. Perineurial glial growth appears supportive but secondary to the main glycinergic function.","confidence":"High","size":20,"edges":73,"triangles":128,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0060012","count":16},{"id":"GO:0051610","count":16},{"id":"GO:0042066","count":16},{"id":"GO:0036233","count":16},{"id":"GO:0015734","count":16}]},{"hash":"1536836579404445994","title":"Skeletal system development and myoblast fusion","description":"The cluster\u2019s top GO terms cluster around skeletal development and muscle precursor fusion (embryonic skeletal system development; myoblast fusion in skeletal muscle regeneration; positive regulation of cartilage and bone development), with supporting signals from neural crest development. A couple of outliers (visual perception, ER protein folding) do not override the dominant skeletal-development theme. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048706","count":2},{"id":"GO:0045026","count":2},{"id":"GO:0014905","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0035751","count":1}]},{"hash":"352828385081829457","title":"Polyamine biosynthesis and transport","description":"The cluster shows a strong enrichment for polyamine metabolic processes, including putrescine and spermidine biosynthesis from arginine/ornithine and related pathways (nor-spermidine), plus positive regulation of polyamine transport. This points to a cohesive function in polyamine biosynthesis and transmembrane transport. Some terms like tRNA dihydrouridine synthesis or kidney development appear less directly related and may reflect broader or cross-species annotations, but the dominant signal is polyamine metabolism. ","confidence":"High","size":20,"edges":140,"triangles":492,"max_degree":19,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0002943","count":3},{"id":"GO:0008295","count":3},{"id":"GO:0001822","count":3},{"id":"GO:0006527","count":3}]},{"hash":"2130965797442739555","title":"Neuronal signaling and blood-nerve barrier functions","description":"The terms point to neural function (substantia nigra development; sensory perception of sound; neuronal action potential propagation; integrin signaling in neurons) along with barrier and trafficking processes (tight junction assembly; xenobiotic transport across the blood-nerve barrier; endosome transport). This suggests a cluster centered on neural signaling linked to barrier integrity and intracellular trafficking, hence the label focusing on neuronal signaling and blood-nerve barrier functions.","confidence":"High","size":20,"edges":41,"triangles":21,"max_degree":11,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:2001046","count":8},{"id":"GO:0070830","count":7},{"id":"GO:0021762","count":5},{"id":"GO:0007605","count":5},{"id":"GO:0060081","count":5}]},{"hash":"2065403127973529747","title":"Neural membrane signaling and barrier organization","description":"The cluster centers on membrane-associated processes that influence neural function and barrier integrity: myelination, tight junction/endothelial barrier establishment, neuronal synaptic plasticity, and membrane domain organization (e.g., membrane raft polarization, eisosome assembly). While there are a few immune-related terms (B cell signaling, death receptor pathways), the prevailing pattern ties membrane signaling and structural organization to neural and barrier systems.","confidence":"Medium","size":20,"edges":185,"triangles":1054,"max_degree":19,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0042552","count":4},{"id":"GO:0070830","count":4},{"id":"GO:0061028","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0050861","count":3}]},{"hash":"2213270237927215100","title":"Neuroimmune Regulation and Dopamine Signaling","description":"These GO terms cluster around CNS-focused immune regulation (negative regulation of inflammatory response, immune response, eosinophil chemotaxis, astrocyte chemotaxis) and glial/neurotrophic activity (GDNF production) alongside dopaminergic functions (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling). The combination suggests a coherent theme of neuroimmune modulation tied to dopamine signaling, even though the network edges are absent. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":16},{"id":"GO:0042493","count":16},{"id":"GO:2000458","count":16},{"id":"GO:1900168","count":16},{"id":"GO:0048245","count":16}]},{"hash":"1737241241388188657","title":"Chemokine signaling and leukocyte chemotaxis","description":"The top terms cluster around immune cell recruitment and signaling: eosinophil, neutrophil, T cell, and macrophage chemotaxis, plus chemokine-mediated signaling and ERK cascade involvement. This points to a cohesive function in leukocyte trafficking and chemokine-driven immune responses, with general immune activation as a secondary aspect. A few terms like insulin secretion regulation may reflect shared signaling cross-talk but do not override the leukocyte chemotaxis theme.","confidence":"High","size":20,"edges":146,"triangles":540,"max_degree":18,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0048245","count":20},{"id":"GO:0006955","count":20},{"id":"GO:0010759","count":20},{"id":"GO:0070374","count":20},{"id":"GO:0051930","count":20}]},{"hash":"35236014306581568","title":"Nervous system development and axon guidance","description":"The top GO terms cluster around nervous system development, peripheral nervous system development, synapse organization, and axon guidance via ROBO signaling, with related cell adhesion and BMP signaling modulation. Together they point to neural development and connectivity processes; angiogenesis and skeletal development likely reflect broader morphogenesis signals but do not overturn the neural-centric theme.","confidence":"High","size":20,"edges":10,"triangles":0,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045162","count":15},{"id":"GO:0007155","count":14},{"id":"GO:0007399","count":14},{"id":"GO:0001525","count":14},{"id":"GO:0001501","count":13}]},{"hash":"437306116156294449","title":"Diverse membrane transporters","description":"GO terms indicate transport across membranes for nitrite, xenobiotics, phosphate, sugars, sialic acid, arabinose, and neurotransmitter loading into synaptic vesicles, plus nitrate assimilation. This convergence on transmembrane transport across diverse substrates suggests these proteins are membrane transporters with varied substrates, hence the name Diverse membrane transporters.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0015707","count":7},{"id":"GO:0006855","count":5},{"id":"GO:0035435","count":5},{"id":"GO:0098700","count":5},{"id":"GO:1900754","count":5}]},{"hash":"156681035045851459","title":"Dopamine signaling and neuroinflammatory regulation","description":"This cluster combines dopaminergic functions (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling) with neuroimmune/glial processes (immune response, negative regulation of inflammatory response, astrocyte chemotaxis, eosinophil chemotaxis, GDNF production, response to xenobiotic stimulus), suggesting a theme of neuroimmune interaction where dopamine pathways intersect with glial and inflammatory regulation.","confidence":"High","size":20,"edges":14,"triangles":7,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":20},{"id":"GO:0042493","count":20},{"id":"GO:2000458","count":20},{"id":"GO:1900168","count":20},{"id":"GO:0048245","count":20}]},{"hash":"1587002401353020008","title":"B cell signaling and antiviral immune regulation","description":"The cluster centers on adaptive immune functions: B cell differentiation and MHC I biosynthetic regulation, coupled with STAT-related signaling (tyrosine phosphorylation), and modulation of Th2 cytokines. The presence of defense against viruses and suppression of viral genome replication indicates antiviral regulation, with an additional note of pregnancy-associated immune tolerance. Together these terms point to a cohesive theme of adaptive immune signaling and antiviral defense.","confidence":"High","size":20,"edges":162,"triangles":791,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0042517","count":16},{"id":"GO:0030183","count":16},{"id":"GO:0033141","count":15},{"id":"GO:0007565","count":15},{"id":"GO:2000663","count":14}]},{"hash":"1403353651911285204","title":"Innate immune response to bacteria","description":"The top GO terms are dominated by innate immune processes and defense against bacteria (innate immune response, defense response to bacterium, negative regulation of LPS signaling), indicating a coherent theme of antibacterial immune signaling. While a few terms touch on neuronal or motor processes, they are much less represented, and the immune-related terms strongly define the cluster\u2019s function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0031665","count":6},{"id":"GO:0042742","count":6},{"id":"GO:0035634","count":3},{"id":"GO:2001268","count":3}]},{"hash":"96461003609980009","title":"Immunological synapse regulation and cell junctions","description":"This cluster centers on processes governing immune cell communication and activity at cell\u2013cell interfaces. Terms such as regulation of synapse assembly, negative regulation of NK cell\u2013mediated cytotoxicity and T cell degranulation point to immunological synapse control, while actin cytoskeleton and cell junction localization terms reflect junctional dynamics that enable this signaling. Some signals (immunoglobulin transcytosis, AV node action potential) suggest broader intercellular communication across tissues, but the shared theme remains immune signaling at cell junctions.","confidence":"Medium","size":20,"edges":116,"triangles":325,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0051963","count":5},{"id":"GO:0046718","count":5},{"id":"GO:0002859","count":5},{"id":"GO:0090138","count":5},{"id":"GO:0043318","count":5}]},{"hash":"1042685973712072156","title":"Membrane transport of cofactors and metabolites","description":"The top GO terms cluster around transmembrane transport of vitamins and metabolic cofactors (thiamine pyrophosphate, coenzyme A, pyridoxal phosphate), amino acid/glycine transport, phosphate ion transport, and mitochondrial metabolite exchange (malate-aspartate shuttle, mitochondrial ATP transport). This points to a coherent function: proteins that move essential metabolites and cofactors across membranes, especially related to mitochondrial metabolism. A few terms touching insulin signaling and necroptosis regulation are secondary context but do not redefine the primary theme. Confidence: High","confidence":"","size":20,"edges":187,"triangles":1088,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0030974","count":18},{"id":"GO:0035435","count":18},{"id":"GO:0035349","count":18},{"id":"GO:0036233","count":18},{"id":"GO:0043490","count":18}]},{"hash":"76079639721483242","title":"Neuroimmune Dopaminergic Signaling","description":"This cluster combines immune/inflammatory regulation terms with dopaminergic signaling and glial-associated processes (astrocyte chemotaxis, GDNF regulation, dopamine transport/metabolism, and PLC-activated dopamine receptor signaling), suggesting proteins that mediate cross-talk between immune responses and neuronal/glial dopamine pathways, i.e., neuroimmune modulation via dopamine and astrocyte activity.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":20},{"id":"GO:0042493","count":20},{"id":"GO:2000458","count":20},{"id":"GO:1900168","count":20},{"id":"GO:0048245","count":20}]},{"hash":"1605887664992183908","title":"Skeletal system development and morphogenesis","description":"This cluster is dominated by GO terms for skeletal system development and morphogenesis, along with broader multicellular organism development and male gonad development, pointing to a developmental program with a skeletal focus. The presence of related terms such as cellular response to hypoxia and mitochondria-nucleus signaling suggests regulatory context during development, and a nod to chromatin regulation is indicated by the histone acetylation term. Overall, the most representative theme is skeletal development within an organismal growth/morphogenesis context.","confidence":"High","size":19,"edges":170,"triangles":952,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043966","count":15},{"id":"GO:0008584","count":14},{"id":"GO:0035264","count":14},{"id":"GO:0071456","count":14},{"id":"GO:0007275","count":14}]},{"hash":"283729531821701249","title":"Embryonic morphogenesis and neural development","description":"The Top Terms point to broad developmental processes (ectoderm formation, female gonad and uterine epithelium development) along with neural differentiation and neuron migration, and cytoskeletal remodeling (actin filament bundle and lamellipodium assembly). This suggests the cluster captures proteins involved in developmental morphogenesis and cell movement with cytoskeletal dynamics. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010735","count":1},{"id":"GO:0072283","count":1},{"id":"GO:0097477","count":1},{"id":"GO:0021526","count":1},{"id":"GO:0051017","count":1}]},{"hash":"1567499980030655963","title":"Developmental Signaling and Differentiation Regulation","description":"This cluster centers on signaling pathways that govern development and cell fate decisions, highlighted by Hippo signaling and positive regulation of Wnt signaling, along with differentiation processes such as keratinocyte differentiation and myoblast fusion. The presence of apoptosis and glial survival terms further supports a theme of coordinated growth, differentiation, and cell survival, with additional terms touching on transcriptional control of ribosomal genes and lipid biosynthesis that underpin these processes.","confidence":"High","size":19,"edges":107,"triangles":401,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006915","count":14},{"id":"GO:0035329","count":14},{"id":"GO:0090263","count":14},{"id":"GO:0030216","count":14},{"id":"GO:0060044","count":14}]},{"hash":"1186497786250188317","title":"Post-Translational Modifications and tRNA Modification with Autophagy","description":"This cluster is dominated by GO terms for conjugation pathways (sumoylation, ufmylation, urmylation, and neddylation) and autophagy-related processes (mitophagy and microautophagy of the nucleus), with tRNA wobble thiolation and cyclic t6A biosynthesis also enriched, suggesting a broader theme of cellular quality control and stress response linking protein modification, RNA modification, and autophagy.","confidence":"Medium","size":19,"edges":115,"triangles":351,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":8},{"id":"GO:0002143","count":6},{"id":"GO:1990592","count":6},{"id":"GO:2000220","count":6},{"id":"GO:0032447","count":6}]},{"hash":"810258519986102592","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":127,"triangles":504,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0032264","count":4},{"id":"GO:0006178","count":4},{"id":"GO:0006207","count":4},{"id":"GO:0044205","count":4}]},{"hash":"539857988235614247","title":"Neural development and organogenesis","description":"The top GO terms cluster around nervous system development (neuron migration, locomotory behavior, regulation of respiratory processes by the nervous system) and organ formation (heart/pulmonary myocardium development, retina development, organ induction, trigeminal ganglion development). This suggests a theme of neural-driven organogenesis and neural maturation. ","confidence":"High","size":19,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":10},{"id":"GO:0007626","count":10},{"id":"GO:0043524","count":10},{"id":"GO:0003350","count":10},{"id":"GO:0001764","count":10}]},{"hash":"432376731327851295","title":"Inflammatory signaling and endosomal trafficking","description":"This cluster centers on TNF-mediated inflammatory signaling and cytokine regulation, with clear ties to endosomal transport between the plasma membrane and endosomes, and related signaling cascades (ERK, NF-kB, HIF-1alpha regulation). While a few terms are outdated or incidental (e.g., DNA recombination), the core themes point to immune signaling intertwined with membrane trafficking.","confidence":"High","size":19,"edges":136,"triangles":586,"max_degree":17,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:2000009","count":6},{"id":"GO:0033209","count":6},{"id":"GO:0032088","count":6},{"id":"GO:0048227","count":6},{"id":"GO:1902072","count":6}]},{"hash":"401204349225570237","title":"Insulin/IGF signaling and GTPase-regulated angiogenesis","description":"This cluster centers on insulin receptor and IGF signaling regulation, coupled with small GTPase (Rac/Rho) pathways and processes controlling endothelial behavior, such as sprouting angiogenesis and vascular permeability. The shared focus on insulin/IGF signaling and Rac/Rho-mediated regulation of angiogenesis/migration supports a cohesive module linking these signaling axes to vascular remodeling. ","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0048009","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0090051","count":2}]},{"hash":"903361009114450277","title":"Nuclear import and chromatin assembly","description":"Most top GO terms point to nuclear processes: import of proteins and ribosomal components into the nucleus, mRNA transport, and chromatin assembly during DNA replication, with additional signals for Pol III transcription regulation and protein desumoylation. A few terms relate to apoptosis/meiosis, but the core theme is nuclear transport and chromatin maintenance.","confidence":"Medium","size":19,"edges":33,"triangles":15,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":4},{"id":"GO:0060188","count":3},{"id":"GO:0071230","count":3},{"id":"GO:1903538","count":3},{"id":"GO:2001241","count":3}]},{"hash":"2065209643161585759","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":160,"triangles":799,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0006368","count":2},{"id":"GO:0007076","count":2},{"id":"GO:0006265","count":2},{"id":"GO:0098789","count":2}]},{"hash":"855898143649884139","title":"Placental and Trophoblast Development and Embryonic Patterning","description":"This cluster shows a strong emphasis on placental and trophoblast differentiation (trophoblast giant cell differentiation, endocrine system development) alongside embryonic patterning processes (left-right formation, cartilage morphogenesis, EMT-related events). The presence of transcriptional regulation terms also points to regulatory factors governing embryogenesis. Overall, it seems to reflect a developmental network centered on placental/trophoblast differentiation and broader embryonic patterning.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0060707","count":4},{"id":"GO:0060536","count":4},{"id":"GO:0060972","count":4},{"id":"GO:0035270","count":4}]},{"hash":"546548540979814449","title":"Ribosome Biogenesis and Translation (Mitochondrial)","description":"This cluster is dominated by ribosome-related processes: ribosome biogenesis, translation, and rRNA maturation, including mitochondrial translation, suggesting a shared function in assembling and operating ribosomes across compartments.","confidence":"High","size":19,"edges":167,"triangles":904,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0070301","count":2},{"id":"GO:0006417","count":1},{"id":"GO:0000470","count":1},{"id":"GO:0000028","count":1}]},{"hash":"1479652554236599831","title":"RNA Stability and Translational Control","description":"This cluster centers on post-transcriptional control of gene expression, including mRNA stability, splicing, and initiation of translation, plus miRNA and ncRNA\u2013mediated silencing. The GO terms emphasize mRNA stability/regulation, translation initiation/preinitiation complex formation, translation reinitiation, and RNA silencing, with blastocyst formation pointing to developmental contexts. Together they indicate a cohesive theme of RNA-level regulation of translation and mRNA turnover.","confidence":"High","size":19,"edges":5,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":3},{"id":"GO:0001825","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0006446","count":3},{"id":"GO:1900363","count":3}]},{"hash":"1784627454000395661","title":"Growth factor signaling and cytoskeleton remodeling","description":"These proteins cluster around growth factor\u2013related signaling (IGF receptor and growth hormone receptor pathways) and GPCR signaling, with strong ties to regulation of Rho signaling and actin cytoskeleton organization. The presence of apoptotic process and PI phospholipid signaling fits within growth-factor\u2013driven survival and cytoskeletal dynamics. Overall, the common theme is growth factor\u2013mediated signaling that orchestrates cytoskeletal remodeling and related cell behaviors.","confidence":"Medium","size":19,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048009","count":6},{"id":"GO:0007205","count":6},{"id":"GO:0035023","count":6},{"id":"GO:0006915","count":5},{"id":"GO:0046856","count":5}]},{"hash":"1816555992571367352","title":"Developmental transcription regulators","description":"The cluster is enriched for transcription-related GO terms (RNA polymerase II transcription, DNA-templated transcription) and several development-specific terms (endocrine pancreas development, brain segmentation, rhombomere development), indicating a group of transcription factors/regulators coordinating developmental programs. Some unrelated terms reflect broader regulatory signals, but the core theme is developmental transcriptional regulation.","confidence":"High","size":19,"edges":71,"triangles":132,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":9},{"id":"GO:0006351","count":7},{"id":"GO:0031018","count":6},{"id":"GO:0035994","count":6},{"id":"GO:1990440","count":6}]},{"hash":"1618586088725733359","title":"Golgi-ER vesicle trafficking and synaptic exocytosis","description":"The terms are centered on vesicle transport between the ER and Golgi, intra-Golgi routing, Golgi ribbon formation, and exocytosis, including calcium-dependent and synaptic vesicle exocytosis (with links to long-term potentiation). This points to a cohesive role in Golgi-ER vesicle trafficking that underpins neuronal exocytosis.","confidence":"High","size":19,"edges":146,"triangles":672,"max_degree":18,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0060291","count":4},{"id":"GO:0048280","count":4},{"id":"GO:0090161","count":4},{"id":"GO:0016079","count":4}]},{"hash":"1216482664020321134","title":"Epigenetic Transcriptional Regulation","description":"The cluster is dominated by GO terms tied to epigenetic control of gene expression\u2014regulation of DNA-templated transcription, DNA methylation, and chromatin organization\u2014suggesting a cohesive role in epigenetic regulation of transcription, with a few developmental terms that may reflect broader lineage involvement.","confidence":"High","size":19,"edges":8,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0010216","count":3},{"id":"GO:0043046","count":3},{"id":"GO:1903709","count":3},{"id":"GO:0061412","count":3}]},{"hash":"2263521809511830946","title":"Embryogenesis and Ubiquitination Regulation","description":"The top GO terms cluster around embryonic development processes (hemopoiesis, prechordal plate formation, epiboly, placental development) together with regulation of transcription and ubiquitination (protein ubiquitination, regulation of ubiquitination, SMAD-related degradation). Although the proteins are not connected by edges, they collectively point to developmental regulation mediated in part by ubiquitin-related control of transcription and signaling pathways, notably TGF-beta/SMAD. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030097","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0030511","count":2},{"id":"GO:0021501","count":2},{"id":"GO:0000209","count":2}]},{"hash":"1536488602918916932","title":"Transcriptional regulation and apoptotic signaling","description":"The proteins are linked by transcriptional control (DNA-templated transcription; RNAP II regulation) and signaling pathways related to apoptosis (extrinsic death receptor\u2013mediated) and NF-kappaB modulation, with additional outward cues from signal transduction and growth-related terms. This suggests a module coordinating gene expression in response to apoptotic and survival signals.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0008625","count":3},{"id":"GO:1900112","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0000122","count":1}]},{"hash":"2216812864645664218","title":"Neural development and cell cycle regulation","description":"The top terms show strong signals for nervous system development and axonogenesis regulation, indicating neural differentiation processes. They are complemented by mitotic cell cycle and cell division terms, suggesting involvement of proliferative control. Additional terms for cell polarity maintenance and Golgi-to-plasma membrane transport point to coordinated trafficking and organization essential for neural cells. Overall, this cluster appears to combine neural development with cell-cycle and polarity-related functions.","confidence":"Medium","size":19,"edges":20,"triangles":8,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0030011","count":4}]},{"hash":"568465243670945294","title":"Secretory vesicle trafficking and endosomal transport","description":"The top GO terms cluster around endosome-to-lysosome transport, endocytic recycling, and dense core granule maturation with related histamine secretion and secretory processes, suggesting a focus on vesicle trafficking and secretion. Additional terms on cilium localization and cell polarity fit within membrane organization and trafficking contexts, while some terms (mitotic cell cycle, fungal sporulation) appear peripheral noise. Overall, the shared theme is secretory/trafficking activity rather than a single narrow function.","confidence":"Medium","size":19,"edges":147,"triangles":654,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008333","count":4},{"id":"GO:1990502","count":4},{"id":"GO:1990126","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0061512","count":3}]},{"hash":"1968485225723333006","title":"Unknown","description":"The top GO terms are highly diverse, ranging from regulation of biosynthetic processes and nitric oxide biosynthesis to centrosome localization, actin assembly, mRNA decay, and telomere maintenance. With no clear shared pathway or function and no edges among proteins, there isn\u2019t a coherent theme to name this cluster beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009890","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0043105","count":1},{"id":"GO:0045428","count":1},{"id":"GO:1904780","count":1}]},{"hash":"591476039276385618","title":"Telomere maintenance regulation","description":"The cluster shows strong enrichment for telomere-related processes: positive/negative regulation of telomere maintenance via telomerase, telomere capping, regulation of telomere maintenance, and localization to telomeric regions, indicating a core telomere biology theme. Some terms related to NOD2 signaling and NF-kappaB regulation appear, but the dominant signal is telomere maintenance and telomeric chromatin context.","confidence":"High","size":19,"edges":5,"triangles":0,"max_degree":4,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0070431","count":12},{"id":"GO:0032088","count":12},{"id":"GO:0000083","count":12},{"id":"GO:0032212","count":9},{"id":"GO:1904355","count":9}]},{"hash":"882567701462273165","title":"Neural development and axon guidance","description":"The top GO terms cluster around neural development: medial motor column neuron differentiation, retinal ganglion cell axon guidance, metencephalon development, and ectoderm formation, with related neuronal survival and locomotory behavior terms. This suggests a cohesive neurodevelopmental program driving neuron differentiation and axon pathfinding, despite some reproductive tissue terms appearing in the set. Overall, the cluster appears to reflect neural development processes rather than unrelated functions.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021526","count":18},{"id":"GO:0060677","count":18},{"id":"GO:0031290","count":18},{"id":"GO:0001705","count":18},{"id":"GO:0008585","count":18}]},{"hash":"1022512982216834279","title":"Adaptive immune signaling and lymphocyte development","description":"The top GO terms cluster around adaptive immunity: IL-7 response, IL-4 production, T cell receptor signaling, B cell affinity maturation, and NK T cell differentiation, all hallmark processes of lymphocyte activation and maturation. Additional terms like cell migration and regulation of Rho signaling support dynamic movement and cytoskeletal rearrangements typical of immune cells. Some terms (insulin signaling, heart development) may reflect broader roles of shared signaling components, but the dominant signal is clearly adaptive immune function.","confidence":"High","size":19,"edges":128,"triangles":443,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0098761","count":9},{"id":"GO:0008286","count":9},{"id":"GO:0032633","count":9},{"id":"GO:0016477","count":9},{"id":"GO:0007507","count":9}]},{"hash":"1991164705181955555","title":"Oxidative stress response and redox homeostasis","description":"Most GO terms point to redox biology: cellular redox homeostasis, cellular oxidant detoxification, oxidative stress response, and protein deglutathionylation. There are additional terms indicating transcriptional regulation by RNA polymerase II, suggesting that redox state may influence transcription in this cluster. Taken together, the proteins in this cluster appear involved in maintaining redox balance and responding to oxidative stress, with a subset linked to redox-sensitive transcriptional control.","confidence":"High","size":19,"edges":134,"triangles":566,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":17},{"id":"GO:0098869","count":17},{"id":"GO:0055114","count":16},{"id":"GO:1903026","count":13},{"id":"GO:0080058","count":13}]},{"hash":"483403613408573002","title":"Unknown","description":"The Top Terms cover a broad mix of processes across bacteria and animals, including secretion systems (type I), peptide export, various transport processes (ceramide, cysteine), immune antigen presentation, and reproductive or developmental processes (sperm capacitation, stem cell proliferation). There isn't a single coherent function uniting these terms, making it hard to assign a specific, concise theme. Therefore the most appropriate label is Unknown.","confidence":"","size":19,"edges":118,"triangles":452,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030253","count":16},{"id":"GO:0051454","count":16},{"id":"GO:0030153","count":16},{"id":"GO:0046689","count":16},{"id":"GO:0048240","count":16}]},{"hash":"539186577802140594","title":"Cell Cycle and Vesicle Trafficking","description":"The cluster shows strong enrichment for cell division and cell cycle terms (cell division, cell cycle, mitotic cell cycle, septum assembly), indicating a core involvement in cell cycle progression. The concurrent presence of vesicle trafficking terms (ER-Golgi transport, endosome-to-lysosome transport, melanosome assembly) and protein ubiquitination suggests coordinated regulation of membranes and protein turnover, which often interfaces with cell cycle control. Together, these signals point to a theme of cell cycle processes coupled with intracellular transport and protein regulation.","confidence":"Medium","size":19,"edges":60,"triangles":64,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0007049","count":6},{"id":"GO:0090529","count":6},{"id":"GO:0000278","count":5},{"id":"GO:1902236","count":5}]},{"hash":"798226079111840021","title":"Actin Cytoskeleton and Microvilli Assembly","description":"The cluster is dominated by GO terms for actin cytoskeleton organization and assembly of microvilli/microspikes, along with related processes like focal adhesion assembly and Rho signaling, and even mitotic spindle/sarcomere organization\u2014indicating a cohesive module of cytoskeletal dynamics and membrane-associated structures.","confidence":"High","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030035","count":9},{"id":"GO:0070493","count":9},{"id":"GO:1902896","count":9},{"id":"GO:0035023","count":9},{"id":"GO:0090307","count":9}]},{"hash":"2163835940936337903","title":"RNA processing and translational regulation","description":"The cluster's top GO terms mainly point to RNA metabolism and regulation of gene expression at the RNA level: mRNA stabilization, stress-associated control of mRNA stability, regulation of translational initiation, and mRNA splice site recognition, with related RNA processing activities like polyadenylation. While there are a couple of developmental terms (fertilization, blastocyst formation), the pervasive theme is RNA processing and translation control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:2001275","count":3},{"id":"GO:0009566","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0048255","count":2}]},{"hash":"1349688713657194961","title":"Immune signaling and lymphoid development with angiogenesis","description":"Top GO terms point to NF-kappaB\u2013related immune signaling, B cell receptor signaling, thymus development, and IL-7\u2013mediated responses, along with PDGF signaling and angiogenesis, plus cell migration and cytoskeleton remodeling. This combination suggests a cluster of proteins coordinating immune cell signaling, lymphoid organ development, and associated vascular remodeling. ","confidence":"High","size":19,"edges":108,"triangles":352,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051092","count":11},{"id":"GO:0045766","count":10},{"id":"GO:0048538","count":9},{"id":"GO:0016477","count":9},{"id":"GO:0043552","count":9}]},{"hash":"1123556303777514622","title":"NF-\u03baB\u2013driven inflammatory and antiviral signaling","description":"The top GO terms cluster around NF-\u03baB activation (positive regulation of NF-\u03baB transcription factor activity and canonical NF-\u03baB signaling), with supporting terms for RIG-I\u2013mediated antiviral signaling and LPS-induced pathways. While a few terms touch on cardiac and pancreatic processes, the dominant theme is innate immune and inflammatory signaling via NF-\u03baB and related antiviral pathways.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051092","count":4},{"id":"GO:0098910","count":4},{"id":"GO:0098907","count":4},{"id":"GO:0043123","count":4},{"id":"GO:1900246","count":3}]},{"hash":"849609489164883881","title":"Cytoskeletal remodeling and cell migration","description":"The terms point to actin organization (actin filament bundle assembly), Rho signaling regulation, response to mechanical stimuli, and cell migration, with related polarity and vascular remodeling terms. Together these suggest cytoskeletal dynamics driving movement and polarity in response to mechanical cues. Some telomere-related terms appear incidental noise rather than core to this cluster, but the dominant theme is actin- and Rho-mediated cytoskeletal remodeling linked to migration. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0051017","count":1},{"id":"GO:0032212","count":1}]},{"hash":"1238931237672007269","title":"T Cell Cytokine Signaling and MAPK Activation","description":"The top GO terms point to immune signaling and T cell\u2013associated pathways, including type I interferon production, IL-4 signaling, IL-7 response, and Th1 differentiation, complemented by ERK1/ERK2 cascade activation. Additional terms like lamellipodium assembly suggest leukocyte migration; proteasomal regulation aligns with antigen processing. Collectively, these indicate a cluster of proteins involved in T cell\u2013driven cytokine signaling and MAPK-mediated responses.","confidence":"High","size":19,"edges":169,"triangles":935,"max_degree":18,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0032481","count":19},{"id":"GO:2001275","count":19},{"id":"GO:0035771","count":19},{"id":"GO:0030032","count":19},{"id":"GO:0046676","count":19}]},{"hash":"563382440656711832","title":"ER-Golgi vesicle trafficking and synaptic exocytosis","description":"This cluster centers on ER-to-Golgi vesicle transport, ER membrane organization, and regulation of synaptic vesicle exocytosis, pointing to a shared role in secretory pathway and presynaptic vesicle dynamics, with some developmental terms likely reflecting broader differentiation/migration functions. ","confidence":"Medium","size":19,"edges":31,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030218","count":2},{"id":"GO:0055072","count":2},{"id":"GO:0060576","count":2},{"id":"GO:0060628","count":2},{"id":"GO:0021814","count":1}]},{"hash":"1175821009350687035","title":"NF-kappaB immune signaling","description":"Several top GO terms point to NF-kappaB regulation (canonical and non-canonical) and immune activity, including innate immune response and T cell proliferation, consistent with NF-kappaB\u2013driven immune signaling. Also, terms related to extrinsic apoptotic signaling and protein homooligomerization align with immune cell signaling and regulation. Less connected terms like tRNA modification and telomere maintenance appear, but do not override the dominant immune/NF-kappaB theme.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070525","count":3},{"id":"GO:0007329","count":3},{"id":"GO:0000722","count":3},{"id":"GO:0051092","count":2},{"id":"GO:1901224","count":2}]},{"hash":"1856758855552894422","title":"Golgi\u2013vacuole trafficking and autophagy","description":"This label captures the dominant pattern of vesicle transport and degradation pathways: Golgi-to-vacuole transport, ER-to-Golgi trafficking, retrograde transport from endosome to Golgi, vesicle fusion with the Golgi, and protein targeting to the vacuole, along with macroautophagy. A couple of terms (DNA-templated transcription and voluntary movement) are less aligned with this core theme, but the cluster is clearly enriched for intracellular trafficking and vacuolar/autophagic processes.","confidence":"Medium","size":19,"edges":111,"triangles":347,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0050882","count":2},{"id":"GO:1903076","count":2},{"id":"GO:0016236","count":2}]},{"hash":"2210632542121003061","title":"Immune signaling and cell motility cluster","description":"This cluster is driven by GO terms linking immune signaling (IL-7 response, NK cell and mast cell regulation) with actin-driven motility (lamellipodium assembly) and vesicle trafficking (transcytosis, vesicular signaling such as EGFR). While development terms (uterus/parathyroid) appear, the dominant theme ties immune response pathways to cell movement and trafficking, suggesting proteins that coordinate immune signaling with cytoskeletal remodeling and vesicle transport.","confidence":"Medium","size":19,"edges":121,"triangles":547,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030032","count":16},{"id":"GO:0098761","count":16},{"id":"GO:0045056","count":16},{"id":"GO:0060065","count":16},{"id":"GO:0010863","count":16}]},{"hash":"483197952437400528","title":"Secretory pathway and Wnt secretion","description":"The cluster centers on ER-Golgi trafficking and secretion: COPI budding, ER exit, ER retention, and ER-to-Golgi transport, with positive regulation of Wnt secretion. This points to a shared role in processing and exporting proteins, including Wnt signals, to the extracellular space. Developmental terms (axis specification, placenta) fit with secreted factors guiding tissue patterning, supporting a cohesive secretory/signaling theme. Confidence: High","confidence":"","size":19,"edges":137,"triangles":543,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0061357","count":2},{"id":"GO:0035964","count":2},{"id":"GO:0070863","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0002121","count":2}]},{"hash":"2110436900806522016","title":"Vacuolar amino acid transport","description":"The top GO terms cluster around transmembrane transport of multiple amino acids (asparagine, arginine, lysine, serine, histidine) into or out of the vacuole, with related ion transport terms. This strongly suggests a group of proteins functioning as vacuolar amino acid transporters, supporting a concise label focused on this shared function; a few unrelated terms appear but do not override the core theme.","confidence":"High","size":19,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006867","count":7},{"id":"GO:1990818","count":7},{"id":"GO:0090517","count":7},{"id":"GO:0089707","count":7},{"id":"GO:0051365","count":7}]},{"hash":"208788423823957936","title":"Dopaminergic synaptic signaling and vesicle transport","description":"The cluster features GO terms tied to dopamine secretion and dopamine receptor signaling, positive regulation of neurotransmitter release, and anterograde synaptic vesicle transport, plus dendrite morphogenesis and kinase activity regulation. This points to neuronal synaptic function with a focus on dopamine-mediated neurotransmission and vesicle trafficking, suggesting a coherent theme of dopaminergic signaling and vesicle dynamics.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071901","count":3},{"id":"GO:0014059","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0032091","count":2},{"id":"GO:0060155","count":2}]},{"hash":"2149710743540063206","title":"Embryonic organogenesis and patterning","description":"Many terms relate to embryonic development and organ formation across tissues (endocardial cushion/heart development, left-right patterning, cartilage morphogenesis, roof of the mouth, pancreas endocrine development, placenta differentiation), suggesting a general morphogenesis theme. A couple of mRNA processing terms appear auxiliary. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003198","count":6},{"id":"GO:0060707","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060972","count":5},{"id":"GO:0035270","count":5}]},{"hash":"893816257935958037","title":"Unknown","description":"Top GO terms span metabolism (cellulose catabolic process, ubiquinone biosynthetic process, oxidation-reduction), secretion, transport (carbon dioxide transport), response (steroid hormone response, cellular response to fluid shear stress), and development (bone resorption, kidney development). There is no clear unifying function tying these terms together, so a single, coherent label is not apparent.","confidence":"","size":19,"edges":150,"triangles":678,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006744","count":2},{"id":"GO:2000984","count":2},{"id":"GO:0048545","count":2}]},{"hash":"2244923693566891017","title":"TLR/NLRP3 Innate Immune Signaling","description":"GO terms point to innate immune sensing and inflammatory signaling in response to bacteria: lipopolysaccharide detection, MyD88-dependent TLR signaling, cellular responses to LPS and diacyl lipopeptides, and NLRP3 inflammasome assembly, with associated coagulation activation. Although a distant term on synapse assembly appears, the dominant pattern is antibacterial innate immunity, so the label TLR/NLRP3 Innate Immune Signaling is representative and specific.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":3},{"id":"GO:0038095","count":3},{"id":"GO:0007596","count":3},{"id":"GO:1900227","count":2},{"id":"GO:0071726","count":2}]},{"hash":"193320925178363818","title":"Embryonic development and organogenesis","description":"These proteins show a shared emphasis on developmental processes across multiple organ systems, including endocrine/pancreas development, placental and cartilage morphogenesis, left-right patterning, and heart-associated epithelial-to-mesenchymal transitions. Some terms reflect basic cellular machinery (ribosomal export, spliceosome-mediated splicing, RNA Pol II regulation), but the predominant theme is embryonic development and organogenesis, suggesting a cluster tied to differentiation and formation of tissues during development.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0003323","count":7},{"id":"GO:0060707","count":7},{"id":"GO:0060536","count":7},{"id":"GO:0060806","count":7},{"id":"GO:0060972","count":7}]},{"hash":"923274187339641533","title":"TLR-Driven Innate Immunity and Inflammasome Activation","description":"The cluster is enriched for TLR signaling (TLR8/10), LPS detection, non-canonical NF-kappaB, NLRP3 inflammasome regulation, and antiviral defense, pointing to a coherent innate immune sensing and inflammasome activation module, with some peripheral terms likely reflecting shared pathways or dataset noise.","confidence":"High","size":19,"edges":133,"triangles":499,"max_degree":18,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042346","count":17},{"id":"GO:0051607","count":17},{"id":"GO:0016525","count":17},{"id":"GO:0032497","count":17},{"id":"GO:0002730","count":17}]},{"hash":"1495390340359054283","title":"Inflammation, Coagulation, and Angiogenesis","description":"The terms cluster around innate immune activation (complement activation, response to lipopolysaccharide), coagulation and its regulation, and vascular remodeling (angiogenesis, prostaglandin biosynthesis, angiotensin maturation), with supportive signals from biomineral tissue development. Some terms like digestion and amyloid precursor protein regulation appear more peripheral, but the core theme is inflammation-linked coagulation and vascular changes.","confidence":"High","size":19,"edges":53,"triangles":78,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":4},{"id":"GO:0007586","count":4},{"id":"GO:0032496","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0030194","count":3}]},{"hash":"1388678648937535524","title":"Ion Transport and pH Regulation","description":"Dominant GO terms center on ion and fluid transport and pH homeostasis\u2014chloride and bicarbonate transport, borate transport, and related fluid movement. While there are a couple of additional terms (lipopolysaccharide response, neuron development) that appear, the core set points to membrane transporters maintaining ionic balance and acidity, justifying the label.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030308","count":3},{"id":"GO:0071222","count":2},{"id":"GO:0042044","count":2},{"id":"GO:0021860","count":2},{"id":"GO:0051453","count":2}]},{"hash":"1990270556733690942","title":"Developmental signaling and morphogenesis","description":"This cluster centers on developmental processes and signaling pathways, with GO terms pointing to bone maturation (ossification) and neural tract morphogenesis (corticospinal tract), as well as cell adhesion and multiple phosphorylation-driven signaling events (autophosphorylation, STAT phosphorylation, and related pathways). The mix suggests proteins coordinating development and morphogenesis through signaling and cell interactions, rather than a single tissue-specific function.","confidence":"Medium","size":19,"edges":11,"triangles":2,"max_degree":5,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043931","count":6},{"id":"GO:0051092","count":5},{"id":"GO:0021957","count":4},{"id":"GO:0032516","count":4},{"id":"GO:0042523","count":4}]},{"hash":"1520736985481644954","title":"Neuroimmune Stress and Neural Development","description":"Top GO terms indicate glucocorticoid response, innate immune activation, and apoptosis, alongside neural development processes like axonogenesis and substantia nigra development, plus ethanol response. This suggests a theme where neuroimmune and stress signaling influence neural development and cell death, making the label appropriate and representative.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0051384","count":7},{"id":"GO:0051092","count":7},{"id":"GO:0006919","count":6},{"id":"GO:0090002","count":6},{"id":"GO:0045087","count":6}]},{"hash":"1007765895625448632","title":"Cardiac and nervous system development","description":"The top GO terms point to developmental processes in heart, nervous system, face, and limbs (e.g., nervous system development, heart development, limb and face morphogenesis, heart contraction, and regulation of cardiac membrane potential), suggesting a cluster of proteins involved in embryonic development with both cardiac and neural emphasis. Some terms reflect cellular organization (ER membrane) that can support development, but the dominant theme is organogenesis and tissue patterning. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031585","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0060325","count":2}]},{"hash":"1175819461060197812","title":"Organ development with neural signaling and immune components","description":"These terms cluster around organ development (multicellular organism development, heart development, glomerular basement membrane development, EMT) and signaling activities, including neural excitability and synaptic regulation, with associated calcium transport. Immune-related terms (complement activation, T cell proliferation) suggest additional immune signaling involvement. Taken together, the proteins appear to participate in developmental programs that integrate neural signaling and immune function during organogenesis.","confidence":"Medium","size":19,"edges":22,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0032836","count":3},{"id":"GO:0042102","count":3},{"id":"GO:0060079","count":2}]},{"hash":"1356975197911788139","title":"Immune signaling and development regulation","description":"The cluster\u2019s top GO terms cluster around inflammatory signaling and immune responses (positive regulation of IL-8 production, defense against Gram-positive bacteria, LPS-mediated signaling, NF-kB-related regulation) as well as pathways involved in cell signaling and cytoskeletal dynamics (Rho signaling) and developmental processes (myoblast differentiation, brain development, angiogenesis). This suggests a theme of immune/inflammatory signaling with ancillary roles in development and tissue remodeling. However, given there are no edges and the terms span both immune and developmental processes, the connection is not tightly cohesive, so the label is a best-fit rather than a tightly defined module.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045416","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0010693","count":2},{"id":"GO:0045663","count":2},{"id":"GO:0031663","count":2}]},{"hash":"1492373405644099995","title":"Central carbon metabolism: glycolysis and TCA cycle","description":"The cluster shows strong enrichment for core energy-producing pathways, notably glycolysis (GO:0006096) and the tricarboxylic acid cycle (GO:0006099), with related malate and oxaloacetate metabolism. While other terms hint at stress signaling (nutrient and xenobiotic responses) and plant-specific photorespiration regulation, the dominant theme is central carbon metabolism and energy production, suggesting enzymes of glycolysis and the TCA cycle clustered together.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":12},{"id":"GO:0055114","count":10},{"id":"GO:0006096","count":10},{"id":"GO:0080093","count":5},{"id":"GO:0007584","count":5}]},{"hash":"407371087561587943","title":"Glycan metabolism and glycosphingolipid biosynthesis","description":"Most top terms cluster around glycan and glycolipid metabolism (N-acetylneuraminate, N-glycan, oligosaccharide metabolism, glycosylceramide, ganglioside biosynthesis). A few terms relate to pollen/olfactory development, which may reflect broader roles of glycans in development rather than a different core function. This supports labeling the cluster as glycan/glycolipid biosynthesis. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006054","count":4},{"id":"GO:0006491","count":4},{"id":"GO:0009860","count":4},{"id":"GO:0009846","count":4},{"id":"GO:0021628","count":4}]},{"hash":"629147504558996198","title":"Glycan biosynthesis in mammary and reproductive tissues","description":"The cluster is enriched for glycan/proteoglycan biosynthesis (keratan sulfate proteoglycan) and mammary gland\u2013related processes (lactose biosynthesis, mammary gland development), as well as reproductive functions (sperm binding to zona pellucida, regulation of acrosome reaction). Together, these suggest a common theme of extracellular matrix and glycan components influencing both mammary biology and fertilization-related events.","confidence":"Medium","size":19,"edges":110,"triangles":310,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":12},{"id":"GO:0006486","count":11},{"id":"GO:0030879","count":10},{"id":"GO:0060046","count":10},{"id":"GO:0060054","count":10}]},{"hash":"473221070529830246","title":"Unknown","description":"The top GO terms are a mixed bag: several point to iron-sulfur cluster biology (2Fe-2S cluster assembly and Fe-S cluster transfer), but many others relate to diverse immune development processes (macrophage differentiation, NK cell cytotoxicity) or epithelial maturation, with no clear, cohesive biological theme linking all 19 proteins. The lack of a unifying function or interaction pattern suggests there isn\u2019t a single interpretable cluster function to label beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051220","count":1},{"id":"GO:0044571","count":1},{"id":"GO:0036086","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0034396","count":1}]},{"hash":"1080330916404218003","title":"Immune organ development and lymphocyte homeostasis","description":"The top terms center on immune system development and lymphocyte homeostasis (T and B cell homeostasis; spleen and thymus development) with an accompanying innate immune response to lipopolysaccharide; a few terms about neurotransmitter handling are present but do not dominate. This supports labeling the cluster as related to immune organ development and lymphocyte maintenance.","confidence":"High","size":19,"edges":54,"triangles":67,"max_degree":10,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0043029","count":5},{"id":"GO:0001782","count":5},{"id":"GO:0048536","count":5},{"id":"GO:0032496","count":4},{"id":"GO:0000122","count":3}]},{"hash":"1316837441100791972","title":"Unknown","description":"The proteins map to a heterogeneous set of GO terms, spanning cofactor and nucleotide metabolism, RNA editing/catabolic processes, and a stress-response term, with no clear shared pathway or cohesive function. The lack of internal edges and the scattered annotations suggest no single biological theme linking the cluster, so a generic Unknown label is most appropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900036","count":1},{"id":"GO:0015938","count":1},{"id":"GO:0046656","count":1},{"id":"GO:0009240","count":1},{"id":"GO:0045337","count":1}]},{"hash":"294402420919939574","title":"Unknown","description":"Top terms span spermatid development, lens morphogenesis, immune regulation, synapse assembly, macrophage activation, and tumor/host interactions, indicating no single cohesive function tying the proteins together. Therefore, this cluster is Unknown with no confident representative label.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0006508","count":3},{"id":"GO:1902414","count":3},{"id":"GO:0002089","count":3}]},{"hash":"965762387655862129","title":"Multitissue Development and Proteoglycan Biosynthesis","description":"The top GO terms point to developmental processes across diverse tissues (nigra, bone/cartilage, fat, kidney) and to biosynthesis of proteoglycans like heparan sulfate and chondroitin sulfate. This suggests the cluster groups proteins involved in broad tissue differentiation and extracellular matrix proteoglycan metabolism rather than a single tissue-specific function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0043931","count":2}]},{"hash":"1933875584817582871","title":"Unknown","description":"The top GO terms span unrelated processes\u2014from DNA repair and cell adhesion to various developmental and tissue-specific events\u2014showing no single cohesive function. With zero edges/triangles and each term represented only once, there is no enriched theme to define a specific cluster label. Therefore, Unknown is appropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006303","count":1},{"id":"GO:0033627","count":1},{"id":"GO:0021750","count":1},{"id":"GO:0003259","count":1},{"id":"GO:0061382","count":1}]},{"hash":"884326873507511862","title":"Cotranslational Translation and SRP Targeting","description":"The top GO terms cluster around SRP-dependent cotranslational protein targeting to the membrane and negative regulation of translational elongation, suggesting these proteins function in translation coupled to membrane targeting. Additional terms like tRNA wobble thiolation and related biosynthetic processes align with translation-related roles, supporting a cohesive theme of cotranslational protein handling at membranes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045900","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:1902455","count":1},{"id":"GO:0035335","count":1}]},{"hash":"2252739447737369391","title":"RNA Pol II Transcription Regulation","description":"These proteins show a clear enrichment for transcription-related GO terms tied to RNA polymerase II, including DNA-templated transcription and negative regulation of Pol II activity. While a couple of terms are obsolete and one refers to hydrogen peroxide biosynthesis (less directly related), the dominant signal is regulation of Pol II\u2013mediated transcription, suggesting a nucleus-localized transcription regulatory role, potentially linked to the cell cycle.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007576","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010729","count":2},{"id":"GO:0070895","count":2},{"id":"GO:0046022","count":2}]},{"hash":"192028124824846819","title":"Microglial Activation and Neuroinflammation","description":"The cluster centers on GO terms about regulating microglial activation (both positive and negative), inflammatory response, and neural activity related to pain perception (regulation of membrane potential and sensory perception of pain). This suggests a cohesive theme of microglia-driven neuroinflammation and nociceptive signaling, with a couple of less central terms like development and coagulation possibly reflecting broader inflammation-related processes. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:1903979","count":4},{"id":"GO:0042391","count":4},{"id":"GO:0051930","count":4},{"id":"GO:1903980","count":4},{"id":"GO:0042691","count":4}]},{"hash":"1564728008750486519","title":"Host Entry and Immune Activation","description":"The cluster's top GO terms center on host-symbiont interaction and immune signaling (symbiont entry into host cell, proteolysis, cell adhesion, T cell costimulation and activation, and regulation of extracellular matrix disassembly). This points to a shared theme of host invasion and immune modulation, with a few seemingly unrelated terms likely representing annotation noise. The overall pattern supports a host\u2013immune interaction theme.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0046718","count":5},{"id":"GO:0006508","count":5},{"id":"GO:0007155","count":5},{"id":"GO:0031295","count":5},{"id":"GO:0015996","count":4}]},{"hash":"737543119449302793","title":"Unknown","description":"The top GO terms show a diverse, non-cohesive mix across development, metabolism, transcription regulation, and signaling, with no single unifying function apparent and no network structure; this suggests the cluster is not functionally cohesive.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001229","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0045137","count":1},{"id":"GO:0035186","count":1},{"id":"GO:0016574","count":1}]},{"hash":"827774162795725311","title":"Multi-tissue Development and Differentiation","description":"The top GO terms span keratinization, hair follicle morphogenesis, keratinocyte migration, lens fiber development, Bergmann glial differentiation, ventricular cardiac muscle development, and PNS axon regeneration, plus hepatocyte apoptosis and autophagy regulation. This suggests proteins involved in diverse tissue-specific differentiation and maturation programs rather than a single pathway, warranting a broad label that reflects multi-tissue development.","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":19},{"id":"GO:0014012","count":19},{"id":"GO:0031069","count":19},{"id":"GO:1904714","count":19},{"id":"GO:0055015","count":19}]},{"hash":"2156844500715739417","title":"Inflammation and vascular regulation","description":"This cluster centers on GO terms for inflammatory and immune responses (inflammatory response, response to lipopolysaccharide, pain perception) together with vascular processes (blood coagulation, positive regulation of vasoconstriction and blood pressure) and signaling pathways (adenylate cyclase-activating GPCR signaling, Rho protein signaling). The combination suggests a theme of inflammation-driven modulation of vascular tone and coagulation, potentially mediated by GPCR and Rho pathways; the electron transport chain term is less directly connected but may reflect mitochondrial involvement in inflammatory energy demands. Overall, the cluster appears to represent inflammation-linked vascular signaling.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0035025","count":16},{"id":"GO:0022900","count":16},{"id":"GO:0045777","count":16},{"id":"GO:0010579","count":16},{"id":"GO:0032496","count":14}]},{"hash":"746450938935421671","title":"Sodium transport and osmotic regulation","description":"Top GO terms such as sodium ion homeostasis, positive regulation of P-type Na+/K+-exchanging transporter activity, and hyperosmotic salinity response converge on a core function of maintaining ionic balance and osmotic pressure in cells, especially in epithelia. While other terms touch on development or immune-related processes, the strongestsignal in the cluster is ion transport and osmoregulation, justifying a label centered on sodium transport and osmotic regulation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040018","count":4},{"id":"GO:0051023","count":4},{"id":"GO:0070977","count":4},{"id":"GO:1903408","count":4},{"id":"GO:0055078","count":4}]},{"hash":"1095510249705193489","title":"Neuronal junctions and endosomal trafficking","description":"The terms point to neural-specific structures and processes: junction assembly (tight/apical), membrane hyperpolarization and action potential propagation, and trafficking of neurotransmitter receptors through endosomes to lysosomes. Endosome transport and ER organization further support a theme of intracellular trafficking linked to neural signaling and barrier functions (e.g., blood-nerve barrier xenobiotic transport). Collectively, these proteins likely participate in maintaining neural junctions and shuttling synaptic components, rather than a single isolated function.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070830","count":4},{"id":"GO:0071786","count":3},{"id":"GO:0060081","count":3},{"id":"GO:0045779","count":3},{"id":"GO:0061772","count":3}]},{"hash":"299294980725749387","title":"Endothelial lipid transport and activation","description":"The cluster is dominated by GO terms linking lipid handling with endothelial biology: endothelial cell activation, lipoprotein metabolic process, and lipid transport, suggesting a vascular-focused lipid metabolism theme. A few outlier terms (regulatory ncRNA silencing, piRNA processing, spermatid development, non-autophagic vacuole fusion, and a lipid-linked post-translational modification) appear less connected to this core function and may reflect multifunctional proteins or annotation noise. Overall, the strongest signal points to lipid transport/metabolism in an endothelial context.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042118","count":5},{"id":"GO:0042157","count":5},{"id":"GO:0006869","count":5},{"id":"GO:0044381","count":2},{"id":"GO:0031047","count":2}]},{"hash":"69463538645162459","title":"Hair Keratinization and Hair Cycle Proteins","description":"Dominant GO terms are keratinization and hair cycle, pointing to skin/hair differentiation processes. While a few terms (e.g., xenobiotic response, visual perception) appear, they are less representative of the cluster's core function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":4},{"id":"GO:0042633","count":3},{"id":"GO:0043154","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0008284","count":2}]},{"hash":"1064427329574225703","title":"Embryonic development and morphogenesis","description":"The top GO terms cluster around broad developmental processes across multiple tissues (endocrine, mesoderm, craniofacial, placenta, and patterning). This suggests the proteins participate in embryonic development and morphogenetic events rather than a single tissue-specific function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":14},{"id":"GO:0060806","count":14},{"id":"GO:0060972","count":14},{"id":"GO:0060536","count":14},{"id":"GO:0003323","count":14}]},{"hash":"1835778801615034161","title":"Diverse Transmembrane Transporters","description":"The top GO terms cluster around transmembrane transport of a variety of ions and small molecules (sodium, phosphate, sugars, xenobiotics, neurotransmitter loading), indicating a group of membrane transport proteins with diverse substrates. Therefore, \"Diverse Transmembrane Transporters\" succinctly captures the shared function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":6},{"id":"GO:0006855","count":5},{"id":"GO:0035435","count":5},{"id":"GO:0098700","count":5},{"id":"GO:1900754","count":5}]},{"hash":"180600658741102603","title":"Embryonic Organogenesis and Tissue Morphogenesis","description":"The top terms cluster around developmental processes across organs (olfactory placode/nerve formation, kidney development, pregnancy), plus tissue remodeling signals such as angiogenesis and collagen fibril organization. Some immune-related terms (innate immune response, complement activation) appear as well, which can occur during development or reflect shared pathways, but the dominant theme centers on organogenesis and tissue morphogenesis rather than a single pathway. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":4},{"id":"GO:0021628","count":3},{"id":"GO:0071699","count":3},{"id":"GO:0001822","count":3},{"id":"GO:0006958","count":3}]},{"hash":"1081429229712519543","title":"Embryonic Development and Organ Morphogenesis","description":"This cluster is dominated by GO terms tied to embryonic development and organ formation, including endocrine system development, placenta and pancreatic cell development, left/right patterning, cartilage morphogenesis, and heart-related EMT processes. The presence of transcriptional regulation terms (negative regulation of transcription by RNA Polymerase II) also fits a developmental gene-expression control theme. Taken together, these proteins appear to participate broadly in embryogenesis and organ morphogenesis, not a single pathway, supporting a label around embryonic development and tissue differentiation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":9},{"id":"GO:0060806","count":9},{"id":"GO:0060972","count":9},{"id":"GO:0060536","count":9},{"id":"GO:0003323","count":9}]},{"hash":"309467523344680911","title":"Glial Dopamine Signaling and Immune Regulation","description":"The GO terms point to both immune/inflammatory processes (immune response, negative regulation of inflammatory response, eosinophil chemotaxis, xenobiotic response) and glial/neuronal signaling (astrocyte chemotaxis regulation, glial-derived neurotrophic factor production, dopamine transport, dopamine metabolic regulation, PLC-activating dopamine receptor signaling). This suggests proteins in the cluster coordinate neuroimmune interactions in glial cells, particularly involving dopaminergic signaling, rather than a purely immune or purely neural function. ","confidence":"High","size":19,"edges":19,"triangles":4,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":19},{"id":"GO:0042493","count":19},{"id":"GO:2000458","count":19},{"id":"GO:1900168","count":19},{"id":"GO:0048245","count":19}]},{"hash":"29515527101403357","title":"Innate and adaptive immune activation","description":"The enrichment of complement activation (classical pathway), phagocytosis recognition and engulfment, innate immune response, and adaptive signaling (B cell receptor signaling, positive regulation of B cell activation, T cell proliferation, and T cell costimulation) indicates a cluster of proteins involved in activating and coordinating immune responses. The presence of both phagocytic processes and lymphocyte signaling suggests a shared function in mounting and regulating immunity rather than a single specific pathway.","confidence":"High","size":19,"edges":56,"triangles":76,"max_degree":12,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":18},{"id":"GO:0006910","count":18},{"id":"GO:0045087","count":18},{"id":"GO:0006911","count":18},{"id":"GO:0050853","count":18}]},{"hash":"1757251049556151822","title":"LPS-responsive development signaling cluster","description":"This cluster shows prominent GO terms for immune/inflammatory processes (response to lipopolysaccharide; chemokine and IL-23 production; B cell apoptosis) alongside developmental cues (in utero embryonic development; kidney and lung development) and Hedgehog signaling (smoothened pathway). The combination suggests a theme of signaling that ties inflammatory responses to developmental processes, though the lack of edges indicates limited direct interactions within the set. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":4},{"id":"GO:0007224","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0032747","count":3},{"id":"GO:0001783","count":3}]},{"hash":"435912004359982502","title":"Dopamine signaling with astrocyte-immune modulation","description":"This cluster centers on dopamine transport/metabolism and dopamine receptor signaling (PLC pathway) while also highlighting astrocyte-related activities (astrocyte chemotaxis, glial-derived neurotrophic factor production) and immune/inflammatory processes (immune response, negative regulation of inflammation) and xenobiotic response. The convergence suggests a module where dopaminergic signaling interfaces with glial/immune regulation, hence the chosen label.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":19},{"id":"GO:0042493","count":19},{"id":"GO:2000458","count":19},{"id":"GO:1900168","count":19},{"id":"GO:0048245","count":19}]},{"hash":"1956822363522107800","title":"Neuroimmune Regulation and Dopaminergic Signaling (CNS)","description":"The top GO terms point to immune and inflammatory regulation (negative regulation of inflammatory response, immune response, eosinophil chemotaxis, response to xenobiotic stimulus) alongside astrocyte-related functions (regulation of astrocyte chemotaxis, GDNF production) and dopaminergic processes (dopamine transport, regulation of dopamine metabolic process, phospholipase C-activating dopamine receptor signaling). This convergence suggests a cohesive theme of CNS neuroimmune modulation with dopaminergic signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":19},{"id":"GO:0042493","count":19},{"id":"GO:2000458","count":19},{"id":"GO:1900168","count":19},{"id":"GO:0048245","count":19}]},{"hash":"1692381139658842081","title":"Ubiquitin-Dependent Degradation and Autophagy","description":"This cluster is dominated by GO terms related to ubiquitin/SUMO post-translational modification and autophagic processes. It includes protein sumoylation, ubiquitin-dependent ERAD, and autoubiquitination, plus several autophagy-related pathways (mitophagy, nucleophagy, and the Cvt pathway). These shared functions point to a module of protein quality control and selective degradation that encompasses both ubiquitin-proteasome and autophagic routes; the immune signaling terms may reflect regulatory cross-talk but do not override the central theme.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":9},{"id":"GO:0030433","count":7},{"id":"GO:0051865","count":6},{"id":"GO:1903265","count":6},{"id":"GO:0034727","count":6}]},{"hash":"1311443467280613853","title":"Wnt-driven neural development and vesicle trafficking","description":"This cluster centers on neural development (substantia nigra development) and synaptic vesicle exocytosis, with supporting roles for canonical Wnt signaling, endothelial barrier formation, and lysosome/phagosome fusion, suggesting a combined theme of neural differentiation and vesicle/lysosome trafficking.","confidence":"Medium","size":18,"edges":116,"triangles":391,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061028","count":18},{"id":"GO:0060070","count":18},{"id":"GO:2000300","count":18},{"id":"GO:0021762","count":18},{"id":"GO:0090385","count":18}]},{"hash":"492530447167475443","title":"Brain development and synaptic/cytoskeletal dynamics","description":"The cluster is dominated by terms tied to brain development (substantia nigra development; endothelial barrier formation via Wnt signaling), and synaptic/cytoskeletal machinery (regulation of synaptic vesicle exocytosis; formin-nucleated actin assembly), with supporting lysosomal/phagosomal processing. This pattern suggests a cohesive theme around neurodevelopment, synaptic function, and cytoskeletal dynamics, rather than a single metabolic pathway.","confidence":"High","size":18,"edges":137,"triangles":590,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061028","count":18},{"id":"GO:0060070","count":18},{"id":"GO:2000300","count":18},{"id":"GO:0021762","count":18},{"id":"GO:0090385","count":18}]},{"hash":"1485573906928585547","title":"Innate Immune Signaling and Cytoskeletal Remodeling","description":"The proteins cluster around antiviral and interferon-related activities (defense response to virus, cellular response to type II interferon, NLRP3 inflammasome assembly, IL-2 regulation), indicating innate immune signaling. They also feature processes tied to cytoskeletal dynamics and membrane trafficking (microtubule depolymerization, ER membrane fusion, regulation of synaptic assembly at the NMJ, GTPase activity regulation, and protein homooligomerization), suggesting coordinated remodeling of the cytoskeleton and vesicle trafficking during immune responses. Overall, the ensemble points to immune activation intertwined with cytoskeletal and membrane dynamics.","confidence":"Medium","size":18,"edges":58,"triangles":61,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0071346","count":3},{"id":"GO:1900041","count":3}]},{"hash":"827168401735830355","title":"Epigenetic regulators: histone methylation and deubiquitination","description":"This cluster is dominated by GO terms pointing to chromatin modification and transcription regulation, including DNA-templated transcription and histone methylation (H3K4/K79) along with multiple deubiquitinase activities (K29, K11, K63) and ubiquitin chain depolymerization, suggesting a set of proteins that regulate gene expression via histone modifications and ubiquitination dynamics. Some terms are labeled obsolete, but the overall theme remains histone modification\u2013mediated transcription control.","confidence":"High","size":18,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0035523","count":6},{"id":"GO:0034729","count":6},{"id":"GO:0051568","count":6},{"id":"GO:0060013","count":5}]},{"hash":"561409998607813319","title":"Immune cytokine signaling and interferon response","description":"The cluster is dominated by GO terms tied to immune signaling and cytokine pathways: positive regulation of type I interferon production; interleukin-4 signaling; interleukin-7 response; and positive regulation of T-helper 1 cell differentiation, plus related signaling processes such as the Sevenless pathway, lamellipodium assembly, and proteasomal ubiquitin-dependent protein degradation. Although a few terms reflect cytoskeletal dynamics and protein turnover, the overarching theme is cytokine- and interferon-mediated signaling networks that govern immune cell communication and activation, rather than a single metabolic or structural function.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032481","count":18},{"id":"GO:2001275","count":18},{"id":"GO:0035771","count":18},{"id":"GO:0030032","count":18},{"id":"GO:0046676","count":18}]},{"hash":"1071234024112817198","title":"Cardiac and skeletal muscle development with signaling","description":"The top GO terms cluster around heart development, SA node action potential regulation, and skeletal muscle tissue development, alongside intracellular signal transduction and transcription regulation, suggesting a module focused on cardiac and skeletal muscle development with associated signaling processes. Some terms (mRNA processing, visual perception, fat cell differentiation) are less central but reflect broader regulatory annotations within the cluster.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006397","count":4},{"id":"GO:0098907","count":4},{"id":"GO:0045444","count":4},{"id":"GO:0035556","count":4},{"id":"GO:0071260","count":4}]},{"hash":"484973181263916592","title":"Rho-driven actin remodeling and innate immune signaling","description":"This cluster centers on actin cytoskeleton dynamics (microspike/filopodium assembly, microtubule regulation) controlled by Rho GTPase signaling, with concurrent innate immune cues (IL-6 production, IL-2 regulation). The convergence of cytoskeletal remodeling and immune signaling terms suggests a shared role in immune cell movement/activation and cytokine regulation.","confidence":"High","size":18,"edges":41,"triangles":23,"max_degree":9,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030035","count":5},{"id":"GO:0043547","count":5},{"id":"GO:2000778","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0007026","count":5}]},{"hash":"765093386699185294","title":"Ciliogenesis and Skeletal Development","description":"The top terms center on skeletal system development and morphogenesis and gastrulation, indicating embryonic tissue patterning, with a strong cue for ciliogenesis via cilium assembly. Supporting processes like vesicle trafficking, mRNA transport, and protein complex assembly further reflect cellular mechanisms underpinning development and ciliary function. Confidence: Medium","confidence":"Medium","size":18,"edges":76,"triangles":131,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":16},{"id":"GO:0048705","count":16},{"id":"GO:0070208","count":16},{"id":"GO:0000348","count":16},{"id":"GO:0031930","count":16}]},{"hash":"2144082821286356375","title":"Mitotic cell cycle and spindle regulation","description":"The top GO terms cluster around mitosis and cell division (cell division, mitotic cell cycle, spindle orientation, APC/C-dependent catabolic process, mitotic DNA replication). Supporting terms like actin filament depolymerization and COPII-coated vesicle budding reflect cytoskeletal and trafficking changes linked to mitotic processes. Together they suggest a cohesive theme of mitotic progression and spindle regulation.","confidence":"High","size":18,"edges":34,"triangles":22,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:1904263","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0000132","count":9},{"id":"GO:0000278","count":8}]},{"hash":"440222016695087230","title":"Neuronal development: dendrite growth and migration","description":"The cluster is dominated by GO terms related to cytoskeletal signaling (Rho/Ras pathways) that regulate neuron shape and motility, combined with terms for dendrite extension, cortical radial glia-guided migration, and synaptic vesicle exocytosis regulation. This pattern points to neural development processes\u2014neurite outgrowth, neuronal migration, and synaptic signaling\u2014as the unifying theme, with a few cross-tissue cytoskeletal processes (e.g., myoblast fusion) that reflect shared regulatory mechanisms. ","confidence":"High","size":18,"edges":4,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":15},{"id":"GO:1903861","count":15},{"id":"GO:0046580","count":15},{"id":"GO:0021814","count":14},{"id":"GO:0007520","count":14}]},{"hash":"2297394869606113655","title":"RNA Processing and Translation Initiation","description":"The top GO terms cluster around RNA metabolism, notably translation initiation (formation of translation preinitiation complex, regulation of translational initiation, IRES-dependent initiation) and mRNA splicing, indicating a core theme of RNA processing and control of protein synthesis; the other terms (DNA repair, mitosis) appear less central but suggest broader genome maintenance roles.","confidence":"Medium","size":18,"edges":116,"triangles":397,"max_degree":17,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0006446","count":5},{"id":"GO:0075522","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0000398","count":4}]},{"hash":"412708819852258856","title":"Meiotic Chromosome Condensation and Segregation","description":"The top GO terms are dominated by meiotic chromosome events: meiotic chromosome condensation, synaptonemal complex assembly, and meiotic chromosome separation, with related regulation of meiotic double-strand break formation. There are also general cell division and RNA-processing terms, but the strongest and most coherent theme is meiosis-related chromosome organization and segregation, so the label highlights that core function.","confidence":"High","size":18,"edges":151,"triangles":785,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0000184","count":3},{"id":"GO:1903342","count":2},{"id":"GO:0010032","count":2}]},{"hash":"2117771571923931882","title":"Cell cycle control and transcription regulation","description":"This cluster is dominated by cell-cycle and transcription-related terms (cell division, APC-dependent processes, DNA-templated transcription, multicellular growth), with additional signaling links (GTPase activity regulation, tyrosine phosphorylation, TGF-beta response). It suggests proteins coordinating cell proliferation with gene expression.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0006351","count":6}]},{"hash":"1641737022696090283","title":"Regulation of signaling and endocytic recycling","description":"The top GO terms cluster around modulation of signaling pathways (Ras, STAT) and membrane trafficking (endocytic and receptor recycling, PI catabolic processes). While some terms relate to broader physiological contexts (cell size, cardiac hypertrophy, locomotion), the shared theme is regulation of cellular signaling and membrane trafficking, rather than a single, specific pathway. This justifies labeling the cluster as Regulation of signaling and endocytic recycling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046580","count":2},{"id":"GO:0032922","count":2},{"id":"GO:0045793","count":1},{"id":"GO:0014898","count":1},{"id":"GO:2001135","count":1}]},{"hash":"141790246711507679","title":"Unknown","description":"The terms include endosomal transport, apoptosis, placental development, DNA integration, viral transport, immune signaling, and ERAD pathways\u2014diverse functions with no clear common theme, and no interactions among proteins. Therefore a specific, representative label cannot be determined.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0097345","count":1},{"id":"GO:0001893","count":1},{"id":"GO:0060137","count":1},{"id":"GO:1903547","count":1}]},{"hash":"366792539581567685","title":"Neurodevelopment and morphogenesis regulators","description":"The top GO terms indicate strong involvement in neural development (brain and spinal cord) and skeletal morphogenesis, together with DNA-templated transcription and transcriptional regulation, pointing to a cluster of factors coordinating developmental processes through gene expression control.","confidence":"High","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0021510","count":4},{"id":"GO:0007584","count":4}]},{"hash":"796072061071908333","title":"Innate Immune Signaling and Xenophagy","description":"The terms cluster around innate immune responses to pathogens: lipopolysaccharide signaling, dsRNA response, interferon-beta production, and overall innate immune activation; also includes xenophagy and ubiquitination, consistent with pathogen clearance and protein regulation during immune responses. Some terms about mitosis and apoptosis may reflect stress during infection, but the core theme is innate immunity and autophagic pathogen handling.","confidence":"High","size":18,"edges":15,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0006915","count":5},{"id":"GO:0031663","count":5},{"id":"GO:1904417","count":5},{"id":"GO:0043330","count":5}]},{"hash":"572485863411779281","title":"Neuronal signaling and endosomal trafficking","description":"These proteins cluster around neuronal excitability (membrane hyperpolarization and action potential propagation) and vesicular receptor trafficking (neurotransmitter receptor transport, endosome transport), with components related to barrier junctions and the blood-nerve barrier (apical/bicellular tight junction assembly, xenobiotic transport). The combination points to a module coordinating neural signaling with endosomal trafficking and barrier junction maintenance.","confidence":"Medium","size":18,"edges":97,"triangles":245,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0060081","count":8},{"id":"GO:0016049","count":8},{"id":"GO:0070830","count":8},{"id":"GO:0045779","count":5},{"id":"GO:0061772","count":5}]},{"hash":"305615487553255183","title":"Chromatin remodeling and cell division","description":"This cluster centers on chromatin dynamics, with nucleosome assembly/disassembly and histone acetylation-related terms, and includes cell-division related processes such as budding/growth and stem cell division, plus hints of microtubule involvement in mitotic contexts. Together these terms point to chromatin remodeling and regulation during cell cycle progression as the dominant theme.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031116","count":1},{"id":"GO:2000617","count":1},{"id":"GO:0007117","count":1},{"id":"GO:2000035","count":1},{"id":"GO:0006337","count":1}]},{"hash":"1338359954094343706","title":"DNA replication, repair, and RNA processing","description":"This cluster centers on DNA metabolism\u2014primarily replication and repair (primer synthesis, unwinding, recombination, SOS response, transcription-coupled repair)\u2014along with RNA processing activities (RNA Pol I transcription termination, prespliceosome assembly, rRNA catabolism). The combination suggests proteins involved in DNA maintenance in the nucleus together with RNA processing pathways, with some overlap to viral genome replication.","confidence":"High","size":18,"edges":107,"triangles":340,"max_degree":17,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006363","count":5},{"id":"GO:0006306","count":5},{"id":"GO:0006269","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0009432","count":5}]},{"hash":"1588439142651268296","title":"Embryonic development and tissue proliferation","description":"The top GO terms are dominated by developmental processes across multiple tissues (angiogenesis, lung mesenchyme development, embryonic pectoral fin morphogenesis, keratinocyte proliferation, white fat cell proliferation) with additional signals related to tissue growth. There is also representation of translation-related terms (translation, regulation of translational fidelity), suggesting a broader link to gene expression during development. Taken together, the cluster seems to reflect a general developmental and proliferative program rather than a single pathway.","confidence":"Medium","size":18,"edges":134,"triangles":561,"max_degree":17,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0006450","count":4},{"id":"GO:0001525","count":4},{"id":"GO:0070858","count":3},{"id":"GO:0043616","count":3}]},{"hash":"507209040417376885","title":"Cytoskeletal regulation during mitosis","description":"The top terms cluster around cytoskeletal dynamics and mitosis\u2014spindle assembly, contractile ring formation, and centrosome maintenance\u2014driven by Rho signaling, with additional hints of broader signaling (thrombin, Wnt) and developmental contexts.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0070493","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0016055","count":4},{"id":"GO:0051661","count":4}]},{"hash":"74544868109614593","title":"Post-transcriptional RNA processing and translation regulation","description":"The cluster centers on mRNA stability, splicing, polyadenylation, and regulation of translation initiation and preinitiation complex formation, plus ncRNA-mediated silencing, indicating a cohesive group focused on post-transcriptional control of gene expression. A developmental term (blastocyst formation) may reflect context rather than core function.","confidence":"High","size":18,"edges":65,"triangles":103,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":15},{"id":"GO:0048025","count":13},{"id":"GO:0031047","count":12},{"id":"GO:0006378","count":12},{"id":"GO:0048255","count":11}]},{"hash":"1977556060117756296","title":"Growth and immune signaling regulators","description":"This cluster is enriched for terms involving modulation of key signaling pathways that govern cell growth and immune responses, including positive regulation of PI3K/AKT and ERK cascades, negative regulation of TOR signaling, and negative regulation of T cell activation, plus associations with cell division and CDK activity. A single term on neuron migration is likely incidental, but overall the proteins appear to function as regulators of growth-related and immune signaling pathways.","confidence":"Medium","size":18,"edges":85,"triangles":169,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0050728","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0032007","count":2}]},{"hash":"1872805749084685444","title":"Bacterial cell-wall and secondary metabolite biosynthesis","description":"The terms point to diverse biosynthetic pathways typical of bacteria, including cell-wall lipid components (lipoteichoic acid), fatty acids, menaquinone, siderophores, and nonribosomal peptide biosynthesis, plus the bioluminescent capability in some species. Energy-related processes like pyruvate fermentation to acetate and malonate catabolism further support a broad bacterial metabolism theme, suggesting a cluster of proteins specialized for bacterial biosynthesis and energy production rather than a single fixed pathway.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0070395","count":18},{"id":"GO:0043041","count":18},{"id":"GO:1902987","count":18},{"id":"GO:0006633","count":18},{"id":"GO:0008206","count":17}]},{"hash":"1557371391641960438","title":"Cytoskeleton Remodeling and Cell Migration","description":"The cluster centers on actin-related processes and movement: actin filament bundle assembly, cell migration, and epithelial cell polarity establishment, with hints of vascular/cardiac tissue dynamics (endothelial delamination and cardiac muscle cell membrane depolarization) where cytoskeletal remodeling is critical. Some terms (telomere maintenance, insulin-stimulated glucose import) appear peripheral or incidental; however, the strongest signal is cytoskeletal organization and motility, supporting a label around cytoskeleton remodeling and cell migration.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0032212","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0016477","count":1}]},{"hash":"1740854240846545469","title":"Neuronal membrane organization and synapse assembly","description":"The top GO terms point to neural development, clustering of voltage-gated sodium channels, and regulation of synapse assembly, which together indicate roles in neuronal membrane organization and synaptic connectivity. Supporting terms on transmembrane transport and maintaining electrochemical gradients reinforce a membrane- and ion-channel\u2013related function. Some terms (e.g., DNA integration, proviral latency, symbiont-mediated apoptosis) appear unrelated and may be noise, but the core signal supports neural membrane/synapse related activity.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0045162","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0075713","count":2}]},{"hash":"110065753000495671","title":"Xenobiotic and nutrient transmembrane transport","description":"The cluster is dominated by GO terms for transmembrane transport across membranes, covering xenobiotics, vitamins, amino acids, long-chain fatty acids into peroxisomes, and potassium ions. This points to a cohesive theme of membrane transporters for diverse substrates. A couple of outlier terms (e.g., heterochromatin formation, insulin response) are less connected but do not outweigh the primary transport signal.","confidence":"High","size":18,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042908","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0032869","count":3}]},{"hash":"1104645531614254846","title":"Embryonic organogenesis and neural crest development","description":"The terms cluster around early developmental processes spanning multiple organs and tissues, including heart development, organ induction, neural crest formation, neuron migration, cranial skeleton morphogenesis, and retinal/visual system development. Together they point to a cohesive theme of embryonic organogenesis and tissue patterning across diverse lineages, with some inclusion of neural and sensory system development.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":15},{"id":"GO:0007601","count":12},{"id":"GO:0007275","count":12},{"id":"GO:0014029","count":11},{"id":"GO:0031290","count":11}]},{"hash":"1548387020644268575","title":"Heat-stress\u2013driven cell cycle and cytoskeleton remodeling","description":"The cluster combines terms for telomere maintenance and capping, cell cycle, and heat response with cytoskeletal processes (actin bundle assembly, cell migration, epithelial polarity, endothelial delamination), suggesting a theme of proliferative and structural adaptation under thermal stress. The label captures the core link between cell division/teleomere regulation and cytoskeletal remodeling in stressed conditions, though some terms reflect broader tissue remodeling contexts.","confidence":"Medium","size":18,"edges":83,"triangles":56,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":16},{"id":"GO:0007049","count":16},{"id":"GO:0009408","count":16},{"id":"GO:2001275","count":8},{"id":"GO:0051017","count":8}]},{"hash":"2237096486214695675","title":"Developmental differentiation and morphogenesis","description":"The top GO terms center on transcriptional regulation (DNA-templated transcription) and various morphogenesis/differentiation processes, including vertebrate heart development (ventricular cardiac muscle cell differentiation, sinoatrial valve morphogenesis), tracheal cartilage development, and primitive streak formation. The ERK5 signaling cascade indicates developmental signaling involvement. Some plant-related terms (flower development, floral meristem identity) may reflect cross-species annotation noise, but the overarching theme is developmental differentiation and tissue morphogenesis driven by transcriptional regulation.","confidence":"Medium","size":18,"edges":150,"triangles":771,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0055012","count":11},{"id":"GO:0060534","count":11},{"id":"GO:0070375","count":10},{"id":"GO:0090009","count":10}]},{"hash":"355314749513018245","title":"Developmental transcriptional regulators","description":"This cluster is defined by GO terms for DNA-templated transcription and transcriptional regulation, coupled with numerous embryonic development terms (neural crest migration, habenula and peripheral nervous system development, ureteric bud branching, odontogenesis, pancreas development, digestive tract morphogenesis). The pattern suggests a set of transcription factors coordinating organogenesis across tissues.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0090190","count":13},{"id":"GO:0021986","count":12},{"id":"GO:0001755","count":11},{"id":"GO:0000122","count":11}]},{"hash":"242024948321276630","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0060386","count":9},{"id":"GO:0016567","count":9},{"id":"GO:0042752","count":7},{"id":"GO:0000209","count":6}]},{"hash":"76682680956700530","title":"Oxidative Detoxification and Metabolic Response","description":"The top GO terms cluster around detoxification of cellular oxidants, glutathione metabolism, and toxin catabolic processes, indicating a redox/metabolic stress program. Additional terms point to broader metabolism (aromatic amino acids), starvation response, and growth regulation, suggesting coordinated cellular adaptation to oxidative stress and nutrient status. Some terms related to calcium signaling and DNA repair appear as broader housekeeping roles, but the dominant theme centers on redox detoxification and metabolic response.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":17},{"id":"GO:0009407","count":16},{"id":"GO:0006749","count":16},{"id":"GO:0014810","count":15},{"id":"GO:0060316","count":15}]},{"hash":"1011565877562499794","title":"Actin Cytoskeleton Dynamics and Rho Signaling","description":"The cluster centers on actin-driven protrusions and cytoskeletal remodeling, with key terms for lamellipodium assembly, actin organization, and regulation of Rho GTPase signaling, plus small GTPase\u2013mediated pathways. This points to a cohesive theme of actin dynamics driving cell motility and morphogenesis (neural migration and related contexts).","confidence":"High","size":18,"edges":114,"triangles":385,"max_degree":17,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0030032","count":9},{"id":"GO:0030036","count":9},{"id":"GO:0035023","count":9},{"id":"GO:0060313","count":9},{"id":"GO:0043314","count":9}]},{"hash":"187212225818989573","title":"Skeletal ECM and Biomineralization","description":"The cluster is dominated by GO terms related to extracellular matrix (ECM) remodeling and skeletal development (growth plate cartilage chondrocyte morphogenesis, biomineral tissue development, negative regulation of ECM assembly), suggesting a theme around cartilage/bone formation and ECM regulation. Some plant-related terms (chlorophyll biosynthetic process, stamen formation) appear but are likely noise; the main signal points to ECM-associated skeletal processes, with proteasome assembly and protein heterotrimerization reflecting general protein complex assembly supporting these functions.","confidence":"Medium","size":18,"edges":64,"triangles":84,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007596","count":8},{"id":"GO:0030194","count":7},{"id":"GO:0031214","count":6},{"id":"GO:0015995","count":6},{"id":"GO:0070208","count":5}]},{"hash":"1390585053557065879","title":"Mitochondrial translation and amino acid biosynthesis","description":"The top GO terms strongly point to mitochondrial protein synthesis, with tRNA processing, mitochondrial phenylalanyl-tRNA aminoacylation, and translation. The accompanying biosynthetic processes for several amino acids, pantothenate, and NADPH regeneration suggest linked mitochondrial metabolism and redox activity. Additional terms like copper ion import and inositol catabolic process imply broader, mitochondria-associated metabolic regulation. Overall, the cluster appears to center on mitochondrial translation machinery with connected metabolic pathways.","confidence":"High","size":18,"edges":19,"triangles":12,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":5},{"id":"GO:0070156","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0015940","count":4},{"id":"GO:0006740","count":4}]},{"hash":"203383008717583540","title":"Photoreceptor GPCR signaling and trafficking","description":"The top GO terms center on phototransduction, opsin-mediated signaling, and GPCR internalization/regulation of receptor internalization, suggesting a functional cluster focused on light-activated GPCR signaling and receptor trafficking in photoreceptor or related cells. While there are a couple of immune-related terms, the core theme is photoreceptor signaling and GPCR trafficking.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032691","count":3},{"id":"GO:0032226","count":2},{"id":"GO:0060613","count":2},{"id":"GO:0002092","count":2},{"id":"GO:0007602","count":2}]},{"hash":"838561464957570989","title":"Estradiol-regulated cell adhesion and motility","description":"This cluster centers on GO terms linking estradiol signaling to changes in cell adhesion and movement (e.g., negative regulation of cell-matrix adhesion and lamellipodium morphogenesis) as well as growth/differentiation pathways (fibroblast proliferation, fat cell differentiation). Additional terms touching metabolism and signaling regulation (glycogen biosynthesis, protein autophosphorylation) fit a broader hormone-regulated cellular behavior theme. While a few terms are peripheral (nitrogen starvation, immune response), the prominent pattern is estradiol-responsive control of adhesion, motility, and growth.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001953","count":4},{"id":"GO:0071392","count":3},{"id":"GO:0048147","count":2},{"id":"GO:0045599","count":2},{"id":"GO:0006995","count":2}]},{"hash":"762853139734968233","title":"TLR2-Mediated Macrophage Innate Immune Activation","description":"The top GO terms cluster around innate immune recognition and inflammatory signaling in macrophages: TLR2 signaling, detection of diacyl lipopeptides, cellular response to LPS, macrophage activation, and NF-kappaB\u2013related pathways driving IL-6 production and antiviral defense. This points to a coherent theme of TLR2-driven macrophage innate immune activation, with a few peripheral terms related to bone remodeling and lymph vessel morphogenesis that are less central to the core function.","confidence":"High","size":18,"edges":63,"triangles":79,"max_degree":14,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045410","count":13},{"id":"GO:0006469","count":13},{"id":"GO:0042346","count":13},{"id":"GO:0051607","count":13},{"id":"GO:0034134","count":13}]},{"hash":"56407589506220396","title":"Heart development and hypoxia-oxidative stress response","description":"The cluster is enriched for heart development and angiogenesis terms, with strong signals for hypoxia response and detoxification of reactive oxygen species (hydrogen peroxide/cellular oxidants), plus NF-kappaB signaling, all of which point to a cardiovascular development module that also handles oxidative stress and inflammatory signaling. Minor links to metabolic remodeling (brown fat differentiation) and tissue remodeling (fibroblast migration) support a broader developmental stress-response context. Confidence: High","confidence":"","size":18,"edges":33,"triangles":21,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007507","count":8},{"id":"GO:0001666","count":7},{"id":"GO:0042744","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0042542","count":6}]},{"hash":"765639308836273324","title":"Multiorgan Development and Differentiation","description":"The top GO terms point to differentiation and morphogenesis across multiple tissues\u2014keratinocytes, cartilage, gonads, palate, kidney (ureteric bud), placenta (labyrinthine layer), and hematopoietic lineages\u2014along with related remodeling processes (stress fiber assembly, fibrinolysis). This suggests a broad developmental theme rather than a single tissue-specific function, making a cross-tissue development label appropriate.","confidence":"Medium","size":18,"edges":86,"triangles":174,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030216","count":5},{"id":"GO:0042730","count":5},{"id":"GO:0008584","count":5},{"id":"GO:0051496","count":5},{"id":"GO:0060021","count":5}]},{"hash":"1505320264875582264","title":"piRNA pathway and germline regulation","description":"The cluster is dominated by GO terms for piRNA processing and regulatory ncRNA-mediated gene silencing, including negative regulation of transposition and spermatid development, pointing to a germline genome-defense/silencing theme. Some broader developmental terms appear but do not override the core piRNA/germline signal.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043086","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0034587","count":2},{"id":"GO:0010529","count":2},{"id":"GO:0007286","count":2}]},{"hash":"878924087772334070","title":"Immune modulation via MHC II and ubiquitination","description":"The top GO terms are largely immune-related, centering on antigen processing and presentation via MHC class II, regulation and suppression of MHC II biosynthesis, regulation of tolerance, and ubiquitin-related processes. This points to a function cluster centered on modulating host immune responses, especially adaptive immunity, rather than a single metabolic pathway. Some terms about suberin/cutin biosynthesis appear but do not define the core theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045347","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0002643","count":1},{"id":"GO:0039648","count":1},{"id":"GO:0039504","count":1}]},{"hash":"1816060090095971573","title":"Cardiac calcium signaling and hypertrophy","description":"The cluster features strong signals for heart development, cardiac muscle hypertrophy in response to stress, and calcium ion transport and sensing, indicating a cardiac calcium signaling module tied to contraction and hypertrophic responses. Also present are inflammatory pathways (NF-kappaB signaling, complement activation) that may reflect cross-talk with cardiac stress signaling; brain development signals are less connected. Overall, the core theme is cardiac calcium signaling and hypertrophy.","confidence":"Medium","size":18,"edges":8,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043123","count":15},{"id":"GO:0007507","count":12},{"id":"GO:0021762","count":11},{"id":"GO:0060316","count":11},{"id":"GO:0070588","count":11}]},{"hash":"2049967020313453140","title":"Embryonic organogenesis and nervous system development","description":"This cluster is characterized by GO terms covering broad embryonic development across multiple tissues, with a clear emphasis on nervous system and sensory organ formation (neural crest, retinal ganglion axon guidance, visual perception) alongside general organogenesis (heart development, ectoderm formation, kidney and reproductive tract development). The mix suggests proteins involved in early developmental differentiation rather than a single pathway, making this label representative.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007601","count":18},{"id":"GO:0007507","count":18},{"id":"GO:0007275","count":18},{"id":"GO:0014029","count":18},{"id":"GO:0021526","count":16}]},{"hash":"1312200348133226777","title":"Developmental Morphogenesis and Protein Synthesis","description":"This cluster shows enrichment for developmental and morphogenetic processes (hair follicle morphogenesis, EMT in endocardial cushion formation, olfactory nerve formation, pollen tube growth/germination) alongside core protein synthesis activities (translational initiation, ribosomal large subunit biogenesis). The combination points to a theme of growth and tissue formation supported by basic biosynthetic machinery.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0031069","count":2},{"id":"GO:0003198","count":2}]},{"hash":"268518754709209595","title":"Osteogenesis and Mesoderm Differentiation","description":"The top GO terms point to bone-related processes (positive regulation of osteoblast differentiation, bone mineralization) and mesodermal lineage development (notochord development, intermediate mesodermal cell differentiation), supplemented by growth-related signaling (PI3K/AKT) and fibroblast proliferation. This pattern suggests a cluster centered on skeletal formation and mesodermal tissue differentiation, with coordinated signaling to promote bone formation and lineage diversification.","confidence":"High","size":18,"edges":144,"triangles":708,"max_degree":17,"top_function":"wound healing","top_go_terms":[{"id":"GO:0050714","count":17},{"id":"GO:2000679","count":17},{"id":"GO:0045669","count":17},{"id":"GO:0043491","count":17},{"id":"GO:0048146","count":17}]},{"hash":"943475202922469969","title":"Embryonic and organ development","description":"This cluster is dominated by GO terms tied to development across multiple tissues and organs (odontogenesis, ectoderm formation, metencephalon development, retinal axon guidance, ureteric bud elongation, gonad and uterine development, myoblast proliferation), suggesting proteins involved in broad developmental programs rather than a single pathway.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042475","count":12},{"id":"GO:0000122","count":12},{"id":"GO:0021526","count":11},{"id":"GO:0060677","count":11},{"id":"GO:0031290","count":11}]},{"hash":"47705958028876496","title":"RNA and Protein Methyltransferases","description":"Top GO terms indicate widespread methyltransferase activity across RNA (rRNA, tRNA wobble) and proteins (arginine/lysine, histone) as well as methylation steps in biosynthetic pathways (chlorophyll, cobalamin, antibiotic biosynthesis), suggesting the cluster is enriched for methyltransferase enzymes involved in diverse substrate modifications and biosynthesis.","confidence":"High","size":18,"edges":112,"triangles":349,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0019919","count":9},{"id":"GO:0017000","count":9},{"id":"GO:0031167","count":9},{"id":"GO:0046690","count":9},{"id":"GO:0002098","count":8}]},{"hash":"1509956911089288282","title":"Neural development and axon fasciculation","description":"The top terms are dominated by neural-development-related processes: positive regulation of synapse assembly, fasciculation of sensory and motor neuron axons, and nervous system development, indicating a core function in neuron growth and axon wiring. Other terms (keratinocyte proliferation, endodermal differentiation, ossification) appear but are less central, suggesting incidental associations rather than the main theme. ","confidence":"High","size":18,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":4},{"id":"GO:0097155","count":4},{"id":"GO:0097156","count":4},{"id":"GO:0048485","count":4},{"id":"GO:0035987","count":4}]},{"hash":"518437221891008296","title":"Neural synapse assembly and maturation","description":"The terms point to neural connectivity and synapse development, including axon guidance, postsynaptic density assembly, and chemical neurotransmission, with supporting developmental context like neural tube closure. Behavioral terms such as vocalization and vocal learning imply involvement of neural circuits underpinning communication, aligning the cluster with synapse formation and maturation in the brain.","confidence":"High","size":18,"edges":18,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":3},{"id":"GO:2000821","count":2},{"id":"GO:0007411","count":2},{"id":"GO:0007268","count":2},{"id":"GO:0097116","count":2}]},{"hash":"1253924162494605684","title":"Plant cell wall biosynthesis and glycosylation","description":"The cluster is enriched for terms related to cell wall organization and various glycan biosynthesis and glycosylation processes, including plant-type secondary cell wall biogenesis. This points to proteins involved in constructing and modifying the plant cell wall through glycosylation and glycoconjugate assembly. Confidence: High","confidence":"","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0071555","count":6},{"id":"GO:0050650","count":4},{"id":"GO:0015012","count":4},{"id":"GO:0016266","count":4},{"id":"GO:0006486","count":4}]},{"hash":"735673823815380085","title":"Embryonic neural and organ development","description":"This set centers on embryonic development across multiple tissues, especially nervous system formation (inner ear, motor column neuron differentiation, retinal ganglion cell axon guidance, metencephalon development) and various organogenesis events (ectoderm formation, gonad and uterine development, ureteric bud elongation, myoblast proliferation, locomotory behavior). The common theme is broad embryonic development rather than a specific pathway.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0048839","count":9},{"id":"GO:0021526","count":8},{"id":"GO:0060677","count":8},{"id":"GO:0031290","count":8},{"id":"GO:0001705","count":8}]},{"hash":"1468306837647247540","title":"RNA Pol II Transcription Regulation","description":"The cluster\u2019s top GO terms are dominated by transcription-related processes involving RNA polymerase II, including DNA-templated transcription and both positive and negative regulation of transcription by RNA Pol II. While a few development terms appear, they are far less represented; the core signal indicates transcriptional control by RNA Pol II as the unifying function of the cluster.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046022","count":16},{"id":"GO:0000122","count":16},{"id":"GO:0006351","count":16},{"id":"GO:0007576","count":16},{"id":"GO:0010729","count":16}]},{"hash":"1317150870496479047","title":"Flavonoid biosynthesis and glycosylation","description":"The top GO terms are dominated by specific flavonoid biosynthesis and sugar-conjugation processes, including cyanidin, kaempferol, and quercetin glucoside biosynthetic steps, as well as related glycosylation activities. Lignin metabolic process also fits within the broader phenylpropanoid pathway, reinforcing a common theme of plant secondary metabolite production. A couple of terms (paranode axon localization, estrogen catabolic process) appear less related and may reflect annotation noise or broad cross-referencing, but the core signal points to flavonoid production and glycosylation. ","confidence":"High","size":18,"edges":99,"triangles":288,"max_degree":17,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009808","count":7},{"id":"GO:0052696","count":7},{"id":"GO:0033485","count":7},{"id":"GO:0002175","count":7},{"id":"GO:0030259","count":7}]},{"hash":"202123683106924233","title":"Purine and nucleobase transport","description":"The top GO terms are dominated by transport of purine nucleobases and related compounds (adenine, guanine, hypoxanthine, uracil, urate, xanthine) across membranes, plus related ascorbate transport. This suggests a cluster of membrane transport proteins specialized for nucleobases and small metabolites. A couple of outliers (sound perception, apoptosis signaling) appear unrelated noise, but the core theme is nucleobase/small-molecule transport.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070904","count":2},{"id":"GO:0098702","count":2},{"id":"GO:0098721","count":2},{"id":"GO:1903825","count":2},{"id":"GO:0035344","count":2}]},{"hash":"1224581101286504790","title":"Cholinergic signaling and myeloid differentiation","description":"Predominant GO terms indicate cholinergic activity (acetylcholine biosynthesis and secretion), suggesting a neuronal signaling aspect, while additional terms point to myeloid lineage differentiation and osteoclast fusion/resorption, implying a link between cholinergic signaling and immune/osteoclastogenic pathways. The outlier plant-related term (sieve element differentiation) does not overpower the overall theme, so the cluster likely reflects cholinergic signaling intertwined with myeloid differentiation processes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008292","count":3},{"id":"GO:0061526","count":3},{"id":"GO:0090603","count":3},{"id":"GO:0071356","count":1},{"id":"GO:0090290","count":1}]},{"hash":"1724369668550378324","title":"Neuronal signaling and proteoglycan biosynthesis","description":"The top terms include neuropeptide signaling and biosynthesis of glycosaminoglycans (chondroitin sulfate and heparan sulfate), with a note on bipolar cell growth regulation, which together point to neuronal communication and extracellular matrix remodeling. While other terms reflect broader metabolic processes (inositol/phosphate, purine) and lipid metabolism, the clustering around neuronal signaling and proteoglycan biosynthesis provides the most coherent theme for this group. ","confidence":"Medium","size":18,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007218","count":3},{"id":"GO:0006144","count":2},{"id":"GO:2001311","count":2},{"id":"GO:0016036","count":2},{"id":"GO:0050650","count":2}]},{"hash":"135756482122246011","title":"Neural development and tissue remodeling (bone and vasculature)","description":"This cluster shows strong signals for nervous system development and synapse assembly, plus ossification and angiogenesis, with accompanying cell adhesion terms and mast cell activity. Together these terms suggest proteins coordinating neural development with structural remodeling of bone and blood vessels, mediated by cell-cell interactions and immune signaling.","confidence":"Medium","size":18,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":6},{"id":"GO:0007156","count":6},{"id":"GO:0007157","count":6},{"id":"GO:0007399","count":5},{"id":"GO:0051965","count":5}]},{"hash":"498300677018583524","title":"Cell adhesion and tissue morphogenesis","description":"The proteins show enrichment for cell adhesion (homophilic and heterophilic) and epithelial differentiation (keratinization), along with planar polarity and axon guidance cues, and morphogenesis-related processes across tissues (hair/body orientation, lung development, heart valve formation, neural guidance). This points to a broad theme of tissue organization and morphogenesis driven by cell adhesion rather than a single, specific pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007156","count":5},{"id":"GO:0007157","count":5},{"id":"GO:0031424","count":4},{"id":"GO:0007626","count":4},{"id":"GO:1904938","count":4}]},{"hash":"1662212853735514530","title":"Golgi-dependent glycosylation in root development","description":"These proteins show GO terms for root development (lateral root development, root hair cell development) alongside Golgi-associated glycosylation and sugar transport processes (GDP-fucose import into Golgi lumen, UDP-glucose transport, fucosylation-related terms). The mix suggests a theme where Golgi-mediated glycan biosynthesis and sugar nucleotide transport influence plant root morphogenesis, supporting a label that emphasizes both Golgi glycosylation and root development. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048527","count":4},{"id":"GO:0036085","count":4},{"id":"GO:0030206","count":4},{"id":"GO:0080147","count":4},{"id":"GO:0015713","count":4}]},{"hash":"398099603195399649","title":"Membrane domain signaling and adhesion","description":"This cluster centers on membrane-associated signaling platforms (rafts/eisosomes) and downstream signaling that regulates cell\u2013cell interactions and immune responses, as seen in endothelial barrier establishment, B cell receptor signaling and differentiation, and adhesion regulation, along with related PKC signaling, apoptotic pathways, and some neuronal terms. While the terms span vascular, immune, neuronal, and membrane biology, the common thread appears to be membrane-domain\u2013driven signaling and adhesion processes. ","confidence":"Medium","size":18,"edges":28,"triangles":21,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0061028","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0050861","count":2},{"id":"GO:0090038","count":2},{"id":"GO:0048169","count":2}]},{"hash":"1688854756112608157","title":"Synaptic organization and learning","description":"The cluster prominently features GO terms for synapse organization and learning, implying neural signaling/plasticity. Receptor internalization and protein tetramerization support synaptic assembly and trafficking, while lipid-related terms may reflect general membrane biology or multifunctional proteins. A minority of terms relate to xenobiotic response, folic acid, plant hormones, or bone development, suggesting some functional noise. Overall, the most coherent theme is neuronal synaptic organization and learning.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090122","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0051593","count":2},{"id":"GO:0050808","count":2},{"id":"GO:0051262","count":2}]},{"hash":"1738408265816819673","title":"Neural-immune signaling cluster","description":"Top terms show a mix of neural/visual perception and immune signaling, with ERK pathway regulation and glial/neurotrophic factors (astrocyte chemotaxis, GDNF production) predominating. This points to a theme of neural-immune cross-talk and glial signaling, rather than a single tissue-specific function; some terms are peripheral but do not negate the central pattern.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":17},{"id":"GO:0006955","count":17},{"id":"GO:0070374","count":17},{"id":"GO:2000484","count":17},{"id":"GO:0007507","count":17}]},{"hash":"936485327113082388","title":"Transmembrane Ion and Metabolite Transport","description":"This cluster is dominated by GO terms for transmembrane transport of ions (potassium, sodium, phosphate, nitrate) and various metabolites (galactose, vitamins, 4-hydroxyphenylacetate), plus a nitrate assimilation term, suggesting the proteins largely function as membrane transporters or channels. An outlier Fc-epsilon receptor signaling term appears but does not define the cluster\u2019s primary function.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":8},{"id":"GO:0038095","count":5},{"id":"GO:0035725","count":5},{"id":"GO:0035435","count":4},{"id":"GO:1900754","count":4}]},{"hash":"74206109924493149","title":"Neuroimmune-Dopaminergic Signaling Regulators","description":"The cluster\u2019s GO terms span immune/inflammatory regulation (negative regulation of inflammatory response, immune response, eosinophil chemotaxis) and neural/glial signaling (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling, astrocyte chemotaxis, GDNF production). This pattern suggests proteins that mediate cross-talk between glial/immune function and dopaminergic signaling, rather than a single simple pathway. ","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":18},{"id":"GO:0042493","count":18},{"id":"GO:2000458","count":18},{"id":"GO:1900168","count":18},{"id":"GO:0048245","count":18}]},{"hash":"2082015112777762238","title":"Neuroimmune and Dopaminergic Signaling","description":"This cluster combines immune-related terms (immune response, regulation of inflammatory response, eosinophil chemotaxis) with CNS/glial context (astrocyte chemotaxis, glial-derived neurotrophic factor production) and dopaminergic processes (dopamine transport, regulation of dopamine metabolism, dopamine receptor signaling), suggesting a coherent theme of neuroimmune crosstalk that modulates dopaminergic signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":18},{"id":"GO:0042493","count":18},{"id":"GO:2000458","count":18},{"id":"GO:1900168","count":18},{"id":"GO:0048245","count":18}]},{"hash":"653285271669466076","title":"Dopaminergic neuroimmune regulation","description":"The cluster shows strong enrichment for dopamine-related processes (dopamine transport; regulation of dopamine metabolic process; phospholipase C-activating dopamine receptor signaling) alongside immune and glial activities (immune response; negative regulation of inflammatory response; astrocyte chemotaxis; glial-derived neurotrophic factor production; eosinophil chemotaxis; response to peptide). Together these terms suggest a cohesive theme where dopaminergic signaling intersects with neuroinflammatory and glial regulation, forming a neuroimmune-dopaminergic module.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":18},{"id":"GO:0042493","count":18},{"id":"GO:2000458","count":18},{"id":"GO:1900168","count":18},{"id":"GO:0048245","count":18}]},{"hash":"46331300586918437","title":"Deubiquitinases Regulating Neuron Cell Cycle","description":"The cluster centers on deubiquitination activities (K29- and K11-linked DUBs) together with cell cycle regulation (G0\u2192G1, cell cycle regulation) and anti-apoptotic/transcriptional control, plus a neuronal context (motor neuron axon guidance) and NFAT/calcium signaling involvement. This suggests a theme where DUBs modulate protein stability and signaling to coordinate neuronal function with cell-cycle decisions. ","confidence":"Medium","size":17,"edges":18,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008045","count":5},{"id":"GO:0070886","count":5},{"id":"GO:0035523","count":4},{"id":"GO:0046832","count":3},{"id":"GO:0045023","count":3}]},{"hash":"51263316920527388","title":"Developmental and Immune Regulation","description":"Reason: The terms cluster around broad regulatory roles\u2014transcription and cell-cycle control, DNA damage response, immune tolerance/modulation, and multiple developmental processes\u2014indicating a general regulatory program rather than a single pathway.","confidence":"Medium","size":17,"edges":78,"triangles":130,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071930","count":6},{"id":"GO:0002513","count":5},{"id":"GO:0001701","count":5},{"id":"GO:0045409","count":5},{"id":"GO:0042593","count":5}]},{"hash":"1812993082835162262","title":"Ubiquitin-Mediated Cell Cycle and DNA Repair","description":"The cluster is dominated by ubiquitination-related processes (K6-linked ubiquitination, neddylation, ubiquitin-protein transferase activity) and APC/C-dependent catabolic processes, along with positive regulation of DNA repair and apoptosis-related terms. This suggests a cohesive role in ubiquitin-driven proteostasis tied to cell cycle regulation and DNA damage response.","confidence":"High","size":17,"edges":71,"triangles":136,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043524","count":17},{"id":"GO:0006344","count":17},{"id":"GO:0031145","count":17},{"id":"GO:0043951","count":17},{"id":"GO:0085020","count":17}]},{"hash":"1802916475272945623","title":"Neural development and axon guidance","description":"The cluster centers on nervous system development and connectivity, with multiple GO terms for neuron development, axon guidance/fasciculation (sensory, dopaminergic, R8 cells), and cerebellar/retinal-related formation, coupled with integrin-mediated adhesion that supports neurite outgrowth. Regulatory signaling (PDGF receptor and non-canonical NF-kappaB) complements these themes, while oxidative-stress\u2013related terms may reflect neuroprotection. Overall, the proteins cohesively point to neural development and axon pathfinding.","confidence":"High","size":17,"edges":127,"triangles":574,"max_degree":16,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0001501","count":10},{"id":"GO:0021688","count":10},{"id":"GO:0033627","count":10},{"id":"GO:2000121","count":10},{"id":"GO:1905217","count":10}]},{"hash":"222101412428326692","title":"RNA processing and transcription regulation cluster","description":"These proteins show strong signals for RNA maturation and gene expression control: mRNA processing, tRNA processing, and spliceosome/tri-snRNP assembly, along with transcription initiation/regulation by RNA polymerase II. While there are also terms related to translation and protein degradation, the dominant themes point to RNA processing and transcriptional regulation as the core functions of this cluster.","confidence":"High","size":17,"edges":86,"triangles":207,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0006367","count":3}]},{"hash":"928702066780836518","title":"DNA replication, repair, and telomere maintenance","description":"Proteins in this cluster are dominated by DNA-centric processes: replication, base-excision repair, nucleotide-excision repair, DNA recombination, and telomere maintenance via telomerase, plus a cellular response to gamma radiation consistent with DNA damage signaling. A translation term is present but less central, supporting a core theme of genome stability and DNA metabolism.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006412","count":6},{"id":"GO:0006284","count":4},{"id":"GO:0016579","count":3},{"id":"GO:0006297","count":3}]},{"hash":"1277519286380716436","title":"Stress-Response Protein Homeostasis and Fe-S Biogenesis","description":"The cluster is enriched for protein quality control under stress (unfolded protein response, chaperone/cofactor-dependent refolding, response to heat) and iron-sulfur cluster assembly, plus oxidative stress and iron handling terms. This points to a cohesive module maintaining protein folding and Fe-S cofactor biosynthesis during stress, despite a few outliers like DNA replication terms.","confidence":"Medium","size":17,"edges":133,"triangles":637,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1900035","count":17},{"id":"GO:0006260","count":17},{"id":"GO:0090084","count":17},{"id":"GO:0031204","count":16},{"id":"GO:0070389","count":16}]},{"hash":"368372243180764634","title":"Developmental morphogenesis and intracellular trafficking","description":"The terms point to broad developmental processes (brain and skeletal development, morphogenesis, gastrulation) coupled with intracellular transport and RNA handling (retrograde Golgi\u2013ER transport, mRNA processing/transport, heterotrimerization) and mitochondria\u2013nucleus signaling. This suggests a cohesive theme around development coordinated with intracellular trafficking and RNA regulation.","confidence":"Medium","size":17,"edges":69,"triangles":136,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007420","count":15},{"id":"GO:0001501","count":14},{"id":"GO:0048705","count":14},{"id":"GO:0070208","count":14},{"id":"GO:0000348","count":14}]},{"hash":"1611422200027128940","title":"Skeletal and Brain Development","description":"This cluster is dominated by developmental terms, especially brain development, osteoblast differentiation, and skeletal system development, suggesting a core focus on neural and skeletal developmental programs. The other terms (ubiquitination, cadmium/ionizing radiation responses, B cell signaling) appear ancillary or context-dependent, not forming a single cohesive alternative theme. ","confidence":"Medium","size":17,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0010898","count":2},{"id":"GO:0001649","count":2}]},{"hash":"1206549021391641918","title":"Developmental Transcription Regulation & Chromatin Remodeling","description":"Based on the dominant GO terms, the cluster centers on transcriptional control and chromatin remodeling (DNA-templated transcription, chromatin remodeling, and negative regulation of Pol II transcription), with relevance to developmental programs (endodermal fate determination, gonad development). Peripheral terms like ER-Golgi transport and immune signaling are present but do not negate the core theme, making this label a reasonable reflection of the cluster\u2019s function.","confidence":"Medium","size":17,"edges":61,"triangles":64,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0043044","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0031134","count":3}]},{"hash":"1532881086131737938","title":"Neural development and innate immune signaling","description":"This cluster is dominated by neural development terms such as corpus callosum development, axonogenesis, and axonal fasciculation, suggesting a role in neural connectivity. It also contains innate immune and inflammatory responses (LPS signaling, response to dsRNA, defense against bacteria, interferon-beta production), implying a neuroimmune or inflammatory dimension accompanying neural development.","confidence":"Medium","size":17,"edges":28,"triangles":30,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0022038","count":10},{"id":"GO:0031663","count":10},{"id":"GO:0007409","count":10},{"id":"GO:0043330","count":10},{"id":"GO:0050830","count":10}]},{"hash":"1274711920572957877","title":"Adherens junctions and microvilli organization","description":"This cluster centers on cell\u2013cell junctions and microvilli, with GO terms for adherens junction maintenance, protein localization to cell junctions, and microvillus assembly, plus membrane signaling involving Rap/Ral/Rac pathways and PI(4,5)P2 turnover. Together these imply a cohesive theme of junctional\u2013cytoskeletal organization and membrane signaling governing cell\u2013cell contacts and microvilli.","confidence":"Medium","size":17,"edges":30,"triangles":14,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007084","count":2},{"id":"GO:0032485","count":2},{"id":"GO:0048009","count":2},{"id":"GO:1902634","count":2},{"id":"GO:1902414","count":2}]},{"hash":"23574259895131826","title":"Neural development and innervation","description":"Most frequent terms point to neural development and innervation (innervation; motor neuron apoptotic process; anterior lateral line development). A subset involves RNA regulation (RISC assembly; mRNA stabilization) that can occur in neurons, with glucose metabolism being less central. Thus label reflects the primary theme of neural development and connectivity, with supportive RNA-level regulation signals.","confidence":"Medium","size":17,"edges":23,"triangles":8,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:2000811","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0035087","count":3},{"id":"GO:0035280","count":3},{"id":"GO:0097049","count":3}]},{"hash":"1432617371616512544","title":"Wnt Signaling and Chromatin Modification","description":"This cluster is anchored by GO terms for the Wnt signaling pathway and its regulation, together with multiple histone acetylation and covalent chromatin modification terms, and transcription by RNA polymerase II. The co-occurrence of signaling and chromatin/transcription terms suggests a theme of Wnt-related control of chromatin state and gene expression, possibly reflecting proteins involved in both signaling and chromatin regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0006357","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0043981","count":2},{"id":"GO:0043983","count":2}]},{"hash":"256988643176461704","title":"Immune cell differentiation and cytokine regulation","description":"The cluster's GO terms include positive regulation of T cell differentiation in thymus, NK cell differentiation, GM-CSF production, and type II interferon production, pointing to immune cell development and cytokine signaling as a unifying theme. Some terms like regulation of Rho signaling, microvillus assembly, and hydroperoxide response appear less specific but do not override the core immune signals.","confidence":"Medium","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0071447","count":2},{"id":"GO:0033089","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1443221033877937000","title":"Regulators of signaling and gene expression","description":"This cluster shows enrichment for signaling regulation (TNF signaling, NF-kappaB regulation) alongside core gene expression processes (DNA-templated transcription, translation). Additional terms touch on vesicle trafficking and genome maintenance, suggesting a broad regulatory role across multiple cellular processes rather than a single, cohesive pathway.","confidence":"Medium","size":17,"edges":81,"triangles":180,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:2000009","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0048227","count":2},{"id":"GO:1902072","count":2}]},{"hash":"868384282859110441","title":"Transcriptional Regulation and Chromatin Remodeling","description":"This cluster centers on transcriptional control and epigenetic regulation, with GO terms for DNA-templated transcription, negative regulation of RNA Pol II transcription, chromatin remodeling, and histone demethylation, indicating a cohesive regulatory module affecting gene expression; accompanying terms related to apoptosis and development (placenta morphogenesis, spermatid differentiation) suggest roles in developmental gene regulation and cell fate decisions.","confidence":"High","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901536","count":4},{"id":"GO:0045869","count":4},{"id":"GO:0060669","count":4},{"id":"GO:0034720","count":4},{"id":"GO:0006915","count":4}]},{"hash":"100631158274611719","title":"RNA processing and transcription regulation","description":"The cluster is dominated by terms related to transcription by RNA polymerase II, splicing/prespliceosome assembly, and mRNA processing, with additional links to stress granule localization and transcription-coupled repair, indicating a cohesive role in RNA processing and transcription control, with some DNA damage response connections.","confidence":"High","size":17,"edges":93,"triangles":364,"max_degree":14,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0009432","count":13},{"id":"GO:0019079","count":12},{"id":"GO:0006283","count":12},{"id":"GO:0006265","count":12},{"id":"GO:0006363","count":12}]},{"hash":"1548522022440129128","title":"Neural development and axon guidance signaling","description":"The top GO terms heavily emphasize neural development and axon pathfinding (axial mesoderm formation and fasciculation of sensory neuron axons) along with neural function (visual learning). While a few terms touch on signaling and metabolism, the dominant theme is neural development and neural signaling. ","confidence":"High","size":17,"edges":21,"triangles":17,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":17},{"id":"GO:0048320","count":17},{"id":"GO:0097155","count":17},{"id":"GO:0032092","count":17},{"id":"GO:0008542","count":17}]},{"hash":"444949322281999899","title":"Actin-driven cell migration and neural development","description":"This cluster is enriched for actin cytoskeleton processes (lamellipodium assembly, actin filament organization) and Rho signaling, plus neural development cues (radial glia\u2013guided migration of Purkinje cells, neuroblast proliferation). The presence of Golgi organization and vesicle-targeting terms suggests trafficking tied to cytoskeleton dynamics, while hedgehog pathway regulation points to developmental signaling. Collectively, the proteins appear to coordinate cytoskeleton remodeling and cell movement with development-related signaling.","confidence":"Medium","size":17,"edges":112,"triangles":408,"max_degree":16,"top_function":"establishment or maintenance of cell polarity","top_go_terms":[{"id":"GO:0030032","count":8},{"id":"GO:0007015","count":6},{"id":"GO:0021942","count":5},{"id":"GO:0007266","count":5},{"id":"GO:0032258","count":4}]},{"hash":"573253891883006505","title":"Vesicle trafficking and lysosome/vacuole targeting","description":"The top GO terms cluster around vesicle-mediated transport, protein targeting to the lysosome and vacuole, and ubiquitin-dependent sorting via the multivesicular body pathway, plus Golgi retention. These indicate a set of proteins involved in intracellular trafficking and degradation pathways, especially delivery to lysosomes/vacuoles and Golgi processing. While there are some signaling-related terms (e.g., Toll and FGF signaling), they likely reflect regulatory connections rather than a cohesive signaling module. Therefore, this label captures the dominant functional theme.","confidence":"Medium","size":17,"edges":42,"triangles":61,"max_degree":9,"top_function":"vesicle-mediated transport","top_go_terms":[{"id":"GO:0031954","count":5},{"id":"GO:0016192","count":4},{"id":"GO:0006622","count":4},{"id":"GO:0043328","count":4},{"id":"GO:0045053","count":4}]},{"hash":"26275841318773458","title":"Ubiquitin-Driven Mitosis and ERAD","description":"This cluster centers on ubiquitin-mediated proteolysis tied to mitosis, with strong signals for K11-linked ubiquitination, APC/C-dependent catabolic processes, and metaphase/anaphase transition, suggesting a cohesive module that governs cell cycle progression and protein quality control via degradation; ERAD-related terms and steroid receptor assembly hints at broader regulatory roles, but the dominant pattern is ubiquitin-driven cell cycle control.","confidence":"High","size":17,"edges":107,"triangles":428,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":11},{"id":"GO:0030433","count":10},{"id":"GO:0051301","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0006463","count":9}]},{"hash":"51960889166349433","title":"Developmental Transcription and Signaling","description":"The GO terms cluster around DNA-templated transcription and transcription regulation (RNA Pol I), TOR signaling, and wing disc morphogenesis, together pointing to a module that links transcriptional control with growth signaling and developmental patterning, particularly in a tissue-specific context. Some terms like lactation and late viral transcription appear as noise, but the core theme remains transcription-regulation intertwined with signaling and development. Medium","confidence":"","size":17,"edges":81,"triangles":179,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0097202","count":3},{"id":"GO:0035308","count":2},{"id":"GO:0045943","count":2},{"id":"GO:0009966","count":2}]},{"hash":"744535231137055038","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster is enriched for maturation of LSU and SSU rRNA, ribosome biogenesis, and export of the large ribosomal subunit from the nucleus, pointing to a cohesive module of ribosome assembly and rRNA maturation. Other GO terms such as DNA-templated transcription and mitotic cell cycle are supplementary and not central to the primary function inferred. Overall, the shared theme is the production and maturation of ribosomes.","confidence":"High","size":17,"edges":133,"triangles":636,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":6},{"id":"GO:0000466","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000055","count":4},{"id":"GO:0000462","count":3}]},{"hash":"928219290007405149","title":"Neural development and axon guidance","description":"The top GO terms cluster around neural development and neurite formation, including CNS projection neuron axonogenesis, dendrite morphogenesis, hippocampus and corpus callosum development, and ephrin receptor signaling (a key axon guidance pathway). ERK signaling modulation and peptidyl-serine phosphorylation further support neural differentiation and neurite maturation; a few terms about early embryonic tissues (e.g., axial mesoderm) reflect development context but the dominant signal is neural development and axonogenesis.","confidence":"High","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":12},{"id":"GO:0048013","count":12},{"id":"GO:0048320","count":11},{"id":"GO:0021952","count":11},{"id":"GO:0070374","count":11}]},{"hash":"642511894036026737","title":"Axon guidance and synapse development","description":"This cluster is dominated by neural connectivity terms: retinal ganglion cell axon guidance, axonal fasciculation, corpus callosum development, and regulation of synapse assembly, pointing to axon pathfinding and synapse formation as the core theme. Some non-neural terms are present (lipid biosynthesis, cell cycle), but they are less representative of the cluster\u2019s main signal.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048681","count":3},{"id":"GO:0007413","count":3},{"id":"GO:0022038","count":3},{"id":"GO:0051965","count":3},{"id":"GO:2000525","count":2}]},{"hash":"1411695923701675506","title":"Antiviral innate immunity and cell cycle control","description":"This cluster\u2019s top GO terms emphasize innate antiviral defense (defense response to virus, cellular response to interferon-alpha, innate immune response) and autophagy, along with centrosome maintenance and mitotic cell cycle terms. Together these suggest a group of proteins that interface antiviral signaling with cell division regulation, despite some outliers. ","confidence":"Medium","size":17,"edges":55,"triangles":67,"max_degree":11,"top_function":"autophagy","top_go_terms":[{"id":"GO:0048496","count":5},{"id":"GO:0051661","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0008584","count":4},{"id":"GO:0009736","count":4}]},{"hash":"1920025600549326327","title":"Complement-Coagulation and Vascular Signaling","description":"The terms point to activation of complement pathways (lectin and classical) and coagulation (Factor XII), with additional signals tied to angiogenesis and vascular regulation (ANP), plus immune signaling (Toll) and developmental pathways (Wnt) that often intersect inflammation and blood vessel biology. This suggests a cluster of proteins coordinating innate immunity and coagulation with vascular signaling.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001867","count":7},{"id":"GO:0006958","count":7},{"id":"GO:0007596","count":6},{"id":"GO:0003050","count":6},{"id":"GO:0045766","count":6}]},{"hash":"742981470078355898","title":"Ubiquitin-regulated transcription and chromatin modification","description":"The Top Terms include DNA-templated transcription, ubiquitin-dependent protein catabolic process, histone methylation, and deubiquitination-related activities, all pointing to control of gene expression through chromatin remodeling and ubiquitin-mediated protein turnover. While virus defense and neural migration terms are present, the core signal centers on transcriptional regulation via ubiquitin signaling and chromatin modification. ","confidence":"High","size":17,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0042787","count":6},{"id":"GO:0034729","count":5},{"id":"GO:0051568","count":5},{"id":"GO:0006511","count":5}]},{"hash":"1425623984919309701","title":"Interferon-driven innate antiviral response","description":"The terms are dominated by innate immunity and antiviral signaling, including cellular responses to interferon-alpha and type I interferon, and defense against virus, indicating a clear IFN-mediated innate defense theme. Some cell cycle and ER stress-related terms appear but are likely ancillary to the primary antiviral signaling. ","confidence":"High","size":17,"edges":8,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0000278","count":6},{"id":"GO:1905515","count":5},{"id":"GO:1903071","count":5},{"id":"GO:0035457","count":5}]},{"hash":"1074165931500058800","title":"DNA replication and RNA processing factors","description":"This cluster centers on nucleic acid metabolism, dominated by DNA replication terms (DNA replication, replication primer synthesis, DNA unwinding) and cell division, with additional RNA processing pathways (transcription-coupled repair, RNAP I termination, prespliceosome assembly, rRNA catabolic process). The presence of viral genome replication hints at shared replication machinery features; overall, the proteins appear to participate in replication-dominated processes with concurrent RNA processing/degradation roles.","confidence":"Medium","size":17,"edges":115,"triangles":440,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0019079","count":6},{"id":"GO:0006269","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0051301","count":5}]},{"hash":"1355361001104633541","title":"IL-27\u2013driven T cell activation and STAT signaling","description":"The top GO terms cluster around IL-27\u2013mediated signaling, Th2 cytokine production, and positive regulation of T cell costimulation, all pointing to immune cytokine signaling and T cell activation via STAT/JAK pathways. While there are a few development-related terms (axial mesoderm formation, axon guidance), the dominant pattern is IL-27\u2013related immune signaling and T cell activation, supported by strong representation of STAT phosphorylation. ","confidence":"High","size":17,"edges":22,"triangles":8,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042517","count":12},{"id":"GO:0070106","count":11},{"id":"GO:0001525","count":11},{"id":"GO:0035745","count":11},{"id":"GO:2000525","count":10}]},{"hash":"1982119374159787860","title":"Developmental Transcriptional Regulation","description":"The cluster centers on transcriptional regulation (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) and development-related processes (myotube development, ureteric bud morphogenesis, pregnancy, respiratory system), with a nod to circadian gene expression. This suggests a cohesive theme of transcription control during organ development and related processes, though the set spans multiple systems.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0032922","count":2},{"id":"GO:0007565","count":2},{"id":"GO:0070294","count":2}]},{"hash":"2076424133932178985","title":"Rho GTPase-driven actin remodeling and endocytosis","description":"This cluster is enriched for terms tied to Rho/Rac GTPase signaling, actin filament organization, and endocytosis, along with membrane remodeling (plasma membrane tubulation). The inclusion of positive regulation of GTPase activity and autophagy/cell-cycle terms suggests a broader link between cytoskeletal dynamics, vesicle trafficking, and growth-related processes. ","confidence":"High","size":17,"edges":35,"triangles":20,"max_degree":10,"top_function":"autophagy","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0035021","count":3},{"id":"GO:1900740","count":3},{"id":"GO:0007015","count":3},{"id":"GO:0043547","count":3}]},{"hash":"601283320471687796","title":"Cytoskeletal remodeling and intracellular trafficking","description":"This cluster centers on actin dynamics (positive regulation of Arp2/3 nucleation, actin cortical patch assembly) and organelle/vesicle movement or sorting (mitochondria distribution, Golgi retention, LDL particle clearance), suggesting coordinated cytoskeletal remodeling with trafficking roles. The cell division and tyrosine phosphorylation themes may reflect signaling linked to cytoskeletal changes during growth and division, reinforcing the trafficking/remodeling theme. ","confidence":"Medium","size":17,"edges":14,"triangles":2,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0045053","count":3},{"id":"GO:0048312","count":3},{"id":"GO:0050731","count":3}]},{"hash":"976647690190423769","title":"Keratinization and multi-tissue morphogenesis","description":"The top terms emphasize keratinization, keratinocyte migration, and hair follicle morphogenesis, with additional development-focused terms such as lens fiber cell development, Bergmann glial differentiation, and cardiac and hepatic development. This suggests a cluster of proteins involved in tissue differentiation and morphogenesis across multiple lineages, anchored by skin-related processes but extending to other organ systems. ","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":17},{"id":"GO:0014012","count":17},{"id":"GO:0031069","count":17},{"id":"GO:1904714","count":17},{"id":"GO:0055015","count":17}]},{"hash":"1643988547615888908","title":"Clathrin-mediated vesicle trafficking and GTPase signaling","description":"This cluster centers on clathrin-dependent endocytosis and synaptic vesicle dynamics (coating, budding) with intracellular transport, plus regulation of small GTPases (Rac) and related signaling, hinting at coordinated vesicle trafficking and cytoskeletal remodeling. The presence of PI(4,5)P2 biosynthesis regulation and cell migration terms supports connections to membrane trafficking and actin dynamics.","confidence":"High","size":17,"edges":38,"triangles":85,"max_degree":9,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":5},{"id":"GO:0072583","count":5},{"id":"GO:0016183","count":5},{"id":"GO:0043547","count":5},{"id":"GO:1990386","count":4}]},{"hash":"1034443523130296060","title":"Rho/Rac-regulated actin dynamics and migration","description":"The top GO terms converge on Rho/Rac GTPase signaling, lamellipodium/microspike assembly, actin crosslinking, and cell migration, pointing to an actin cytoskeleton remodeling module driving movement. Some terms about thymus development and interleukin-7 response may reflect immune-related roles, but the core theme is actin-mediated motility regulated by Rho family GTPases.","confidence":"High","size":17,"edges":52,"triangles":115,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0030032","count":2},{"id":"GO:0035021","count":2},{"id":"GO:0048538","count":2},{"id":"GO:0016477","count":2}]},{"hash":"458110213024325640","title":"Eye development and lens differentiation","description":"The dominant GO terms are centered on the visual system and eye structures (visual perception, camera-type eye development, lens fiber cell differentiation, and eye development), suggesting the cluster primarily relates to ocular development and lens biology; other terms like heart development/angiogenesis are less specific to this cluster.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0090190","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0001525","count":3}]},{"hash":"709372979756169682","title":"Neural development and dopaminergic signaling","description":"The terms mainly reflect neural development: regulation of neuron maturation, nerve branching morphogenesis, and neuronal tangential migration to the olfactory bulb. They also include dopaminergic signaling components (cellular response to dopamine, positive regulation of dopamine receptor signaling) and actin cytoskeleton remodeling (actin filament severing), which are key for neuron differentiation and growth. A few innate-immune terms (TLR1 signaling, detection of bacterial lipopeptide) appear but seem less central to the core cluster. Overall, the shared theme appears to be neural development with dopaminergic signaling and cytoskeletal dynamics.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035751","count":3},{"id":"GO:2000172","count":3},{"id":"GO:0014041","count":3},{"id":"GO:0070340","count":3},{"id":"GO:0035564","count":3}]},{"hash":"656448055167777363","title":"Rho-dependent cytoskeleton remodeling and adhesion signaling","description":"The cluster is dominated by GO terms for Rho signal regulation, stress fiber and actin cytoskeleton dynamics, and integrin/podosome\u2013mediated adhesion, pointing to a cohesive theme of cytoskeletal remodeling coupled with cell\u2013matrix signaling. Growth factor and T cell signaling terms are also present but secondary to cytoskeletal regulation.","confidence":"High","size":17,"edges":120,"triangles":487,"max_degree":16,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0035023","count":17},{"id":"GO:0071560","count":17},{"id":"GO:0051492","count":17},{"id":"GO:0007229","count":17},{"id":"GO:0042518","count":17}]},{"hash":"87035618495323676","title":"Spermatogenesis and germline stem cell regulation","description":"The top terms point to male germline development and meiosis, including seminiferous tubule development, male meiosis I, and asymmetric division of male germ-line stem cells, with supporting signals from DNA damage response and apoptosis pathways, suggesting a cluster centered on spermatogenesis and germline maintenance.","confidence":"High","size":17,"edges":96,"triangles":288,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0030511","count":4},{"id":"GO:0072520","count":4},{"id":"GO:0007141","count":4},{"id":"GO:0048133","count":4},{"id":"GO:0006978","count":4}]},{"hash":"1797844751567763531","title":"Insect Development and Hormone Signaling","description":"The cluster includes terms tied to developmental patterning (gonad morphogenesis, axis specification, epithelial\u2013mesenchymal transitions in heart-related formation) and hormone-mediated responses (ecdysone signaling), plus transcriptional regulation and related behaviors, suggesting proteins involved in insect development coordinated by hormonal signaling. The set is coherent but diverse across development and behavior, so confidence is Medium.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061040","count":3},{"id":"GO:0007352","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0006351","count":2}]},{"hash":"401050089688768074","title":"Embryonic Development and Tissue Morphogenesis","description":"The top GO terms cluster around broad embryonic development and organ/tissue morphogenesis, including endocrine and placental development, left-right patterning, cartilage and palate formation, hair follicle morphogenesis, and EMT-related heart development. This suggests the proteins are involved in early developmental programs across multiple tissues, rather than a single specific pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":15},{"id":"GO:0060806","count":15},{"id":"GO:0060972","count":15},{"id":"GO:0060536","count":15},{"id":"GO:0060021","count":15}]},{"hash":"78233499742603976","title":"Spindle Assembly and Cytokinesis","description":"The top GO terms point to mitotic/meiotic spindle dynamics (meiotic spindle disassembly; chromosome passenger complex localization to spindle midzone) and cytokinesis-related processes (actomyosin contractile ring maturation; septation initiation signaling), suggesting a cohesive theme around cell division machinery and its regulation. Some terms regarding stress response and apoptosis appear tangential, but the core cluster centers on spindle function and division-related contractile structures.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0071470","count":17},{"id":"GO:2000808","count":17},{"id":"GO:0051229","count":17},{"id":"GO:0035853","count":17},{"id":"GO:1902310","count":17}]},{"hash":"2148648899378527240","title":"Mitochondrial protein import and calcium regulation","description":"The dominant terms describe mitochondrial biogenesis: complex IV assembly, protein import into the mitochondrial matrix, protein folding, and regulation of mitochondrial calcium concentration, pointing to a cohesive mitochondrial function with calcium homeostasis. The vascular/development terms are likely incidental.","confidence":"High","size":17,"edges":64,"triangles":94,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":4},{"id":"GO:0006457","count":2},{"id":"GO:0036444","count":2},{"id":"GO:0051561","count":2},{"id":"GO:0030150","count":2}]},{"hash":"68099616651160865","title":"Ribosome and Translation Machinery","description":"The top GO terms are dominated by translation-related processes (translation; cytoplasmic translation; ribosomal large subunit assembly), indicating proteins primarily involved in protein synthesis and ribosome assembly. A few other terms (apoptotic process, oogenesis, cell differentiation) occur at low frequencies and likely reflect secondary or context-dependent roles. Overall, the cluster is best described as components of the protein synthesis machinery.","confidence":"High","size":17,"edges":45,"triangles":46,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0000027","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0043066","count":1},{"id":"GO:0030154","count":1}]},{"hash":"1873108255924929941","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000070","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1346217065041340436","title":"Craniofacial skeletal development and ECM remodeling","description":"The terms are dominated by embryonic craniofacial morphogenesis, endochondral ossification, face morphogenesis, and collagen fibril organization, with proteolysis and mechanotransduction indicating extracellular matrix remodeling. Wound healing and EGFR signaling further support coordinated tissue growth and remodeling during craniofacial development. Altogether, the cluster likely centers on craniofacial skeletal formation and ECM-driven morphogenesis.","confidence":"High","size":17,"edges":108,"triangles":344,"max_degree":15,"top_function":"wound healing","top_go_terms":[{"id":"GO:0071260","count":14},{"id":"GO:0006508","count":13},{"id":"GO:0001958","count":13},{"id":"GO:0035987","count":13},{"id":"GO:0048701","count":13}]},{"hash":"2090968844652306297","title":"Axon guidance and neural crest migration","description":"Top terms point to neuronal development and wiring: semaphorin-plexin signaling in axon guidance, sympathetic and branchiomotor neuron projection extension/guidance, and ventral trunk neural crest cell migration, with associated cell adhesion. Collectively these indicate a cohesive function in directing neuronal axons and neural crest-derived cells during development, with some apoptotic process terms likely related to developmental remodeling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0035640","count":5},{"id":"GO:0006915","count":4},{"id":"GO:0097490","count":4},{"id":"GO:0021785","count":4},{"id":"GO:0043277","count":4}]},{"hash":"180891395062320754","title":"Keratinocyte and Hair Follicle Development","description":"The cluster is dominated by epithelial differentiation processes: keratinization, hair follicle morphogenesis, and keratinocyte migration. These skin- and hair-related GO terms are the most represented, suggesting a shared role in epidermal development, despite a few other tissue-development terms present.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":17},{"id":"GO:0014012","count":17},{"id":"GO:0031069","count":17},{"id":"GO:1904714","count":17},{"id":"GO:0055015","count":17}]},{"hash":"1793887383777738837","title":"Neural development and cadherin-mediated adhesion","description":"This cluster is driven by strong enrichment for nervous system development, neuron cell\u2013cell adhesion, and synapse assembly, with emphasis on cadherin-mediated adhesion (homophilic/heterophilic). While there are some broader developmental terms (ossification, nephron development), the neural development and adhesion terms dominate, suggesting a cohesive role in neural connectivity and synapse organization.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":11},{"id":"GO:0007156","count":11},{"id":"GO:0051965","count":11},{"id":"GO:0007157","count":10},{"id":"GO:0007158","count":9}]},{"hash":"331580097468761525","title":"Neural development and dopamine metabolism","description":"The cluster shows a core signal around neural precursor cell proliferation and dopamine metabolic processes, pointing to neurodevelopment and neurotransmitter regulation. Supportive terms include tetrahydrofolate and thiamine biosynthesis (essential cofactors for neural metabolism) and stress/response terms (xenobiotic, lipopolysaccharide, cold), suggesting accompanying metabolic and stress-related contexts. Overall, the dominant theme appears to be neural development linked to dopamine metabolism, with metabolic and stress-response processes acting as broader contextual support.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046653","count":5},{"id":"GO:0009228","count":5},{"id":"GO:2000179","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0032496","count":4}]},{"hash":"2251134253808792560","title":"Unknown","description":"The GO terms are highly diverse and span pancreatic cell differentiation, calcium transport, bleb assembly, integrin signaling, bone mineralization, visual perception, blood coagulation, and monocyte chemotaxis. There isn\u2019t a single dominant biological process tying these proteins together, making it unclear what cohesive function the cluster represents. Unknown; no clear theme detected.","confidence":"","size":17,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090104","count":2},{"id":"GO:2000227","count":2},{"id":"GO:2000077","count":2},{"id":"GO:0007601","count":2},{"id":"GO:2001046","count":2}]},{"hash":"1186100393014279031","title":"Innate Immune Chemotaxis and Inflammatory Signaling","description":"Based on the dominant GO terms, this cluster centers on recruitment of immune cells (neutrophil and monocyte chemotaxis), receptor internalization, and inflammatory signaling (calcium-mediated signaling and TNF production). While there are a few RNA silencing-related terms present, these appear peripheral to the main inflammatory/chemotactic theme, making Innate Immune Chemotaxis and Inflammatory Signaling a concise, representative label.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031623","count":3},{"id":"GO:0050850","count":3},{"id":"GO:0030593","count":3},{"id":"GO:0032760","count":3},{"id":"GO:0031047","count":2}]},{"hash":"449455700602544156","title":"Neural development and immune regulation cluster","description":"The top terms converge on nervous system development, synapse assembly, and angiogenesis, pointing to neural development and connectivity. They are accompanied by immune-regulatory terms (macrophage, NK, and T cell activity) and cytoskeleton/cell-adhesion regulation, suggesting a theme where neural development processes intertwine with immune signaling and cytoskeletal dynamics. This combination supports a cohesive label centered on neural development with immune modulation.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0032516","count":11},{"id":"GO:0001525","count":11},{"id":"GO:0001501","count":11},{"id":"GO:0051963","count":11},{"id":"GO:0043031","count":11}]},{"hash":"993877881393287388","title":"Neural development and synaptic signaling","description":"This cluster centers on neural development and synaptic communication, as indicated by retinal ganglion cell axon guidance, regulation of ephrin receptor signaling, and positive regulation of synaptic plasticity via receptor localization to synapse. Ubiquitination/ERAD terms suggest regulation of signaling components, while axial mesoderm formation points to early developmental processes that shape neural structures. Vitamin D response and lipid biosynthesis may contribute to broader regulatory or membrane-related roles, but the core theme is neural development and synaptic signaling.","confidence":"Medium","size":17,"edges":22,"triangles":10,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0016567","count":3},{"id":"GO:1900383","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1024726714872833139","title":"Proteoglycan and glycosaminoglycan biosynthesis","description":"The top GO terms point to proteoglycan and glycosaminoglycan biosynthesis (chondroitin sulfate, heparan sulfate, heparin proteoglycan) and related carbohydrate metabolism (N-acetylglucosamine, sulfate assimilation, sulfation). This suggests a shared function in assembling sulfated glycosaminoglycans on proteoglycans. Some terms such as catecholamine metabolic process and regulation of angiotensin levels are present but appear less central to the core theme. Overall, the dominant signal is proteoglycan/glycosaminoglycan biosynthesis.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030206","count":4},{"id":"GO:0015015","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0009090","count":3},{"id":"GO:0009088","count":3}]},{"hash":"1284984221772725540","title":"Ciliary Assembly and Hedgehog Signaling","description":"Two terms clearly point to ciliary biology (non-motile cilium assembly; smoothened signaling pathway), suggesting a possible ciliary/hedgehog signaling theme. However, the other terms span metal ion transport, dephosphorylation, amino acid biosynthesis, and metabolism, indicating a rather heterogeneous set. This provides a plausible but partial signal, so the label is best kept with medium confidence.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905515","count":1},{"id":"GO:0007224","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0071577","count":1}]},{"hash":"652505999786823863","title":"RNA Pol II Transcription Regulation","description":"Based on the top GO terms, the proteins cluster around transcriptional processes driven by RNA polymerase II, including DNA-templated transcription and negative regulation of transcription by RNA Pol II. Although several terms are obsolete, the recurring theme is transcription regulation via RNA Pol II, with at least one term pointing to regulation of transcription during the mitotic cell cycle. Together, these suggest a functional grouping of factors involved in transcription control rather than, for example, signaling or metabolism.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007576","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0010729","count":1},{"id":"GO:0070895","count":1},{"id":"GO:0046022","count":1}]},{"hash":"1061984674407444264","title":"Immune response modulation","description":"Based on multiple immune-related GO terms (mast cell degranulation, complement activation, macrophage activation regulation, CD8+ T cell apoptosis, IL-10 production, tumor cell detection), the cluster appears to group proteins involved in immune signaling and regulation, despite a few development-related terms present. This core theme justifies the label, though some annotation noise may exist.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043303","count":5},{"id":"GO:0035018","count":4},{"id":"GO:1902414","count":4},{"id":"GO:0002089","count":4},{"id":"GO:1905404","count":4}]},{"hash":"54140409659507619","title":"Viral genome integration and proviral latency","description":"This cluster\u2019s GO terms cluster around viral entry into host cells, nuclear penetration, DNA recombination and integration, RNA-templated DNA biosynthesis (reverse transcription), and establishment of integrated proviral latency, all pointing to retroviral-like genome integration and latency maintenance alongside host apoptosis modulation. The theme is coherent despite one obsolete term, suggesting a retroviral integration/latency function.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":1},{"id":"GO:0075732","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0075713","count":1},{"id":"GO:1903704","count":1}]},{"hash":"2145736006551975031","title":"Cytoskeleton remodeling and cell adhesion signaling","description":"The cluster top terms point to cytoskeletal dynamics (lamellipodium assembly, microtubule anchoring) and cell\u2013cell/cell\u2013matrix adhesion (zonula adherens, epithelial adhesion, integrin signaling, Rho signaling), with several migration-related terms (neutrophil chemotaxis, neuron projection development). This suggests proteins coordinating cytoskeletal remodeling with adhesion and signaling at interfaces. A few terms are peripheral to adhesion (e.g., B cell signaling), but overall the theme is cohesive around cytoskeleton and adhesion processes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031175","count":3},{"id":"GO:0034453","count":2},{"id":"GO:0030593","count":2},{"id":"GO:0045218","count":2},{"id":"GO:0043552","count":2}]},{"hash":"444846073432011149","title":"Retinoic Acid Signaling in Organ and Neural Morphogenesis","description":"The top GO terms cluster around retinoic acid receptor signaling and broad morphogenesis across multiple organs and neural structures (heart morphogenesis, inner ear morphogenesis, nucleus accumbens development, ureter maturation, righting reflex). This suggests a cohesive developmental program guided by retinoic acid signaling affecting organ formation and brain/neuronal development, with supportive endothelial proliferation regulation tying into developmental angiogenesis.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0048384","count":16},{"id":"GO:0060013","count":16},{"id":"GO:0001936","count":16},{"id":"GO:0032180","count":16},{"id":"GO:0009258","count":16}]},{"hash":"1517264208847324413","title":"Developmental morphogenesis and signaling","description":"This cluster is enriched for terms tied to tissue and organ development (olfactory placode/nerve formation, pollen tube growth), and includes signaling pathway terms (Smoothened). Additional terms on glycosylation and metabolism suggest protein maturation linked to developmental processes, supporting a shared theme of morphogenesis and signaling across systems.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071699","count":3},{"id":"GO:0021628","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0007224","count":2}]},{"hash":"1902957750643624639","title":"Immune Regulation and Cell Adhesion","description":"Most terms point to immune signaling and regulation, e.g., negative regulation of macrophage activation, regulation of T cell proliferation, and IL-10 production, along with heterophilic cell-cell adhesion and localization to cell junctions. This suggests proteins functioning at immune interfaces where cells interact and modulate activation states. A few terms (lens morphogenesis, spermatid development) are less clearly connected and may reflect annotation noise or broader structural roles, but the core theme appears to be immune modulation at cell junctions.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043031","count":10},{"id":"GO:0007157","count":10},{"id":"GO:1902414","count":9},{"id":"GO:0002089","count":9},{"id":"GO:1905404","count":9}]},{"hash":"842509115327816096","title":"Cortical neuron migration and synaptic vesicle trafficking","description":"The top GO terms point to cortical neuron development (radial glia-guided migration and reelin signaling) and synaptic vesicle functions (exocytosis, priming), suggesting a cohesive theme around neuronal maturation and synaptic machinery, with some membrane and remodeling aspects also present.","confidence":"High","size":17,"edges":7,"triangles":4,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0021814","count":17},{"id":"GO:0007520","count":17},{"id":"GO:0002692","count":17},{"id":"GO:2000300","count":17},{"id":"GO:0099526","count":17}]},{"hash":"1141230246379511301","title":"Plant secondary metabolism and detoxification","description":"The GO terms point to broad metabolic processing, including cellular oxidant detoxification, alkaloid and antibiotic biosynthesis, beta-ketoadipate aromatic compound catabolism, PHB biosynthesis, uracil catabolism, and a plant development term (secondary shoot formation). Although the proteins lack network connectivity, the shared theme is involvement in detoxification and diverse secondary/metabolic pathways typical of plant metabolism. Therefore the label captures a representative function of the cluster without overstretching to a single pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:2000124","count":2},{"id":"GO:0042952","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0010223","count":2}]},{"hash":"475365093861860881","title":"Mixed neural, immune, and membrane signaling","description":"The terms include neural-related processes (myelination, sensory perception of sound, regulation of neuronal synaptic plasticity), immune signaling (B cell receptor signaling, B cell differentiation), endothelial barrier establishment, apoptotic signaling, and membrane organization (eisosome assembly, membrane raft polarization), as well as signaling modulation (negative regulation of PKC). This combination points to a cluster driven by broad, membrane-associated signaling roles across multiple systems rather than a single, cohesive function. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042552","count":3},{"id":"GO:0061028","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0050861","count":2},{"id":"GO:0090038","count":2}]},{"hash":"2097369789943247368","title":"Epithelial Secretory Trafficking","description":"The cluster centers on vesicle trafficking, membrane localization and secretion in epithelial contexts: protein transport, calcium-dependent exocytosis, and transepithelial chloride transport, with palmitoylation linking to membrane-associated secretory machinery. Vacuole fusion supports vesicle dynamics, while sebaceous gland development hints at skin-specific secretory functions. Visual perception terms are present but appear exploratory; overall, the theme is epithelial secretion and transport.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":3},{"id":"GO:0018230","count":3},{"id":"GO:0048733","count":3},{"id":"GO:0015031","count":2},{"id":"GO:0030321","count":1}]},{"hash":"810031979460487590","title":"Glycan processing and glycosphingolipid biosynthesis","description":"The top GO terms are dominated by glycosylation and glycosphingolipid pathways (N-glycan processing, N-linked glycosylation, oligosaccharide metabolism, glycosylceramide metabolism, ganglioside biosynthesis, and sialic acid-related metabolism). While a few pollen-related terms appear, the common thread across the cluster is glycans and glycosphingolipids, suggesting a cohesive focus on glycan processing and glycosphingolipid biosynthesis.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006054","count":4},{"id":"GO:0006491","count":4},{"id":"GO:0009860","count":4},{"id":"GO:0009846","count":4},{"id":"GO:0021628","count":4}]},{"hash":"1889110589445306277","title":"Embryonic development and organ morphogenesis","description":"The top GO terms cluster around developmental programs such as placental/trophoblast differentiation, endocrine system development, left-right patterning, and cardiac EMT/morphogenesis, pointing to a role in embryonic organogenesis rather than a single specific process.","confidence":"High","size":17,"edges":9,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007576","count":17},{"id":"GO:0060707","count":17},{"id":"GO:0006351","count":17},{"id":"GO:0060536","count":17},{"id":"GO:0060806","count":17}]},{"hash":"571489524719105557","title":"Membrane raft\u2013dependent signaling in neurons and B cells","description":"The cluster centers on membrane microdomain organization and signaling, with GO terms spanning neural functions (myelination, synaptic plasticity, sound perception) and immune processes (B cell receptor signaling, B-1a differentiation), plus membrane-raft/eisososome\u2013related terms and PKC signaling regulation. This suggests proteins that function in signaling modulated by lipid rafts or eisosomes across neural and immune cell contexts.","confidence":"Medium","size":17,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042552","count":6},{"id":"GO:0061028","count":4},{"id":"GO:0007605","count":4},{"id":"GO:0050861","count":4},{"id":"GO:0090038","count":4}]},{"hash":"1495068065578189770","title":"Membrane organization and signaling","description":"This cluster centers on membrane-associated processes: tight junction assembly and endothelial barrier establishment point to cell\u2013cell junctions, while membrane raft polarization and eisosome assembly reflect membrane domain organization; the included signaling terms (PKC regulation, B cell receptor signaling, extrinsic apoptotic signaling) suggest a shared theme of membrane-driven signal transduction across cell types, even though several terms point to tissue-specific roles like auditory perception and neuronal plasticity.","confidence":"Medium","size":17,"edges":28,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070830","count":5},{"id":"GO:0061028","count":4},{"id":"GO:0007605","count":4},{"id":"GO:0050861","count":4},{"id":"GO:0090038","count":4}]},{"hash":"1532203491913130626","title":"Immune Activation and Adhesion","description":"This cluster\u2019s top GO terms center on innate immune signaling and leukocyte behavior: regulation of macrophage activation, dendritic cell differentiation, monocyte chemotaxis, and heterophilic cell-cell adhesion, pointing to immune cell recruitment and activation. The presence of symbiont entry into host cell reinforces host-pathogen interaction context. Some terms (cuticle pattern formation, skeletal development) seem unrelated outliers, likely annotation spillover. Overall, the dominant theme is immune regulation and cell interactions.","confidence":"Medium","size":17,"edges":40,"triangles":50,"max_degree":10,"top_function":"establishment or maintenance of cell polarity","top_go_terms":[{"id":"GO:0035018","count":7},{"id":"GO:0051963","count":7},{"id":"GO:0043031","count":7},{"id":"GO:0071639","count":7},{"id":"GO:2001200","count":7}]},{"hash":"2099334834906073041","title":"GPCR Signaling Across Immune and Neural Processes","description":"The cluster centers on GPCR signaling (GO:0007186) and includes immune-related pathways (Fc-epsilon receptor signaling; dendritic cell differentiation) as well as neural-associated processes (synaptic vesicle endocytosis, visual perception). It also touches on broader cellular response themes (autophagy regulation, p53-mediated apoptotic signaling). This combination suggests a broad signaling network that links immune, neural, and stress-response functions.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001199","count":2},{"id":"GO:0038095","count":2},{"id":"GO:0019236","count":2},{"id":"GO:0007186","count":2},{"id":"GO:0048488","count":1}]},{"hash":"734903996798087563","title":"Xenobiotic response and redox metabolism","description":"This cluster is dominated by GO terms related to sensing and processing foreign compounds (response to xenobiotic stimulus, camphor catabolic process, LPS response) and maintaining redox balance (redox homeostasis, oxidation-reduction). Capsule biosynthesis also points to a bacterial metabolic/defense context. A couple of terms (gastrulation, spliceosome-related splicing, histone methylation) are outliers and may reflect annotation noise, but the core signal supports a xenobiotic response with redox metabolism theme.","confidence":"Medium","size":17,"edges":20,"triangles":21,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0019383","count":10},{"id":"GO:0042493","count":9},{"id":"GO:0007369","count":9},{"id":"GO:0045454","count":9}]},{"hash":"1270484049817711576","title":"Neuronal signaling and synaptic plasticity","description":"The Top Terms show strong enrichment for brain-related processes: substantia nigra development, long-term memory, regulation of long-term neuronal synaptic plasticity, activation of adenylate cyclase activity (cAMP signaling), and modulation of PKC signaling. Together they point to neuronal signaling pathways and plasticity mechanisms underlying memory and brain development. Some terms (cardiac hypertrophy, B cell signaling, eisosome, endothelial barrier) are peripheral or reflect pleiotropy, but the dominant theme is neuronal signaling and plasticity.","confidence":"High","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":4},{"id":"GO:1903244","count":3},{"id":"GO:0007616","count":3},{"id":"GO:0007190","count":3},{"id":"GO:0061028","count":2}]},{"hash":"1101120222308675315","title":"Membrane Transport and Secretion","description":"The cluster centers on various transmembrane transport processes (xenobiotic, chloride, amino acids, phospholipids) and secretion-related activities (Type I secretion system), with supporting terms related to membrane potential and pH regulation. This suggests a cohesive theme of membrane-associated transport and secretory functions across substrates and contexts.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:0045332","count":4},{"id":"GO:1902476","count":4},{"id":"GO:0060081","count":4},{"id":"GO:0030253","count":3}]},{"hash":"902105865924015129","title":"Neuronal synaptic transmission and myelination","description":"This cluster centers on neuronal function, with key GO terms for excitatory postsynaptic potentials, action potential propagation, and regulation of synaptic plasticity, plus myelination and membrane hyperpolarization. Additional terms on endosomal trafficking and transport across the blood-nerve barrier support a nerve-specific signaling/insulation theme, though a few outliers (e.g., bone resorption) are present. Overall, it represents neuronal signaling and myelin-related processes.","confidence":"High","size":17,"edges":134,"triangles":651,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0070830","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0048169","count":2},{"id":"GO:0042552","count":2},{"id":"GO:0060081","count":2}]},{"hash":"1175680536922602526","title":"Immune cell adhesion and synapse regulation","description":"The top terms cluster around cell\u2013cell adhesion and immune synapse formation, including regulation of actin cytoskeleton during adhesion, and negative regulation of NK/T cell functions and macrophage activation, suggesting a theme of immune cell communication and signaling via adhesion. Some outliers like symbiont entry and cuticle pattern formation are present but don\u2019t override the main immune-adhesion signal.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051963","count":12},{"id":"GO:0046718","count":12},{"id":"GO:0002859","count":12},{"id":"GO:0090138","count":12},{"id":"GO:0043318","count":12}]},{"hash":"2100118876560709656","title":"Neuroimmune modulation and dopaminergic signaling","description":"The terms cluster around immune responses and inflammatory regulation, glial cell activity (astrocyte chemotaxis, neurotrophic factor production), xenobiotic response, and dopaminergic processes (dopamine transport and metabolism). This points to a theme of neuroimmune interactions influencing dopamine signaling and related behaviors (e.g., grooming), likely involving glial-neuronal regulation.","confidence":"High","size":17,"edges":59,"triangles":83,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007625","count":15},{"id":"GO:0050728","count":14},{"id":"GO:0042493","count":14},{"id":"GO:2000458","count":14},{"id":"GO:1900168","count":14}]},{"hash":"1668164097059540367","title":"Neuroimmune signaling and glial chemotaxis","description":"This cluster is dominated by terms linking nervous system signaling with immune and glial cell activity, including positive regulation of astrocyte chemotaxis, glial-derived neurotrophic factor production, eosinophil chemotaxis, and immune/inflammatory regulation. The combination suggests neuroimmune cross-talk centered on glial cells, with supporting GPCR/Rho signaling and xenobiotic/metabolic context. Overall, the theme points to neuroinflammation and glial signaling rather than pure metabolism or isolated immune response.","confidence":"Medium","size":17,"edges":89,"triangles":207,"max_degree":15,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0035025","count":14},{"id":"GO:0022900","count":14},{"id":"GO:0045777","count":14},{"id":"GO:0010579","count":14},{"id":"GO:0050728","count":13}]},{"hash":"501642529887338743","title":"Neuroimmune Dopamine Signaling and Glial Regulation","description":"These terms cluster around dopaminergic signaling (dopamine transport, dopamine metabolism, dopamine receptor\u2013related pathways), glial involvement (astrocyte chemotaxis, glial-derived neurotrophic factor production), and neuroimmune modulation (immune response, negative regulation of inflammatory response, eosinophil chemotaxis) with a xenobiotic response component. Together, they suggest a theme of interactions between dopamine signaling, glial activity, and immune/neuroinflammatory processes.","confidence":"High","size":17,"edges":20,"triangles":3,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":16},{"id":"GO:0042493","count":16},{"id":"GO:2000458","count":16},{"id":"GO:1900168","count":16},{"id":"GO:0048245","count":16}]},{"hash":"1797335503808127401","title":"Cytochrome P450 omega-oxidation and xenobiotic metabolism","description":"These proteins show enrichment for cytochrome P450\u2013mediated metabolism: omega-oxidation of fatty acids and xenobiotic processing (insecticides, alkaloids, retinoids). The GO terms point to a detoxification/metabolism theme via P450 pathways, even though some development terms appear in the list as contextual signals. Overall, the central function is P450-driven metabolic processing of diverse compounds.","confidence":"High","size":17,"edges":90,"triangles":256,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":17},{"id":"GO:0010193","count":17},{"id":"GO:0008585","count":17},{"id":"GO:0097267","count":17},{"id":"GO:0009822","count":17}]},{"hash":"2248714707031796792","title":"Neuroimmune Dopaminergic Signaling","description":"This cluster centers on neuroimmune interactions in the CNS, with terms like negative regulation of inflammatory response, immune response, astrocyte chemotaxis, and glial-derived neurotrophic factor production. It also includes dopaminergic components such as dopamine transport and signaling pathways, suggesting a convergence between immune regulation and dopaminergic neurotransmission. The combined emphasis on glial/neural immune processes and dopamine biology justifies a label reflecting both neuroinflammation and dopaminergic signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":17},{"id":"GO:0042493","count":17},{"id":"GO:2000458","count":17},{"id":"GO:1900168","count":17},{"id":"GO:0048245","count":17}]},{"hash":"253389680803814437","title":"Neuroimmune-Dopaminergic Regulation","description":"This cluster combines GO terms tied to immune/inflammatory control (negative regulation of inflammatory response, immune response, eosinophil chemotaxis, response to xenobiotic stimulus) with dopaminergic signaling (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling) and glial involvement (astrocyte chemotaxis, glial neurotrophic factor production), suggesting a cohesive theme of neuroimmune modulation linked to dopamine pathways.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":17},{"id":"GO:0042493","count":17},{"id":"GO:2000458","count":17},{"id":"GO:1900168","count":17},{"id":"GO:0048245","count":17}]},{"hash":"1467678362979600181","title":"Dopaminergic Neuroimmune Regulation","description":"This cluster combines proteins involved in dopamine transport and dopamine receptor signaling (dopamine transport, regulation of dopamine metabolic process, phospholipase C-activating dopamine receptor signaling pathway) with immune/neuroglial-related functions (negative regulation of inflammatory response, regulation of astrocyte chemotaxis, glial-derived neurotrophic factor production), suggesting a link between dopaminergic signaling and neuroimmune/glial regulation, possibly in xenobiotic response contexts.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":16},{"id":"GO:0042493","count":16},{"id":"GO:2000458","count":16},{"id":"GO:1900168","count":16},{"id":"GO:0048245","count":16}]},{"hash":"746076302466646497","title":"Dopamine signaling and neuroimmune interactions","description":"The cluster centers on dopaminergic processes (dopamine transport, dopamine metabolic regulation, dopamine receptor signaling) and neuroimmune/glial-related functions (immune response, astrocyte/eosinophil chemotaxis, glial-derived neurotrophic factor production), suggesting a cohesive theme of how dopamine signaling interfaces with neuroimmune and glial regulation in the CNS.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":17},{"id":"GO:0042493","count":17},{"id":"GO:2000458","count":17},{"id":"GO:1900168","count":17},{"id":"GO:0048245","count":17}]},{"hash":"1859080871209547696","title":"Neuroinflammation and Dopaminergic Signaling","description":"This cluster is characterized by GO terms centered on immune/glial regulation (negative regulation of inflammatory response, immune response, astrocyte chemotaxis, GDNF production) and dopaminergic processes (dopamine transport, regulation of dopamine metabolism, dopamine receptor signaling). The combination suggests a cohesive neuroimmune module where glial signaling modulates inflammation and dopamine pathways are engaged, possibly in CNS contexts. The xenobiotic response term also aligns with CNS inflammatory responses to foreign compounds. Overall, the theme is neuroinflammation linked to dopaminergic signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":17},{"id":"GO:0042493","count":17},{"id":"GO:2000458","count":17},{"id":"GO:1900168","count":17},{"id":"GO:0048245","count":17}]},{"hash":"73261422571514870","title":"Neuroimmune Modulation of Dopaminergic Signaling","description":"This cluster links immune/glial functions (immune response, anti-inflammatory regulation, astrocyte chemotaxis, eosinophil chemotaxis, GDNF production) with dopaminergic processes (dopamine transport and metabolism, PLC-activated dopamine signaling) and xenobiotic response, indicating neuroimmune modulation of dopamine pathways.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":15},{"id":"GO:0042493","count":15},{"id":"GO:2000458","count":15},{"id":"GO:1900168","count":15},{"id":"GO:0048245","count":15}]},{"hash":"237127878504361344","title":"Neural signaling and drug response","description":"This cluster is dominated by neuronal-related GO terms such as excitatory postsynaptic potential, responses to cocaine and morphine, and Schwann cell development, pointing to neural signaling and psychoactive substance response. The presence of insulin signaling and cell-cycle/DNA replication terms suggests additional multifunctional factors or pleiotropy, but the primary theme remains neural signaling and drug response.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008286","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0000082","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0034501","count":5}]},{"hash":"205720112401829278","title":"mRNA decay and miRNA silencing in stress granules","description":"This cluster centers on post-transcriptional regulation: mRNA processing and decay pathways (NMD, deadenylation-dependent/independent decapping), mRNA localization to cytoplasmic stress granules, and miRNA-mediated gene silencing, indicating coordinated control of mRNA turnover and translational repression within RNP granules, consistent with stress-related and gene-silencing functions (including oskar mRNA localization).","confidence":"High","size":16,"edges":42,"triangles":31,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:1903608","count":3},{"id":"GO:0045451","count":3},{"id":"GO:0034428","count":2},{"id":"GO:0000184","count":2},{"id":"GO:0000290","count":2}]},{"hash":"1224047725273780090","title":"Plant ion homeostasis and lipid metabolism","description":"The top GO terms center on intracellular phosphate ion homeostasis, glycerol metabolic processes, and phosphatidylglycerol catabolism, with additional related terms like monoatomic cation transmembrane transport and guard cell morphogenesis. This suggests a plant-specific module where ion balance and lipid turnover relate to guard cell development. Some unrelated terms (e.g., collagen fibril organization) may reflect annotation noise, but the core theme remains ion/homeostasis and lipid metabolism in plant cells.","confidence":"Medium","size":16,"edges":55,"triangles":80,"max_degree":13,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0030643","count":7},{"id":"GO:0034478","count":7},{"id":"GO:0006071","count":7},{"id":"GO:0010442","count":7},{"id":"GO:0036292","count":4}]},{"hash":"794574526948839707","title":"NF-kappaB-linked inflammation and apoptosis","description":"The terms cluster around NF-kappaB signaling, apoptotic pathways, inflammatory response, and T cell activation-induced cell death, suggesting a role in NF-kappaB\u2013mediated inflammation and apoptosis regulation.","confidence":"High","size":16,"edges":41,"triangles":45,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043123","count":5},{"id":"GO:2001241","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0006954","count":4}]},{"hash":"1401428049894002105","title":"Innate immune signaling and transcriptional regulation","description":"This cluster is dominated by terms tied to innate immunity (innate immune response, NF-kappaB transcription factor activity regulation) and transcriptional control (DNA-templated transcription), with related regulation of proteasomal protein degradation and signaling cascades (JNK). While there are some development-related terms (axon fasciculation, axial mesoderm formation), the strongest signal centers on immune signaling and transcriptional regulation, suggesting a cohesive module of immune response regulation and gene expression control.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051092","count":16},{"id":"GO:0045087","count":16},{"id":"GO:0035372","count":16},{"id":"GO:0046329","count":15},{"id":"GO:0032436","count":15}]},{"hash":"299989243321014754","title":"Embryogenesis and Signaling Pathways","description":"The cluster aligns with vertebrate embryonic development and core signaling cascades (Wnt, Rho, insulin), with processes like neural tube closure, heart and thymus development, and cell migration, plus apoptosis and endocytic regulation. This suggests a cohesive theme of morphogenesis guided by signaling networks.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016477","count":9},{"id":"GO:0006915","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0001843","count":7},{"id":"GO:0007266","count":7}]},{"hash":"1537436128405831469","title":"NF-kappaB\u2013driven Immune Activation","description":"The top GO terms point to innate and adaptive immune signaling, including innate immune response, IL-1 signaling, LPS response, and T cell receptor signaling, all centered on NF-\u03baB transcription factor activity; together they indicate proteins functioning in inflammatory signaling networks, with NF-\u03baB as a key regulator, despite a few broader terms like neural tube closure or general transcription that are less defining for this cluster.","confidence":"High","size":16,"edges":95,"triangles":310,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051092","count":14},{"id":"GO:0001843","count":14},{"id":"GO:0045087","count":14},{"id":"GO:0070498","count":13},{"id":"GO:0071222","count":13}]},{"hash":"1899838842265516062","title":"Embryogenesis and organ morphogenesis","description":"The top GO terms cluster around embryonic development across multiple tissues\u2014trophoblast differentiation, cartilage morphogenesis, left-right patterning, endocrine pancreas and placenta development, EMT in heart cushion formation, semicircular canal morphogenesis, and forebrain proliferation\u2014pointing to a shared theme of developmental patterning and organ morphogenesis.","confidence":"High","size":16,"edges":39,"triangles":44,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":7},{"id":"GO:0060536","count":7},{"id":"GO:0060972","count":7},{"id":"GO:0035270","count":7},{"id":"GO:0003323","count":7}]},{"hash":"775005614674623843","title":"Signaling Regulation and Neuronal Development","description":"This cluster shows a convergence on regulation of signaling pathways (positive/negative regulation, receptor clustering, JNK cascade regulation), together with developmental processes linked to neural tissue (axial mesoderm formation and fasciculation of sensory neuron axons). Although a few terms touch on metabolism or immune signaling (e.g., interleukin-7 response), the dominant theme is coordinated signaling regulation and neural development/connectivity, suggesting proteins that modulate signaling networks during neural development.","confidence":"Medium","size":16,"edges":100,"triangles":356,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":16},{"id":"GO:0048320","count":16},{"id":"GO:0097155","count":16},{"id":"GO:0032092","count":16},{"id":"GO:0008542","count":16}]},{"hash":"636804365134003961","title":"Neural development and neurotransmission with calcium signaling","description":"The top terms point to brain development and clear neurotransmitter signaling (glutamate and GABA pathways), along with calcium-related processes (calcium transport and store-operated calcium channels). This pattern suggests a cluster centered on neural development and calcium-dependent synaptic signaling, despite a few terms referencing other organ systems. ","confidence":"Medium","size":16,"edges":32,"triangles":23,"max_degree":11,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":11},{"id":"GO:2000560","count":10},{"id":"GO:0051282","count":10},{"id":"GO:0007215","count":10},{"id":"GO:0007214","count":10}]},{"hash":"135110090773813413","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":21,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0007099","count":3},{"id":"GO:0034414","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0017001","count":2}]},{"hash":"1785777387328784234","title":"Cytoskeletal dynamics in immune signaling","description":"The top GO terms cluster around actin cytoskeleton organization, microtubule-based movement, and cell migration, indicating cytoskeletal remodeling. At the same time, multiple immune-related pathways appear (B cell receptor signaling, inflammatory response, NOD2 signaling, defense against Gram-positive bacteria), suggesting the proteins collectively link cytoskeletal dynamics with immune signaling and response. Some neural development terms are present but are likely secondary, making the cytoskeleton-immune theme the most representative.","confidence":"High","size":16,"edges":56,"triangles":81,"max_degree":12,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0030036","count":7},{"id":"GO:0016477","count":6},{"id":"GO:0050853","count":6},{"id":"GO:0007018","count":6},{"id":"GO:0021510","count":6}]},{"hash":"1334538621095628821","title":"Keratinocyte differentiation and antiviral signaling","description":"The cluster shows a clear theme around skin/epithelial biology\u2014keratinocyte differentiation and proliferation, epithelial differentiation (including mammary gland), and a mechanical stimulus response\u2014paired with innate antiviral defense (defense response to virus and interferon-alpha production). Transcriptional regulation (DNA-templated transcription and histone acetylation) reinforces a developmental, differentiation-associated program that also engages antiviral signaling.","confidence":"High","size":16,"edges":56,"triangles":83,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006915","count":8},{"id":"GO:0051607","count":7},{"id":"GO:0071260","count":7},{"id":"GO:0030216","count":7}]},{"hash":"841989053355007557","title":"Neural development and inflammatory signaling","description":"These proteins appear linked to neural development and brain signaling (forebrain development, DNA-templated transcription, mitotic cell cycle) and to stress/inflammatory pathways (JNK cascade, IL-1 signaling, NF-kappaB signaling, LPS signaling), with a note of neural activity modulation evidenced by the behavioral response to cocaine. This combination suggests a cluster centered on neural development coupled with inflammatory/stress signaling mechanisms.","confidence":"Medium","size":16,"edges":89,"triangles":243,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0048148","count":4},{"id":"GO:0046330","count":4}]},{"hash":"1239793708553521555","title":"Hippo signaling and developmental apoptosis","description":"The cluster centers on Hippo pathway signaling and related developmental processes (heart and hippocampus development) with accompanying neurotrophin signaling and apoptosis execution terms, indicating a cohesive theme of growth control and programmed cell death in neural/cardiac contexts; xenobiotic/nicotine responses appear peripheral but not contradictory.","confidence":"High","size":16,"edges":92,"triangles":294,"max_degree":15,"top_function":"wound healing","top_go_terms":[{"id":"GO:0035329","count":9},{"id":"GO:0051092","count":9},{"id":"GO:0097194","count":9},{"id":"GO:0021766","count":9},{"id":"GO:0048011","count":9}]},{"hash":"177244066307680435","title":"Cell cycle regulation and telomere maintenance","description":"Reasoning: The top terms cluster around mitotic/spindle assembly processes, general cell cycle control, and telomere maintenance (including telomerase regulation and telomere capping), with additional input from ubiquitination and proteasome assembly, suggesting a module focused on cell division and genome stability. A Wnt signaling entry aligns with proliferation context but does not dominate the theme.","confidence":"Medium","size":16,"edges":34,"triangles":14,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0016055","count":5},{"id":"GO:1904908","count":4},{"id":"GO:0051225","count":4},{"id":"GO:0016567","count":4}]},{"hash":"1202658707180480635","title":"Cytoskeletal remodeling and cell migration signaling","description":"This cluster centers on lamellipodium assembly, microtubule-based movement, and membrane tubulation, plus Rho-mediated signaling, indicating a shared theme of cytoskeletal reorganization driving cell shape changes and movement. The presence of multiple receptor signaling terms (insulin receptor, thrombin-activated receptor, GM-CSF stimulus) suggests these signals orchestrate cytoskeletal dynamics rather than a single metabolic process. Developmental terms like spinal cord development may reflect contexts where such remodeling is important, reinforcing the motion/morphology theme. Overall, the proteins appear tied to cytoskeletal dynamics regulated by diverse signaling inputs, i.e., migration and morphological change. ","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0097011","count":6},{"id":"GO:0008286","count":6},{"id":"GO:0070493","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0007018","count":5}]},{"hash":"979936429046768787","title":"Renin-Angiotensin Axis and Peptide Processing","description":"The top GO terms center on angiotensin maturation and regulation of blood volume via the renin-angiotensin system, plus related peptide processing (proteolysis and digestion) and thirst-related behavior. While some immune-related terms appear, the dominant signal points to peptide hormone maturation and proteolysis within the angiotensin axis and digestive context, suggesting a cohesive theme of peptide processing linked to blood pressure regulation and digestion. ","confidence":"Medium","size":16,"edges":7,"triangles":1,"max_degree":4,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042756","count":10},{"id":"GO:0002016","count":10},{"id":"GO:0048469","count":10},{"id":"GO:0002003","count":10},{"id":"GO:0032496","count":10}]},{"hash":"436074199249754240","title":"Immune cell development and signaling","description":"This cluster is enriched for immune-related terms such as B cell affinity maturation, NK T cell differentiation, and hemopoiesis, along with cytokine signaling (IL-7, IL-4) and development cues. The presence of lamellipodium assembly and Rho signaling indicates cytoskeletal remodeling and cell migration common to differentiating immune cells. Although insulin/IGF signaling appears, the dominant pattern is immune lineage specification and signaling.","confidence":"High","size":16,"edges":92,"triangles":304,"max_degree":15,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:2001275","count":14},{"id":"GO:0048009","count":13},{"id":"GO:0098761","count":13},{"id":"GO:0032633","count":13},{"id":"GO:0002344","count":13}]},{"hash":"2240074249895142619","title":"Antiviral Innate Immune Response","description":"The top GO terms cluster around innate immunity and antiviral signaling: cellular response to dsRNA, response to type I interferon, and innate immune response, with negative regulation of defense against virus by host. This points to interferon-driven antiviral signaling as the core function of the cluster. Some unrelated terms (plant hormone signaling, prostate development) may be annotations artifacts but do not change the primary antiviral/immune theme.","confidence":"High","size":16,"edges":63,"triangles":80,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0008277","count":6},{"id":"GO:0071360","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0071357","count":5}]},{"hash":"1908296261932753751","title":"Intestinal microvilli cytoskeleton remodeling and signaling","description":"This cluster centers on intestinal epithelial cytoskeleton dynamics (actin remodeling, terminal web, microvillus length) and associated signaling (Rho GTPases, focal adhesions, receptor tyrosine kinase pathways, NF-kB via I-kappaB), plus intestinal glucose absorption, indicating a coherent module of microvilli structure and signaling.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031532","count":5},{"id":"GO:1902896","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0007252","count":3},{"id":"GO:0032532","count":3}]},{"hash":"322476293206608615","title":"Cell differentiation, polarity, and division","description":"This cluster highlights proteins involved in cell differentiation and maintenance of cell polarity, with several terms pointing to cell cycle and division (spindle assembly in meiosis, general cell division). Additional signals include neuron projection development and Rho signaling, suggesting cytoskeletal and developmental coordination. A couple of RNA processing terms (tRNA modification, ribosomal export) indicate some housekeeping roles, but the dominant themes center on development, polarity, and division. Overall, the label captures the main shared functions across the GO terms.","confidence":"Medium","size":16,"edges":18,"triangles":7,"max_degree":6,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030154","count":4},{"id":"GO:0030011","count":4},{"id":"GO:0006400","count":4},{"id":"GO:0031175","count":4},{"id":"GO:0035023","count":3}]},{"hash":"502841536884786970","title":"Mitotic cell cycle regulators","description":"These proteins show a strong enrichment for cell division and mitotic cell cycle terms, suggesting roles in mitosis and regulation of cell division. Additional annotations for protein complex assembly and phosphorylation-mediated signaling support involvement in mitotic machinery, though some components also have development or immune-related functions, indicating broader, context-dependent roles. Overall, the dominant theme is mitosis and cell cycle control.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051291","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006817","count":3},{"id":"GO:0021766","count":2}]},{"hash":"346932748627125318","title":"Signaling and Membrane Trafficking","description":"The cluster centers on PI-mediated signaling, endosome transport, cilium localization, and regulation of cell polarity, suggesting a unifying theme of intracellular signaling coupled with membrane trafficking; a few terms (sporulation membrane formation, osteoblast fate) are more context-specific but do not override the common signaling/trafficking pattern.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032120","count":4},{"id":"GO:0048015","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0060315","count":3},{"id":"GO:0061512","count":2}]},{"hash":"2001003827706023988","title":"Neural and Visual System Development","description":"The cluster shows strong representation of neural and visual system processes (retina layer formation, visual perception, substantia nigra development) along with synaptic signaling and calcium-channel regulation, suggesting a cohesive theme around CNS/retinal development and synaptic communication.","confidence":"Medium","size":16,"edges":6,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0038095","count":13},{"id":"GO:0007601","count":13},{"id":"GO:0007507","count":13},{"id":"GO:0016061","count":12},{"id":"GO:2000300","count":12}]},{"hash":"1225035533803615660","title":"Neural and Skeletal Muscle Development","description":"The proteins cluster around neural and muscular differentiation processes: neurogenesis, nervous system development, skeletal muscle differentiation, myoblast differentiation, and myelination. While some terms touch heart and pancreas development, the strongest signal is neuromuscular development, justifying this label as representative of the cluster\u2019s function. ","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902416","count":3},{"id":"GO:2000637","count":3},{"id":"GO:0035914","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0007399","count":2}]},{"hash":"561232232719595401","title":"Exocytosis and innate immune signaling","description":"The cluster centers on secretory processes: exocytosis, exocyst localization, SNARE complex regulation, and peptide hormone secretion. It also includes innate-immune terms such as Toll-like receptor 2 signaling, macrophage activation, and defense responses to virus and Gram-negative bacteria, suggesting secretory vesicle trafficking linked to immune signaling in immune cells. A term like rhabdomere membrane biogenesis may reflect membrane trafficking contexts as well, but the dominant pattern ties vesicle trafficking and secretion to immune response.","confidence":"Medium","size":16,"edges":42,"triangles":47,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":6},{"id":"GO:0045313","count":6},{"id":"GO:0051601","count":6},{"id":"GO:0006887","count":6},{"id":"GO:0030072","count":6}]},{"hash":"845368353660806704","title":"GTPase-driven actin remodeling and cell migration","description":"This cluster centers on positive regulation of GTPase activity and actin cytoskeleton organization (actin filament bundle assembly), with several signaling pathways (TGF-beta, PDGF receptor, estrogen receptor) linked to cytoskeletal dynamics and cellular movement. The inclusion of cell migration and related processes supports a cohesive theme of signaling guiding actin remodeling to drive movement. ","confidence":"High","size":16,"edges":99,"triangles":354,"max_degree":15,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043547","count":13},{"id":"GO:0071560","count":12},{"id":"GO:0050731","count":12},{"id":"GO:0000747","count":12},{"id":"GO:0033146","count":11}]},{"hash":"1596918427748745790","title":"Developmental transcription and morphogenesis","description":"The top GO terms cluster around RNA polymerase II\u2013mediated transcription and diverse developmental processes across multiple tissues (cardioblast migration, Malpighian tubule and seminal vesicle differentiation, pancreatic cell development, vestibular nucleus development, etc.), with some cell adhesion involvement. This suggests a broad role in developmental regulation and tissue patterning rather than a single pathway, so a label emphasizing developmental transcription and morphogenesis fits best.","confidence":"Medium","size":16,"edges":89,"triangles":263,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":13},{"id":"GO:0033627","count":9},{"id":"GO:0021750","count":9},{"id":"GO:0003259","count":9},{"id":"GO:0061382","count":9}]},{"hash":"499866860383171883","title":"Neural development and angiogenesis with TGF-beta signaling","description":"The top GO terms cluster around nervous system development (nervous system development, forebrain development, neural tube closure) and angiogenesis, all related to development and vascularization, with cellular responses to TGF-beta stimulus tying them together. Immune terms appear but likely reflect pleiotropic roles of TGF-beta or broader gene functions rather than a primary immune module. Overall, the dominant theme is neural and vascular development under TGF-beta\u2013mediated signaling.","confidence":"High","size":16,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":4},{"id":"GO:0035264","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0050830","count":3}]},{"hash":"1295989080992135028","title":"Translational control and growth signaling","description":"Top GO terms suggest a central theme of regulating protein synthesis in response to nutrient and hormonal cues, including IRES-dependent translational initiation, regulation of translation initiation, TOR signaling, insulin receptor signaling, and responses to amino acid starvation and dexamethasone. Coupled with cell-cycle notes (G1/S transition) this points to a cohesive cluster about coordinating growth and metabolism through translational control, rather than a structural or purely signaling module. The mixture of translation regulation with nutrient/hormone signaling supports this interpretation, though the sparse, heterogeneous annotations temper certainty.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002192","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0045931","count":1},{"id":"GO:0071549","count":1},{"id":"GO:0000082","count":1}]},{"hash":"273551115431148305","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":80,"triangles":218,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0060213","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0000472","count":3}]},{"hash":"529128924527038925","title":"Spermatogenesis-linked transcription machinery assembly","description":"This cluster shows enrichment for spermatogenesis along with terms for RNA polymerase I/II/III assembly and transcription elongation regulation, plus supporting processes like protein folding and tubulin complex assembly. Together, these points suggest a theme around germ cell development requiring coordinated transcription machinery assembly and cytoskeletal dynamics, with some regulation of apoptosis and RNA silencing as ancillary gene expression controls. ","confidence":"Medium","size":16,"edges":94,"triangles":289,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:1990114","count":2},{"id":"GO:1990113","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0007021","count":2}]},{"hash":"222952668011502842","title":"Intracellular vesicle trafficking and autophagy signaling","description":"Most terms point to membrane trafficking (PI-mediated signaling, endosome-to-Golgi transport, lysosome localization, intracellular protein transport) and autophagy (autophagosome maturation) with involvement of small GTPases (GTPase activity, Rap signaling). A minor mention of muscle differentiation is present, but the core theme is vesicle trafficking and autophagy.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0034499","count":3},{"id":"GO:0051146","count":2},{"id":"GO:0000902","count":2}]},{"hash":"1120733188279860447","title":"Microtubule Dynamics and Cell Cycle Control","description":"Based on the GO terms, the cluster centers on microtubule-related processes: cellular response to mechanical stimulus and plus-end-directed vesicle transport along microtubules, plus mitotic spindle assembly checkpoint signaling, indicating roles in microtubule dynamics and cell-cycle control. Some terms (miRNA processing, histone ubiquitination, isotype switching, Rap signaling) are more divergent and may reflect broader or incidental functions, but the dominant signal is cytoskeleton- and division-associated.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0009190","count":1},{"id":"GO:0044810","count":1},{"id":"GO:0032487","count":1},{"id":"GO:0090055","count":1}]},{"hash":"722346269196407302","title":"Nucleotide biosynthesis and salvage","description":"This cluster is dominated by GO terms for phosphorylation and nucleotide metabolism (e.g., phosphorylation, nucleoside monophosphate phosphorylation, ADP and CDP biosynthesis, AMP salvage, purine ribonucleotide interconversion), indicating a cohesive role in nucleotide synthesis and turnover. The brain and liver development terms appear as ancillary associations rather than the defining function. ","confidence":"High","size":16,"edges":115,"triangles":500,"max_degree":15,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046939","count":7},{"id":"GO:0046940","count":7},{"id":"GO:0016310","count":7},{"id":"GO:0015951","count":6},{"id":"GO:0006172","count":6}]},{"hash":"1367810821895007136","title":"Mitochondrial dynamics and membrane adhesion signaling","description":"The cluster features multiple terms centered on mitochondrial maintenance and dynamics (stress-induced mitochondrial fusion, inner mitochondrial membrane organization, mitochondrion inheritance) alongside membrane-related processes (protein localization to membrane raft, cadherin-mediated cell-cell adhesion). This suggests a cohesive theme linking mitochondrial function with membrane organization and adhesion, despite some additional regulatory terms present.","confidence":"Medium","size":16,"edges":107,"triangles":421,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0045541","count":6},{"id":"GO:0032226","count":6},{"id":"GO:1990046","count":6},{"id":"GO:0000001","count":6}]},{"hash":"2193449129127410657","title":"Mammary gland development and lactation signaling","description":"This cluster is strongly linked to mammary biology: lactation, mammary gland epithelial cell proliferation, leptin response, and canonical Wnt signaling, which together suggest functions in mammary gland development and lactation. Supporting terms like epithelial differentiation regulation and cell division align with growth and remodeling, while autophagy-related signaling (ULK1) can support cellular remodeling. A few terms (stomatal opening, late viral transcription, antiviral genome replication) appear as outliers but do not override the mammary-focused signal.","confidence":"Medium","size":16,"edges":82,"triangles":214,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007595","count":3},{"id":"GO:0019086","count":3},{"id":"GO:0030857","count":3},{"id":"GO:0033598","count":3},{"id":"GO:0044321","count":3}]},{"hash":"504922004232245332","title":"Immune Signaling and Developmental Regulation","description":"The cluster is enriched for innate immune response and interferon-alpha\u2013related terms, plus transcription and cell division, with developmental signals like substantia nigra development and non-motile cilium assembly. This suggests a mixed set of proteins involved in immune signaling alongside broader regulatory roles in development and proliferation, though the connection is not tightly cohesive across all terms.","confidence":"Medium","size":16,"edges":26,"triangles":4,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0006463","count":2}]},{"hash":"754737293541955113","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0080188","count":2}]},{"hash":"1848793699507600623","title":"Rho GTPase and PI signaling in endocytosis and cytokinesis","description":"This cluster centers on Rho/Rho-like GTPase signaling, phosphoinositide-mediated signaling, and links to endosomal transport and regulation of cytokinesis and the mitotic cell cycle, suggesting a coherent role in coordinating vesicular trafficking with cytoskeletal signaling during cell division.","confidence":"High","size":16,"edges":83,"triangles":220,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0032465","count":2},{"id":"GO:0008333","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0071901","count":2}]},{"hash":"1635195347872646115","title":"Embryonic Development and Organ Morphogenesis","description":"Genes in this cluster are enriched for embryonic and organ development terms across multiple tissues (eye, spinal cord, heart, prostate) and developmental processes, with supporting roles in cell\u2013matrix adhesion and signaling, suggesting a cohesive theme of developmental regulation and organogenesis.","confidence":"High","size":16,"edges":6,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008286","count":6},{"id":"GO:0007095","count":6},{"id":"GO:0007160","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0043010","count":4}]},{"hash":"1379837819886993268","title":"Neural\u2013Cardiovascular Regulation and Plasticity","description":"In this cluster, the top GO terms cluster around neural plasticity (short-term memory, long-term synaptic potentiation) and cardiovascular regulation (heart rate, renin-angiotensin pathway) with supporting signals in vascular growth (angiogenesis) and metabolic/transcriptional control (triglyceride metabolism, transcription regulation). Mast cell immunity adds an inflammatory signaling layer. The set suggests proteins involved in coordinated signaling that links neural activity, vascular function, and metabolic regulation rather than a single narrow pathway. ","confidence":"Medium","size":16,"edges":12,"triangles":10,"max_degree":5,"top_function":"protein maturation","top_go_terms":[{"id":"GO:0007614","count":11},{"id":"GO:0002027","count":11},{"id":"GO:0001525","count":11},{"id":"GO:0060291","count":11},{"id":"GO:2001275","count":10}]},{"hash":"2159775608112507773","title":"NF-kappaB-driven innate immune signaling","description":"This cluster is dominated by GO terms related to canonical NF-kappaB signaling and innate immune response, suggesting proteins involved in NF-kappaB\u2013mediated immunity. Other terms touch on calcium signaling and development, which may reflect cross-talk with signaling and cell fate processes; overall the core theme is NF-kappaB\u2013regulated innate immune signaling.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":3},{"id":"GO:0090201","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1123469686102248383","title":"ECM remodeling and angiogenesis","description":"These terms cluster around extracellular matrix organization (collagen fibril organization, proteoglycan catabolic process) and angiogenic signaling pathways (VEGF signaling, endothelial tube morphogenesis, integrin signaling, BMP response). Together they suggest a module of cartilage/ECM remodeling coupled with vascular development. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0032331","count":15},{"id":"GO:1900748","count":15},{"id":"GO:0001542","count":14},{"id":"GO:0045636","count":14},{"id":"GO:2001113","count":14}]},{"hash":"1258671890562312950","title":"Neurite outgrowth and microtubule dynamics","description":"The top GO terms point to neuron projection development, axonogenesis, and cytoskeletal/microtubule regulation (including microtubule organization and depolymerization/polymerization), plus a cellular response to nerve growth factor. Taken together, these terms indicate neuronal morphogenesis driven by microtubule remodeling and neurite/axon extension, with regulatory inputs such as Rac signaling. This makes \u201cneurite outgrowth and microtubule dynamics\u201d a precise and representative label.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031175","count":1},{"id":"GO:0007409","count":1},{"id":"GO:0031117","count":1},{"id":"GO:0010977","count":1},{"id":"GO:0007026","count":1}]},{"hash":"1817612037144185398","title":"Germline Development and Gametogenesis","description":"These proteins are tied to germ-cell development across sexes, including oogenesis, spermatogenesis, and meiotic processes, along with germline stem cell maintenance. Post-transcriptional regulation terms (translation repression, deadenylation) reflect germline-specific RNA control. Overall, the cluster represents germline development and gametogenesis.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008354","count":1},{"id":"GO:0045886","count":1},{"id":"GO:0045835","count":1},{"id":"GO:0001555","count":1},{"id":"GO:0017148","count":1}]},{"hash":"1892033228111859359","title":"Cardiac development and electrophysiology","description":"This cluster centers on heart development (GO:0007507) and cardiac electrical activity, with terms for SA node action potential regulation (GO:0098907) and clustering of voltage-gated potassium channels (GO:0045163), pointing to a shared cardiac development and electrophysiology theme. Some developmental terms beyond the heart appear, but the cardiac signals are the strongest link.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0045163","count":3},{"id":"GO:0035502","count":3}]},{"hash":"816073341049930100","title":"Neuronal Mitochondrial Dynamics and Membrane Organization","description":"The top GO terms cluster around mitochondrial maintenance\u2014inheritance, inner membrane organization, and stress-induced fusion\u2014indicating a core mitochondrial dynamics theme. Supporting terms point to neuronal membrane signaling and adhesion (dopaminergic synaptic transmission, membrane rafts, cadherin-mediated adhesion), suggesting a link between mitochondrial dynamics and neuronal membrane organization and signaling. Overall, the cluster seems best described by mitochondrial maintenance in neurons with associated membrane and signaling roles.","confidence":"Medium","size":16,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0045541","count":2},{"id":"GO:0032226","count":2},{"id":"GO:1990046","count":2}]},{"hash":"825965050200308524","title":"Epithelial Innate Immunity and Gland Development","description":"The top GO terms cluster around epithelial tissues (skin, tracheal and salivary glands) development and barrier features (tight junction regulation), along with innate immune responses (monocyte chemotaxis, phagocytosis, LPS signaling, inflammatory responses). This suggests a cohesive theme of mucosal/epithelial immunity linked to gland morphogenesis and barrier remodeling.","confidence":"High","size":16,"edges":73,"triangles":159,"max_degree":13,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0071230","count":10},{"id":"GO:0043588","count":10},{"id":"GO:0031663","count":7},{"id":"GO:0060662","count":6},{"id":"GO:0002439","count":6}]},{"hash":"1868812759997972541","title":"Chondrogenesis and Cartilage Development (BMP Signaling)","description":"The cluster is enriched for cartilage-related processes: cartilage condensation, chondrocyte differentiation, cartilage development, and positive regulation of BMP signaling, plus involvement of ERK1/2 cascades and cell-matrix adhesion, all pointing to BMP-driven chondrogenesis and cartilage formation. Some vascular and remodeling terms appear as secondary associations, but the dominant theme is cartilage development and BMP pathway regulation.","confidence":"High","size":16,"edges":104,"triangles":375,"max_degree":15,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0001502","count":10},{"id":"GO:0007596","count":9},{"id":"GO:0060716","count":8},{"id":"GO:0030513","count":8},{"id":"GO:0007160","count":8}]},{"hash":"1407932645594874600","title":"Unknown","description":"The GO terms span metabolism (catabolic processes and ferredoxin metabolism), energy production (ATP synthesis coupling), transport (sodium ion transport), and regulatory roles in lactation and vascular development, with an outlier nitrogen fixation term. The set lacks a cohesive, single function tying the cluster, so a general Unknown label is most appropriate.","confidence":"","size":16,"edges":66,"triangles":159,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":5},{"id":"GO:0042773","count":5},{"id":"GO:0007595","count":4},{"id":"GO:0009115","count":4},{"id":"GO:0045602","count":4}]},{"hash":"1437191743151660652","title":"T cell receptor signaling and proliferation regulation","description":"The top GO terms are dominated by T cell\u2013related processes: T cell receptor signaling pathway and positive/negative regulation of T cell proliferation. While there are additional terms relating to development and hormone signaling, the strongest and most representative signals in the cluster point to immune signaling, especially T cell\u2013mediated responses and proliferation control. This justifies a label centered on T cell signaling, with an acknowledgment of broader functional diversity.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":2},{"id":"GO:0042102","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0071372","count":2},{"id":"GO:0072178","count":2}]},{"hash":"1470030238901772726","title":"Central carbon metabolism and metabolic stress","description":"The cluster shows strong signals from core metabolic pathways (glycolysis, TCA cycle, oxaloacetate, one-carbon metabolism) and multiple \u201cresponse to\u201d terms (nutrients, hypoxia, glucose, hydrogen peroxide, cAMP), indicating integration of energy production with redox and nutrient signaling.","confidence":"High","size":16,"edges":79,"triangles":206,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":6},{"id":"GO:0007584","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0001666","count":4},{"id":"GO:0006730","count":4}]},{"hash":"1993111705465028976","title":"Hematopoietic and immune cell development regulation","description":"The GO terms show positive regulation of hematopoiesis (embryonic hemopoiesis, bone marrow proliferation) and immune-lineage differentiation (dendritic cells, NK cells) along with osteoclast proliferation. This suggests the cluster is centered on signaling-mediated control of blood/immune system development; a few muscle-related terms exist, but the dominant theme is hematopoietic/immune development regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":2},{"id":"GO:0090290","count":2},{"id":"GO:0001934","count":2},{"id":"GO:0030885","count":2},{"id":"GO:0035162","count":2}]},{"hash":"2039891403464303721","title":"Neuroimmune signaling and synapse formation","description":"This cluster is enriched for neural development and synapse assembly terms (nervous system development; positive regulation of synapse assembly) alongside immune/antiviral signals (defense response to virus; interferon-related terms; PI3K/AKT and PDGF signaling). The combination suggests proteins linking neural development with immune signaling and antiviral responses, i.e., neuroimmune coordination.","confidence":"Medium","size":16,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051897","count":4},{"id":"GO:0007399","count":3},{"id":"GO:0051965","count":3},{"id":"GO:0032703","count":3},{"id":"GO:0010641","count":3}]},{"hash":"789689863906905089","title":"Lens and eye development","description":"This cluster is dominated by GO terms tied to the eye and lens, including lens fiber cell differentiation, lens development and morphogenesis in camera-type eyes, retina morphogenesis, and visual perception. While a kidney development term appears among the top terms, the majority point to lens/eye structure formation and function, suggesting the proteins co-cluster around lens and camera-type eye development. Therefore, naming it Lens and eye development accurately reflects the main theme of the cluster.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":4},{"id":"GO:0001822","count":3},{"id":"GO:0060042","count":3},{"id":"GO:0032836","count":3},{"id":"GO:0007601","count":2}]},{"hash":"2162452745633686777","title":"Developmental Differentiation and Cell Polarity","description":"The top GO terms span cell differentiation, multicellular development, spermatogenesis, and keratinization, indicating development and tissue differentiation. Supporting terms like Cdc42 signaling and establishment of bipolar cell polarity point to regulation of cell shape and morphogenesis during development, suggesting a cohesive theme of differentiation with polarity rather than a single lineage. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030154","count":2},{"id":"GO:0007283","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0031424","count":2},{"id":"GO:0032488","count":1}]},{"hash":"1055324855426718000","title":"Developmental differentiation and apoptosis regulation","description":"The Top Terms indicate a focus on development and differentiation (multicellular organism development, exocrine pancreas development, cell differentiation) with accompanying signals about cell cycle and negative regulation of apoptosis, suggesting a broad developmental program rather than a single pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900118","count":1},{"id":"GO:0090156","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0031017","count":1},{"id":"GO:0030154","count":1}]},{"hash":"879899434283785837","title":"Fatty acid biosynthesis and catabolism","description":"This cluster is dominated by GO terms for fatty acid metabolism, with multiple entries for biosynthetic and catabolic processes of fatty acids and fatty-acyl-CoA species (palmitic acid, medium- and long-chain). The recurring themes indicate coordinated lipid metabolism rather than a single narrow function. Some terms such as enterobactin biosynthesis and phenylacetate catabolic process appear as possible annotations from broader metabolic roles or noise, but the clear majority centers on fatty acid biosynthesis and degradation, justifying a label around lipid metabolism.","confidence":"High","size":16,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900535","count":3},{"id":"GO:0051792","count":3},{"id":"GO:0036114","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0009239","count":3}]},{"hash":"1314137523021634906","title":"Unknown","description":"The top GO terms are highly diverse (immune differentiation, neural and muscle development, gliogenesis, uterine/germline-related morphogenesis, regulation of signaling), with no clear, single shared function or pathway connecting the proteins. There are no edges, so there is no cohesive interaction context to anchor a specific label. Therefore, I cannot assign a concrete functional theme beyond Unknown, with no confidence in a representative label.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033082","count":1},{"id":"GO:1900006","count":1},{"id":"GO:1903709","count":1},{"id":"GO:0014904","count":1},{"id":"GO:0014013","count":1}]},{"hash":"993486279064124497","title":"Peroxisomal lipid metabolism","description":"The set is dominated by lipid- and peroxisome-related GO terms: fatty acid beta-oxidation, acetyl-CoA catabolic processes, and glyoxysome organization, which together point to peroxisomal lipid metabolism as a core function. Other terms extend to hormone response and development (adipose and brain), and additional metabolic processes across organisms, suggesting a cluster centered on energy metabolism with peroxisomal involvement. Confidence reflects a cohesive thread around peroxisomal lipid metabolism, tempered by broader, less-related terms. ","confidence":"Medium","size":16,"edges":93,"triangles":288,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0009725","count":7},{"id":"GO:0019619","count":7},{"id":"GO:0042619","count":7},{"id":"GO:0046356","count":7},{"id":"GO:0060612","count":7}]},{"hash":"1665147083933539785","title":"Neurovascular development","description":"This cluster is dominated by terms tied to neural and vascular development and patterning, such as angiogenesis, neuron migration, axon guidance, and establishment of the blood-brain barrier, suggesting proteins that function in coordinated neurovascular morphogenesis and maturation. While other terms touch on general development or metabolism, the strongest signal is for neurovascular development. ","confidence":"Medium","size":16,"edges":7,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":16},{"id":"GO:0001764","count":16},{"id":"GO:0043435","count":16},{"id":"GO:0072520","count":16},{"id":"GO:0071329","count":16}]},{"hash":"415289708174392254","title":"Rho-driven actin remodeling and cell shape control","description":"This cluster centers on cytoskeletal dynamics: Rho signaling, actin filament polymerization, pseudopodium assembly, and regulation of cell shape, plus the JNK cascade, suggesting coordinated actin remodeling during morphogenesis. A few DNA repair terms appear in the list but are likely incidental annotations rather than representing a core function. Overall, the proteins seem linked by actin dynamics and morphology regulation.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000495","count":1},{"id":"GO:0072327","count":1},{"id":"GO:0007266","count":1},{"id":"GO:0031274","count":1},{"id":"GO:0007254","count":1}]},{"hash":"636245212011448958","title":"Redox homeostasis and oxidative stress response","description":"The proteins cluster around redox biology: strong enrichment for cellular oxidant detoxification, redox homeostasis, and response to oxidative stress, plus protein deglutathionylation, indicating a coherent redox regulatory role. A few unrelated terms appear but the dominant theme is redox regulation.","confidence":"High","size":16,"edges":104,"triangles":385,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":14},{"id":"GO:0045454","count":12},{"id":"GO:0030416","count":10},{"id":"GO:0055114","count":8},{"id":"GO:0034599","count":8}]},{"hash":"998178373387505697","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning apoptosis (p53-mediated DNA damage response), endosome regulation and receptor recycling, Rho signaling, transcription regulation, angiogenesis, and even synaptic transmission, with several obsolete terms. There is no single cohesive function or pathway that dominates the cluster, so a unified label isn\u2019t supported.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":2},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0034968","count":1}]},{"hash":"449893702973709687","title":"MHC I Antigen Presentation and Cytotoxic Immunity","description":"This cluster is dominated by GO terms for antigen processing and presentation via MHC class I (both endogenous and TAP-dependent pathways), along with interferon signaling (type I and II) and cytotoxic effector activities (NK cell\u2013 and T cell\u2013mediated cytotoxicity), plus IL-1\u03b2 and IL-17 production. These collectively point to a cohesive immune activation focusing on antigen presentation and cytotoxic responses. Some terms (bitter taste detection, iron import) appear peripheral or context-dependent but do not override the core immune theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002479","count":2},{"id":"GO:0032611","count":2},{"id":"GO:0060337","count":2},{"id":"GO:0001916","count":2},{"id":"GO:0098711","count":2}]},{"hash":"1221773559456329307","title":"Unknown","description":"The Top Terms are a highly diverse mix (chlorophyll catabolic process, regulation of endocannabinoid signaling, T cell activation, ECM disassembly regulation, beta-ketoadipate pathway, formaldehyde catabolic process, PHB biosynthesis, secondary shoot formation, cellular response to strigolactone, and oxidation-reduction process), with no edges or shared function linking them. This lack of a coherent theme means a concise, representative label cannot be assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015996","count":1},{"id":"GO:2000124","count":1},{"id":"GO:0042110","count":1},{"id":"GO:0010716","count":1},{"id":"GO:0042952","count":1}]},{"hash":"1098612964632500191","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":1},{"id":"GO:2000344","count":1},{"id":"GO:2000884","count":1},{"id":"GO:0016042","count":1},{"id":"GO:0016239","count":1}]},{"hash":"2301356144744137518","title":"Mitotic spindle assembly and chromosome segregation","description":"Top GO terms indicate a focus on mitosis and spindle dynamics, including spindle assembly, kinetochore-microtubule interactions, and metaphase chromosome maintenance. While there are also mitochondrial and development-related terms present, the strongest and most recurrent signals relate to cell-division machinery, suggesting the cluster centers on mitotic processes rather than metabolism or development. This makes \"Mitotic spindle assembly and chromosome segregation\" a concise, representative label for the cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0072092","count":1},{"id":"GO:0048364","count":1},{"id":"GO:0099607","count":1}]},{"hash":"2220403730666020139","title":"Adhesion Molecules and Synaptic Regulation","description":"The dominant terms are cell-cell adhesion (homophilic and heterophilic) and regulation of synapse assembly, with connections to actin cytoskeleton organization driven by adhesion and neuronal localization (juxtaparanode, AV node). This points to a cluster enriched in adhesion molecules and synaptic organizers, with some immune-regulatory cues likely arising from shared adhesion-related pathways. Overall, the theme centers on adhesion-mediated synaptic and cellular messaging rather than a single enzymatic or signaling function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007156","count":10},{"id":"GO:0051963","count":9},{"id":"GO:0043031","count":9},{"id":"GO:0046718","count":9},{"id":"GO:0002859","count":9}]},{"hash":"1166869063324143177","title":"Neural development and FGFR/MAPK signaling","description":"These proteins cluster around nervous system development with neuron axonogenesis and corpus callosum formation, and prominently feature FGFR-related signaling and downstream MAPK/ERK cascades, consistent with coordinated neural growth and patterning. The presence of organ induction and endothelial chemotaxis to FGFs supports broader developmental signaling, though neural development is the strongest theme; a few outlier terms (fertilization, cardiac repolarization) are less central. ","confidence":"High","size":16,"edges":49,"triangles":43,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0007342","count":2},{"id":"GO:0021952","count":2},{"id":"GO:0070374","count":2}]},{"hash":"995099774636225909","title":"Neuroimmune and Dopaminergic Signaling","description":"This cluster converges on CNS neuroimmune interactions and dopamine biology: terms for immune response, regulation of inflammation, astrocyte chemotaxis, and glial-derived neurotrophic factor production point to glial-mediated modulation; alongside dopamine transport, regulation of dopamine metabolism, and a phospholipase C-activating dopamine receptor pathway, these imply a coordinated neuroimmune-dopaminergic module, with xenobiotic response supporting a broader CNS stress/detox context.","confidence":"High","size":16,"edges":5,"triangles":0,"max_degree":4,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":14},{"id":"GO:0042493","count":14},{"id":"GO:2000458","count":14},{"id":"GO:1900168","count":14},{"id":"GO:0048245","count":14}]},{"hash":"226827462170329701","title":"RNA Pol II Transcription Regulation in Development","description":"The cluster centers on transcriptional control by RNA polymerase II (DNA-templated transcription and regulation of transcription by RNA Pol II), with several terms describing regulatory roles during the cell cycle. The accompanying developmental terms (left/right pattern formation, cartilage morphogenesis, trophoblast giant cell differentiation, endocrine system development) suggest these proteins also participate in developmental differentiation. Together, they indicate a group of factors coordinating transcription regulation in developmental contexts, rather than a single pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007576","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0010729","count":6},{"id":"GO:0070895","count":6},{"id":"GO:0046022","count":6}]},{"hash":"722927294771828436","title":"Diverse Substrate Transmembrane Transport","description":"The top GO terms cluster around transmembrane transport of a wide range of substrates, including xenobiotics, phosphate ions, sugars (galactose, arabinose, sialic acid), nitrite/nitrate, and even neurotransmitter loading into synaptic vesicles. This pattern points to a group of membrane transporter proteins with broad substrate specificity rather than a single-substrate family.","confidence":"Medium","size":16,"edges":5,"triangles":1,"max_degree":2,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0006855","count":7},{"id":"GO:0035435","count":7},{"id":"GO:0098700","count":7},{"id":"GO:1900754","count":7},{"id":"GO:0042128","count":7}]},{"hash":"1136298655233788656","title":"Heparan sulfate proteoglycan biosynthesis and cell adhesion","description":"This cluster centers on biosynthesis of heparan sulfate proteoglycans and related glycosaminoglycans (GO:0015012, GO:0015015, GO:0030210) and on heterophilic cell\u2013cell adhesion (GO:0007157), suggesting a shared role in extracellular matrix composition and cell interactions. Additional terms reflect related metabolic processes and potential vascular/immune signaling connections (e.g., regulation of angiotensin levels, catecholamine metabolism, macrophage activation). Overall, the theme is proteoglycan biosynthesis linked to cell adhesion and signaling in tissue context.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015012","count":2},{"id":"GO:0007157","count":2},{"id":"GO:0043031","count":2},{"id":"GO:0015015","count":1},{"id":"GO:0000103","count":1}]},{"hash":"1775891409307354335","title":"Developmental cell fate specification and organogenesis","description":"This cluster shows several terms tied to cell fate decisions and tissue development (cone cell fate commitment, wing cell fate specification, pronephric glomerulus development, spermatid differentiation) with supporting growth and signaling processes, suggesting a unifying theme around developmental differentiation across tissues. Some terms are broader (unfolded protein response, progesterone response, NK cell regulation), but the core signal centers on development and organogenesis.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904211","count":2},{"id":"GO:0032570","count":2},{"id":"GO:0072137","count":1},{"id":"GO:0039021","count":1},{"id":"GO:0038005","count":1}]},{"hash":"361797943560386299","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":56,"triangles":92,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":4},{"id":"GO:0006874","count":4},{"id":"GO:0097171","count":4},{"id":"GO:0071318","count":3},{"id":"GO:0030836","count":3}]},{"hash":"5517800116818401","title":"Transmembrane Transporters","description":"The top GO terms are all about transport across membranes for diverse substrates (sialic acid, galactose, arabinose, nitrite/nitrate, phosphate, xenobiotics) and vesicular neurotransmitter loading, indicating a cluster of membrane transporter proteins with varied substrates.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":15},{"id":"GO:0006855","count":14},{"id":"GO:0035435","count":14},{"id":"GO:0098700","count":14},{"id":"GO:1900754","count":14}]},{"hash":"2278756582532335671","title":"Cardiac conduction and mechanosensory ion channels","description":"This cluster is anchored by GO terms for atrial and AV node action potentials and potassium transmembrane transport, pointing to cardiac electrophysiology and ion-channel function. It also includes mechanosensation-related terms (detection of mechanical stimulus, vestibular nucleus development), suggesting shared ion-channel roles in mechanosensory signaling, with a few peripheral terms that may reflect broader tissue-specific functions.","confidence":"Medium","size":16,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098914","count":16},{"id":"GO:0050976","count":16},{"id":"GO:0071805","count":14},{"id":"GO:0021750","count":13},{"id":"GO:0010754","count":13}]},{"hash":"404953792307623788","title":"TLR2-Mediated Innate Immune Activation","description":"The cluster is enriched for innate immune signaling genes, centered on TLR2 signaling, LPS and diacyl lipopeptide detection, and macrophage activation, with regulation of IL-6 production and non-canonical NF-kappaB signaling, indicating a TLR2-driven defense program in macrophages. A few terms about bone morphogenesis appear peripherally but do not define the main theme.","confidence":"High","size":16,"edges":101,"triangles":355,"max_degree":15,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":16},{"id":"GO:0045410","count":16},{"id":"GO:0042346","count":16},{"id":"GO:0051607","count":16},{"id":"GO:0034134","count":16}]},{"hash":"66237072895945786","title":"CYP450 Xenobiotic and Lipid Metabolism","description":"The cluster is strongly driven by GO terms for omega-hydroxylase P450 pathways, fatty acid omega-oxidation, retinoic acid catabolic processes, and metabolism of alkaloids and macrolides, all pointing to cytochrome P450\u2013mediated processing of both endogenous lipids and a range of xenobiotics. The reproductive development terms may reflect tissue-specific expression of P450s but are secondary to the central metabolic theme. Overall, the common thread is CYP450-driven metabolism across lipids, vitamins, and xenobiotics.","confidence":"High","size":16,"edges":20,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":16},{"id":"GO:0010193","count":16},{"id":"GO:0008585","count":16},{"id":"GO:0097267","count":16},{"id":"GO:0009822","count":16}]},{"hash":"1039971094594912680","title":"Immune signaling and apoptosis regulation","description":"This cluster centers on immune modulation (T cell cytotoxicity regulation; T cell homeostasis) and cell fate signaling (extrinsic apoptotic pathway), with additional, broader signal transduction terms (zinc response, bitter taste detection, viral fusion). The mixture suggests a general signaling/immune-regulation theme with apoptosis as a core component, rather than a single precise pathway. ","confidence":"Medium","size":16,"edges":44,"triangles":50,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010043","count":3},{"id":"GO:0001916","count":3},{"id":"GO:0001580","count":2},{"id":"GO:0019064","count":2},{"id":"GO:0097191","count":2}]},{"hash":"1337629264134288952","title":"Cartilage and bone development via BMP signaling","description":"GO terms cluster around chondrocyte differentiation, cartilage development and condensation, and osteoblast differentiation, with emphasis on BMP signaling regulation. This points to a skeletal development module orchestrated by BMP pathways, with additional, broader developmental terms likely reflecting tissue remodeling processes beyond cartilage/bone. ","confidence":"High","size":16,"edges":91,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051496","count":6},{"id":"GO:0002062","count":6},{"id":"GO:0061036","count":4},{"id":"GO:0001502","count":4},{"id":"GO:0045669","count":4}]},{"hash":"1451449478167380436","title":"Neural development and axon guidance","description":"Top GO terms indicate a focus on nervous system development and signaling, with motor neuron axon guidance, corpus callosum development, and MAPK (ERK/JNK) cascade involvement. While there are outliers like keratinization and metal/cadmium, the prevalent themes point to neural connectivity and signaling pathways guiding axon growth and neuronal responses. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":4},{"id":"GO:0030517","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0048148","count":2},{"id":"GO:0071732","count":2}]},{"hash":"1164515631756508458","title":"Organogenesis and immune-vascular development","description":"The top GO terms point to developmental processes across organs (mesonephric duct and metanephric kidney development, cartilage condensation, lymphatic morphogenesis) alongside immune and vascular signaling (lectin pathway, C-type lectin receptor signaling, leukocyte tethering, NK cell regulation, and platelet activation). This suggests a broad theme of organogenesis with concurrent immune-vascular interactions, rather than a single, narrow function.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0072177","count":15},{"id":"GO:0001502","count":15},{"id":"GO:0072218","count":15},{"id":"GO:0060355","count":15},{"id":"GO:0050901","count":15}]},{"hash":"2142561293985000255","title":"Neuroimmune Dopaminergic Signaling with Glial Modulation","description":"The cluster combines dopamine-related processes (transport, metabolism, and receptor signaling) with immune and glial functions (immune response, astrocyte/lglial chemotaxis, glial-derived neurotrophic factor production, eosinophil chemotaxis, xenobiotic response), suggesting a cohesive theme of dopaminergic signaling intertwined with neuroinflammatory and glial regulation in the CNS.","confidence":"Medium","size":16,"edges":90,"triangles":239,"max_degree":15,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":15},{"id":"GO:0042493","count":15},{"id":"GO:2000458","count":15},{"id":"GO:1900168","count":15},{"id":"GO:0048245","count":15}]},{"hash":"1443965687294774051","title":"Neuroimmune modulation and dopamine signaling","description":"The proteins link immune-related processes (immune response, regulation of inflammatory response, xenobiotic response, chemotaxis of immune cells and astrocytes) with dopaminergic signaling (dopamine transport, regulation of dopamine metabolism, and PLC-activating dopamine receptor signaling), suggesting coordinated CNS immune activity alongside dopamine pathways.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":16},{"id":"GO:0042493","count":16},{"id":"GO:2000458","count":16},{"id":"GO:1900168","count":16},{"id":"GO:0048245","count":16}]},{"hash":"1430597726875195444","title":"Neuroimmune Dopaminergic Signaling","description":"These terms link immune/neuroinflammatory processes with dopaminergic signaling and glial regulation. The cluster includes negative and overall immune responses, eosinophil chemotaxis, xenobiotic response, astrocyte chemotaxis, and glial-derived neurotrophic factor regulation, alongside dopamine transport, dopamine metabolism, and dopamine receptor signaling via phospholipase C. Together they point to a CNS neuroimmune-dopaminergic module.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":13},{"id":"GO:0042493","count":13},{"id":"GO:2000458","count":13},{"id":"GO:1900168","count":13},{"id":"GO:0048245","count":13}]},{"hash":"2104616926221918325","title":"Neuroimmune regulation and dopaminergic signaling","description":"The cluster\u2019s top GO terms span immune/inflammatory regulation (negative regulation of inflammatory response, immune response, xenobiotic response, eosinophil chemotaxis) and neural/dopaminergic processes (dopamine transport, regulation of dopamine metabolism, dopamine receptor signaling, astrocyte-related regulation). This points to a cohesive theme of CNS neuroimmune cross-talk with dopaminergic signaling and glial involvement (e.g., astrocyte chemotaxis and GDNF production). Confidence that this label captures the cluster\u2019s shared function is Medium.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":16},{"id":"GO:0042493","count":16},{"id":"GO:2000458","count":16},{"id":"GO:1900168","count":16},{"id":"GO:0048245","count":16}]},{"hash":"1231150147086705828","title":"Developmental Transcription and Stress Signaling","description":"The top GO terms point to transcriptional control (DNA-templated transcription) and hormone/nuclear receptor signaling (glucocorticoid pathway), along with stress responses (DNA damage response, premature senescence) and development in neural and skin lineages (keratinocyte differentiation, cerebral cortex and hippocampus development). This pattern suggests proteins that coordinate developmental gene regulation with stress-responsive signaling across multiple tissues, rather than a single specialized function. ","confidence":"Medium","size":15,"edges":72,"triangles":173,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030216","count":7},{"id":"GO:0035729","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0090400","count":6},{"id":"GO:0021987","count":6}]},{"hash":"444116303216135680","title":"Developmental transcription and RNA processing","description":"This cluster emphasizes developmental regulation of gene expression, with DNA-templated transcription and RNA processing (branch site recognition), plus protein complex formation and mitochondria\u2013nucleus signaling. The included terms point to diverse developmental programs (eye lens, testes, skeletal morphogenesis), suggesting a general theme of transcriptional control and assembly in development rather than a tissue-specific function.","confidence":"Medium","size":15,"edges":46,"triangles":52,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0070306","count":7},{"id":"GO:0072520","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0001845","count":6}]},{"hash":"679740247832984293","title":"Neuronal migration and axon guidance","description":"The terms cluster around cell migration, integrin-mediated adhesion, actin filament organization, and neural guidance events (retinal ganglion axon guidance, sensory neuron axon fasciculation), indicating a common theme of neural development, cytoskeletal remodeling, and pathfinding. Cadmium response is present but secondary to the dominant neural development signal.","confidence":"High","size":15,"edges":41,"triangles":31,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0033628","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0000278","count":4},{"id":"GO:2001275","count":3}]},{"hash":"626058080517337778","title":"Chromatin modification and NF-\u03baB signaling","description":"The cluster shows strong representation of histone modification and ubiquitination processes (acetylation/methylation regulation, histone ubiquitination, histone catabolic process) alongside NF-\u03baB pathway activation (NIK activity) and JNK cascade regulation, with V(D)J recombination suggesting immune-related chromatin regulation. This points to a cohesive theme of chromatin-state control linked to immune signaling.","confidence":"Medium","size":15,"edges":55,"triangles":114,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":8},{"id":"GO:2000620","count":8},{"id":"GO:0070512","count":8},{"id":"GO:0046328","count":8},{"id":"GO:1903762","count":8}]},{"hash":"699932373629116850","title":"NF-kB-driven cytokine production and T cell activation","description":"This cluster centers on NF-kB signaling and cytokine production (TNF, IFN-\u03b3) with processes that promote T cell proliferation and extrinsic apoptotic signaling, indicating an inflammatory immune response with apoptotic regulation. A minor portion relates to mechanosensing or other regulatory processes, but the dominant theme is immune activation and inflammation.","confidence":"High","size":15,"edges":65,"triangles":111,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":3},{"id":"GO:0032729","count":2},{"id":"GO:0032760","count":2},{"id":"GO:0097194","count":2},{"id":"GO:0097202","count":2}]},{"hash":"368707271476410463","title":"ER-Golgi trafficking and Rho GTPase signaling","description":"The top GO terms center on ER-to-Golgi vesicle transport, mRNA transport, and regulation of Rho signaling with associated phosphorylation events, suggesting a cluster that coordinates intracellular trafficking with cytoskeletal signaling and phosphorylation regulation; additional terms like mitotic cycle and hypoxia response indicate broader cellular regulation but do not override the core trafficking/signaling theme.","confidence":"Medium","size":15,"edges":51,"triangles":85,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051028","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006470","count":2}]},{"hash":"1221475269517852210","title":"Mitochondrial quality control and proteostasis","description":"The top GO terms converge on mitochondrial dynamics (both positive and negative regulation of mitochondrial fusion), mitophagy, and protein homeostasis (aggresome assembly, autoubiquitination), complemented by stress responses (cellular response to toxic substances, TNF signaling). This suggests a cohesive cluster of proteins centered on maintaining mitochondrial integrity and overall proteostasis under cellular stress.","confidence":"High","size":15,"edges":23,"triangles":10,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:1904049","count":3},{"id":"GO:0010637","count":3},{"id":"GO:0070842","count":3},{"id":"GO:0097237","count":3},{"id":"GO:0051865","count":3}]},{"hash":"1123619803784033787","title":"Neuronal development and synaptic signaling","description":"The terms cluster around neural development and synaptic remodeling: dendritic spine morphogenesis, ERK/MAPK and PI3K/AKT signaling, cell migration in development, and behavioral responses to cocaine, all pointing to neuronal differentiation and synaptic regulation rather than generic cell-cycle processes. Some proliferation-related terms appear but are less representative of the main theme. ","confidence":"High","size":15,"edges":20,"triangles":4,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008285","count":9},{"id":"GO:0000082","count":9},{"id":"GO:0051897","count":8},{"id":"GO:0060997","count":8},{"id":"GO:0070374","count":8}]},{"hash":"1017723220079153704","title":"Embryonic Organogenesis and Vascular Development","description":"The cluster centers on developmental processes across organs (multicellular organism development; atrial septum morphogenesis; lung alveolus development) and vascular formation (endothelial cell proliferation), with supporting regulatory signals (Wnt pathway regulation) and transcriptional control. This points to a cohesive theme of embryonic organogenesis and vascular/heart-lung development rather than a single signaling pathway.","confidence":"High","size":15,"edges":41,"triangles":79,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0001755","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0090090","count":6},{"id":"GO:0048286","count":6}]},{"hash":"2132005855182375274","title":"Stress response and protein neddylation/ubiquitination regulation","description":"This cluster centers on cellular stress responses (hypoxia, UV-C, gamma radiation) alongside immune signaling, and shows multiple terms related to protein post-translational modification via neddylation and ubiquitin pathways, including both positive and negative regulation. A unifying theme is stress-induced signaling coupled with regulation of protein modification systems that govern protein turnover and signaling.","confidence":"Medium","size":15,"edges":29,"triangles":15,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:0006955","count":2},{"id":"GO:2000436","count":1},{"id":"GO:0010225","count":1},{"id":"GO:0010332","count":1}]},{"hash":"1421169137303515365","title":"Rho/Rap GTPase Signaling and Membrane Traffic","description":"This cluster centers on small GTPase\u2013mediated signaling (Rho, Rap) coupled to membrane trafficking and cytoskeleton-related processes, as seen in terms like activation of GTPase activity, Rap signaling, regulation of Rho signaling, and microvillus assembly. While there are broader terms present (e.g., B cell receptor signaling, transcription), the strongest recurring theme is GTPase-driven signaling coordinating transport and cytoskeletal dynamics.","confidence":"Medium","size":15,"edges":7,"triangles":0,"max_degree":3,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0032120","count":3},{"id":"GO:0032486","count":3}]},{"hash":"643161273187670766","title":"mRNA processing and translation regulation","description":"The cluster is enriched for post-transcriptional RNA metabolism: spliceosome-mediated mRNA splicing, splice site recognition, and regulation of mRNA stability, alongside translation-related processes and initiation regulation, indicating a cohesive module in RNA processing and control of gene expression.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000380","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0048255","count":3}]},{"hash":"1422988162318863219","title":"Exocytosis and Golgi-to-plasma membrane trafficking","description":"The cluster is enriched for vesicle tethering, docking, and exocytosis terms, along with Golgi-to-membrane transport, pointing to a cohesive role in vesicle trafficking and secretion from the Golgi to the plasma membrane. Some peripheral terms (e.g., platelet aggregation, phototaxis) are less directly related but don\u2019t override the main exocytosis theme. This makes the label a strong representation of the cluster\u2019s function.","confidence":"High","size":15,"edges":86,"triangles":261,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0090522","count":5},{"id":"GO:0007266","count":4},{"id":"GO:0006904","count":3},{"id":"GO:0006896","count":3},{"id":"GO:0006887","count":3}]},{"hash":"617755442106731658","title":"Unknown","description":"This cluster's top GO terms span development (growth, bone maturation, oviduct epithelium development), immune regulation, ion transport, and metabolic signaling, with no single unifying function. Without a cohesive biological theme, a specific label would be speculative.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040018","count":3},{"id":"GO:0051023","count":3},{"id":"GO:0070977","count":3},{"id":"GO:1903408","count":3},{"id":"GO:0055078","count":3}]},{"hash":"961664358335166219","title":"Embryonic neural and organ morphogenesis","description":"This cluster shows strong emphasis on developmental processes across the nervous system (retinal ganglion axon guidance, metencephalon development, neural crest migration, medial motor column neuron differentiation) and visceral organ morphogenesis (ureteric bud morphogenesis/elongation, endocrine pancreas development, embryonic digestive tract morphogenesis), with transcriptional regulation activity also present. The shared theme is embryonic morphogenesis across multiple tissues, suggesting a coordinated developmental program.","confidence":"High","size":15,"edges":23,"triangles":15,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0031290","count":6},{"id":"GO:0045617","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0022037","count":5},{"id":"GO:0001755","count":5}]},{"hash":"1182909422384529261","title":"Inflammation-Responsive Gene Expression Regulation","description":"This cluster centers on inflammatory signaling (TNF production regulation, LPS response, prostaglandin response) and on broad regulation of gene expression (RNA splicing, transcription elongation, mRNA export) plus chromatin-related processes and cell-cycle regulation, suggesting proteins that link inflammatory cues to transcriptional and RNA-processing control.","confidence":"Medium","size":15,"edges":16,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032720","count":1},{"id":"GO:0043484","count":1},{"id":"GO:0071380","count":1},{"id":"GO:0032784","count":1},{"id":"GO:0044839","count":1}]},{"hash":"852772331234558053","title":"Gametogenesis and Developmental Signaling","description":"The cluster shows a concentration of gamete development terms (oocyte maturation, fertilization) alongside chromatin-related processes (protein localization to chromatin, DNA-templated transcription), and includes developmental signaling and morphogenesis references (Wnt signalosome assembly, imaginal disc polarity, neural migration). This suggests a set of proteins involved in gamete development and broader developmental signaling rather than a single specific function.","confidence":"Medium","size":15,"edges":10,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071168","count":2},{"id":"GO:0001556","count":2},{"id":"GO:0009566","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043046","count":2}]},{"hash":"742856249310276336","title":"Spliceosome-driven mRNA processing and translation initiation","description":"The top GO terms cluster around spliceosome-mediated mRNA processing (alternative splicing, splice site recognition, and regulation of splicing) and factors related to mRNA stability and the initiation of translation (preinitiation complex formation and regulation of translational initiation), with a note on stress-responsive mRNA regulation and a developmental term (blastocyst formation). This suggests proteins that coordinate RNA maturation and post-transcriptional control of gene expression from splicing decisions to translation initiation, justifying a combined label focused on RNA processing and translation control.","confidence":"High","size":15,"edges":20,"triangles":3,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":8},{"id":"GO:0000380","count":7},{"id":"GO:0000381","count":7},{"id":"GO:0048255","count":6},{"id":"GO:0001825","count":6}]},{"hash":"1391936268822452742","title":"TLR-Mediated Innate Immunity and NF-\u03baB Regulation","description":"The cluster is driven by innate immune and TLR signaling terms, including Toll-like receptor 9 and 2 pathways, innate immune response, and defense against virus, with negative regulation of canonical NF-\u03baB signaling suggesting a modulatory role. Some associated terms (regulatory ncRNA-mediated gene silencing, positive regulation of mRNA splicing) appear peripheral, and a couple entries like rRNA export and defecation rhythm likely reflect noise. Overall, the proteins are best grouped by their involvement in TLR-driven innate immunity and NF-\u03baB regulation.","confidence":"Medium","size":15,"edges":67,"triangles":143,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0043124","count":4},{"id":"GO:0006407","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0034162","count":4},{"id":"GO:0031047","count":4}]},{"hash":"1367773502367327890","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":8,"triangles":2,"max_degree":4,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":10},{"id":"GO:1901253","count":9},{"id":"GO:0031664","count":9},{"id":"GO:0051607","count":9},{"id":"GO:0061158","count":9}]},{"hash":"1314887556726867294","title":"Membrane-anchored immune signaling","description":"This cluster centers on GO terms related to membrane-related processes (protein insertion and targeting to membrane) and immune signaling (type II interferon production, chemokine and IL-6 production, and non-canonical NF-kappaB signaling), suggesting a theme around membrane receptors that drive inflammatory cytokine responses. A few outliers (mRNA decay, monocyte aggregation) are present but don\u2019t override the core membrane-immune motif. Confidence in this label is Moderate.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051205","count":2},{"id":"GO:0001580","count":2},{"id":"GO:0006612","count":2},{"id":"GO:1904780","count":1},{"id":"GO:0070966","count":1}]},{"hash":"1889628052878299554","title":"Embryonic development and morphogenesis","description":"The dominant GO terms describe embryonic development and tissue morphogenesis\u2014left-right patterning, placental and trophoblast differentiation, cartilage and pancreatic cell development, and EMT-related processes\u2014indicating a cohesive developmental program, with a few general RNA processing terms as ancillary functions.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000055","count":4},{"id":"GO:0035270","count":4},{"id":"GO:0060806","count":4},{"id":"GO:0060972","count":4},{"id":"GO:0060536","count":4}]},{"hash":"2264858884046702842","title":"RNA and protein methylation machinery","description":"This cluster is dominated by methylation-related GO terms, including RNA methylation (tRNA, rRNA, mRNA capping, guanine-N7 methylation) and various protein methylations (arginine, N-terminal, histone), suggesting a core function in methyltransferase activities coordinating RNA processing and epigenetic modifications.","confidence":"High","size":15,"edges":94,"triangles":335,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":9},{"id":"GO:0043985","count":8},{"id":"GO:0019919","count":8},{"id":"GO:0030488","count":8},{"id":"GO:0031167","count":8}]},{"hash":"2166911387715536353","title":"Endothelial angiogenesis and permeability signaling","description":"This cluster centers on endothelial cell\u2013driven angiogenesis and barrier regulation. GO terms point to sprouting angiogenesis and endothelial tube lumen extension, along with regulation of vascular permeability and extravasation. The presence of small GTPase (Rac/Rho) signaling, IGF receptor pathways, BMP secretion, and TNF production modulation suggests integrated signaling that coordinates growth factor responses, cytoskeletal dynamics, and inflammatory cues to drive vessel formation while controlling permeability.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048009","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0090051","count":3},{"id":"GO:0043114","count":3},{"id":"GO:0002692","count":3}]},{"hash":"1757074354109189252","title":"ERBB2/EGFR Signaling and Junction Dynamics","description":"Dominant signal is ERBB2 signaling, with strong representation for adherens junction organization and epithelial migration, plus modulation of tyrosine phosphorylation and related pathways (e.g., p38MAPK). The presence of neuronal synapse-related terms hints at broader signaling impacts, but the core cluster centers on growth factor receptor signaling and cell\u2013cell adhesion control.","confidence":"High","size":15,"edges":102,"triangles":418,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":15},{"id":"GO:0048679","count":15},{"id":"GO:0010633","count":15},{"id":"GO:1903753","count":15},{"id":"GO:0042059","count":15}]},{"hash":"568896215810536655","title":"RNAP II Transcription Repression with Redox/ER Stress","description":"The cluster centers on transcriptional control by RNA polymerase II\u2014negative regulation of RNAP II\u2013mediated transcription, together with DNA-templated transcription\u2014plus redox-related processes (cell redox homeostasis, protein deglutathionylation) and ER stress response, suggesting a theme of transcriptional repression linked to redox/ER stress signaling.","confidence":"Medium","size":15,"edges":51,"triangles":79,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0046826","count":11},{"id":"GO:0045454","count":8},{"id":"GO:1903206","count":7},{"id":"GO:1903026","count":7}]},{"hash":"665081894699489720","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":91,"triangles":312,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0044205","count":7},{"id":"GO:0042493","count":7},{"id":"GO:0009636","count":6},{"id":"GO:0045880","count":5},{"id":"GO:0001542","count":5}]},{"hash":"1474045159471668945","title":"MAPK signaling regulation and cell cycle control","description":"GO terms emphasize dephosphorylation events (tyrosine/threonine), negative regulation of ERK/MAPK cascades, and cell cycle control, with ancillary links to VEGF and T cell receptor signaling. This points to a cohesive module of phosphatases and regulators that modulate MAPK signaling to influence cell proliferation and immune signaling cross-talk. Confidence: High","confidence":"","size":15,"edges":46,"triangles":70,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":13},{"id":"GO:0007049","count":13},{"id":"GO:0070373","count":12},{"id":"GO:0050860","count":12},{"id":"GO:0000200","count":12}]},{"hash":"1017349658587996294","title":"MAPK signaling in neuronal development and dendrite morphogenesis","description":"This cluster is characterized by enrichment of MAPK-related terms (p38MAPK cascade, ERK1/ERK2 cascade) alongside stimuli-responsive pathways (PMA, EGF, GM-CSF) and neuronal development processes (nervous system development, dendrite morphogenesis, hippocampus development). The convergence of signaling cascades and neuronal morphogenesis terms suggests MAPK-driven signaling roles in neuronal differentiation and dendritic/hippocampal development.","confidence":"High","size":15,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904628","count":3},{"id":"GO:0038066","count":3},{"id":"GO:0070371","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0031532","count":3}]},{"hash":"1054176612449458244","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":22,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0006189","count":4},{"id":"GO:0009229","count":4},{"id":"GO:0009228","count":4}]},{"hash":"1508989140773191075","title":"Nervous and muscular development","description":"This cluster\u2019s top GO terms center on development of neural and muscular tissues, including nervous system development, hippocampus development, skeletal muscle tissue development, heart development, and sarcomere organization, indicating a theme of coordinated neural and muscle tissue formation. There are also terms related to cell adhesion and migration (filopodium/adhesion spreading, fibroblast migration) and signaling. The presence of an outlier immune signaling term (B cell receptor signaling) suggests some noise, but the dominant pattern is neural and muscular development with supportive signaling and adhesion processes. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0045214","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0007519","count":3},{"id":"GO:0033138","count":3}]},{"hash":"1541578179384700323","title":"Lamellipodium Formation and GTPase Signaling","description":"The top GO terms cluster around actin-driven lamellipodium assembly and activation of GTPase activity, pointing to cytoskeletal remodeling and cell migration. Additional terms on ubiquitin-dependent protein catabolism, phosphatidylinositol and tyrosine dephosphorylation suggest coordinated signaling regulation of these processes. Some outliers related to myelination and peroxisome inheritance hint at broader cellular organization roles, but the core theme remains cytoskeleton dynamics and signaling control of movement and proliferation.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0051262","count":2}]},{"hash":"1211366329664898030","title":"Developmental transcriptional regulation","description":"The cluster shows strong representation of transcription-related GO terms (DNA-templated transcription; positive regulation of transcription by RNA polymerase II) together with multiple development-related processes across various tissues (liver, placenta, gliogenesis, T cell differentiation, myotube/dendrite development, etc.), suggesting a role in controlling gene expression during development.","confidence":"Medium","size":15,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045944","count":3},{"id":"GO:0097421","count":3},{"id":"GO:0001892","count":2},{"id":"GO:0033082","count":2}]},{"hash":"1200425926244540483","title":"Bacteriocin secretion, transport, and immunity","description":"The top GO terms cluster around secretion and transporter activities related to bacteriocins\u2014protein secretion by a Type I system, bacteriocin transport, and bacteriocin immunity\u2014along with related peptide export and various transmembrane transport processes. This points to a cohesive group of membrane-associated proteins involved in exporting bacteriocins or peptide signals and providing immunity, with additional xenobiotic and cysteine transport reflected in the neighborhood terms. A few outliers (mercury response, MHC I\u2013related antigen processing) may be noise or cross-species annotations, but the dominant signal is bacteriocin-related secretion and transport.","confidence":"High","size":15,"edges":74,"triangles":191,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030253","count":10},{"id":"GO:0030153","count":10},{"id":"GO:0046689","count":10},{"id":"GO:0072089","count":10},{"id":"GO:0019885","count":10}]},{"hash":"340557022700919183","title":"Tagatose-6-phosphate and Lactose Catabolism","description":"The cluster is dominated by sugar metabolism terms, notably D-tagatose 6-phosphate catabolic and lactose catabolic processes via tagatose-6-phosphate, plus glycolytic steps through fructose-6-phosphate and responses to various sugars (fructose, sucrose). This points to a cohesive sugar catabolic module centered on tagatose/lactose utilization, with auxiliary links to broader carbohydrate biosynthesis pathways (e.g., ADP-L-glycero-beta-D-manno-heptose and inositol phosphate biosynthesis). Confidence in this theme is high.","confidence":"High","size":15,"edges":31,"triangles":25,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:2001059","count":4},{"id":"GO:0009750","count":4},{"id":"GO:0006175","count":4},{"id":"GO:0006169","count":4},{"id":"GO:0061615","count":4}]},{"hash":"918148959109415025","title":"Pore-forming pyroptosis and innate defense","description":"This cluster centers on GO terms for pore formation and assembly, pyroptotic inflammatory response, apoptotic signaling, and defense against bacteria, suggesting a shared role in inflammasome-driven pore-forming cell death and innate immunity. Some other terms (sensory organ development) appear less related and may reflect broad annotations.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035915","count":2},{"id":"GO:0070269","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0036331","count":2},{"id":"GO:2001244","count":2}]},{"hash":"1398894471716563880","title":"Nervous system development and motor function","description":"This cluster is dominated by terms related to neural structure and motor activity: neural development signals (Wnt regulation), neurofilament cytoskeleton organization, Schwann cell migration, neuromuscular processes, visual perception, and musculoskeletal movement. Membrane transport and lipid signaling terms appear as supporting components but do not override the neural/motor theme.","confidence":"High","size":15,"edges":22,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030111","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0001306","count":2},{"id":"GO:1900148","count":2}]},{"hash":"1904577667076464081","title":"Genome Integrity and Translation","description":"The cluster shows enrichment for genome maintenance processes (DNA repair, DNA recombination, telomere maintenance, cell cycle checkpoint) together with translation-related activities (protein synthesis and mitochondrial tRNA aminoacylation). This suggests a functional module linking genome stability with the translation machinery, with embryonic development likely reflecting developmental roles of these processes. ","confidence":"Medium","size":15,"edges":24,"triangles":35,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0001701","count":4},{"id":"GO:0006310","count":3},{"id":"GO:0072581","count":3},{"id":"GO:0070200","count":3}]},{"hash":"1495409224620428972","title":"RNA and protein methylation","description":"This cluster centers on methylation and RNA/protein modification, with GO terms for tRNA methylation, tRNA wobble uridine modification, 7-methylguanosine mRNA capping, and peptidyl-arginine/histone methylation, implying a core set of methyltransferases. Some terms like cobalamin biosynthesis, antibiotic biosynthesis, and nodulation may reflect linked metabolic enzymes or annotation noise, but the dominant signal is methylation-related biology.","confidence":"Medium","size":15,"edges":44,"triangles":50,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":13},{"id":"GO:0030488","count":12},{"id":"GO:0002098","count":9},{"id":"GO:0019919","count":9},{"id":"GO:0046690","count":9}]},{"hash":"229421733971151519","title":"Telomere Maintenance and Wnt Signaling Regulators","description":"The top GO terms point to telomere maintenance and capping, with localization to the telomeric chromosome region, indicating a core telomere protection/maintenance theme. Additional terms reference Wnt signaling, suggesting occasional cross-talk or shared regulatory components. Overall, the cluster appears to group proteins involved in telomere biology with some signaling-related roles rather than a single pathway.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0016055","count":2},{"id":"GO:1904908","count":2},{"id":"GO:1904743","count":2}]},{"hash":"334784427999743561","title":"Innate Immune Activation and Coagulation","description":"The top GO terms cluster around innate immune and inflammatory processes (leukocyte migration, LPS response, Toll signaling, IL-1\u03b2 production) and coagulation (Factor XII activation, seminal clot liquefaction). The combination suggests coordinated immune response and coagulation pathway cross-talk, with some broader signaling (GPCR and Wnt) that are secondary to the dominant immune/coagulation theme. Confidence: High","confidence":"","size":15,"edges":66,"triangles":131,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0002523","count":13},{"id":"GO:0001867","count":11},{"id":"GO:0042127","count":10},{"id":"GO:1900738","count":10},{"id":"GO:0002542","count":10}]},{"hash":"717999269545737149","title":"Immune signaling and developmental pathways","description":"Rationale: Top GO terms include immune activation (response to lipopolysaccharide, Toll signaling, interleukin-1 beta production) and developmental cues (Wnt signaling, pancreas morphogenesis), with additional coagulation-related terms (Factor XII activation, seminal clot liquefaction). The cluster appears to connect immune signaling with developmental processes and coagulation, rather than a single narrow function.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042127","count":14},{"id":"GO:1900738","count":14},{"id":"GO:0002542","count":14},{"id":"GO:0016055","count":14},{"id":"GO:0045752","count":14}]},{"hash":"2162393213643560065","title":"Peripheral neuron axon guidance and neural crest migration","description":"The top GO terms cluster around axonogenesis, axon extension and guidance, and neural crest\u2013related neuron projection and organization (e.g., semaphorin-plexin signaling, sympathetic and trigeminal neuron guidance, neural crest migration). A couple of terms about foam cell differentiation and blood coagulation appear minor compared to the dominant axon guidance theme, supporting a cohesive label for this cluster as axon guidance and neural crest\u2013driven peripheral neuron development.","confidence":"High","size":15,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060385","count":4},{"id":"GO:0097490","count":4},{"id":"GO:0021785","count":4},{"id":"GO:0048846","count":4},{"id":"GO:1902287","count":4}]},{"hash":"1345578084352755297","title":"EGFR/ERBB2 Signaling Regulation and Cell Adhesion","description":"The cluster centers on modulation of growth factor signaling (ERBB2/EGFR; p38 MAPK) and regulation of cell\u2013cell adhesion and migration (adherens junction organization, epithelial migration). Neural remodeling terms (axon regeneration, dendritic spine development) accompany these signaling and adhesion aspects, suggesting a cohesive program of signaling attenuation linked to adhesion and tissue remodeling.","confidence":"High","size":15,"edges":75,"triangles":196,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":15},{"id":"GO:0048679","count":15},{"id":"GO:0010633","count":15},{"id":"GO:1903753","count":15},{"id":"GO:0042059","count":15}]},{"hash":"1084546283709792231","title":"LPS-induced innate immune signaling and macrophage activation","description":"GO terms indicate a cohesive theme of innate immune response to lipopolysaccharide, with downstream ERK and PI3K/AKT signaling and positive regulation of macrophage chemotaxis, highlighting LPS-triggered inflammatory signaling and macrophage activation.","confidence":"High","size":15,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014068","count":7},{"id":"GO:0043552","count":6},{"id":"GO:0016525","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0071222","count":5}]},{"hash":"898512763243971439","title":"Neuronal development and synapse formation","description":"The cluster is dominated by GO terms for nervous system development, synapse assembly, and neuron cell\u2013cell adhesion, along with myelination, indicating roles in neural differentiation, connectivity, and nerve fiber maturation. The presence of ossification and angiogenesis terms may reflect broader developmental contexts or non-neural roles intersecting with neural development, but the strongest signal remains neural development and synaptic adhesion/formation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0051965","count":6},{"id":"GO:0007158","count":5},{"id":"GO:0043931","count":5},{"id":"GO:0007156","count":5}]},{"hash":"1703841632177450472","title":"Neural development and myelination","description":"The cluster is dominated by GO terms tied to nervous system development and function\u2014peripheral nervous system development, synapse organization, nerve impulse transmission, voltage-gated sodium channel clustering, and myelination\u2014suggesting a cohesive role in neural differentiation and myelin formation. Hedgehog/BMP signaling terms further support developmental signaling relevant to neural tissues, with only a few terms (kidney development, myoblast differentiation) as peripheral notes.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045663","count":13},{"id":"GO:0050808","count":12},{"id":"GO:0007422","count":12},{"id":"GO:0030513","count":12},{"id":"GO:0001822","count":12}]},{"hash":"475746416206609413","title":"Neural and cardiac development signaling","description":"This cluster centers on broad signaling and developmental processes across nervous system and heart/muscle tissues, with terms like NF-kappaB signaling, synaptic vesicle exocytosis regulation, myoblast fusion, retina layer formation, and substantia nigra development, plus heart contraction regulation, indicating a set of proteins involved in developmental and neuronal/cardiac signaling and function.","confidence":"Medium","size":15,"edges":101,"triangles":409,"max_degree":14,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0043123","count":15},{"id":"GO:0007165","count":15},{"id":"GO:0016061","count":14},{"id":"GO:0007520","count":14},{"id":"GO:0006469","count":14}]},{"hash":"155310059643393385","title":"Mitochondrial Electron Transport Chain","description":"These proteins are centered on mitochondrial respiration and ATP production, including assembly of complexes III and IV and the respirasome, proton pumping, and overall electron transport chain activity.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":5},{"id":"GO:0009060","count":4},{"id":"GO:0033617","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0034551","count":2}]},{"hash":"1633117506076895120","title":"RNA stability and translational control","description":"The cluster\u2019s terms cluster around post-transcriptional gene regulation, focusing on mRNA stability, translational initiation/reinitiation, and RNA silencing by miRNAs and regulatory ncRNAs, with supporting roles in splice site recognition and preinitiation complex formation. This indicates a coherent theme of RNA-level control rather than transcriptional regulation.","confidence":"High","size":15,"edges":102,"triangles":417,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":15},{"id":"GO:0048255","count":13},{"id":"GO:0001825","count":13},{"id":"GO:0006446","count":13},{"id":"GO:1900363","count":13}]},{"hash":"559938597462962608","title":"Unknown","description":"The GO terms across this cluster are highly diverse, including cardiac muscle processes, cold/stress responses, peroxisome autophagy, transport, iron-sulfur cluster assembly, redox processes, immune differentiation, transcription regulation, and ergosterol biosynthesis regulation. There isn\u2019t a single cohesive functional theme tying most proteins together, so a precise, representative label is not reliable.","confidence":"","size":15,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055119","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0050826","count":2},{"id":"GO:0030242","count":2},{"id":"GO:0006810","count":2}]},{"hash":"1752467976271567491","title":"Neuronal development and axon guidance","description":"Most terms point to neural development and axon pathfinding (pyramidal neuron development, olfactory lobe development, axonal fasciculation, axon extension in guidance) and signaling via receptor tyrosine kinases. The presence of protein ubiquitination and centrosome localization supports neuronal morphology and trafficking processes. A few outliers (e.g., male gonad development) may reflect broader gene roles or annotation noise, but the dominant theme is neuronal development and axon guidance.","confidence":"High","size":15,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0014068","count":5},{"id":"GO:0014912","count":3},{"id":"GO:0007413","count":3},{"id":"GO:0007169","count":3},{"id":"GO:0048846","count":3}]},{"hash":"387299434664309435","title":"Innate Immune NF-kappaB Signaling","description":"The prevalent GO terms point to innate immune response and NF-kappaB pathway regulation (response to lipopolysaccharide, positive/negative regulation of NF-kappaB signaling). These together suggest the cluster\u2019s proteins function in immune signaling and inflammatory transcription control, despite some orthogonal terms that may reflect broader annotations.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0046688","count":2},{"id":"GO:0043123","count":2}]},{"hash":"686951489972628478","title":"Innate immune defense against bacteria","description":"This cluster is dominated by GO terms related to defense response to bacteria and innate immune response, with several entries touching on regulation of LPS signaling, indicating a cohesive theme of antibacterial innate immunity. Some terms may reflect broader or pleiotropic gene functions, but the core signals point to antibacterial innate defense.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042742","count":4},{"id":"GO:0031665","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0021762","count":2},{"id":"GO:0045944","count":2}]},{"hash":"1570549966572098813","title":"Embryonic Development and Organogenesis","description":"The top GO terms point to broad embryonic development across multiple tissues and organ systems: placental/trophoblast differentiation, heart development, left-right patterning, endocrine organ development, cartilage morphogenesis, EMT in heart structures, and nervous system maturation, suggesting a cohesive cluster of proteins involved in embryogenesis and organ morphogenesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":6},{"id":"GO:0060536","count":6},{"id":"GO:0060972","count":6},{"id":"GO:0035270","count":6},{"id":"GO:0003323","count":6}]},{"hash":"1591275303009974311","title":"Embryogenesis and Organogenesis","description":"The GO terms are dominated by embryonic development processes (placentation, trophoblast differentiation, left-right patterning, cartilage morphogenesis, endocrine system development, and EMT in heart development), indicating a cohesive theme of embryo formation and organogenesis across multiple tissues, including placental development.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":3},{"id":"GO:0060536","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0035270","count":3},{"id":"GO:0003323","count":3}]},{"hash":"944504625243744221","title":"Unknown","description":"The top GO terms span many different biological areas (respiratory system, osteoclast differentiation, prostaglandin biosynthesis, circadian gene expression, pregnancy, renal ion handling, ureteric bud morphogenesis, skeletal muscle development, BMP signaling, and intestinal stem cell homeostasis), with no clear single function or pathway linking them. The lack of edges also suggests no strong interaction-based cohesion, so there isn\u2019t a coherent cluster theme to name meaningfully.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003016","count":2},{"id":"GO:0045670","count":2},{"id":"GO:0001516","count":2},{"id":"GO:0032922","count":1},{"id":"GO:0007565","count":1}]},{"hash":"1242670011052399986","title":"Oxidative Metabolism and Catabolic Processes","description":"The cluster\u2019s GO terms are dominated by oxidation-related and diverse catabolic activities, including oxidation-reduction, formaldehyde and amino acid catabolism, fatty acid omega-oxidation, prostaglandin metabolism, and lignin biosynthesis, with related respiration and stress-response terms. This suggests proteins participating broadly in oxidative metabolism and the breakdown of various substrates, rather than a single specific pathway. ","confidence":"High","size":15,"edges":17,"triangles":13,"max_degree":6,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0046294","count":6},{"id":"GO:0019518","count":5},{"id":"GO:0006693","count":5},{"id":"GO:0000947","count":5}]},{"hash":"2262337643496929684","title":"Peripheral nerve development and neuron\u2013Schwann cell function","description":"This cluster features motor neuron differentiation, neuromuscular process activity, and Schwann cell migration/regulation, along with neurofilament cytoskeleton organization and matrix/lipid biosynthesis (collagen and ceramide) that support nerve structure and neurotransmission. Together, these terms point to peripheral nervous system development, maintenance, and neuron\u2013Schwann cell interactions driving neuromuscular signaling.","confidence":"High","size":15,"edges":99,"triangles":386,"max_degree":14,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0044257","count":3},{"id":"GO:0001306","count":3},{"id":"GO:0021523","count":3},{"id":"GO:0051935","count":3},{"id":"GO:0050884","count":3}]},{"hash":"1388362075285861158","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":74,"triangles":182,"max_degree":14,"top_function":"wound healing","top_go_terms":[{"id":"GO:0045669","count":8},{"id":"GO:0048839","count":7},{"id":"GO:0045216","count":7},{"id":"GO:0003181","count":7},{"id":"GO:0001501","count":7}]},{"hash":"1381348690641042198","title":"Neuronal Calcium Signaling and Synaptic Transmission","description":"Several top GO terms point to neuronal function: neuronal action potential, chemical synaptic transmission, detection of calcium ion, and potassium ion transport. This suggests a cluster centered on Ca2+-dependent signaling and synaptic communication in neurons. Other terms like ER-to-Golgi vesicle transport reflect general vesicle trafficking that complements neuronal activity. A few terms related to inflammation and fibrinolysis appear as noise rather than central to the cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042730","count":2},{"id":"GO:0050766","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0006813","count":1},{"id":"GO:0005513","count":1}]},{"hash":"459254647257285687","title":"Epithelial Innate Immunity and Stress Response","description":"Most top terms cluster around innate immune signaling (innate immune response, classical complement activation), stress and damage responses (response to hydrogen peroxide, apoptotic process), and development/maintenance of epithelial tissues (eye development, epidermis development, GI epithelium maintenance). There is one outlier term about collateral sprouting, but the majority points to epithelial barrier immunity and cellular stress responses.","confidence":"Medium","size":15,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048672","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0070301","count":3}]},{"hash":"1206385430804464494","title":"Nuclear envelope and chromatin dynamics","description":"The prevalent GO terms cluster around nuclear architecture and chromatin organization, including nucleokinesis and nuclear migration along microfilaments, telomere tethering at the nuclear periphery, meiotic telomere attachment to the nuclear envelope, and centromere clustering at the nuclear envelope, suggesting a cohesive theme of nuclear positioning during cell movement and division, with related cytoskeletal anchoring terms. A few terms such as immunoglobulin production, magnesium ion transport, and bone remodeling appear unrelated and may reflect noise in the data.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002377","count":2},{"id":"GO:0015693","count":2},{"id":"GO:0021817","count":2},{"id":"GO:0046850","count":2},{"id":"GO:0031022","count":2}]},{"hash":"277880048615946038","title":"Embryonic Development and Morphogenesis","description":"The top GO terms point to various morphogenetic and developmental processes across multiple tissues (trophoblast giant cell differentiation, mesoderm, cartilage, hair follicle, palate development, left-right patterning, endocrine development). While a few terms are general cellular machinery (splicing, ribosomal export), the dominant signal is embryonic development and tissue morphogenesis, justifying a developmental label.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":4},{"id":"GO:0000055","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0007498","count":4},{"id":"GO:0060536","count":4}]},{"hash":"1603170062481470685","title":"Neuronal signaling and receptor trafficking","description":"This cluster is dominated by GO terms related to neuronal activity and trafficking of receptors and endosomes (calcium transport, action potential propagation, postsynaptic receptor transport, endosome-to-lysosome pathways), suggesting a cohesive theme of neural signaling and intracellular receptor handling. Some terms about adhesion or bone resorption appear tangential, but the neural-focused terms predominate. ","confidence":"Medium","size":15,"edges":91,"triangles":306,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0070588","count":9},{"id":"GO:2001046","count":9},{"id":"GO:0060081","count":8},{"id":"GO:0045779","count":8},{"id":"GO:0061772","count":8}]},{"hash":"2193009178779319713","title":"Neural development and signaling","description":"The cluster contains GO terms centered on nervous system development and neuron survival/apoptosis regulation, along with neuronal GPCR signaling (e.g., opioid receptor signaling). This suggests a neural development/signaling theme as the core function. However, there are outlier terms such as ergosterol biosynthesis and lipid transport that do not fit neatly with neural processes, indicating only partial coherence. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040008","count":2},{"id":"GO:1903507","count":2},{"id":"GO:2001199","count":1},{"id":"GO:0038095","count":1},{"id":"GO:0070207","count":1}]},{"hash":"64912849033239911","title":"FGF-MAPK Signaling in Organ Development","description":"This cluster centers on FGFR signaling feeding into MAPK/ERK cascades, with GO terms spanning nervous system development, organ induction, angiogenesis, and tissue morphogenesis (lung mesenchyme, salivary gland branching). The repeated mentions of ERK/MAPK cascades and FGFR-mediated regulation, along with development and vascular processes, point to a coherent theme of FGF-driven MAPK signaling governing organogenesis and allied morphogenetic events.","confidence":"High","size":15,"edges":6,"triangles":2,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":9},{"id":"GO:0060484","count":8},{"id":"GO:0070374","count":8},{"id":"GO:0001759","count":8},{"id":"GO:2000546","count":8}]},{"hash":"631258014438940984","title":"Nephrogenesis with immune-vascular interactions","description":"The prominent GO terms point to kidney development (mesonephric duct and metanephric limb growth) alongside features of vascular and immune processes (lymph vessel morphogenesis, leukocyte tethering/rolling, C-type lectin receptor signaling, complement activation via lectin pathway, and platelet activation). This suggests a cluster of proteins involved in organogenesis that is closely linked to vascular and immune signaling, rather than a single enzyme or receptor pathway. Therefore a compact label focusing on nephrogenesis with immune-vascular interactions fits best.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072177","count":15},{"id":"GO:0001502","count":15},{"id":"GO:0072218","count":15},{"id":"GO:0060355","count":15},{"id":"GO:0050901","count":15}]},{"hash":"357866029798150682","title":"Lipid and steroid biosynthesis","description":"The top GO terms are dominated by biosynthetic processes, especially fatty acid elongation and very long-chain fatty acid biosynthesis, with glucocorticoid biosynthetic process also appearing. This suggests a core theme of lipid and steroid biosynthesis, with some peripheral biosynthetic pathways (phylloquinone catabolic, BH4 biosynthesis, antibiotic biosynthesis) accompanying them. Confidence: High","confidence":"","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030497","count":15},{"id":"GO:0006704","count":15},{"id":"GO:0042376","count":15},{"id":"GO:0042619","count":15},{"id":"GO:0055114","count":15}]},{"hash":"880592717213788722","title":"Gram-positive cell wall glycan and antibiotic biosynthesis","description":"This cluster is characterized by strong signals for biosynthetic processes, including antibiotic biosynthesis/metabolism and various glycan-related assembly steps (lipoteichoic acid, dolichol-linked oligosaccharides) that are typical of Gram-positive bacterial cell walls, with carbohydrate metabolism and cell division terms supporting a broader biosynthetic, growth-associated theme.","confidence":"Medium","size":15,"edges":77,"triangles":247,"max_degree":13,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0017000","count":12},{"id":"GO:0051301","count":9},{"id":"GO:0007049","count":9},{"id":"GO:0009718","count":9},{"id":"GO:0030259","count":8}]},{"hash":"113814211735922932","title":"Unknown","description":"The top GO terms cover a wide range of functions (nuclear pore complex assembly; taste perception; skin development; peroxisome organization; detoxification; synaptic activity regulation; signaling; apoptotic and cardiac contraction processes). There is no single dominant biological process or shared function tying the proteins together, and the lack of edges supports a lack of cohesive interaction, so a specific label cannot be reliably inferred.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051292","count":3},{"id":"GO:0050913","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0050916","count":2},{"id":"GO:0032581","count":2}]},{"hash":"1120822393972405599","title":"Innate immunity and tissue remodeling","description":"The top GO terms cluster around innate immune response, coagulation, and vascular/tissue remodeling (sprouting angiogenesis, smooth muscle proliferation, embryo implantation, ossification), suggesting an inflammation-driven remodeling theme across tissues. A few neural-associated terms appear, likely due to broad annotations, but the dominant signal is immune-related remodeling. ","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0043113","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0002040","count":3},{"id":"GO:0048661","count":3}]},{"hash":"246080817095302036","title":"Neuro-immune signaling","description":"This cluster combines nervous system-related terms (locomotory behavior, visual perception) with glial activity (astrocyte chemotaxis, glial-derived neurotrophic factor production) and immune/inflammatory terms (immune response, eosinophil chemotaxis, inflammatory regulation) as well as xenobiotic response and coagulation. The mix suggests a theme of neuro-immune communication and its role in behavior, though the terms span several related but distinct processes, so the label is plausible but not strongly cohesive. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007626","count":12},{"id":"GO:0007601","count":11},{"id":"GO:0007596","count":11},{"id":"GO:0050728","count":10},{"id":"GO:0042493","count":10}]},{"hash":"1361117187139252628","title":"Embryonic craniofacial and neural development","description":"These proteins are tied to early embryonic morphogenesis across skeletal/craniofacial structures (palate, cranial skeleton, digits, limbs) and neural development (motor neuron differentiation, cerebral cortex regionalization). The dominance of developmental GO terms across both skeletal and neural tissues suggests a cohesive embryonic morphogenesis theme, justifying this label.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":6},{"id":"GO:0035115","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0021524","count":4},{"id":"GO:0021983","count":4}]},{"hash":"1526120169568710900","title":"Antiviral Immune Response and Humoral Immunity","description":"The cluster\u2019s top GO terms converge on antiviral defense, cytokine regulation (including Th2/IL-5), antigen presentation (MHC I biosynthesis), and STAT signaling, pointing to coordinated immune signaling against viral infections with adaptive (humoral) aspects. Coagulation and host-immunomodulatory terms further reflect inflammation linked to antiviral responses. Overall, the theme is antiviral immune response with humoral involvement.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2000663","count":14},{"id":"GO:0051607","count":14},{"id":"GO:2000552","count":14},{"id":"GO:0046597","count":14},{"id":"GO:0045343","count":14}]},{"hash":"2055203906732222995","title":"Axon Guidance and Neural Development","description":"The top GO terms cluster around neuronal development and axon wiring, including axonal fasciculation, branchiomotor neuron axon guidance, sympathetic neuron projection extension, and semaphorin-plexin signaling in axon guidance, plus multicellular organism development. Immune-related terms (complement activation, chemokine production) are present but secondary to the strong neural guidance signal. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":3},{"id":"GO:0090197","count":3},{"id":"GO:0007413","count":3},{"id":"GO:0001798","count":3},{"id":"GO:0006958","count":3}]},{"hash":"880985823981008393","title":"Inhibitory Synapse Assembly and Vesicle Trafficking","description":"This cluster centers on inhibitory synapse features, including gephyrin clustering and postsynaptic density assembly, regulation of inhibitory postsynaptic potentials, and synaptic vesicle exo- and endocytosis, with associated cytoskeletal organization at the active zone, indicating a coherent set of proteins involved in GABAergic synapse formation and vesicle cycling.","confidence":"High","size":15,"edges":94,"triangles":341,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":15},{"id":"GO:0048789","count":15},{"id":"GO:0002087","count":15},{"id":"GO:0097151","count":15},{"id":"GO:1900244","count":15}]},{"hash":"396586605981234237","title":"Neuroimmune modulation and dopamine signaling","description":"This cluster centers on immune and inflammatory processes (negative regulation of inflammatory response; immune response; response to xenobiotic stimulus; eosinophil and astrocyte chemotaxis; glial cell-derived neurotrophic factor production) and, in the same proteins, dopaminergic pathways (dopamine transport; regulation of dopamine metabolic process; phospholipase C-activating dopamine receptor signaling). The co-occurrence suggests a functional theme of glial/neuronal communication where immune signaling intersects with dopaminergic signaling, as seen in neuroinflammation and xenobiotic responses affecting astrocyte behavior and dopamine dynamics.","confidence":"Medium","size":15,"edges":22,"triangles":7,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":15},{"id":"GO:0042493","count":15},{"id":"GO:2000458","count":15},{"id":"GO:1900168","count":15},{"id":"GO:0048245","count":15}]},{"hash":"2147296602591684501","title":"Immune and inflammatory signaling with development","description":"This cluster is dominated by immune/inflammatory terms (immune response, LPS response, prostaglandin signaling, xenobiotic response, negative regulation of inflammation) and includes development-related processes (bone remodeling, heart development). The coexistence of inflammatory signaling with developmental processes suggests a shared immune\u2013development axis, with some behavioral regulation terms likely reflecting integrated signaling pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006955","count":8},{"id":"GO:0046849","count":8},{"id":"GO:0007626","count":8},{"id":"GO:0032496","count":7},{"id":"GO:0008284","count":7}]},{"hash":"1091803297793443183","title":"Dopaminergic Neuroimmune Modulation","description":"The cluster combines immune/inflammatory GO terms with glial/neural context and dopamine signaling (dopamine transport and PLC-activating dopamine receptor pathway), suggesting a common theme where dopamine modulates neuroimmune and glial functions.","confidence":"Medium","size":15,"edges":85,"triangles":248,"max_degree":14,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":15},{"id":"GO:0042493","count":15},{"id":"GO:2000458","count":15},{"id":"GO:1900168","count":15},{"id":"GO:0048245","count":15}]},{"hash":"1085497168335441426","title":"Neuroimmune regulation of dopamine signaling","description":"These proteins appear to coordinately relate to immune processes within the nervous system and dopaminergic signaling, as suggested by GO terms for inflammatory regulation, xenobiotic response, astrocyte and eosinophil chemotaxis, glial-derived neurotrophic factor production, immune response, and dopamine transport and PLC-activated dopamine receptor signaling. The shared theme points to neuroinflammation intersecting with dopamine pathways, involving glial cells and neurotrophic support. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":15},{"id":"GO:0042493","count":15},{"id":"GO:2000458","count":15},{"id":"GO:1900168","count":15},{"id":"GO:0048245","count":15}]},{"hash":"1374190813562716585","title":"Dopamine signaling and glial-immune regulation","description":"The cluster\u2019s top GO terms cluster around immune/inflammatory regulation (negative regulation of inflammatory response, immune response, eosinophil chemotaxis) alongside glial/astrocyte processes (regulation of astrocyte chemotaxis, glial cell-derived neurotrophic factor production) and dopaminergic signaling components (dopamine transport, regulation of dopamine metabolic process, phospholipase C-activating dopamine receptor signaling). This suggests a coherent theme where dopamine signaling interfaces with glial/immune functions in the neural environment, supporting a combined role in neural immune modulation. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":15},{"id":"GO:0042493","count":15},{"id":"GO:2000458","count":15},{"id":"GO:1900168","count":15},{"id":"GO:0048245","count":15}]},{"hash":"1913214444278817021","title":"GTPase-driven cell polarity and trafficking","description":"The cluster clusters around actions regulated by GTPases (positive regulation of GTPase activity), localization to cilia, lamellipodium formation, and endosome trafficking, all of which tie to cell polarity and cytoskeletal remodeling. There are also occasional outliers (osteoblast fate commitment, histamine secretion) that may reflect broader signaling roles in specific tissues, but the dominant pattern points to coordinated signaling, trafficking, and morphogenesis.","confidence":"Medium","size":14,"edges":36,"triangles":44,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0061512","count":2},{"id":"GO:0002051","count":2},{"id":"GO:0032005","count":2},{"id":"GO:2000769","count":2}]},{"hash":"1180480363355218535","title":"Ubiquitin/Neddylation Regulation of Cell Cycle and Apoptosis","description":"This cluster centers on ubiquitin- and Nedd8-related regulation, with terms for K6-linked ubiquitination, neddylation, and positive regulation of ubiquitin transferase activity, plus APC/C-dependent catabolic processes. The presence of apoptotic and DNA repair regulation hints suggests a cohesive theme around protein turnover and DNA damage response intertwined with cell-cycle control.","confidence":"High","size":14,"edges":53,"triangles":103,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043524","count":13},{"id":"GO:0006344","count":13},{"id":"GO:0031145","count":13},{"id":"GO:0043951","count":13},{"id":"GO:0085020","count":13}]},{"hash":"948079055599346086","title":"RNA Transcription and Ribosome Biogenesis","description":"This cluster centers on transcription machinery across RNA polymerases I, II, and III and on ribosome biogenesis, as shown by GO terms for RNA-templated transcription, Pol I/II/III transcription, and ribosome assembly. The combination of transcription initiation/elongation/termination terms and ribosome biogenesis points to a cohesive functional module governing RNA production and ribosome production, with cell division and development terms playing supportive roles.","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001172","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0006366","count":5},{"id":"GO:0042797","count":5},{"id":"GO:0006386","count":4}]},{"hash":"247602519832001366","title":"Developmental and ciliogenesis cluster","description":"This cluster is dominated by developmental terms, especially skeletal system development and morphogenesis, as well as gastrulation and cilium assembly, which together point to vertebrate development and ciliogenesis. While other terms touch on protein assembly and intracellular transport, the clearest signal is a developmental/ciliogenesis theme.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":14},{"id":"GO:0048705","count":14},{"id":"GO:0070208","count":14},{"id":"GO:0000348","count":14},{"id":"GO:0031930","count":14}]},{"hash":"1629723393995033665","title":"Meiosis-Associated Golgi\u2013Endosome Trafficking","description":"This cluster combines cell-cycle and meiosis-related terms (mitotic cell cycle, synaptonemal complex assembly, ascospore-type prospore membrane formation) with vesicle trafficking and Golgi-endosome transport processes (protein retention in Golgi, intralumenal vesicle formation, late endosome to Golgi transport) and related signaling (GTPase activity, phosphatidylinositol-mediated signaling), indicating a group of proteins coordinating membrane remodeling and trafficking during meiosis/sporulation.","confidence":"High","size":14,"edges":37,"triangles":47,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007130","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0045053","count":2}]},{"hash":"1017650775909231506","title":"Neural development and myelination signaling","description":"This cluster centers on ephrin receptor signaling, regulation of myelination, spinal cord development, and cytoskeletal remodeling (microtubule movement, GTPase activity, focal adhesion regulation), all of which point to neural development and glial maturation. While there are heart development signals present, the dominant themes are neural differentiation, neurite outgrowth, and myelination-related processes, supported by PI3K/AKT signaling and cytoskeletal dynamics. Confidence: High","confidence":"","size":14,"edges":8,"triangles":1,"max_degree":2,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0031641","count":5},{"id":"GO:0048013","count":5},{"id":"GO:0051291","count":4},{"id":"GO:0051893","count":4},{"id":"GO:0007507","count":4}]},{"hash":"2193752784652433853","title":"Developmental transcription and chromatin regulation","description":"These proteins appear to cluster around regulation of gene expression and chromatin state (RNA Pol II\u2013related transcription control, histone modification topics) with an overarching developmental signaling context (canonical Wnt) and differentiation processes (macrophage differentiation, follicle cell stalk formation). The spindle assembly term adds a cell-cycle/mitosis aspect common to developing tissues. Overall, the theme is transcriptional control and chromatin regulation in development.","confidence":"Medium","size":14,"edges":84,"triangles":291,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0061087","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0043981","count":3},{"id":"GO:0006367","count":3}]},{"hash":"1378821892596737059","title":"Embryonic Development and Morphogenesis","description":"The cluster is enriched for brain development, skeletal development, skeletal morphogenesis, and gastrulation, pointing to a core role in embryonic development and tissue patterning. Additional terms like mRNA transport and mitochondria-nucleus signaling suggest supporting cellular processes that accompany development, while a couple of obsolete annotations reflect historical naming. Overall, the proteins appear linked to developmental pathways governing embryo formation and morphogenesis.","confidence":"High","size":14,"edges":18,"triangles":2,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":11},{"id":"GO:0007420","count":11},{"id":"GO:0001501","count":10},{"id":"GO:0048705","count":10},{"id":"GO:0070208","count":10}]},{"hash":"666253986953485069","title":"Rab-regulated neural vesicle trafficking","description":"This cluster is dominated by Rab signaling and regulation of synaptic vesicle exocytosis, with supporting neural development terms such as axonogenesis inhibition and substantia nigra development, plus Wnt signaling. Together these indicate a core theme of vesicle trafficking coordinated with neural development and synaptic function, with additional, more general cell polarity/development context reflected by epithelial/endothelial terms.","confidence":"High","size":14,"edges":89,"triangles":341,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050771","count":14},{"id":"GO:0032482","count":14},{"id":"GO:0061028","count":12},{"id":"GO:0060070","count":12},{"id":"GO:2000300","count":12}]},{"hash":"1030536273852062459","title":"Developmental Gene Expression and Epigenetic Regulation","description":"This cluster centers on regulation of gene expression in development, as indicated by translation, mRNA export, and histone-related modifications, alongside developmental processes such as semicircular canal morphogenesis, sebaceous gland development, and abdomen segment identity. The mix suggests a broader theme of how gene expression and epigenetic state govern developmental patterning and differentiation.","confidence":"Medium","size":14,"edges":29,"triangles":23,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0048752","count":2},{"id":"GO:0048733","count":2},{"id":"GO:0071894","count":2}]},{"hash":"866487837384324299","title":"Tissue Development and Differentiation","description":"This cluster aggregates proteins associated with multiple developmental processes across diverse tissues (skin/hair follicle, skeletal system, bladder, nervous system, muscle) and differentiation pathways (keratinocytes, myotubes, T-helper cells) as well as general transcription and cell-cycle regulation. The common theme is developmental progression and lineage-specific differentiation rather than a single pathway, justifying a broad \u201cTissue Development and Differentiation\u201d label.","confidence":"High","size":14,"edges":8,"triangles":4,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0048485","count":5},{"id":"GO:0060157","count":5},{"id":"GO:0031069","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0046533","count":5}]},{"hash":"1145880554157212309","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0071222","count":3},{"id":"GO:1900165","count":3},{"id":"GO:1904628","count":2},{"id":"GO:0061014","count":2}]},{"hash":"1342937158684570391","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":23,"triangles":15,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903608","count":5},{"id":"GO:0034414","count":4},{"id":"GO:0072752","count":4},{"id":"GO:0006396","count":4},{"id":"GO:0007053","count":4}]},{"hash":"948239646678380436","title":"DNA Damage Response and Immunoglobulin Diversification","description":"The terms cluster around DNA damage recognition and repair (base/excision, nucleotide-excision repair), response to gamma radiation, and intrinsic apoptotic signaling in DNA damage, as well as immunoglobulin gene diversification processes (somatic hypermutation and V-D-J recombination). This suggests a coherent theme of genome maintenance coupled with immune receptor diversification, with a few peripheral terms (aging, salivary gland morphogenesis) being less central. ","confidence":"High","size":14,"edges":65,"triangles":149,"max_degree":13,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0016446","count":5},{"id":"GO:0007568","count":4},{"id":"GO:0006297","count":4},{"id":"GO:0006284","count":4},{"id":"GO:0006286","count":4}]},{"hash":"948825672327659145","title":"Innate antiviral immunity and inflammasome regulation","description":"Most terms point to antiviral defense and innate immunity, with specific references to NLRP3 inflammasome regulation, IL-1\u03b2 production, and ubiquitin-mediated control of immune signaling. A few terms about cell division appear but do not define the cluster; the prevalent pattern is innate immune defense and inflammatory regulation.","confidence":"High","size":14,"edges":12,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051607","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:1900226","count":2}]},{"hash":"1510060391075840051","title":"DNA Damage Response and Genome Stability","description":"The top GO terms cluster around DNA damage response and genome stability, notably double-strand break repair via classical NHEJ, DNA break association with the nuclear envelope, and telomere maintenance dynamics. While there are ancillary signaling-related terms (e.g., TGF-beta signaling, extracellular growth regulation), the strongest and recurring themes center on DNA repair and genome integrity, suggesting this label captures the core function of the cluster.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010735","count":1},{"id":"GO:0006471","count":1},{"id":"GO:0097680","count":1},{"id":"GO:0030511","count":1},{"id":"GO:0001560","count":1}]},{"hash":"369904991678077941","title":"Unknown","description":"The top GO terms are highly diverse, spanning plasma membrane localization, plant defense responses, cilium assembly, hair follicle morphogenesis, mitochondrial membrane regulation and import, and cell cycle regulation, plus several obsolete terms. This mix covers plant immunity, development, organelle functions, and cell-cycle processes with no clear, unified theme, so a concise, representative label cannot be assigned. ","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072661","count":2},{"id":"GO:0080185","count":1},{"id":"GO:1905515","count":1},{"id":"GO:1901622","count":1},{"id":"GO:0031069","count":1}]},{"hash":"576859477462819013","title":"mRNA Splicing and Translation Regulation","description":"This cluster centers on post-transcriptional control, with multiple GO terms for spliceosome-mediated splicing, splice site recognition, mRNA stability, and regulation of translational initiation, plus formation of translation preinitiation complexes. These together point to coordinated regulation of gene expression at RNA processing and translation initiation stages. Some development-related terms appear but the dominant theme is mRNA processing and translation control.","confidence":"High","size":14,"edges":56,"triangles":138,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048025","count":4},{"id":"GO:0000380","count":4},{"id":"GO:0035041","count":3},{"id":"GO:0048255","count":3},{"id":"GO:0001825","count":3}]},{"hash":"726613145773184697","title":"Translation Machinery and Regulation","description":"The top terms are dominated by translation-related processes, including cytoplasmic and mitochondrial translation, along with explicit positive/negative regulation of translation and related transcription termination terms. This pattern points to core protein synthesis machinery and its regulation as the common theme of the cluster, with minor signals related to stress responses.","confidence":"High","size":14,"edges":64,"triangles":146,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0006353","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0002181","count":2},{"id":"GO:1990090","count":2}]},{"hash":"473211389107787297","title":"Unknown","description":"The cluster's top GO terms cover diverse themes: adaptive immune signaling (B cell receptor signaling, germinal center formation, type 2 immune response) alongside protein ubiquitination, responses to mechanical stimuli, circadian sleep/wake cycles, and some odd developmental annotations. This lack of a coherent single function across the terms suggests there isn\u2019t a clear, unified biological role for the cluster, so a generic Unknown label is most appropriate.","confidence":"","size":14,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0002467","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0045497","count":2}]},{"hash":"824055893047326634","title":"Oxidative Stress Response and Redox Homeostasis","description":"The top GO terms show cellular redox homeostasis, oxidation-reduction processes, oxidant detoxification, and responses to oxidative stress, with deglutathionylation as a redox-linked modification. A few terms about prolyl hydroxylation and nuclear regulation may reflect downstream effects, but the dominant theme is redox biology and oxidative stress management.","confidence":"High","size":14,"edges":86,"triangles":314,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":13},{"id":"GO:0055114","count":11},{"id":"GO:0018401","count":11},{"id":"GO:0098869","count":10},{"id":"GO:0034599","count":9}]},{"hash":"1163181487289755969","title":"Ribosome biogenesis and translation","description":"The top terms point strongly to ribosome assembly and function: maturation of rRNA (SSU/LSU/5.8S), ribosome biogenesis, translation, and translational initiation. While some terms touch on RNA processing and transcription, the dominant signal is the protein synthesis machinery and its maturation. Overall, the cluster appears to represent ribosome biogenesis and active translation.","confidence":"High","size":14,"edges":64,"triangles":182,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000462","count":4},{"id":"GO:0031564","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0042254","count":3}]},{"hash":"379627878373637356","title":"Rho GTPase signaling and cytoskeleton remodeling","description":"This cluster centers on regulation of GTPase activity and Rho pathway signaling, plus protein localization to microtubules, pointing to cytoskeletal dynamics and related signaling processes. Additional terms like spinal cord development, ubiquitination, and dephosphorylation suggest broader regulatory roles but still align with signaling-driven remodeling of cytoskeletal networks. ","confidence":"Medium","size":14,"edges":29,"triangles":12,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0033280","count":2}]},{"hash":"1315116349507668389","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":77,"triangles":231,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000289","count":5},{"id":"GO:0070301","count":5},{"id":"GO:0034415","count":4},{"id":"GO:0000738","count":4},{"id":"GO:0010606","count":4}]},{"hash":"2279419587874484459","title":"Innate Immune Signaling and Macrophage Activation","description":"This cluster\u2019s GO terms point to innate immune sensing and macrophage responses, featuring NOD2 and TLR2 signaling, defense against viruses, macrophage activation, and actin remodeling for cell migration, together indicating a cohesive immune activation module. Some peripheral/obsolete terms appear but do not undermine the core immune-related theme.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0070431","count":5},{"id":"GO:0032088","count":5},{"id":"GO:0000083","count":3},{"id":"GO:0035882","count":3},{"id":"GO:0051607","count":3}]},{"hash":"1547280594548795584","title":"Translation Machinery and Ribosome Regulation","description":"This cluster centers on core translation processes and ribosome dynamics, including initiation, elongation, termination, and ribosome disassembly, plus selenocysteine incorporation. Also related are mRNA turnover processes that impact translation efficiency and an antibiotic response that often targets translation. Overall, the common theme is protein synthesis machinery and its regulation.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:2000767","count":11},{"id":"GO:0001514","count":11},{"id":"GO:0046677","count":11},{"id":"GO:0014009","count":11}]},{"hash":"188419590475009094","title":"Innate antiviral immunity and cellular stress responses","description":"Based on the top GO terms, the cluster centers on defense against viruses and innate immune activity, complemented by stress-related pathways such as ER stress\u2013driven translation, mitochondrial fission regulation, and protein targeting to membranes. The inclusion of microtubule/centrosome organization and cell cycle regulation suggests coordinated cellular responses during infection or stress. Taken together, these proteins likely function in antiviral defense alongside cellular stress adaptation.","confidence":"Medium","size":14,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0090141","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0045842","count":2},{"id":"GO:1903071","count":1}]},{"hash":"1788262916992106780","title":"Nuclear transcription and ubiquitin-proteasome proteostasis","description":"The cluster centers on DNA-templated transcription and mRNA processing, with strong links to ubiquitination/deubiquitination and proteasome/ERAD pathways, suggesting coordination between transcriptional regulation and protein quality control/turnover.","confidence":"Medium","size":14,"edges":28,"triangles":17,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:1904378","count":5},{"id":"GO:0006397","count":5},{"id":"GO:0043433","count":4},{"id":"GO:1904379","count":4}]},{"hash":"968417673345315585","title":"Nucleotide and Cofactor Metabolism","description":"The top GO terms cluster around biosynthesis and catabolism of cofactors and nucleotides (CoA, folic acid, IPP/FP, dGTP) as well as nucleobase-containing small molecules, with additional RNA-focused terms (adenosine to inosine editing; snoRNA catabolic process). This points to a broad theme of nucleotide/cofactor metabolism and related RNA processing, though the mix includes some RNA-specific processes and an obsolete term, suggesting a somewhat heterogeneous but related functional group. ","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0015938","count":3},{"id":"GO:0046656","count":3},{"id":"GO:0009240","count":3},{"id":"GO:0045337","count":3},{"id":"GO:1901639","count":3}]},{"hash":"697484861712509636","title":"Developmental transcription regulators","description":"This cluster shows enrichment for transcription-related GO terms (DNA-templated transcription and negative regulation of transcription by RNA polymerase II) alongside diverse developmental processes (ureteric bud branching, peripheral nervous system development, Sertoli cell development, oligodendrocyte differentiation, satellite cell activation). Together, these suggest the proteins act as transcription regulators critical for development across multiple tissues.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0090190","count":3},{"id":"GO:0007422","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1297227344517762081","title":"Neural and cardiac development with cytoskeletal signaling","description":"The top GO terms point to developmental processes in heart and nervous system, plus synaptic transmission, and cytoskeletal dynamics (filopodium assembly, Rho signaling). These together suggest a cluster centered on development of neural/cardiac systems with actin-based remodeling, even though other terms touch on vascular, muscle, placenta, and immune aspects, indicating a broad developmental program rather than a single pathway. Confidence: Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0035249","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0046847","count":3}]},{"hash":"1482514543600193182","title":"Growth Factor and Cytokine Signaling Driving Migration","description":"This cluster is dominated by signaling related to insulin receptor signaling, VEGF and prostaglandin responses, and cytokines (IL-7 and IL-4), plus terms linked to cell migration and vascular development (labyrinthine layer blood vessel development, fibroblast migration). Taken together, these GO terms point to coordinated growth factor/cytokine signaling that promotes cellular movement in vascular remodeling contexts. ","confidence":"High","size":14,"edges":47,"triangles":84,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":13},{"id":"GO:0046329","count":13},{"id":"GO:0098761","count":13},{"id":"GO:0060716","count":13},{"id":"GO:0035924","count":13}]},{"hash":"214343894874837403","title":"Spermatogenesis and Telomere Maintenance","description":"The top GO terms show strong signals for male germ cell development (spermatogenesis, spermatid development) together with telomere maintenance (telomere lengthening, telomerase regulation) and DNA replication regulation, suggesting a cluster of proteins involved in meiosis/germline maturation with telomere dynamics. Mitochondrion inheritance also appears, which can be associated with germline processes, while terms like regulation of GTPase activity and cell proliferation provide broader context but do not override the germline-telomere theme.","confidence":"Medium","size":14,"edges":22,"triangles":15,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":3},{"id":"GO:0090314","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0007283","count":2}]},{"hash":"1519432389175919386","title":"Unknown","description":"The top terms point to diverse biological themes: retinal development, dopamine metabolism, monocyte differentiation, immune signaling, and cardiac calcium handling. The cluster lacks a unifying pathway or tissue-specific function; the terms appear to reflect separate processes rather than a cohesive module. Because there is no clear common function tying these proteins together, I label the cluster Unknown.","confidence":"","size":14,"edges":76,"triangles":243,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046549","count":12},{"id":"GO:1903206","count":12},{"id":"GO:0032729","count":12},{"id":"GO:0055119","count":12},{"id":"GO:0042053","count":12}]},{"hash":"2107141507941400921","title":"Steroid and lipid metabolism with mammary development","description":"This cluster is dominated by GO terms for steroid hormone biosynthesis (testosterone) and androgen metabolism, plus prostaglandin and triglyceride metabolism, indicating a lipid/hormone metabolism theme. The appearance of mammary gland development suggests a tissue-specific, hormone-regulated aspect, while terms related to signaling regulation (ERK cascade, GTPase activity) and ubiquitin-mediated proteolysis imply coordinated control of these metabolic processes. Overall, the proteins seem linked to hormone-driven lipid metabolism and associated developmental signaling.","confidence":"Medium","size":14,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0061370","count":5},{"id":"GO:0008209","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0006641","count":4}]},{"hash":"1101717951190381543","title":"ECM remodeling and developmental morphogenesis","description":"This cluster centers on extracellular matrix organization and skeletal/embryonic morphogenesis (collagen fibril organization, skeletal system morphogenesis, embryonic cranial skeleton morphogenesis) with signals for broader development (multicellular organism development) and mechanotransduction (cellular response to mechanical stimulus). The presence of EGFR pathway regulation and motor neuron axon fasciculation suggests integration of growth signaling with neural patterning, supporting a cohesive theme of development driven by ECM remodeling and morphogenesis. Peptidoglycan turnover terms appear unrelated noise.","confidence":"Medium","size":14,"edges":54,"triangles":85,"max_degree":11,"top_function":"wound healing","top_go_terms":[{"id":"GO:0071260","count":7},{"id":"GO:1904707","count":7},{"id":"GO:0045742","count":7},{"id":"GO:0030199","count":7},{"id":"GO:0009254","count":6}]},{"hash":"2224774517975364608","title":"Immune signaling and leukocyte trafficking","description":"This cluster is driven by innate immune processes: phagocytosis recognition, leukocyte tethering/rolling, C-type lectin receptor signaling, and complement activation via the lectin pathway, with additional NK cell chemotaxis regulation and lymph vessel morphogenesis. A few developmental terms are present, but the predominant theme centers on immune recognition and leukocyte movement, supporting a label for innate immune activation and trafficking.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006910","count":9},{"id":"GO:0072177","count":6},{"id":"GO:0001502","count":6},{"id":"GO:0072218","count":6},{"id":"GO:0060355","count":6}]},{"hash":"1482059250577341919","title":"RNA processing and antiviral defense","description":"The top GO terms point to post-transcriptional regulation of gene expression\u2014mRNA stability, translational initiation, and nuclear RNA export\u2014and to stress- and defense-related immune responses (innate immunity and defense against virus). The presence of ubiquitination also fits with regulatory control of these processes. Collectively, the proteins appear to coordinate RNA metabolism with antiviral signaling, rather than a single clean enzymatic pathway. ","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0002230","count":2},{"id":"GO:0048255","count":2}]},{"hash":"1510666509819604323","title":"Mammary gland development and lactation signaling","description":"The cluster\u2019s top GO terms cluster around mammary biology and related signaling: lactation, mammary gland epithelial cell proliferation, response to leptin, and canonical Wnt signaling, all pointing to development and lactation regulation. Additional terms like cell division and autophagy-related assembly support general growth/survival processes, while a few outliers (stomatal opening, late viral transcription, host antiviral response) may reflect annotation breadth or cross-species noise rather than a core theme. Overall, the dominant theme is mammary gland development and lactation signaling.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007595","count":1},{"id":"GO:0019086","count":1},{"id":"GO:0030857","count":1},{"id":"GO:0033598","count":1},{"id":"GO:0044321","count":1}]},{"hash":"332824950097051048","title":"Secretory vesicle transport and exocytosis","description":"GO terms point to vesicle trafficking along Golgi-ER and endosome-Golgi routes, retrograde transport, and vesicle fusion with the Golgi, complemented by degranulation events in NK and neutrophils and histamine secretion. Together, these suggest a cohesive theme of secretory pathway dynamics and granule-mediated release, with supporting protein maturation and quality-control processes (CAAX processing and ubiquitin-dependent ERAD). ","confidence":"High","size":14,"edges":43,"triangles":62,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0071586","count":2},{"id":"GO:0043320","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0043312","count":1}]},{"hash":"2208276927309251861","title":"Innate immune signaling and inflammation","description":"I labeled this cluster Innate immune signaling and inflammation because several top GO terms point to inflammatory and immune pathways, including response to lipopolysaccharide, positive regulation of Toll signaling, and interleukin-1 beta production, as well as GPCR-PLC signaling common in immune cells. Factor XII activation links coagulation with inflammation, reinforcing the inflammatory theme. Although there are developmental terms such as Wnt signaling and pancreas morphogenesis present, the strongest shared signal among the enriched terms is innate immune activation and inflammatory signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042127","count":14},{"id":"GO:1900738","count":14},{"id":"GO:0002542","count":14},{"id":"GO:0016055","count":14},{"id":"GO:0045752","count":14}]},{"hash":"982700063056266909","title":"Ribosome Biogenesis and Translation","description":"The dominant GO terms center on ribosome assembly and function: biogenesis of both ribosomal subunits, export of the large subunit from the nucleus, and cytoplasmic translation, along with tRNA modification. This suggests a cohesive cluster focused on ribosome production and protein synthesis, with other growth-related terms playing a minor role.","confidence":"High","size":14,"edges":4,"triangles":1,"max_degree":3,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0000055","count":8},{"id":"GO:0051301","count":8},{"id":"GO:0090529","count":6},{"id":"GO:0006400","count":6},{"id":"GO:0042254","count":6}]},{"hash":"676091886435654399","title":"Transcriptional Regulation in Development","description":"The top GO terms cluster around RNA polymerase II\u2013mediated transcription and its negative regulation, suggesting a shared role in controlling gene expression. Development-related terms (hair follicle morphogenesis, endocrine system development, left-right pattern formation) indicate these proteins participate in developmental regulation that relies on transcriptional control.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":1},{"id":"GO:0031069","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0046022","count":1}]},{"hash":"552832649630347711","title":"Ubiquitin-mediated signaling and degradation","description":"The cluster centers on ubiquitin-related processes (K6-linked ubiquitination, autoubiquitination, ubiquitin-dependent ERAD) and regulation of signaling pathways (RIG-I, JNK), as well as receptor turnover (Wnt receptor catabolic process). While a couple of terms touch broader chromatin/genome regulation (V(D)J recombination, dosage compensation), the common theme is ubiquitin-driven control of protein fate and signaling in immune and stress pathways.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033151","count":4},{"id":"GO:0085020","count":4},{"id":"GO:0038018","count":4},{"id":"GO:0009048","count":4},{"id":"GO:0051865","count":4}]},{"hash":"821398756372240622","title":"Unknown","description":"The GO terms span nucleotide catabolism, lipid biosynthesis/transport, cofactor biosynthesis, and even eukaryotic-like processes (endothelial proliferation) alongside DNA transposition and sporulation, indicating no single cohesive function or pathway linking the proteins. The lack of edges reinforces a heterogeneous set rather than a unified module, so no specific label is appropriate.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046079","count":3},{"id":"GO:0045332","count":2},{"id":"GO:0001935","count":2},{"id":"GO:0006313","count":2},{"id":"GO:0015941","count":1}]},{"hash":"1011046341902293147","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":46,"triangles":83,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1990966","count":3},{"id":"GO:0009611","count":3},{"id":"GO:0019350","count":3},{"id":"GO:0046444","count":3},{"id":"GO:0097171","count":3}]},{"hash":"1971433647605786531","title":"Rho GTPase\u2013driven cell migration and morphogenesis","description":"The top GO terms cluster around cell migration, cell morphogenesis, and Rho protein signaling, with activation of GTPase activity, suggesting a common theme of cytoskeletal remodeling and motility governed by Rho-family GTPases. Some terms like telomere maintenance and mRNA processing are less central, but the dominant signal is migratory and morphogenetic control via Rho pathways.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0000902","count":4},{"id":"GO:0007266","count":4},{"id":"GO:0051534","count":3},{"id":"GO:0090630","count":3}]},{"hash":"545098941466956100","title":"TLR2-driven macrophage innate immune activation","description":"This cluster centers on innate immune sensing and macrophage responses: TLR2 signaling, detection of diacyl lipopeptides, NF-kappaB\u2013related pathways, IL-6 production, and macrophage activation, all pointing to a coordinated macrophage-driven defense response. Some terms appear tangential (lysosomal pH regulation, bone formation), but the core theme is TLR2-mediated innate immunity and NF-\u03baB\u2013dependent activation.","confidence":"High","size":14,"edges":74,"triangles":192,"max_degree":13,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045410","count":14},{"id":"GO:0006469","count":14},{"id":"GO:0042346","count":14},{"id":"GO:0051607","count":14},{"id":"GO:0034134","count":14}]},{"hash":"1447952637640175591","title":"Microtubule organization and vesicle transport","description":"These terms cluster around microtubule organization, tubulin complex assembly, and regulation of microtubule polymerization, together with anterograde synaptic vesicle transport and proteostasis via chaperones and the ubiquitin-proteasome system. Occasional cell division and chromosome segregation terms further reflect spindle-associated microtubules. The overarching theme is microtubule dynamics and microtubule-dependent transport, with supporting protein quality control. ","confidence":"High","size":14,"edges":29,"triangles":16,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043622","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0071629","count":2},{"id":"GO:0007021","count":2},{"id":"GO:0032968","count":2}]},{"hash":"277053353845658150","title":"Angiogenesis and vascular remodeling","description":"The prominent GO terms cluster around blood vessel development and remodeling: angiogenesis, branching in blood vessel morphogenesis, and positive regulation of smooth muscle cell migration. Additional terms like regulation of Rho protein signaling and protein dephosphorylation point to cytoskeletal dynamics and signaling control that facilitate endothelial and mural cell movement during vessel formation. Although nervous system development and synapse-related localization appear in the set, the dominant theme is vascular development and vessel morphogenesis.","confidence":"High","size":14,"edges":28,"triangles":31,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0006470","count":4},{"id":"GO:0001569","count":4},{"id":"GO:0014068","count":4},{"id":"GO:0007399","count":4}]},{"hash":"1366344157417733833","title":"Diverse Metabolic Biosynthesis","description":"Top GO terms cluster around biosynthetic and metabolic processes across a wide range of compounds (phenylpropanoid, sporopollenin, ether lipids, poly-hydroxybutyrate, galactose metabolism, L-glutamine metabolism, etc.), with some catabolic terms as well. This suggests a general theme of metabolism and biomolecule synthesis rather than a single, cohesive pathway. Confidence in this label is Medium.","confidence":"Medium","size":14,"edges":46,"triangles":120,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0009699","count":10},{"id":"GO:1902987","count":10},{"id":"GO:0006012","count":10},{"id":"GO:0080110","count":10}]},{"hash":"1546056047778528852","title":"Antigen Presentation and Phagocytosis","description":"This cluster is strongly enriched for immune-related GO terms: phagocytosis, antigen processing and presentation via MHC class I and II (including TAP-dependent pathways), and B cell receptor signaling, all pointing to proteins involved in capturing, processing, and presenting antigens and in adaptive immune activation. Additional terms for Gram-negative defense and polysaccharide binding support a pattern of innate/acute immune responses linked to antigen presentation. Together, these terms suggest a cohesive immune-function cluster centered on antigen handling and presentation.","confidence":"High","size":14,"edges":54,"triangles":119,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006911","count":14},{"id":"GO:0050853","count":14},{"id":"GO:0019886","count":14},{"id":"GO:0042493","count":13},{"id":"GO:0002506","count":13}]},{"hash":"1168468215885381020","title":"Signaling and differentiation in epithelial and placental tissues","description":"The Top Terms point to epithelial development (hair follicle development) and placental differentiation (chorionic trophoblast), alongside cell surface receptor tyrosine kinase signaling and responses to prostaglandin, heparin, and xenobiotic stimuli. The presence of metabolic processes (electron transport chain) and insulin regulation suggests these proteins operate at the intersection of growth signaling and tissue-specific differentiation, spanning skin/epithelial and placental lineages. Overall, a coherent theme is signaling-driven differentiation in epithelial and placental contexts, with metabolic and xenobiotic responsiveness.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042493","count":14},{"id":"GO:0022900","count":14},{"id":"GO:0071380","count":14},{"id":"GO:0007169","count":14},{"id":"GO:0071504","count":12}]},{"hash":"1029780346392189092","title":"Mitochondrial Transport and Membrane Dynamics","description":"Top GO terms cluster around mitochondrial transmembrane transport and membrane dynamics, including ADP, NAD, phosphate transport, malate-aspartate shuttle, and pyrimidine import into mitochondria, as well as regulation of membrane permeability and fission. This combination points to a cohesive mitochondria-centered transport/dynamics function for the proteins.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0097274","count":8},{"id":"GO:0035435","count":6},{"id":"GO:0043490","count":6},{"id":"GO:0090149","count":6},{"id":"GO:0000066","count":6}]},{"hash":"847797135017272515","title":"Neural development and Hedgehog signaling","description":"The top terms show strong ties to nervous system development and neural connectivity (neuron adhesion, synapse assembly) and include Hedgehog pathway activity (smoothened signaling). There are also broader developmental terms (kidney development, axial mesoderm formation), suggesting these proteins participate in embryonic patterning where neural differentiation occurs. Overall, the cluster appears to reflect embryonic neural development with Hedgehog signaling as a central axis, plus some broader developmental roles.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0001822","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0007224","count":5},{"id":"GO:0007156","count":5},{"id":"GO:0006998","count":5}]},{"hash":"351836745903592662","title":"Neuronal membrane signaling and transport","description":"Top terms emphasize neuronal function and membrane processes: action potential propagation, postsynaptic membrane assembly, membrane hyperpolarization, and ion transmembrane transport, along with endosomal trafficking and xenobiotic transport across barriers. While there are outlier terms (amelogenesis, bone resorption, viral release) that seem less connected, the strongest signal points to neural membrane signaling and intracellular transport as the cluster's shared theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097186","count":3},{"id":"GO:0019227","count":3},{"id":"GO:0019076","count":3},{"id":"GO:0097104","count":2},{"id":"GO:0034765","count":2}]},{"hash":"1946181706934809552","title":"Neuronal growth and synapse formation","description":"The top terms center on axon extension, lamellipodium assembly, synapse assembly, and glutamatergic synaptic transmission, indicating neural development and the establishment of synaptic connectivity. Although some terms are obsolete, the remaining signals point to growth and communication in neurons, rather than generic cellular processes. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:1903955","count":4},{"id":"GO:0045773","count":4},{"id":"GO:0007626","count":4},{"id":"GO:0007416","count":4},{"id":"GO:0090527","count":3}]},{"hash":"1656220839397390999","title":"Multi-tissue Development and Transcription Regulation","description":"These proteins appear to participate in broad developmental programs across tissues, unified by transcriptional control (RNA Pol II) and downstream differentiation/morphogenesis events (adhesion, heart rhythm regulation, organ morphogenesis in multiple tissues). The label captures the cross-tissue developmental theme suggested by the top GO terms.","confidence":"Medium","size":14,"edges":65,"triangles":147,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0033627","count":10},{"id":"GO:0021750","count":10},{"id":"GO:0003259","count":10},{"id":"GO:0061382","count":10}]},{"hash":"841497345306418497","title":"Mitochondrial respiration and ETC assembly","description":"The cluster is characterized by strong signals for mitochondrial energy production: assembly of respiratory chain complexes (including complex IV and ATP synthase), cytochrome assembly, TCA cycle, and aerobic respiration, indicating a cohesive theme of mitochondrial oxidative phosphorylation. A single outlier term on synaptic vesicle endocytosis appears secondary to the energy context. ","confidence":"High","size":14,"edges":26,"triangles":22,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0090201","count":2},{"id":"GO:0008203","count":1},{"id":"GO:0033615","count":1},{"id":"GO:0017004","count":1}]},{"hash":"567778891369370611","title":"Embryonic Development and Organogenesis","description":"These proteins are linked to broad developmental processes across multiple tissues (pancreas, pituitary, gonads, spinal cord, neural crest, ureteric bud, etc.), plus transcriptional regulation by RNA Pol II, suggesting a set of regulatory factors involved in embryogenesis and organ formation rather than a single pathway. Confidence is Medium.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0031018","count":6},{"id":"GO:0021521","count":6},{"id":"GO:0006366","count":6},{"id":"GO:2000288","count":5}]},{"hash":"1779493059905174060","title":"Cerebellar Development and Granule Cell Differentiation","description":"The top GO terms cluster around cerebellar development, granule cell migration and maturation, and Purkinje cell differentiation, with a note on neuropeptide signaling and related behaviors (feeding and walking). This pattern strongly indicates a functional theme in cerebellar neurodevelopment and signaling, particularly involving the granule cell lineage and cerebellar circuitry.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007218","count":1},{"id":"GO:0007631","count":1},{"id":"GO:0021933","count":1},{"id":"GO:0021686","count":1},{"id":"GO:0007628","count":1}]},{"hash":"2088065075531580549","title":"Neuromuscular signaling and movement control","description":"The top GO terms center on neural and motor function (locomotory behavior, cholinergic synaptic transmission, neuromuscular process controlling posture, and movement-related signaling). Some terms reference proteolysis and plasminogen activation (fibrinolysis, urokinase signaling), which can relate to remodeling in neuromuscular contexts, while a few others are broader stress or signaling responses. The strongest pattern is neuromuscular control of movement, so this label reflects the cluster\u2019s core theme, with moderate confidence due to some outlier terms.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035634","count":2},{"id":"GO:2001268","count":2},{"id":"GO:0007626","count":2},{"id":"GO:0051006","count":2},{"id":"GO:0007271","count":2}]},{"hash":"288924898627514268","title":"Developmental ECM and RTK signaling","description":"The cluster\u2019s terms strongly point to developmental processes that depend on an extracellular collagen framework (collagen fibril organization, endochondral ossification) and signaling through receptor tyrosine kinases (cell surface receptor protein tyrosine kinase signaling pathway), with examples of organ- and tissue-specific development (corpus callosum development, endodermal differentiation, FSH response). Immune and neuronal-related terms are present but less central. Overall, the dominant theme is development shaped by an collagen-rich extracellular matrix and RTK signaling.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":3},{"id":"GO:0001958","count":2},{"id":"GO:0035987","count":2},{"id":"GO:0043277","count":2},{"id":"GO:0045087","count":2}]},{"hash":"2158550191139186063","title":"RNA and histone methylation regulating transcription","description":"The cluster is dominated by methylation-related GO terms across RNA processing (rRNA methylation, mRNA capping, RNA methylation) and histone/protein methylation (histone H4-R3 methylation, peptidyl-arginine/lysine methylation), with a link to transcriptional control (negative regulation of RNA Pol II). This suggests a cohesive role in methylation-mediated regulation of RNA processing and chromatin state, impacting cell growth and senescence.","confidence":"High","size":14,"edges":45,"triangles":51,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":7},{"id":"GO:0009236","count":5},{"id":"GO:0016049","count":5},{"id":"GO:0043985","count":5},{"id":"GO:0019919","count":5}]},{"hash":"1596805964889085222","title":"Developmental Transcription Regulation","description":"Top GO terms reveal a strong emphasis on transcriptional control by RNA polymerase II, with several development-associated terms (endocrine system development, left-right pattern formation, cartilage morphogenesis, placental development). This suggests the proteins function as transcription regulators coordinating gene expression during development and organogenesis, rather than a single enzymatic activity. Confidence reflects a coherent developmental transcription theme across the cluster.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0035270","count":8},{"id":"GO:0046022","count":8},{"id":"GO:0060806","count":8}]},{"hash":"81573865513115775","title":"Membrane Transporters","description":"The top GO terms point to transmembrane transport across membranes for a wide range of substrates\u2014ions (potassium, phosphate, nitrite), sugars (galactose, arabinose), sialic acid, xenobiotics, and even neurotransmitter loading into synaptic vesicles. This cohesive pattern indicates proteins whose primary function is membrane transport, spanning diverse substrates, so \"Membrane Transporters\" captures the shared theme. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":9},{"id":"GO:0015739","count":8},{"id":"GO:0006855","count":7},{"id":"GO:0035435","count":7},{"id":"GO:0098700","count":7}]},{"hash":"241886712162788564","title":"Cytochrome P450 Xenobiotic and Lipid Metabolism","description":"The prominent GO terms point to omega-hydroxylation/omega-oxidation and fatty acid metabolism, alkaloid and insecticide metabolism, and retinoic acid catabolism, all characteristic of cytochrome P450 enzymes involved in detoxification and lipid processing. The mammary gland and female gonad development terms likely reflect hormone metabolism or signaling modulated by P450 activity, linking development to these metabolic functions. Overall, the cluster appears to center on P450-mediated xenobiotic and lipid metabolism rather than a single non-metabolic process.","confidence":"High","size":14,"edges":39,"triangles":60,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":14},{"id":"GO:0010193","count":14},{"id":"GO:0008585","count":14},{"id":"GO:0097267","count":14},{"id":"GO:0009822","count":14}]},{"hash":"1031530754850508037","title":"Mitochondrial lipid biosynthesis and remodeling","description":"The cluster shows strong representation of lipid biosynthesis and remodeling processes, including cardiolipin acyl-chain remodeling, phosphatidylcholine remodeling, CDP-diacylglycerol biosynthesis, triglyceride and ether lipid biosynthesis, and mitochondrial ATP synthesis coupled to electron transport, which together suggest a cohesive theme of mitochondrial lipid metabolism. A couple of development terms (cerebellum morphogenesis, glandular epithelial maturation) may reflect broader tissue roles but do not outweigh the core lipid-centric signals.","confidence":"High","size":14,"edges":75,"triangles":231,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":7},{"id":"GO:0016024","count":6},{"id":"GO:0042775","count":5},{"id":"GO:2001246","count":5},{"id":"GO:0008611","count":5}]},{"hash":"1016474061350971928","title":"Embryonic development and morphogenesis","description":"The proteins are tied to a broad set of developmental and morphogenetic processes across multiple tissues (tooth dentin formation, retina morphogenesis, genitalia morphogenesis, fat differentiation, EMT in heart cushion, bone mineralization regulation, forebrain proliferation, etc.). There isn\u2019t a single unified function, but the shared theme is developmental patterning and tissue morphogenesis.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0001580","count":3},{"id":"GO:0042475","count":2},{"id":"GO:0060059","count":2},{"id":"GO:0048807","count":2}]},{"hash":"1661616716146004802","title":"mRNA stability and translation regulation","description":"The GO terms are dominated by post-transcriptional control: mRNA stabilization, stress-related regulation of mRNA stability, regulation of translational initiation, preinitiation complex formation, translation reinitiation, and miRNA/ncRNA-mediated gene silencing. Together they point to a cohesive cluster of proteins involved in RNA processing and control of translation, rather than a single pathway.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0010610","count":1},{"id":"GO:0006446","count":1},{"id":"GO:1900363","count":1}]},{"hash":"1410359891358247697","title":"Neural cell adhesion and nervous system development","description":"This cluster is dominated by cadherin-mediated cell adhesion terms (homophilic/heterophilic adhesion, cell-cell adhesion, cadherin-mediated adhesion) and neural-related functions (neuron cell adhesion, nervous system development, positive regulation of synapse assembly). Additional terms on planar polarity and tissue patterning (bone maturation, hair orientation) suggest adhesion proteins coordinating neural connectivity with broader tissue organization. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007156","count":9},{"id":"GO:0007157","count":9},{"id":"GO:0007158","count":7},{"id":"GO:0043931","count":7},{"id":"GO:0051965","count":7}]},{"hash":"1866914588635608922","title":"Autophagy-Lysosome Proteostasis","description":"This cluster shows strong enrichment for autophagy- and lysosome-related processes (autophagosome maturation; chaperone-mediated autophagy; lysosomal protein catabolic process; Golgi to lysosome transport) along with protein stabilization and proteasomal regulation. Together these terms indicate a module focused on protein quality control through autophagy-lysosome pathways and proteostasis, rather than a single signaling pathway.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050821","count":3},{"id":"GO:2001199","count":2},{"id":"GO:0038095","count":2},{"id":"GO:0035455","count":2},{"id":"GO:0090160","count":2}]},{"hash":"1958526018025860385","title":"Cardiovascular development and coagulation","description":"The cluster is enriched for terms tied to heart development, angiogenesis, blood coagulation, fibrinolysis, and complement activation, pointing to vascular biology and hemostasis. While a few terms are obsolete or peripheral (e.g., stilbenoid response and PI3K signaling), the core theme centers on cardiovascular formation, vascular remodeling, and coagulation pathways.","confidence":"Medium","size":14,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045766","count":4},{"id":"GO:0042730","count":4},{"id":"GO:0006958","count":4},{"id":"GO:0007596","count":3},{"id":"GO:0003050","count":3}]},{"hash":"611216256503450124","title":"Neuroimmune Dopaminergic Signaling","description":"This cluster combines strong signals for immune/inflammatory regulation (negative regulation of inflammatory response, immune response, eosinophil and astrocyte-related chemotaxis) with robust dopamine-related processes (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling), plus glial-neurotrophic interactions, suggesting a coherent theme at the intersection of neuroinflammation and dopaminergic signaling.","confidence":"Medium","size":14,"edges":15,"triangles":6,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":14},{"id":"GO:0042493","count":14},{"id":"GO:2000458","count":14},{"id":"GO:1900168","count":14},{"id":"GO:0048245","count":14}]},{"hash":"1056656348620134936","title":"Endothelial Coagulation Signaling","description":"Endothelial cells and coagulation pathways dominate the top GO terms, including positive regulation of endothelial apoptosis, activation and general coagulation cascades, and membrane signaling events such as calcium-activated phosphatidylcholine scrambling and bleb formation. While there are a few outliers (bone mineralization, insulin secretion), the cluster overall centers on endothelial signaling coordinating coagulation and related membrane dynamics, justifying a label focused on endothelial coagulation signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":2},{"id":"GO:0045794","count":2},{"id":"GO:0030501","count":2},{"id":"GO:1902304","count":2},{"id":"GO:0061590","count":2}]},{"hash":"2198999208303386357","title":"Embryonic Morphogenesis and Placental Development","description":"The top GO terms point to development and morphogenesis: left/right pattern formation, cartilage morphogenesis, trophoblast giant cell differentiation, placental development and EMT in heart cushion formation, and endocrine/pancreatic beta-cell development. While there are some immune-related terms (complement activation), the dominant pattern is embryonic and placental differentiation and tissue morphogenesis, suggesting proteins co-function in developmental programs. Overall, a coherent label focusing on embryonic morphogenesis and placental development fits best.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006957","count":2},{"id":"GO:0006958","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0060536","count":2},{"id":"GO:0060972","count":2}]},{"hash":"1621661857855666404","title":"Central Carbon Metabolism: Glycolysis and Gluconeogenesis","description":"This cluster is driven by strong signals for canonical glycolysis and gluconeogenesis, plus starvation and redox-related processes, suggesting a group of central energy metabolism enzymes that may function as oligomers (tetramers). The terms imply focus on glucose metabolism and energy balance under stress, with structural enzyme associations.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":5},{"id":"GO:0051289","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0070542","count":3},{"id":"GO:0071353","count":3}]},{"hash":"511536518999743499","title":"Embryonic development and morphogenesis","description":"The top terms cluster around diverse developmental and morphogenic processes across tissues (placental differentiation, mesoderm formation, left/right patterning, and organ-specific morphogenesis such as cartilage, hair follicles, and facial structures), indicating a theme of broad embryonic development and tissue morphogenesis rather than a single tissue-specific function.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":10},{"id":"GO:0060536","count":10},{"id":"GO:0060806","count":10},{"id":"GO:0060972","count":10},{"id":"GO:0035270","count":10}]},{"hash":"425800481506474483","title":"Mucosal immune signaling and epithelial maintenance","description":"The top terms center on immune regulation (B cell signaling, complement activation, and cytokine production such as IL-10, IL-13, GM-CSF) and epithelial/ palatal context (roof of mouth development, maintenance of gastrointestinal epithelium), suggesting a theme of mucosal immunity and tissue homeostasis. Some terms (Rho signaling, glutamatergic transmission) are less directly tied but may reflect broader signaling roles in mucosal tissues. Overall, the cluster appears related to immune signaling in mucosal epithelium and its maintenance.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0035249","count":2},{"id":"GO:2000667","count":2},{"id":"GO:2001181","count":2}]},{"hash":"865717860700838313","title":"Embryonic organogenesis and skeletal morphogenesis","description":"The top GO terms cluster around developmental biology, with strong emphasis on skeletal system development, organ induction, and outer ear morphogenesis (and related lung mesenchyme development). Additional terms point to signaling and regulatory processes (protein autophosphorylation, chemokine production, and cell activation), which are commonly involved in coordinating embryonic organogenesis. Together, these suggest a group of proteins tied to developmental morphogenesis rather than a single specific tissue, hence the \u201cEmbryonic organogenesis and skeletal morphogenesis\u201d label.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0001501","count":11},{"id":"GO:1905065","count":11},{"id":"GO:0060484","count":11},{"id":"GO:0046777","count":11},{"id":"GO:0050808","count":11}]},{"hash":"19398935698201645","title":"Dopaminergic Neuroimmune Signaling","description":"Top GO terms indicate both immune/inflammatory regulation and dopaminergic signaling, plus glial-related processes (astrocyte chemotaxis and neurotrophic factor production). This points to a theme of dopaminergic modulation of neuroimmune and glial activity, with some xenobiotic response context.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":14},{"id":"GO:0042493","count":14},{"id":"GO:2000458","count":14},{"id":"GO:1900168","count":14},{"id":"GO:0048245","count":14}]},{"hash":"1820395507459039294","title":"Embryonic neural development and transcription regulation","description":"These terms cluster around embryogenesis and neural development (blastocyst formation; neural tube closure initiation; midbrain-hindbrain boundary morphogenesis; third ventricle development; axis specification), with supporting roles for transcriptional and mRNA stability regulation and some developmental/post-translational modification processes. The dominant theme is developmental morphogenesis with a focus on neural contexts, aided by gene expression control mechanisms.","confidence":"Medium","size":13,"edges":30,"triangles":36,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001825","count":5},{"id":"GO:0010610","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0021678","count":3},{"id":"GO:0021555","count":3}]},{"hash":"782262338808873862","title":"Actin Cytoskeleton Remodeling and Integrin Signaling","description":"This cluster centers on actin cytoskeleton dynamics (reorganization, stress fiber assembly), Rho-mediated and integrin signaling, and related adhesion processes, pointing to coordinated cytoskeletal remodeling and cell\u2013matrix communication. Neural development terms (axonogenesis, corpus callosum development) and apoptosis suggest roles in neurite outgrowth and cell fate decisions that rely on cytoskeletal and adhesion signaling. The mixture of cytoskeletal, adhesion, and signaling terms, with some developmental/immune-related connections, supports a cohesive theme of cytoskeleton-driven signaling. Confidence: Medium","confidence":"","size":13,"edges":37,"triangles":44,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":5},{"id":"GO:0032092","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0022038","count":4},{"id":"GO:0031663","count":4}]},{"hash":"1867094020377573334","title":"Immune cell apoptosis and inflammatory regulation","description":"This cluster is centered on programmed cell death and inflammatory signaling within immune contexts: multiple GO terms point to apoptosis (TRAIL-activated signaling, activation-induced T cell death, endothelial and motor neuron apoptotic processes) and inflammatory regulation (negative regulation of inflammatory response, cytokine production like IL-5/IL-10, fever-related prostaglandin signaling). The dominant theme is apoptosis intertwined with immune/inflammatory regulation, with a few peripheral terms related to cell division. ","confidence":"High","size":13,"edges":59,"triangles":150,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":10},{"id":"GO:0006925","count":10},{"id":"GO:0006924","count":10},{"id":"GO:0009786","count":10},{"id":"GO:0036462","count":10}]},{"hash":"912901140935365794","title":"Cytoskeleton and Golgi trafficking in development","description":"This cluster centers on processes like exocytosis, actin cytoskeleton organization, and Golgi localization, plus neuron migration and GTPase regulation, all of which point to coordinated cytoskeletal remodeling and vesicle trafficking during development. While some terms (e.g., sensory perception of sound, bone development, glucan biosynthesis) may reflect broader developmental roles or annotation noise, the dominant themes converge on how cells organize and transport materials to support growth and cellular movement.","confidence":"Medium","size":13,"edges":26,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006887","count":3},{"id":"GO:0030036","count":3},{"id":"GO:0051683","count":3},{"id":"GO:0090557","count":3},{"id":"GO:0007605","count":3}]},{"hash":"644730689012183648","title":"Proteostasis and Vesicle Trafficking","description":"These terms cluster around protein quality control and trafficking: misfolded protein response, ER/Golgi quality control (retention in Golgi, ER polarization), mitochondrial protein import, SNARE complex disassembly, autophagy, and proteasome assembly. Together they point to proteostasis and vesicular transport pathways that manage protein folding, degradation, and trafficking. Some nodes like nonfunctional rRNA decay and microtubule dynamics indicate broader quality-control and cytoskeletal roles but do not contradict the core theme.","confidence":"High","size":13,"edges":59,"triangles":138,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070651","count":6},{"id":"GO:0045053","count":5},{"id":"GO:0071218","count":5},{"id":"GO:0045041","count":4},{"id":"GO:0006272","count":4}]},{"hash":"897179968477891088","title":"Ubiquitin-mediated proteolysis and signaling","description":"The terms are dominated by ubiquitination activities (autoubiquitination, K48- and K63-linked), and ubiquitin-dependent protein catabolic processes, which imply roles in targeting proteins for degradation. Additional GO terms connect ubiquitination to chromatin regulation (histone catabolic process) and to signaling and transcription regulation (TNF signaling, JNK cascade, RNA Pol II repression). This suggests a cohesive cluster of proteins that modify ubiquitin to control protein turnover, chromatin dynamics, and signaling pathways.","confidence":"High","size":13,"edges":25,"triangles":12,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":9},{"id":"GO:0085020","count":8},{"id":"GO:0036205","count":8},{"id":"GO:1903265","count":8},{"id":"GO:0042787","count":8}]},{"hash":"2049325387643925562","title":"Protein quality control via ubiquitin-proteasome system","description":"The cluster\u2019s top GO terms heavily center on ubiquitin-dependent protein degradation (ERAD, proteasomal catabolic processes, aggresome assembly, deubiquitination/deneddylation) and regulation of translation initiation, which together indicate a cohesive proteostasis module for tagging, degrading misfolded proteins, and managing aggregates. Occasional links to nucleotide excision repair appear less central. Overall, this set strongly supports a protein quality control function.","confidence":"High","size":13,"edges":75,"triangles":255,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070911","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0032436","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0070842","count":3}]},{"hash":"1269635500926766915","title":"Regulation of proliferation and cytoskeleton dynamics","description":"This cluster centers on control of cell growth and division (negative regulation of proliferation, apoptotic regulation, chromatin assembly) and on cytoskeletal dynamics and cell movement (microtubule regulation, cell migration, GTPase activity, ciliogenesis docking). Additional terms like mRNA transport and ribosomal protein import suggest broader biosynthetic regulation tied to growth. Taken together, the proteins seem to coordinate proliferation control with cytoskeletal and ciliogenesis processes, making the label representative but not perfectly specific. ","confidence":"Medium","size":13,"edges":45,"triangles":68,"max_degree":11,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0008285","count":5},{"id":"GO:0007026","count":4},{"id":"GO:0071230","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0051028","count":4}]},{"hash":"1376765728773684729","title":"Ubiquitin-Proteasome System and Signaling","description":"The top terms are dominated by ubiquitination processes (autoubiquitination, ubiquitin-dependent ERAD, ubiquitin-dependent protein catabolic process, K6-linked ubiquitination) and downstream signaling (regulation of JNK cascade, NF-kappaB activation). This pattern points to a cluster of proteins involved in tagging substrates for degradation and regulating signaling pathways via ubiquitin-mediated mechanisms, with a few terms hinting at immune system processes and chromatin-related regulation (V(D)J recombination, dosage compensation) that can be linked to ubiquitin-mediated control. Overall, it represents the ubiquitin-proteasome system and related signaling rather than a single metabolic or structural pathway. ","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":11},{"id":"GO:0030433","count":10},{"id":"GO:0042787","count":10},{"id":"GO:0033151","count":9},{"id":"GO:0085020","count":9}]},{"hash":"81019667645104875","title":"Cross-Species Developmental and Reproductive Processes","description":"The top GO terms span diverse developmental and reproductive themes across species (caudal fin development, notochord vacuolation, pollen and embryo sac development, cilium assembly) plus related cellular processes (DNA repair during meiosis, vacuolar acidification, proton transport). This suggests a cluster centered on developmental and reproductive biology across plants and animals, with some accompanying cellular housekeeping functions. Confidence: Medium","confidence":"Medium","size":13,"edges":48,"triangles":94,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0042777","count":2},{"id":"GO:0033336","count":2},{"id":"GO:0060036","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0015991","count":2}]},{"hash":"222171867207797991","title":"Chromatin Silencing and Transcription Regulation","description":"The cluster is dominated by GO terms related to epigenetic control of gene expression, including negative regulation of transcription by RNA polymerase II, histone H3-K27 methylation regulation, and heterochromatin formation (subtelomeric and rDNA). These indicate a common theme of chromatin-mediated transcriptional silencing and chromosomal regulation, with dosage compensation and sex chromosome-related processes further supporting a chromatin-centric regulatory role. Some outliers (like plasmid partitioning) may reflect broader chromosomal segregation connections, but the core signal is epigenetic transcriptional control.","confidence":"Medium","size":13,"edges":31,"triangles":33,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0061086","count":5},{"id":"GO:1900363","count":4},{"id":"GO:0030543","count":4},{"id":"GO:0035023","count":4}]},{"hash":"775685565080062870","title":"Chromatin silencing and heterochromatin formation","description":"This cluster shows a strong emphasis on chromatin organization, with multiple GO terms for heterochromatin formation (subtelomeric, pericentric, rDNA) and negative regulation of transcription by RNA polymerase II, plus related histone methylation regulation and dosage compensation/spermatogenesis contexts. The plasmid partitioning term likely reflects shared chromatin-based partitioning mechanisms. Overall, the common theme is chromatin silencing and heterochromatin maintenance.","confidence":"High","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0030543","count":13},{"id":"GO:0035023","count":13},{"id":"GO:0031509","count":13},{"id":"GO:0007296","count":13},{"id":"GO:0007549","count":13}]},{"hash":"936559130790219446","title":"Neural and skeletal muscle development","description":"The top GO terms cluster around nervous system development (including corpus callosum development and axonal fasciculation) and skeletal muscle/muscle tissue development with sarcomere organization, indicating a cohesive theme of neural and muscular development. Additional neural activity-related terms like cellular response to dopamine and behavioral responses to pain support a neural focus, while some immune-related terms may reflect broader multifunctionality or annotation noise. Overall, the dominant signal points to neurodevelopmental and myogenic processes.","confidence":"Medium","size":13,"edges":50,"triangles":80,"max_degree":12,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":7},{"id":"GO:0045214","count":7},{"id":"GO:0050853","count":7},{"id":"GO:0007519","count":7},{"id":"GO:0022038","count":6}]},{"hash":"2014765714236412858","title":"Circadian Gene Regulation and Kidney Development","description":"The top GO terms cluster around circadian regulation of gene expression and kidney-related developmental and functional processes (ureteric bud branching, renal sodium absorption), with supporting transcriptional regulation terms and some broader systemic roles. This suggests a theme of circadian control of gene expression in kidney development and function, with some ancillary regulatory terms. Therefore, this label emphasizes the circadian transcriptional regulation linked to renal development.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0032922","count":4},{"id":"GO:0007565","count":4},{"id":"GO:0070294","count":4},{"id":"GO:0090190","count":4},{"id":"GO:0003016","count":4}]},{"hash":"529986225957407263","title":"Post-transcriptional mRNA processing and translation control","description":"The cluster centers on mRNA splicing via the spliceosome, mRNA stability, and regulation of translation initiation and reinitiation, plus miRNA-mediated translational silencing. Together these terms indicate a coherent focus on post-transcriptional gene expression regulation, with some developmental context suggested by blastocyst formation.","confidence":"High","size":13,"edges":45,"triangles":90,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0048255","count":4},{"id":"GO:0001825","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0006446","count":4}]},{"hash":"443869150091300641","title":"Golgi-ER and endosomal vesicle trafficking","description":"This cluster is dominated by GO terms for vesicle transport across the secretory pathway (ER\u2013Golgi, Golgi\u2013ER, Golgi to plasma membrane, endocytosis, endosome\u2013Golgi) and protein targeting/sorting. These terms cohere into a vesicle trafficking/sorting module; additional terms like dendrite development and Wnt signaling likely reflect downstream roles that depend on proper trafficking. ","confidence":"High","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":12},{"id":"GO:0006888","count":12},{"id":"GO:0090316","count":10},{"id":"GO:0006897","count":10},{"id":"GO:0043001","count":9}]},{"hash":"522203973722359970","title":"Muscle/Heart/CNS Development and Signaling Control","description":"The cluster centers on developmental processes across muscle, heart, and central nervous system, with positive/negative regulation of BMP and Wnt signaling, and broader cell differentiation and proliferation control. This suggests a cohesive module of developmental differentiation guided by signaling pathway regulation.","confidence":"Medium","size":13,"edges":15,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035914","count":5},{"id":"GO:0046827","count":4},{"id":"GO:0030514","count":4},{"id":"GO:1905453","count":3},{"id":"GO:0060914","count":3}]},{"hash":"1754252665423847362","title":"Mammary gland growth and lactation signaling","description":"Based on the top GO terms, the cluster is enriched for processes central to mammary tissue biology: mammary gland epithelial cell proliferation, lactation, and hormonal signaling via leptin, together with canonical Wnt signaling and cell division, suggesting coordinated growth and lactation-related regulation. Some terms like Atg1/ULK1 and epithelial differentiation imply remodeling and maturation processes, while a few viral-related terms appear less central to the main theme. Confidence in this thematic label is high.","confidence":"High","size":13,"edges":67,"triangles":186,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007595","count":3},{"id":"GO:0019086","count":3},{"id":"GO:0030857","count":3},{"id":"GO:0033598","count":3}]},{"hash":"1112969323257916567","title":"Yeast invasive/pseudohyphal growth under glucose limitation","description":"This cluster centers on transcriptional activity (RNA Pol II and preinitiation complex assembly) alongside morphological responses to nutrient stress (invasive and pseudohyphal growth) and cytoskeletal (actin bundle) remodeling, suggesting a coordinated transcriptional program driving yeast morphogenesis under glucose limitation. Some histone modification terms further imply chromatin regulation accompanying this switch.","confidence":"Medium","size":13,"edges":12,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":3},{"id":"GO:0051123","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0007124","count":2}]},{"hash":"1967886782604745072","title":"Ubiquitin-specific deubiquitinases (DUBs)","description":"This cluster is dominated by deubiquitination terms across multiple ubiquitin linkages (K11, K29, K63) and substrate categories, including histone deubiquitination and ubiquitin-dependent transcription, suggesting the proteins act as DUBs with broader roles in chromatin regulation and ubiquitin signaling. Some terms touch on neuronal behavior, likely reflecting downstream effects rather than defining function.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060013","count":4},{"id":"GO:0035192","count":4},{"id":"GO:0010995","count":4},{"id":"GO:0035871","count":4},{"id":"GO:0035520","count":4}]},{"hash":"556385495459283084","title":"DNA replication, recombination, and integration","description":"This cluster centers on genome remodeling and integration, as indicated by terms for DNA replication, recombination, DNA integration, and RNA-templated DNA biosynthesis, plus proviral latency. Some viral entry/host interaction terms appear but the dominant theme is DNA synthesis and genome integration, including retroviral-like processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":2},{"id":"GO:0003351","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0075732","count":2},{"id":"GO:0006310","count":2}]},{"hash":"1162083323158844400","title":"Ribosome Biogenesis and Translation","description":"The cluster shows a strong focus on ribosome- and translation-related processes: translation is highly represented (GO:0006412, 10 occurrences), with significant signals for ribosome biogenesis (GO:0042254, 3) and ribosome assembly (GO:0042255, 2), plus rRNA processing/export terms. The presence of some antibiotic and virus response terms likely reflects ribosome-targeting stresses or defense connections rather than a separate pathway. Overall, the dominant theme is components and regulation of ribosome biogenesis and protein synthesis.","confidence":"High","size":13,"edges":44,"triangles":63,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0046677","count":5},{"id":"GO:0042254","count":3},{"id":"GO:0042255","count":2},{"id":"GO:0006407","count":2}]},{"hash":"183242139675180604","title":"Inflammatory Cytokine Signaling","description":"The cluster\u2019s GO terms center on immune response and cytokine-driven signaling, including positive regulation of interferon, interleukin-6 production, fever generation, monocyte aggregation, and NF-kappaB/PI3K-AKT pathways. Together these point to an inflammatory immune activation program. A few terms (spermatid development, mitotic nuclear division) are less related, but the dominant pattern supports cytokine-mediated immune signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033674","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0042095","count":1},{"id":"GO:0070487","count":1},{"id":"GO:0045410","count":1}]},{"hash":"672943309991865253","title":"Endoplasmic Reticulum Stress and ER-to-Golgi Trafficking","description":"The top GO terms cluster around ER-wide processes: unfolded protein response and ER localization, plus COPII vesicle budding and ER-to-Golgi trafficking, with calcium homeostasis in the ER, indicating a cohesive theme of ER stress response and protein export. A few terms about host-virus interactions appear as outliers/noise but do not override the dominant ER-centric pattern.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006987","count":2},{"id":"GO:0006874","count":2},{"id":"GO:0060304","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0044828","count":2}]},{"hash":"1640587294714788456","title":"ER stress\u2013driven apoptosis and innate immune signaling","description":"This cluster is dominated by ER-stress\u2013induced apoptotic signaling and related transcriptional responses, with additional immune-related terms (macrophage differentiation, NK cell cytotoxicity) suggesting a link between cellular stress responses and innate immune activation. Other terms on development and general transcription are less central to the core theme, giving a moderate level of confidence in the label.","confidence":"Medium","size":13,"edges":65,"triangles":181,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070059","count":7},{"id":"GO:0006366","count":6},{"id":"GO:0021983","count":5},{"id":"GO:1990418","count":5},{"id":"GO:0030225","count":5}]},{"hash":"1786309976421495108","title":"Complement Activation and Immune Regulation","description":"The proteins in this cluster cluster around classical and alternative complement activation and its regulation, along with immune cell adhesion, leukocyte trafficking, anti-inflammatory IL-10 production, and apoptosis-related signaling. This combination suggests a cohesive immune-regulatory module centered on the complement system and related leukocyte interactions, with an incidental outlier term for vocalization behavior.","confidence":"High","size":13,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071625","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0007157","count":3},{"id":"GO:0006924","count":2},{"id":"GO:0045959","count":2}]},{"hash":"1396248878552892649","title":"Immune signaling and developmental morphogenesis","description":"The top GO terms show a mix of immune-related activities (interleukin-4 response, macrophage differentiation, microglial activation, NK cell cytotoxicity) and developmental/morphogenesis processes (imaginal disc fusion, outflow tract morphogenesis, epithelial maturation in salivary gland development). This combination suggests a cluster of proteins involved in both immune signaling and developmental regulation, rather than a single narrow function. Confidence: Medium","confidence":"","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071353","count":4},{"id":"GO:0061614","count":3},{"id":"GO:0046529","count":3},{"id":"GO:0003151","count":3},{"id":"GO:1990418","count":3}]},{"hash":"260760857342176786","title":"Ubiquitination and Protein Degradation","description":"The top GO terms are dominated by ubiquitination-related processes (ubiquitin-dependent protein catabolic process, protein ubiquitination, polyubiquitination, autoubiquitination, K6-linked ubiquitination), with additional related regulatory terms (e.g., regulation of JNK cascade) and a few broader processes that can be influenced by ubiquitin signaling. This suggests the cluster centers on ubiquitin tagging and protein turnover pathways.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0016567","count":6},{"id":"GO:0000209","count":6},{"id":"GO:0051865","count":6},{"id":"GO:1901253","count":6}]},{"hash":"2274039734559120444","title":"Chaperone-mediated folding and protein quality control","description":"The top GO terms point to chaperone activity and protein folding/refolding, along with protein complex oligomerization, membrane targeting, and ER-associated degradation, which together suggest a cluster of proteostasis and maturation factors coordinating folding, assembly, and quality control of proteins. The presence of related, albeit less cohesive terms like DNA replication and tRNA import may reflect broader cellular context or annotation overlap, but the dominant signal is chaperone-driven protein maturation and quality control.","confidence":"Medium","size":13,"edges":66,"triangles":180,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051259","count":10},{"id":"GO:0032781","count":10},{"id":"GO:0097428","count":10},{"id":"GO:0090084","count":9},{"id":"GO:1900035","count":9}]},{"hash":"1029347445132136097","title":"Tissue development and remodeling","description":"The top GO terms point to diverse developmental and structural processes across tissues\u2014endothelial barrier establishment, cortical microtubule organization, somite axis specification, muscle development, brush border assembly, and neuron remodeling\u2014suggesting a generic theme of tissue formation and organization rather than a single specialized function. Some terms (receptor internalization, p38MAPK regulation) relate to signaling but do not dominate the cluster. This supports a label of tissue development and morphogenesis as the overarching concept, with some peripheral signals present. ","confidence":"Medium","size":13,"edges":8,"triangles":1,"max_degree":5,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0061028","count":12},{"id":"GO:0043622","count":12},{"id":"GO:0007527","count":12},{"id":"GO:0032092","count":12},{"id":"GO:1903753","count":12}]},{"hash":"1743419158231075872","title":"Neural Development and Migration","description":"The top GO terms are dominated by neural-related processes: regulation of neuron maturation, tangential migration to the olfactory bulb, and branching morphogenesis of a nerve, indicating a focus on neural development and neuronal migration. While some terms are general (protein heterooligomerization, cell division), the prominent neural development terms suggest this cluster centers on brain development and neuronal movement. ","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0035751","count":4},{"id":"GO:2000172","count":4}]},{"hash":"1987125935377590160","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster centers on ubiquitin signaling and proteolysis, with GO terms for ubiquitin-dependent protein catabolic processes, ERAD, autoubiquitination, and K6-linked ubiquitination dominating; histone turnover and transcriptional regulation also tie in via ubiquitin pathways, indicating a cohesive theme of protein turnover controlled by ubiquitination.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0036205","count":8},{"id":"GO:0000122","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0033151","count":7},{"id":"GO:0085020","count":7}]},{"hash":"2162009898677131155","title":"Membrane lipid biosynthesis and cytoskeletal dynamics","description":"The Top Terms include lipid biosynthetic processes (phosphatidylcholine and phosphatidylethanolamine), suggesting membrane lipid metabolism, and microtubule-related terms (bundle formation, polymerization), indicating cytoskeletal remodeling. While there are also terms related to mitochondrial fusion regulation, protein processing, and ethylene signaling/phagocytosis, the most cohesive theme is membrane lipid metabolism linked with cytoskeletal dynamics, justifying this label with Medium confidence.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006656","count":1},{"id":"GO:0010636","count":1},{"id":"GO:0016540","count":1},{"id":"GO:0006646","count":1},{"id":"GO:0010954","count":1}]},{"hash":"1815800041765928236","title":"Calcium-Dependent Neuronal Signaling and NFAT Regulation","description":"These proteins are enriched for calcium-related signaling and neural activity, including detection of calcium, neurotransmitter secretion, memory, and regulation of the calcineurin-NFAT pathway, as well as cAMP-responsive processes. While there are peripheral terms like angiogenesis and cuticle development, the strongest and most coherent theme is calcium-driven neuronal signaling and NFAT-mediated transcriptional regulation, with memory and neurotransmission as core features.","confidence":"Medium","size":13,"edges":21,"triangles":10,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051533","count":6},{"id":"GO:0007269","count":6},{"id":"GO:0005513","count":6},{"id":"GO:0001525","count":4},{"id":"GO:0048745","count":4}]},{"hash":"2024942268726157017","title":"DNA Damage Response and Apoptosis Regulation","description":"This cluster is dominated by terms related to DNA repair, DNA damage checkpoints, and both promoting and inhibiting apoptotic pathways, with additional signals for circadian regulation and protein deacetylation. The combination suggests a cohesive module coordinating genome integrity maintenance with cell fate decisions and growth control.","confidence":"High","size":13,"edges":39,"triangles":51,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0043653","count":1},{"id":"GO:0043065","count":1},{"id":"GO:0090263","count":1},{"id":"GO:0032435","count":1}]},{"hash":"960302197545446809","title":"Embryonic Organogenesis and Tissue Development","description":"The terms point to broad roles in embryonic development across multiple organs and tissues (gonads, heart, eye, placenta, hindlimb, habenula, etc.) and include transcriptional regulation, signaling a general organogenesis theme rather than a single pathway.","confidence":"High","size":13,"edges":40,"triangles":58,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008584","count":9},{"id":"GO:0048048","count":9},{"id":"GO:2000288","count":8},{"id":"GO:0007507","count":8},{"id":"GO:0001890","count":8}]},{"hash":"1044658781054246010","title":"Neurovascular development and cytoskeletal remodeling","description":"The GO terms point to neural development (neuron projection development, nervous system development) and angiogenesis, with a focus on cell movement and membrane ruffle formation, which ties to cytoskeletal remodeling. A few metabolic terms (UTP/CTP biosynthesis) appear but do not define the cluster's main theme; overall it suggests proteins involved in neurovascular development and cell migration.","confidence":"Medium","size":13,"edges":20,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0071398","count":2},{"id":"GO:1900029","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0051259","count":1}]},{"hash":"1490513940519774784","title":"Developmental morphogenesis and actin dynamics","description":"These proteins show enrichment for morphogenesis-related GO terms (seed morphogenesis, plant ovule morphogenesis, ectoderm formation) together with actin cytoskeleton processes (actin filament bundle assembly, lamellipodium assembly) and neuronal differentiation/migration (medial/lateral motor column neuron differentiation). The common thread is coordination of tissue morphogenesis and cell movement via actin remodeling, with some regulatory terms suggesting gene expression control during development. Overall, a cohesive theme of developmental morphogenesis linked to cytoskeletal dynamics. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":8},{"id":"GO:0048317","count":8},{"id":"GO:0048482","count":8},{"id":"GO:0010735","count":7},{"id":"GO:0072283","count":7}]},{"hash":"1994569836196922754","title":"Post-transcriptional mRNA regulation and translation control","description":"The enriched GO terms center on mRNA stability, splicing, polyadenylation regulation, and initiation/reinitiation of translation, indicating proteins focused on post-transcriptional gene expression control rather than transcription. Some terms relate to development (blastocyst formation), but the dominant theme is mRNA processing and translation regulation.","confidence":"High","size":13,"edges":32,"triangles":23,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":12},{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0048255","count":11},{"id":"GO:0001825","count":11}]},{"hash":"1837810991524204147","title":"Stimulus-Responsive Transcription Regulation","description":"The top terms repeatedly point to DNA-templated transcription and its positive regulation, indicating a core theme of transcriptional control. While there are additional, broader signals related to responses to stimuli (mechanical stress, heat), the strongest and most consistent signal is transcription regulation in response to environmental cues, justifying a transcription-focused cluster name with moderate confidence due to weaker connectivity among terms overall.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0002448","count":1}]},{"hash":"1920215389483107742","title":"Sphingolipid biosynthesis and ceramide turnover","description":"The cluster is enriched for sphingolipid-related processes (sphingosine biosynthesis, phytosphingosine biosynthesis, ceramide catabolic process), pointing to coordinated sphingolipid metabolism. Additional terms related to keratinocyte differentiation and stress/adhesion responses suggest an epidermal biology context where sphingolipids are key for barrier function and signaling. Overall, the dominant theme is sphingolipid metabolism with ceramide turnover.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0046512","count":5},{"id":"GO:0035690","count":4},{"id":"GO:0071277","count":4},{"id":"GO:0010446","count":4},{"id":"GO:0030216","count":4}]},{"hash":"2203776828531601269","title":"Wnt signaling and adipocyte differentiation","description":"The top GO terms show strong enrichment for Wnt signaling (GO:0016055) and fat cell differentiation (GO:0045444), suggesting a core role in adipogenesis regulation. Supporting terms related to transcriptional control, mRNA processing, and ubiquitin-dependent protein turnover hint at broader regulatory mechanisms coordinating adipocyte formation and cell cycle-related processes.","confidence":"Medium","size":13,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0000083","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0006397","count":3}]},{"hash":"1329823711719517495","title":"Cell Cycle and Differentiation Signaling","description":"The top GO terms cluster around cell proliferation and DNA synthesis (mitotic cell cycle, DNA-templated transcription, positive regulation of DNA replication) along with fate decisions and differentiation (apoptotic process, keratinocyte differentiation, hippocampus development) and signaling pathways (positive regulation of ERK1/ERK2 cascade). This suggests a coordinated set of proteins influencing growth, transcriptional control, and lineage differentiation rather than a single tissue-specific function.","confidence":"Medium","size":13,"edges":14,"triangles":3,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009636","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0045740","count":4},{"id":"GO:0006915","count":4}]},{"hash":"123648422958264381","title":"Organelle protein targeting and translocation","description":"The cluster is enriched for terms related to directing nascent and mature proteins to membranes and organelles\u2014SRP-dependent cotranslational targeting to membranes, Sec-dependent transport, mitochondrial import, ER-to-cytosol retrograde transport, and Golgi retention\u2014indicating a cohesive theme of protein trafficking and translocation across organelles. A single term about DNA replication appears as an outlier.","confidence":"Medium","size":13,"edges":70,"triangles":209,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0031204","count":4},{"id":"GO:0006616","count":4},{"id":"GO:0032979","count":3}]},{"hash":"746217234817063693","title":"Unknown","description":"The top GO terms span very different biological areas (angiogenesis-related migration, cholesterol transport, floral organ identity, heart morphogenesis, circadian rhythm, hormone signaling, steroid synthesis, integument development), including plant- and animal-specific processes. With no shared function or pathway across the proteins and no interactions observed, there is no coherent theme to label a specific cluster function. I therefore assign Unknown with no confidence.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090051","count":1},{"id":"GO:0032367","count":1},{"id":"GO:0048497","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0097498","count":1}]},{"hash":"567398320740654377","title":"Actin-driven cytoskeleton remodeling and trafficking","description":"The cluster shows strong representation of actin dynamics terms (lamellipodium and podosome assembly, actin nucleation) plus vesicle trafficking processes (transcytosis, synaptic vesicle uncoating), indicating a cohesive role in cytoskeleton remodeling linked to membrane and vesicle movement during development and signaling.","confidence":"High","size":13,"edges":69,"triangles":203,"max_degree":12,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0002051","count":13},{"id":"GO:0030032","count":13},{"id":"GO:0051127","count":13},{"id":"GO:0098761","count":13},{"id":"GO:0016191","count":13}]},{"hash":"1785757123884865372","title":"Adaptive immune signaling and hematopoiesis","description":"The top GO terms strongly point to adaptive immune pathways (Fc-epsilon receptor signaling, B cell receptor signaling, adaptive immune response, IL-2 production) and hematopoietic processes (megakaryocyte development, Kit signaling), suggesting coordinated immune signaling with blood cell development, despite some term obsolescence. ","confidence":"Medium","size":13,"edges":39,"triangles":52,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0038095","count":11},{"id":"GO:0050853","count":11},{"id":"GO:0002250","count":11},{"id":"GO:1900042","count":11},{"id":"GO:0043552","count":10}]},{"hash":"2077471471022376303","title":"Unknown","description":"The top GO terms describe a highly diverse set of processes\u2014from carbohydrate and amino acid catabolism and aldehyde metabolism to lignin biosynthesis, respiration, response to lipopolysaccharide, and extracellular signaling regulation\u2014without a single cohesive biological theme. This lack of a clear shared function makes a concise, specific cluster label unreliable, so the appropriate label is Unknown.","confidence":"","size":13,"edges":11,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019595","count":2},{"id":"GO:0019518","count":2},{"id":"GO:0000947","count":2},{"id":"GO:0010430","count":2},{"id":"GO:0009809","count":2}]},{"hash":"224410266730660287","title":"Neural development and tissue morphogenesis","description":"The terms cluster nervous system development and synapse assembly, with broader developmental processes (mesoderm and osteoblast differentiation) and cytoskeletal remodeling, suggesting proteins involved in developmental programs across tissues and neural connectivity.","confidence":"Medium","size":13,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0045162","count":3},{"id":"GO:0001649","count":3},{"id":"GO:0051965","count":3}]},{"hash":"819046373481629161","title":"TLR2-Mediated Macrophage Activation and Antiviral Defense","description":"Most terms point to innate immune signaling, especially TLR2 pathways, macrophage activation, and defenses against viral/microbial stimuli (e.g., diacyl lipopeptide detection, IL-6 production, NF-kappaB signaling). These together suggest a coordinated TLR2-driven macrophage response with regulatory kinase activity. ","confidence":"High","size":13,"edges":36,"triangles":51,"max_degree":10,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045410","count":13},{"id":"GO:0006469","count":13},{"id":"GO:0042346","count":13},{"id":"GO:0051607","count":13},{"id":"GO:0034134","count":13}]},{"hash":"1931656894017629060","title":"Immune signaling and vascular development","description":"The GO terms point to signaling pathways (MAPK, AKT, STAT signaling; insulin signaling cross-talk) together with immune-defense processes (defense response to virus, response to LPS) and vascular-related processes (angiogenesis, adherens junction organization). This suggests a cluster of proteins coordinating immune signaling with vascular and cell\u2013cell adhesion functions, rather than a single specialized pathway.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0046627","count":2},{"id":"GO:0000187","count":2},{"id":"GO:0034332","count":2},{"id":"GO:0045071","count":2}]},{"hash":"1886740658272455772","title":"Embryonic Development and Organ Morphogenesis","description":"The terms cluster around embryonic development processes, including heart-related EMT and endocardial cushion formation, palate and facial morphogenesis, left-right patterning, cartilage morphogenesis, pancreas development, and placental regulation. This suggests a cohesive theme of embryonic tissue and organ formation, with some transcriptional regulation involved, making a label focused on developmental morphogenesis appropriate.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0003198","count":5},{"id":"GO:0060021","count":4},{"id":"GO:0060707","count":4},{"id":"GO:0060536","count":4},{"id":"GO:0060972","count":4}]},{"hash":"637386989264404609","title":"Developmental morphogenesis and tissue differentiation","description":"These terms point to embryonic development, tissue morphogenesis, and lineage specification across multiple organs (salivary gland, digestive tract, inner ear, hair follicle, endoderm), with extracellular matrix remodeling and SMAD signaling contributing to differentiation and proliferation. The common theme is broad developmental morphogenesis and tissue-specific differentiation.","confidence":"High","size":13,"edges":15,"triangles":6,"max_degree":5,"top_function":"wound healing","top_go_terms":[{"id":"GO:0060445","count":6},{"id":"GO:0007502","count":6},{"id":"GO:0060113","count":6},{"id":"GO:0001942","count":6},{"id":"GO:0035987","count":6}]},{"hash":"355568690967028140","title":"Angiogenesis and vascular morphogenesis","description":"This cluster is dominated by GO terms related to blood vessel formation and migration (angiogenesis, regulation of endothelial cell migration, angioblast migration, lymph vessel development) and to adhesion regulation (focal adhesion assembly, integrin-mediated adhesion). While a few terms touch on neural guidance or differentiation in other tissues, the prevailing signal is vascular development and associated cell-adhesion processes, justifying the label.","confidence":"High","size":13,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030316","count":2},{"id":"GO:0043535","count":2},{"id":"GO:0035475","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0071372","count":2}]},{"hash":"489607404251168871","title":"Protein Tyrosine Phosphatases Regulating MAPK Signaling","description":"The strongest signals are negative regulation of ERK/MAPK cascade and peptidyl-tyrosine dephosphorylation, which point to protein tyrosine phosphatases controlling MAPK signaling. Additional terms cover T cell receptor signaling, cell growth, and spindle-associated processes, suggesting phosphatases also influence cell-cycle Regulation. Together, these imply a cohesive phosphatase-centered cluster modulating signaling and growth, with some cell-cycle connections.","confidence":"Medium","size":13,"edges":66,"triangles":189,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0070373","count":12},{"id":"GO:0050860","count":12},{"id":"GO:0000200","count":12},{"id":"GO:0035335","count":10},{"id":"GO:0071470","count":9}]},{"hash":"134947391801711505","title":"Embryonic organ morphogenesis and differentiation","description":"This cluster centers on developmental morphogenesis across multiple organs (kidney structures like ureteric bud branching and nephron tubule formation; lacrimal gland and otic placode formation; skeletal muscle differentiation) and includes transcriptional regulation during development, indicating a common theme of embryonic organogenesis and lineage differentiation.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0035019","count":8},{"id":"GO:1902262","count":8},{"id":"GO:0060033","count":7},{"id":"GO:0032808","count":7}]},{"hash":"1930067665163392682","title":"Histone acetylation and transcription regulation","description":"The presence of GO terms for histone H4 acetylation (K16, K5, K8) and for positive regulation of DNA-templated transcription points to a theme of chromatin modification driving gene expression. Other terms (metabolic processes, gravitaxis, antibiotic response) appear less cohesive with this core signal and may reflect noise or multifunctional proteins, but the dominant connection is chromatin modification and transcription control.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043984","count":3},{"id":"GO:0042332","count":3},{"id":"GO:0043981","count":3},{"id":"GO:0043982","count":3},{"id":"GO:0051685","count":1}]},{"hash":"2241318097725927345","title":"TLR2-Driven Antiviral and Antibacterial Defense","description":"Based on the enriched GO terms, the proteins cluster around TLR2-mediated innate immune responses. Key terms include defense response to virus and to Gram-negative bacterium, toll-like receptor 2 signaling, macrophage activation, and regulation of dendritic cell cytokine production and IL-8. This points to a group involved in sensing pathogens and coordinating innate immune activation, with some unrelated neural development and lysosomal pH terms likely incidental.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0034134","count":3},{"id":"GO:0035751","count":3},{"id":"GO:1900155","count":3},{"id":"GO:0042116","count":3}]},{"hash":"509040747823704036","title":"Adaptive antiviral immune regulation","description":"The cluster is enriched for immune-related GO terms centered on antiviral defense and adaptive immunity, including defense response to virus, adaptive and humoral immune responses, and regulation of MHC class I biosynthesis. It also features regulatory actions on cytokine production (IL-5, Th2), STAT signaling, and suppression of viral genome replication, pointing to coordinated immune activation with tight regulation. The presence of inflammation/coagulation terms further supports an immune response context.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":11},{"id":"GO:0002250","count":11},{"id":"GO:2000663","count":10},{"id":"GO:2000552","count":10},{"id":"GO:0046597","count":10}]},{"hash":"813787484861717179","title":"Neuroinflammation and glial chemotaxis","description":"The terms cluster around immune/inflammatory processes (immune response, prostaglandin stimulus, eosinophil chemotaxis, xenobiotic response) and CNS-supportive glial signaling (regulation of astrocyte chemotaxis, GDNF production), with a nod to neuronal signaling (dopamine receptor pathway). This points to a coordinated neuroimmune/glial activity theme, justifying the label.","confidence":"Medium","size":13,"edges":58,"triangles":135,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071380","count":12},{"id":"GO:0008283","count":12},{"id":"GO:0007191","count":12},{"id":"GO:0050728","count":11},{"id":"GO:0042493","count":11}]},{"hash":"2088812537967353582","title":"Neural cell adhesion and synapse assembly","description":"This cluster is dominated by neural adhesion and synapse-related GO terms: neuron cell\u2013cell adhesion, homophilic/heterophilic adhesion, nervous system development, and positive regulation of synapse assembly, indicating functions in neural connectivity and synaptogenesis. The inclusion of collagen fibril organization suggests ECM support for neural networks. A subset of terms related to innate immunity and complement may reflect CNS immune interactions or remodeling, but the core signal is neuronal adhesion and synapse formation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007158","count":4},{"id":"GO:0007156","count":4},{"id":"GO:0030199","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0007157","count":3}]},{"hash":"801934083986813627","title":"Cardiac development and cytoskeletal signaling","description":"This cluster centers on heart-related processes (heart development and regulation of heart contraction) and cytoskeletal dynamics (lamellipodium assembly, small GTPase and Rho signaling), suggesting a coordinated role in cardiac muscle signaling and cytoskeletal remodeling. Other terms (cytokine production and ceramide transport) point to broader signaling networks but do not outweigh the core cardiac and cytoskeletal theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0030032","count":5},{"id":"GO:0007507","count":5},{"id":"GO:2001275","count":4},{"id":"GO:0045988","count":4},{"id":"GO:0098761","count":4}]},{"hash":"141620489123580511","title":"DNA-templated transcription with metabolic context","description":"This cluster's top term is DNA-templated transcription (GO:0006351), suggesting a primary role in gene expression regulation. The presence of a few metabolic and biosynthetic terms (glutamine metabolism, colanic acid and lignan biosynthesis) may reflect broader functional context or annotation noise, but the dominant signal points to transcriptional regulation as the shared function.","confidence":"Medium","size":13,"edges":37,"triangles":46,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0001081","count":1},{"id":"GO:0006541","count":1},{"id":"GO:1902131","count":1}]},{"hash":"1715887277067352818","title":"Auditory hair cell and neural signaling","description":"The top terms center on auditory sensory transduction (stereocilium organization and detection of mechanical stimulus in sound) and neural activity (action potential propagation, membrane hyperpolarization), suggesting a coherent theme of hair cell\u2013mediated hearing and downstream neuronal signaling, with a few ancillary terms related to barriers or development that are less central to the core function.","confidence":"Medium","size":13,"edges":10,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001954","count":3},{"id":"GO:0060088","count":2},{"id":"GO:0050910","count":2},{"id":"GO:0001713","count":2},{"id":"GO:0034765","count":2}]},{"hash":"1608027327269250747","title":"Embryonic Development and Morphogenesis","description":"The cluster includes GO terms spanning multiple embryonic tissues and processes\u2014placental/trophoblast differentiation, mesoderm development, cartilage and hair follicle morphogenesis, left-right patterning, palate formation, endocrine system development, and EMT in heart cushion formation\u2014pointing to a broad role in embryogenesis and tissue morphogenesis rather than a single tissue-specific function.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060707","count":12},{"id":"GO:0007498","count":12},{"id":"GO:0060536","count":12},{"id":"GO:0060806","count":12},{"id":"GO:0031069","count":12}]},{"hash":"387241482694623846","title":"Neurotransmitter Uptake and Synaptic Transmission","description":"Based on top GO terms, multiple uptake/transport functions for neurotransmitters dominate: serotonin uptake, dopamine uptake, and glycine import, with regulation of glycinergic synaptic transmission. This points to a cluster enriched in proteins involved in neurotransmitter handling and synaptic signaling. The development-related terms are less central to transport, possibly reflecting tissue-specific expression; overall, the core theme is neural signaling via neurotransmitter uptake.","confidence":"High","size":13,"edges":35,"triangles":24,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051610","count":11},{"id":"GO:0042066","count":11},{"id":"GO:0036233","count":11},{"id":"GO:1905847","count":11},{"id":"GO:0021794","count":11}]},{"hash":"2261850089242848853","title":"NF-kB-driven inflammatory chemotaxis","description":"This cluster centers on immune cell recruitment and inflammatory signaling: neutrophil, macrophage, and lymphocyte chemotaxis; acute-phase response; IL-1 production; and I-kappaB phosphorylation pointing to NF-kB pathway activation. Calcium signaling modulation also fits with activation and chemotaxis processes. A few terms like lipoprotein biosynthesis and stilbenoid response are less central but do not override the core inflammatory/chemotactic theme.","confidence":"High","size":13,"edges":56,"triangles":123,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007252","count":3},{"id":"GO:0042158","count":2},{"id":"GO:0050716","count":2},{"id":"GO:1990266","count":2},{"id":"GO:0006953","count":2}]},{"hash":"1700116225863309543","title":"Membrane Nutrient and Ion Transporters","description":"Most of the top GO terms are transmembrane transport processes for nutrients and ions (glucose, biotin, myo-inositol, pantothenate, and sodium export). This points to proteins functioning mainly as membrane transporters that move small molecules across membranes, with some neural signaling context reflected by acetylcholine and dopamine-related terms. Confidence: Medium","confidence":"","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008292","count":6},{"id":"GO:1904659","count":6},{"id":"GO:0071436","count":6},{"id":"GO:0015878","count":6},{"id":"GO:0015798","count":6}]},{"hash":"1778690891154715701","title":"Osteoclast differentiation and tooth development","description":"These proteins cluster around bone remodeling and tooth formation, with strong links to positive regulation of osteoclast differentiation and bone resorption, and odontogenesis of dentin-containing tooth. Other terms like response to steroid hormone and secretion hint at hormonal regulation of these processes, while a few terms reflect broader developmental contexts. Overall, the dominant theme is regulation of bone resorption and tooth development. ","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048545","count":1},{"id":"GO:0046903","count":1},{"id":"GO:0015670","count":1},{"id":"GO:0071498","count":1},{"id":"GO:0045780","count":1}]},{"hash":"2129159565989546794","title":"Diverse solute transmembrane transporters","description":"This cluster\u2019s dominant GO terms all point to transport across membranes for a wide range of substrates\u2014xenobiotics, phosphate, sugars, amino/sialic acid derivatives, nitrate/nitrite, and even neurotransmitter loading into vesicles\u2014indicating a group of membrane transporter proteins with diverse substrates.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":6},{"id":"GO:0035435","count":6},{"id":"GO:0098700","count":6},{"id":"GO:1900754","count":6},{"id":"GO:0042128","count":6}]},{"hash":"412571608635550064","title":"Lipoprotein Metabolism and Cholesterol Homeostasis","description":"This cluster is dominated by terms on triglyceride turnover, cholesterol transport, and remodeling of HDL/VLDL particles, plus general lipoprotein metabolism and cholesterol homeostasis. Together these terms indicate a cohesive function in lipid processing and cholesterol balance. A single term about cellular defense response is present but not central to the main theme.","confidence":"Medium","size":13,"edges":23,"triangles":12,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":5},{"id":"GO:0043691","count":5},{"id":"GO:0019432","count":5},{"id":"GO:0042632","count":5},{"id":"GO:0034375","count":5}]},{"hash":"295409301613259969","title":"Oxidative and inflammatory stress response","description":"The top GO terms point to cellular stress and immune-related responses, including xenobiotic stimulus, hydrogen peroxide, lipopolysaccharide, and inflammatory processes, along with apoptosis and kinase activity regulation. While terms like eye development and visual perception appear, the majority of annotations center on oxidative stress and inflammatory signaling, suggesting a cohesive theme around stress responses with some tissue-specific annotations. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0007601","count":3}]},{"hash":"2223236859365309587","title":"Unknown","description":"The top terms span metabolism (electron transport chain), broad signaling (GPCR signaling), cardiovascular regulation, behavior, cytolysis, immune defense, and even viral-related processes, with no clear single functional theme linking all proteins, especially given zero edges. This suggests no cohesive cluster function can be inferred.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":7},{"id":"GO:0045777","count":6},{"id":"GO:0010579","count":6},{"id":"GO:0007626","count":5},{"id":"GO:0051482","count":5}]},{"hash":"641320376239773601","title":"Unknown","description":"The GO terms are heterogeneous: transcription-related terms (DNA-templated transcription and transcription regulation), development (in utero embryonic development), cellular organization (apical/basal polarity), and sensory/pheromone responses, with several obsolete terms. The lack of a clear, shared function or pathway makes it inappropriate to assign a focused label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007576","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0010729","count":1},{"id":"GO:0070895","count":1},{"id":"GO:0046022","count":1}]},{"hash":"633752999586061540","title":"Lipid metabolism and adipogenesis","description":"The GO terms cluster around lipid synthesis and fatty acid processing, including monounsaturated fatty acid biosynthesis, sphinganine/sphingolipid metabolism, response to fatty acids, and cholesterol esterification. Additional signals point to adipocyte differentiation (white fat cell differentiation) and skin lipid-barrier aspects (water loss regulation). Some terms are obsolete or context-specific, but the dominant function appears to be lipid metabolism and fat-cell development.","confidence":"High","size":13,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0010873","count":7},{"id":"GO:1903699","count":7},{"id":"GO:0044130","count":7},{"id":"GO:0006667","count":7},{"id":"GO:0010205","count":7}]},{"hash":"1826379463636223690","title":"Mucosal innate antibacterial defense","description":"Based on the Top Terms, the cluster is enriched for antibacterial humoral response, defense responses to Gram-positive and Gram-negative bacteria, and innate immune response in mucosa, pointing to a shared role in mucosal antibacterial defense and innate immunity. While a couple of terms refer to obsolete signaling pathways or unrelated processes, they appear incidental. Overall, proteins likely participate in antibacterial defense at mucosal surfaces.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019731","count":11},{"id":"GO:0035584","count":11},{"id":"GO:0050830","count":11},{"id":"GO:0002227","count":11},{"id":"GO:0019933","count":11}]},{"hash":"1421514472982581387","title":"Dopaminergic Neuroimmune Signaling","description":"The top terms point to a blend of neuroimmune activity (immune response, negative regulation of inflammation, astrocyte chemotaxis, glial-derived neurotrophic factor production, eosinophil chemotaxis) and dopaminergic pathways (dopamine transport, regulation of dopamine metabolism, and phospholipase C-activating dopamine receptor signaling), suggesting a theme of cross-talk between glial/immune processes and dopamine signaling in the brain. ","confidence":"Medium","size":13,"edges":62,"triangles":147,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":12},{"id":"GO:0042493","count":12},{"id":"GO:2000458","count":12},{"id":"GO:1900168","count":12},{"id":"GO:0048245","count":12}]},{"hash":"1221508277610476040","title":"Dopamine Signaling and Neuroinflammation","description":"These terms point to a theme where dopaminergic signaling intersects with neuroimmune/glial activity (dopamine transport and signaling, astrocyte chemotaxis, glial neurotrophic factor production, and immune/inflammatory regulation). The cluster likely represents proteins involved in CNS dopaminergic-immune modulation rather than a purely metabolic pathway.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":13},{"id":"GO:0042493","count":13},{"id":"GO:2000458","count":13},{"id":"GO:1900168","count":13},{"id":"GO:0048245","count":13}]},{"hash":"1949413731415995694","title":"Neuroimmune-Dopaminergic Signaling","description":"The cluster shows enrichment for immune and inflammatory terms (negative regulation of inflammatory response, immune response, eosinophil chemotaxis) alongside neural/dopaminergic terms (dopamine transport, regulation of dopamine metabolism, dopamine receptor signaling via PLC, astrocyte chemotaxis). This pattern suggests a theme of neuroimmune interactions influencing dopaminergic signaling, possibly glial-mediated modulation of dopamine pathways, rather than a purely immune or purely neural function cluster.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":13},{"id":"GO:0042493","count":13},{"id":"GO:2000458","count":13},{"id":"GO:1900168","count":13},{"id":"GO:0048245","count":13}]},{"hash":"62081627173421163","title":"Neuroimmune Signaling and Dopamine Transport","description":"This cluster mixes immune/inflammatory regulation (negative regulation of inflammatory response, immune response, eosinophil chemotaxis, xenobiotic response) with neural/glial activity (astrocyte chemotaxis regulation, glial cell-derived neurotrophic factor production) and dopaminergic processes (dopamine transport, regulation of dopamine metabolism, dopamine receptor signaling). The recurring theme appears to be neuroimmune interactions in the CNS that influence dopamine signaling pathways, likely reflecting glia-mediated modulation of immune responses and dopaminergic function.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":13},{"id":"GO:0042493","count":13},{"id":"GO:2000458","count":13},{"id":"GO:1900168","count":13},{"id":"GO:0048245","count":13}]},{"hash":"1990273708284369141","title":"Dopaminergic signaling and neuroimmune regulation","description":"This cluster centers on dopamine-related processes (dopamine transport, regulation of dopamine metabolism, and PLC-activating dopamine receptor signaling) alongside immune and glial-related terms (immune response, negative regulation of inflammatory response, eosinophil and astrocyte chemotaxis, and GDNF production). The co-occurrence of neural signaling and neuroimmune/glial modulation terms suggests a cohesive theme of dopaminergic pathways interfacing with immune and glial functions. Therefore, a label capturing both dopaminergic signaling and neuroimmune regulation seems most representative.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":13},{"id":"GO:0042493","count":13},{"id":"GO:2000458","count":13},{"id":"GO:1900168","count":13},{"id":"GO:0048245","count":13}]},{"hash":"1284191853407436101","title":"Regulation of transcription, apoptosis, and development","description":"Top GO terms point to regulation of gene expression (transcription and chromatin-related marks), apoptosis control, and developmental processes (vasculogenesis, cardiac development) along with neuronal synapse organization. This suggests a cluster of proteins that orchestrate cell fate and developmental signaling through transcriptional regulation and survival pathways, rather than carrying out a single effector function.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0046642","count":12},{"id":"GO:0043524","count":10},{"id":"GO:0050808","count":10},{"id":"GO:0000413","count":10},{"id":"GO:0019089","count":10}]},{"hash":"1676098040224536892","title":"Neural development and synaptic organization","description":"This cluster is driven by GO terms pointing to neural differentiation and connectivity, including dendrite development, synapse organization, receptor clustering, and cerebellar Purkinje cell layer formation, as well as sensory functions like sound perception. While a couple of terms (bile acid secretion, carnitine transport) are less obviously linked, the dominant neural development and synaptic themes suggest a cohesive neural maturation module.","confidence":"High","size":12,"edges":29,"triangles":56,"max_degree":7,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0032782","count":9},{"id":"GO:0007266","count":9},{"id":"GO:0070830","count":9},{"id":"GO:0015879","count":8},{"id":"GO:0051612","count":8}]},{"hash":"2243175571003500044","title":"Ubiquitin-mediated regulation of cell cycle and DNA repair","description":"Proteins here show strong links to ubiquitination and related modifications (K6-linked ubiquitination, neddylation, ubiquitin-protein transferase activity) and to APC/C-dependent degradation, with alignment to DNA repair and apoptotic processes. The shared theme is post-translational tagging to regulate cell cycle, DNA damage response, and cell fate.","confidence":"High","size":12,"edges":52,"triangles":112,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043524","count":12},{"id":"GO:0006344","count":12},{"id":"GO:0031145","count":12},{"id":"GO:0043951","count":12},{"id":"GO:0085020","count":12}]},{"hash":"554116506885114218","title":"Cytoskeleton dynamics and cell polarity","description":"The top terms cluster around actin-related processes: actin filament bundle assembly, podosome assembly, terminal web assembly, and regulation of planar polarity, all indicative of cytoskeleton organization and cell polarity establishment. Ubiquitin-proteasome\u2013related terms suggest regulation of protein turnover that can modulate cytoskeletal dynamics. Some terms (chlorophyll biosynthesis, stamen formation) appear incidental, but the dominant signal points to cytoskeleton and polarity control.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0015995","count":4},{"id":"GO:0048455","count":4},{"id":"GO:0006511","count":4},{"id":"GO:0043248","count":4},{"id":"GO:0006303","count":3}]},{"hash":"1866538986218605089","title":"Insulin Signaling in Cardiac and Neural Development","description":"The cluster centers on insulin signaling (insulin receptor pathway) and its roles in heart development, neural structure formation (cerebellar cortex) and neural regeneration (axon regeneration), with supporting involvement in cell migration and muscle activity. Additional terms about protein stability and cell proliferation regulation fit into growth and remodeling during development, suggesting a cohesive theme of insulin-mediated developmental processes in heart and nervous tissue.","confidence":"Medium","size":12,"edges":30,"triangles":27,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2001275","count":6},{"id":"GO:0008286","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0016477","count":5}]},{"hash":"965454457237204202","title":"Meiosis and DNA Repair in Germline","description":"Most high-frequency GO terms center on meiosis and DNA repair (cell cycle, late meiotic recombination nodule assembly, double-strand break repair via break-induced replication, female gamete generation). A few terms relate to broader developmental signaling, but the meiosis/repair theme dominates, supporting a label focused on meiotic recombination and germline DNA repair.","confidence":"High","size":12,"edges":53,"triangles":122,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0048478","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0044320","count":2},{"id":"GO:0033327","count":2}]},{"hash":"839983429506712746","title":"Ubiquitin-mediated regulation of NF-kappaB signaling","description":"The GO terms cluster around ubiquitination (K6- and K48-linked, autoubiquitination) and positive regulation of canonical NF-kappaB signaling, indicating a shared role in ubiquitin-dependent control of immune and signaling pathways. Some terms related to intracellular transport or chromatin turnover appear ancillary.","confidence":"Medium","size":12,"edges":15,"triangles":0,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":3},{"id":"GO:0060546","count":2},{"id":"GO:0046597","count":2},{"id":"GO:0085020","count":2},{"id":"GO:0070936","count":2}]},{"hash":"2138090400914228829","title":"Apoptosis and NF-kB signaling with ubiquitination","description":"The top terms cluster around regulation of apoptotic signaling (extrinsic pathway, caspase activity) and key survival pathways (PI3K-AKT and canonical NF-kappaB), with a notable role for ubiquitin-mediated regulation (K11-linked ubiquitination). Additional terms about proliferation and development (endothelial and dendrite growth) fit with downstream effects of these signaling networks. Together, these proteins appear to coordinate cell fate decisions and growth via ubiquitin-regulated signaling cascades, rather than a single isolated function. Therefore, the label captures the main thematic connection among the GO terms.","confidence":"Medium","size":12,"edges":12,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":3},{"id":"GO:0006924","count":2},{"id":"GO:0006919","count":2},{"id":"GO:0043491","count":2},{"id":"GO:0043123","count":2}]},{"hash":"1604352614993073229","title":"Wnt-driven cochlear morphogenesis and epithelial polarity","description":"Top GO terms indicate a focus on Wnt signaling and developmental morphogenesis, especially cochlear morphogenesis, with accompanying processes in EMT regulation, epithelial cell polarity, cell migration, and actin cytoskeleton organization. Telomere maintenance terms suggest proliferative context, aligning with development. Overall, the cluster appears to center on signaling and cytoskeletal dynamics guiding cochlear epithelial development and polarity.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:0090103","count":2},{"id":"GO:0010719","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0051017","count":2}]},{"hash":"2213076889556092360","title":"Dephosphorylation-driven Cell Cycle Regulation","description":"The cluster is dominated by dephosphorylation terms (tyrosine and threonine), with several items tied to cell cycle control, spindle pole/body localization, and meiotic spindle dynamics, suggesting phosphatase activities coordinating mitosis/meiosis and signaling. A couple of terms reference broader signaling pathways (ERK, VEGF), which fits with phosphatases modulating these cascades; one term about symbiont-mediated interferon suppression is less connected, possibly annotation noise.","confidence":"Medium","size":12,"edges":18,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":8},{"id":"GO:1900746","count":6},{"id":"GO:0031031","count":6},{"id":"GO:0071850","count":6},{"id":"GO:0035970","count":6}]},{"hash":"288542097139132697","title":"Neural development signaling regulators","description":"The terms cluster around neural development and signaling control, including negative regulation of neuroblast proliferation, perineurial glial growth, and regulation of Rho/Rac signaling, all of which point to neural progenitor dynamics and glial function. Blastocyst development adds a broader developmental context, while a DNA repair term suggests additional maintenance roles. Overall, the cohesive theme is neural development and signaling regulation.","confidence":"Medium","size":12,"edges":13,"triangles":3,"max_degree":5,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0001824","count":3},{"id":"GO:2000212","count":2},{"id":"GO:0042066","count":2},{"id":"GO:0035023","count":2}]},{"hash":"914843678743011319","title":"EGFR Signaling and Cell Migration","description":"Top GO terms cluster around epidermal growth factor receptor signaling and motility-related processes: EGFR signaling, lamellipodium assembly, and cell migration. Additional terms reference related signaling regulation (Ral and JNK) and vesicle turnover (catecholamine secretion), supporting a theme of growth factor\u2013driven signaling coordinating cytoskeletal dynamics and movement.","confidence":"High","size":12,"edges":4,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007173","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0032485","count":3},{"id":"GO:0050432","count":3},{"id":"GO:0030259","count":3}]},{"hash":"155682734841186927","title":"Rho-regulated neuronal development","description":"The key terms center on Rho protein signal transduction and its regulation, plus neuronal development processes such as dendrite development, neuron maturation, and neural crest cell migration, along with transcriptional control. This points to a cluster of proteins coordinating cytoskeletal signaling with gene expression to drive neuronal differentiation and neural connectivity. The inclusion of related functions like response to muscle activity is compatible with neuromuscular signaling; overall, a cohesive theme of Rho-mediated neuronal development.","confidence":"High","size":12,"edges":18,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0007266","count":3},{"id":"GO:0008542","count":2},{"id":"GO:0001755","count":2}]},{"hash":"260126862804037012","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":24,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006368","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0016973","count":2},{"id":"GO:0051096","count":2}]},{"hash":"1984461504921656326","title":"Developmental Signaling and Morphogenesis","description":"The top GO terms include heart development, CNS development, Notch signaling regulation, GTPase activation, and lamellipodium assembly, pointing to a cluster of proteins involved in developmental signaling and cell movement that shape tissue morphogenesis across multiple organs. The mix of developmental and cytoskeletal processes supports a cohesive theme rather than disparate functions.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0045746","count":2},{"id":"GO:0007417","count":2},{"id":"GO:2001275","count":2}]},{"hash":"352063049421301441","title":"Development and Differentiation Across Tissues","description":"The GO terms span germline and embryonic development (germarium cyst encapsulation, egg chamber stalk formation, preblastoderm mitotic cycle regulation, embryonic skeletal development) and multiple hematopoietic differentiations (granulocytes, macrophages, megakaryocytes, erythrocytes) indicating a broad theme of developmental processes and cell fate specification across tissues. ","confidence":"High","size":12,"edges":15,"triangles":6,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030708","count":3},{"id":"GO:0030713","count":3},{"id":"GO:0048706","count":3},{"id":"GO:0035190","count":3},{"id":"GO:0030851","count":3}]},{"hash":"1543837471869252610","title":"Unknown","description":"The top GO terms cover very diverse processes across different organisms (transcription, signaling, circadian rhythm, development such as nail and pollen, and various metabolic responses). There is no single coherent function or pathway tying these terms together, suggesting either a heterogeneous mix of proteins or annotation noise, so a concise, representative label cannot be assigned.","confidence":"","size":12,"edges":11,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007165","count":2},{"id":"GO:0007623","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0051291","count":2}]},{"hash":"1318005354101331185","title":"NF-kappaB\u2013driven inflammatory cytokine signaling","description":"The cluster centers on TNF responses, TNF and IL-6 production, interferon production (type II and alpha), and canonical NF-kappaB signaling, with dendritic cell proliferation and regulatory touches on NF-kappaB. This points to an integrated innate immune and cytokine signaling module dominated by NF-kappaB\u2013mediated transcription of inflammatory mediators, with some ubiquitin-regulation and stress responses layered in. ","confidence":"High","size":12,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071356","count":2},{"id":"GO:0032635","count":2},{"id":"GO:0007249","count":2},{"id":"GO:0032640","count":2},{"id":"GO:0032609","count":2}]},{"hash":"1421852489952392791","title":"Synaptic signaling and actin remodeling","description":"This cluster is enriched for GO terms linking GPCR/PKC signaling and ephrin receptor pathways to neuronal development, especially receptor localization at synapses and regulation of synaptic plasticity, together with actin cytoskeleton dynamics (lamellipodium/filopodium assembly). The overlap of synaptic signaling with actin remodeling suggests coordinated control of neuron projection development and synapse structure.","confidence":"High","size":12,"edges":42,"triangles":65,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1900383","count":3},{"id":"GO:0007205","count":3},{"id":"GO:1901187","count":3},{"id":"GO:0031175","count":2},{"id":"GO:0010591","count":2}]},{"hash":"812312889748148150","title":"Endocytic recycling and vesicle trafficking","description":"The top GO terms cluster around endocytosis, vesicle dynamics, receptor recycling, and phosphoinositide metabolism, including synaptic and Golgi vesicle uncoating and PI biosynthesis/dephosphorylation. This points to a shared function in vesicle formation, trafficking, and recycling, with possible neuronal context. A couple of terms (myelin assembly, cardiac hypertrophy) are less central, but overall the focus is membrane trafficking.","confidence":"Medium","size":12,"edges":11,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032288","count":1},{"id":"GO:0014898","count":1},{"id":"GO:0046856","count":1},{"id":"GO:2001135","count":1},{"id":"GO:0036092","count":1}]},{"hash":"1029073776200535344","title":"Cardiac morphogenesis and conduction signaling","description":"This cluster\u2019s top GO terms strongly point to heart development (outflow tract and left ventricular morphogenesis) and cardiac electrophysiology (Purkinje signaling, SA node action potential regulation, and SR calcium release), suggesting proteins involved in cardiac structure and electrical activity. A few terms like skin development or pancreatic apoptotic processes appear ancillary and likely reflect broader gene functions, but they do not dominate the cluster. ","confidence":"High","size":12,"edges":10,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043588","count":7},{"id":"GO:0014808","count":7},{"id":"GO:0086029","count":7},{"id":"GO:1903244","count":7},{"id":"GO:0071313","count":7}]},{"hash":"1070239825324739458","title":"Neuronal signaling and cytoskeleton remodeling","description":"This cluster includes terms for GABAergic synaptic transmission, catecholamine secretion, and lamellipodium assembly, plus regulation of Rho and Ral signaling, which together point to neurotransmitter release linked with actin cytoskeleton dynamics. While there are lipid biosynthesis and placenta development terms present, the dominant theme appears to be neuronal communication and cytoskeletal remodeling. ","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030259","count":3},{"id":"GO:0051932","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0016126","count":3},{"id":"GO:0051262","count":3}]},{"hash":"397410909986297816","title":"Chromatin Modification and Transcription Regulation","description":"This cluster centers on epigenetic control of gene expression, with GO terms for regulation of DNA-templated transcription and various chromatin-related modifications (histone exchange, histone H3K27 methylation, heterochromatin formation). Despite obsolete annotations, the common thread is chromatin state modulation influencing transcription and development (stem cell maintenance, spermatid differentiation).","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0043486","count":2},{"id":"GO:2000270","count":1},{"id":"GO:0016569","count":1},{"id":"GO:0035019","count":1}]},{"hash":"1448125919884868085","title":"Cardiac conduction and vascular development","description":"The strongest signals are in heart/vascular biology: AV node action potential and membrane depolarization point to cardiac conduction, while endothelial delamination and guanylyl cyclase signaling relate to vascular development and signaling. Potassium import supports membrane potential changes relevant to cardiac function. Some terms on T cells and vestibular/skin development appear as noise, but the dominant pattern connects excitable tissue signaling with vascular development. ","confidence":"Medium","size":12,"edges":15,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":5},{"id":"GO:0021750","count":4},{"id":"GO:0010754","count":4},{"id":"GO:0086016","count":4},{"id":"GO:0043588","count":4}]},{"hash":"2070224553363681127","title":"RNA and protein methylation","description":"The top GO terms are dominated by various methylation activities\u2014N-terminal methylation (peptidyl-alanine/glycine), arginine methylation, histone methylation, and tRNA methylation\u2014indicating the cluster centers on modification processes affecting both nucleic acids and proteins, rather than a single metabolic pathway.","confidence":"High","size":12,"edges":63,"triangles":193,"max_degree":11,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0018012","count":8},{"id":"GO:0009236","count":8},{"id":"GO:0002098","count":7},{"id":"GO:0043985","count":7},{"id":"GO:0016126","count":7}]},{"hash":"1281564848929608336","title":"Embryonic Development and Tissue Morphogenesis","description":"The GO terms are dominated by developmental and morphogenetic processes across various tissues (endocrine system development, left-right patterning, cartilage and hair follicle morphogenesis, pancreatic cell development, and EMT in heart cushion formation), suggesting a theme of embryonic tissue development and organ morphogenesis. A spliceosome term is present but does not override the central developmental signal.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":10},{"id":"GO:0060806","count":10},{"id":"GO:0060972","count":10},{"id":"GO:0060536","count":10},{"id":"GO:0003323","count":10}]},{"hash":"1529956601926392052","title":"Epithelial Development and Wnt Signaling Regulation","description":"This cluster centers on developmental processes in epithelial tissues, highlighted by terms related to skin development, hindgut morphogenesis, and centriole assembly in multiciliated epithelium, along with multiple entries for regulation of Wnt signaling (canonical and planar cell polarity) and related pathways, plus a note on JNK cascade modulation. The combination suggests a cohesive theme of epithelial morphogenesis with coordinated signaling control, though individual terms are not strongly enriched, supporting a Medium confidence.","confidence":"Medium","size":12,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0098535","count":1},{"id":"GO:0003009","count":1},{"id":"GO:1900108","count":1},{"id":"GO:0048619","count":1},{"id":"GO:0032092","count":1}]},{"hash":"2090098324417767762","title":"Golgi vesicle trafficking and calcium transport","description":"The top GO terms point to vesicle trafficking in the secretory pathway (retrograde Golgi-to-ER transport, endocytosis, Golgi vesicle budding) and ion movement, especially calcium, plus maintenance of electrochemical gradients and related membrane organization. This suggests a cohesive cluster of proteins involved in vesicle trafficking with calcium-dependent processes, rather than disparate functions.","confidence":"High","size":12,"edges":41,"triangles":70,"max_degree":10,"top_function":"establishment or maintenance of cell polarity","top_go_terms":[{"id":"GO:0006890","count":11},{"id":"GO:0006897","count":11},{"id":"GO:0048194","count":10},{"id":"GO:0099132","count":7},{"id":"GO:0031448","count":7}]},{"hash":"1397498116647214585","title":"Diverse lipid and small-molecule biosynthesis","description":"This cluster is enriched for several biosynthetic processes spanning lipids (fatty acid elongation, very long-chain fatty acid biosynthesis), steroids (glucocorticoid biosynthesis), cofactors (tetrahydrobiopterin biosynthesis), quinones (phylloquinone catabolic process), and secondary metabolites (antibiotic biosynthetic process and antibiotic response), as well as PHB biosynthesis. The common theme is broad production of diverse biomolecules rather than a single, narrow pathway, with transcription regulation appearing less central. ","confidence":"Medium","size":12,"edges":5,"triangles":1,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030497","count":3},{"id":"GO:0006704","count":3},{"id":"GO:0042376","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0055114","count":3}]},{"hash":"102482385576439676","title":"Neural and muscular developmental signaling","description":"Top GO terms cluster around neural development and sensory signaling (visual perception, opsin signaling, astrocyte differentiation, regulation of long-term potentiation) and muscular development (skeletal muscle fiber development, satellite cell activation), with related terms for broader development (multicellular organism development, heart development, DNA binding regulation). This points to a theme of developmental signaling in neural and muscular tissues.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0043547","count":2},{"id":"GO:1900271","count":2},{"id":"GO:0022400","count":2}]},{"hash":"1240876876044666258","title":"Lipid transport and lipoprotein remodeling","description":"This cluster centers on lipid metabolism and lipoprotein remodeling, with GO terms for triglyceride and cholesterol homeostasis, triglyceride catabolic process, cholesterol and phospholipid efflux, and HDL/VLDL remodeling and chylomicron remnant clearance. A regulatory signaling term (Cdc42) is present but appears less central to the main lipid-transport theme.","confidence":"High","size":12,"edges":21,"triangles":13,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0070328","count":2},{"id":"GO:0042632","count":2},{"id":"GO:0032489","count":2},{"id":"GO:0034382","count":2},{"id":"GO:0035634","count":2}]},{"hash":"223373335417890417","title":"RNA processing and translational regulation","description":"The GO terms cluster around mRNA stability, mRNA processing/stability in stress, regulation of translational initiation, preinitiation complex formation, translation reinitiation, and RNA silencing by miRNA and regulatory ncRNA, indicating a coherent module of post-transcriptional gene expression control, spanning RNA processing to translation regulation.","confidence":"High","size":12,"edges":20,"triangles":16,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":5},{"id":"GO:0001825","count":5},{"id":"GO:0010610","count":5},{"id":"GO:0006446","count":5},{"id":"GO:1900363","count":5}]},{"hash":"754417272973712280","title":"Developmental Signaling and Transcription Regulation","description":"The cluster's terms emphasize regulation of signaling pathways (GTPase activity, phosphorylation/dephosphorylation), Notch signaling, and differentiation (myoblast/osteoblast), plus DNA-templated transcription, pointing to developmental control and transcriptional regulation as a common theme. Metabolic and transport terms appear less central but may reflect ancillary cellular processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:1902476","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0006195","count":1},{"id":"GO:0046085","count":1}]},{"hash":"241066007897136077","title":"Myelin lipid biosynthesis","description":"The top GO terms are galactosylceramide biosynthetic process and myelination, both strongly pointing to lipid production for myelin in neural tissues; other terms are more heterogeneous, but the clearest shared function is myelin-related lipid synthesis.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042552","count":2},{"id":"GO:0006682","count":2},{"id":"GO:0090528","count":2},{"id":"GO:0006308","count":2},{"id":"GO:2000327","count":2}]},{"hash":"581858814300223599","title":"Kidney and lymphatic development with immune signaling","description":"The cluster includes kidney development terms (mesonephric duct development, metanephric ascending thin limb development) and lymphatic vessel morphogenesis, together with immune-related processes (C-type lectin receptor signaling, lectin pathway complement activation, leukocyte adhesion). This suggests proteins involved in organogenesis with immune-vascular interactions, rather than a single narrow function.","confidence":"Medium","size":12,"edges":21,"triangles":11,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0072177","count":11},{"id":"GO:0090403","count":11},{"id":"GO:0001502","count":9},{"id":"GO:0072218","count":9},{"id":"GO:0060355","count":9}]},{"hash":"423127769341454023","title":"Lung mesenchyme and vascular development","description":"These proteins are enriched for terms tied to mesenchymal development and differentiation in lung and vascular tissues (lung-associated mesenchyme development, vascular smooth muscle differentiation) along with skeletal system development. The extra terms (cell adhesion, synapse organization, chemokine regulation, autophosphorylation) reflect coordinated cell signaling and adhesion during tissue formation. Together, they point to a developmental program for mesenchymal tissue organization in lung/vascular contexts, with active cell signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000649","count":4},{"id":"GO:0007157","count":4},{"id":"GO:0001501","count":3},{"id":"GO:1905065","count":3},{"id":"GO:0060484","count":3}]},{"hash":"1809972607247205242","title":"Embryonic organ development and patterning","description":"These terms cluster around embryonic development and tissue morphogenesis across multiple organs (placenta/trophoblast, left/right patterning, cartilage, palate, pancreas, muscle). A single overarching theme is embryonic organ development and patterning; the spliceosome term appears as a minor exception.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060972","count":5},{"id":"GO:0035270","count":5},{"id":"GO:0003323","count":5}]},{"hash":"1119863725566705078","title":"B Cell Signaling and Phagocytic Innate Immunity","description":"The dominating GO terms show B cell receptor signaling, complement activation, innate immune response, and phagocytosis (recognition and engulfment), with additional signals for B cell activation and xenobiotic response. This points to a cluster of proteins involved in coordinated adaptive and innate immune functions, particularly signaling and phagocytic activity; a retina homeostasis term may be context-specific noise but does not override the immune-centric theme.","confidence":"High","size":12,"edges":47,"triangles":88,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":11},{"id":"GO:0006958","count":10},{"id":"GO:0045087","count":10},{"id":"GO:0006910","count":10},{"id":"GO:0050871","count":10}]},{"hash":"199138229228955920","title":"Collagen-driven connective tissue development","description":"The dominant terms point to collagen fibril organization, cartilage development, skin development, and collagen-activated signaling, indicating a cohesive theme of extracellular matrix organization and connective tissue morphogenesis (including aspects like eye development). Some peripheral terms, such as blood coagulation and lipoprotein clearance, appear but do not override the collagen/connective tissue theme.","confidence":"High","size":12,"edges":16,"triangles":10,"max_degree":5,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030199","count":6},{"id":"GO:0071230","count":5},{"id":"GO:0070208","count":5},{"id":"GO:0060351","count":5},{"id":"GO:0038063","count":5}]},{"hash":"1255502457522465712","title":"Embryonic morphogenesis and organ development","description":"The top GO terms point to broad developmental and organogenesis processes across multiple tissues (mesoderm, placenta, pancreas, hair follicles, palate, etc.), including patterning and morphogenesis events. This suggests a general role in embryonic development and tissue formation rather than a single specific pathway, so the label captures the shared theme.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035270","count":12},{"id":"GO:0060806","count":12},{"id":"GO:0060972","count":12},{"id":"GO:0060536","count":12},{"id":"GO:0003323","count":12}]},{"hash":"544445403666740380","title":"Unknown","description":"The top GO terms span immune regulation (macrophage and NK T cell activity), epithelial transport and adhesion, tissue-specific processes (eye lens morphogenesis, AV node action potential), and adipogenesis, with no single cohesive function linking the proteins. This incoherence suggests no clear shared biological role for the cluster.","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043031","count":7},{"id":"GO:0007156","count":7},{"id":"GO:1902414","count":6},{"id":"GO:0070352","count":6},{"id":"GO:0002415","count":6}]},{"hash":"182820315622233569","title":"Unknown","description":"The top GO terms are a mix of glycosylation (GPI anchor biosynthetic process; dolichol-linked oligosaccharide biosynthesis) and diverse processes such as pollen tube guidance, bitter taste perception, synaptic regulation, muscle development, and heart contraction. This heterogeneous set provides no single cohesive function or theme for the entire cluster, so a concise, representative label isn\u2019t defensible. ","confidence":"","size":12,"edges":13,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":4},{"id":"GO:0006488","count":3},{"id":"GO:0010183","count":3},{"id":"GO:0060025","count":2},{"id":"GO:0048016","count":2}]},{"hash":"1535122508561807612","title":"Macrophage cholesterol homeostasis and lipoprotein regulation","description":"This cluster centers on cholesterol and lipoprotein management in macrophages, with terms like regulation of plasma lipoprotein particle levels, cholesterol homeostasis, triglyceride biosynthesis, and cholesterol efflux, as well as foam cell differentiation. While there are a few additional processes shown (e.g., palmitoylation and SHH signaling), the dominant theme is lipid handling and cholesterol metabolism in macrophages, suggesting a role in atherosclerosis-related pathways.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0097006","count":3},{"id":"GO:0007224","count":3},{"id":"GO:0019432","count":3},{"id":"GO:0042632","count":3},{"id":"GO:0034435","count":3}]},{"hash":"1716851666443332935","title":"Membrane-associated trafficking and signaling proteins","description":"This cluster mixes terms for membrane organization (GPI anchor biosynthesis, eisosome assembly, raft polarization), vesicular trafficking (endosome-to-vacuole transport), and diverse signaling roles (B cell receptor signaling, PKC signaling modulation, neuronal synaptic plasticity, and extrinsic apoptotic signaling), suggesting a broad membrane-centric functional grouping rather than a single pathway.","confidence":"Medium","size":12,"edges":62,"triangles":182,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0032511","count":1},{"id":"GO:0061028","count":1},{"id":"GO:0007605","count":1},{"id":"GO:0050861","count":1}]},{"hash":"1851828916560436229","title":"Ion Transport and Homeostasis","description":"The set is dominated by terms for transporting Na+, K+, and H+ across membranes and maintaining cell volume and ion homeostasis, including import/export across the plasma membrane and vacuolar acidification. This points to a cluster of membrane transporters and regulators that sustain ionic balance and osmotic stress responses, consistent with salt stress or osmotic adaptation. One GO term is obsolete, but the remaining terms clearly indicate ion transport and homeostasis.","confidence":"High","size":12,"edges":14,"triangles":5,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903281","count":7},{"id":"GO:0036376","count":7},{"id":"GO:0097623","count":7},{"id":"GO:0006884","count":7},{"id":"GO:0098719","count":7}]},{"hash":"1847440291155661287","title":"Mitochondrial protein import and membrane assembly","description":"This cluster is dominated by GO terms for importing proteins into the mitochondrial matrix, inserting proteins into mitochondrial inner/outer membranes, and assembling respiratory chain complexes (notably Complex IV). These collectively point to a function of targeting and integrating nuclear-encoded proteins into mitochondria and assembling respiratory machinery. Some terms related to ER folding or chloroplast import may reflect shared chaperone systems or dual targeting, but the mitochondrial processes clearly predominate, supporting this as the core theme.","confidence":"Medium","size":12,"edges":56,"triangles":165,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":4},{"id":"GO:0030150","count":3},{"id":"GO:0015693","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0045039","count":2}]},{"hash":"1993341575197798723","title":"Cholesterol Homeostasis and Lipid Metabolism","description":"These proteins show a coherent emphasis on lipid handling: regulation of plasma lipoprotein particle levels, cholesterol homeostasis and efflux, triglyceride biosynthesis, and cholesterol esterification, along with foam cell differentiation in macrophages. Lipid modifications (palmitoylation/palmitoleylation) and links to lipid-mediated signaling (e.g., Smoothened pathway) further support a lipid-centric theme, making cholesterol homeostasis and lipid metabolism the most representative label.","confidence":"High","size":12,"edges":53,"triangles":141,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0097006","count":7},{"id":"GO:0007224","count":7},{"id":"GO:0019432","count":7},{"id":"GO:0042632","count":7},{"id":"GO:0034435","count":7}]},{"hash":"765351804432618522","title":"Epithelial differentiation and cartilage morphogenesis","description":"The top GO terms point to keratinization (epithelial differentiation) and cartilage morphogenesis, with related developmental processes (left-right patterning) and transcriptional regulation, suggesting a cohesive theme around developmental differentiation in epithelia and skeletal cartilage, supported by transcription control roles.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":4},{"id":"GO:0035270","count":2},{"id":"GO:0046022","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0000122","count":2}]},{"hash":"866386526647849196","title":"Dopamine signaling and neuroimmune regulation","description":"This cluster's GO terms link immune/inflammatory processes (negative regulation of inflammatory response, immune response, eosinophil chemotaxis, xenobiotic response) with dopaminergic signaling (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling) and glial involvement (astrocyte chemotaxis, glial-derived neurotrophic factor production). This suggests a cohesive theme where dopamine signaling modulates neuroimmune/glial activity, connecting immune responses with dopaminergic pathways in neural contexts.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":12},{"id":"GO:0042493","count":12},{"id":"GO:2000458","count":12},{"id":"GO:1900168","count":12},{"id":"GO:0048245","count":12}]},{"hash":"2282802657459013405","title":"Dopamine signaling and neuroinflammation","description":"This cluster links dopamine transport and signaling (dopamine transport; regulation of dopamine metabolic process; phospholipase C-activating dopamine receptor signaling pathway) with glial/immune functions (negative regulation of inflammatory response; regulation of astrocyte chemotaxis; eosinophil chemotaxis; immune response) and xenobiotic response, plus neurotrophic support (positive regulation of GDNF production). The convergence of dopaminergic pathways with astrocyte/microglial\u2013immune processes suggests a module where dopamine signaling is modulated by neuroinflammatory and glial activity, including xenobiotic/drug response. Confidence reflects a coherent dopaminergic-neuroimmune theme. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":12},{"id":"GO:0042493","count":12},{"id":"GO:2000458","count":12},{"id":"GO:1900168","count":12},{"id":"GO:0048245","count":12}]},{"hash":"365112737967638685","title":"NMJ Synaptic Assembly and Immune Signaling","description":"The cluster centers on neuromuscular junction synaptic assembly and its regulation, with supporting signals from immune pathways (defense against virus, IFN response, IL-2 regulation, NLRP3 inflammasome) and cellular trafficking/cytoskeletal processes (ER/Golgi organization, microtubule depolymerization) that together influence synapse formation and maintenance.","confidence":"Medium","size":11,"edges":19,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":7},{"id":"GO:0071346","count":6},{"id":"GO:1900041","count":6},{"id":"GO:1900025","count":6},{"id":"GO:0008582","count":6}]},{"hash":"1480723987935374809","title":"EGFR-MAPK signaling and immune regulation","description":"This cluster centers on EGFR-related signaling control (negative regulation of EGFR and MAP kinase activity, and EGFR signaling) while also featuring diverse immune and inflammatory processes (type I interferon production, IL-4 signaling, leukotriene biosynthesis) and growth regulation, suggesting a theme of growth signaling intertwined with immune modulation.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007175","count":11},{"id":"GO:0043066","count":11},{"id":"GO:0007173","count":11},{"id":"GO:0043407","count":11},{"id":"GO:0032481","count":10}]},{"hash":"2113815096807957391","title":"Sensory Perception and Signaling","description":"The cluster centers on sensory modalities and their intracellular signaling: receptor guanylyl cyclase signaling, photoreception, and taste detection, plus broad intracellular signal transduction. While a few terms touch on development or metabolism (e.g., lateral line development, electron transport chain, oocyte maturation regulation), the dominant terms point to sensory transduction and downstream signaling processes across multiple senses, including light and sweet taste perception.","confidence":"Medium","size":11,"edges":34,"triangles":65,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007168","count":10},{"id":"GO:0022900","count":10},{"id":"GO:0021586","count":9},{"id":"GO:0001582","count":9},{"id":"GO:0035556","count":9}]},{"hash":"1601679144041445921","title":"TLR2-Mediated Innate Immune Activation","description":"GO terms such as innate immune response, defense response to virus, macrophage activation, defense response to Gram-negative bacteria, and the Toll-like receptor 2 signaling pathway point to a cluster focused on innate immune signaling and macrophage-driven defense; a few terms related to lysosomal pH regulation and neuronal development appear incidental.","confidence":"High","size":11,"edges":52,"triangles":139,"max_degree":10,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0051607","count":3},{"id":"GO:0034134","count":3},{"id":"GO:0035751","count":3},{"id":"GO:1900155","count":3}]},{"hash":"701106888380987064","title":"Epithelial cytoskeleton remodeling and adhesion structures","description":"This cluster centers on actin cytoskeleton dynamics and epithelial cell adhesion, with terms for Rho signaling, focal adhesions, podosomes, terminal web/microvilli organization, and EMT, pointing to coordinated cytoskeletal remodeling and cell-surface adhesion in epithelial contexts. An outlier term (ascospore formation) likely reflects annotation noise rather than a core function.","confidence":"High","size":11,"edges":33,"triangles":39,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001837","count":4},{"id":"GO:1902896","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0048041","count":3},{"id":"GO:0032532","count":3}]},{"hash":"1860304054400312128","title":"Iron transport and detoxification","description":"This cluster is dominated by GO terms related to iron ion transport, siderophore-iron import, and detoxification of iron, pointing to proteins involved in iron homeostasis. While a few terms like stress response appear, the iron-centered functions prevail, justifying the name.","confidence":"Medium","size":11,"edges":14,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006950","count":3},{"id":"GO:0030261","count":3},{"id":"GO:0097286","count":3},{"id":"GO:1904234","count":3}]},{"hash":"1148769436752230943","title":"Telomere Chromatin Silencing and DNA Replication","description":"The cluster combines telomere- and subtelomere-associated chromatin silencing terms (silent mating-type cassette heterochromatin formation; subtelomeric heterochromatin formation) with core DNA replication and DNA damage response terms (DNA replication; break-induced replication repair; mitotic G1 DNA damage checkpoint signaling). This pattern points to a theme of genome maintenance centered on telomere-associated chromatin regulation and replication/repair processes. While a few terms relate to broader stress responses or cell proliferation, the dominant signal is telomere chromatin state coupled to replication and repair.","confidence":"High","size":11,"edges":50,"triangles":124,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000727","count":3},{"id":"GO:0031939","count":3},{"id":"GO:0030466","count":3},{"id":"GO:0071466","count":3}]},{"hash":"1491192730758123004","title":"Cell fate specification across lineages","description":"This cluster centers on diverse lineage differentiation events, including immune cell differentiation (eosinophils, basophils, Th2 cytokine production), cardiac development (ventricular septum and cardioblast fate), and pancreatic alpha cell differentiation, as well as regulation of differentiation-related factors like TGF-beta. The unifying theme is cell fate specification guiding lineage commitment across multiple tissues, not a single specialized function.","confidence":"High","size":11,"edges":47,"triangles":106,"max_degree":10,"top_function":"autophagy","top_go_terms":[{"id":"GO:2000667","count":7},{"id":"GO:0003281","count":7},{"id":"GO:0070345","count":7},{"id":"GO:0035854","count":7},{"id":"GO:0021691","count":7}]},{"hash":"603375224623209747","title":"Developmental cell migration and morphogenesis","description":"The top terms cluster around cell movement and tissue formation, including germ and hemocyte migration, axon fasciculation, and tracheal/morphogenetic growth, along with related ECM and cytoskeletal processes (collagen organization, Rho signaling). Some terms touch neural learning or innate immunity, but the dominant pattern is developmental migration and morphogenesis.","confidence":"Medium","size":11,"edges":33,"triangles":65,"max_degree":8,"top_function":"wound healing","top_go_terms":[{"id":"GO:0008542","count":7},{"id":"GO:0034142","count":7},{"id":"GO:0002042","count":7},{"id":"GO:0030199","count":6},{"id":"GO:0035099","count":6}]},{"hash":"61281015161883361","title":"RNA Pseudouridylation Enzymes","description":"The cluster is dominated by GO terms for pseudouridine synthesis across snRNA, mRNA, and tRNA, indicating the proteins are likely RNA modification enzymes that install pseudouridine. While a few other terms (development, DNA damage response, and various cellular stress responses) appear, they are less central and may reflect broader or pleiotropic roles. Overall, the core signal points to RNA pseudouridylation activity as the defining theme of this group.","confidence":"High","size":11,"edges":37,"triangles":56,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031120","count":2},{"id":"GO:1990481","count":2},{"id":"GO:0031119","count":2},{"id":"GO:0007488","count":1},{"id":"GO:0071480","count":1}]},{"hash":"326546999544414120","title":"Glutamatergic synapse signaling and dendrite morphogenesis","description":"These proteins mainly align with glutamatergic synaptic activity and dendritic development: multiple terms point to glutamatergic synaptic transmission, excitatory postsynaptic potentials, and receptor clustering, along with dendrite morphogenesis. A couple of terms related to transcription and cell cycle appear, which may reflect multifunctional or housekeeping roles, but the dominant signal is a synaptic/dendritic function.","confidence":"High","size":11,"edges":11,"triangles":4,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008542","count":5},{"id":"GO:0043113","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0035249","count":5}]},{"hash":"281103777185979213","title":"Innate Immune Signaling and Cytokine Regulation","description":"Most frequent GO terms describe immune signaling and cytokine regulation (defense response to virus; lipopolysaccharide-mediated signaling pathway; negative regulation of interleukin-6 production; negative regulation of NF-kappaB transcription factor activity). While there are a few terms pointing to neural signaling (nitric oxide\u2013mediated retrograde signaling) or metabolic assembly (iron-sulfur cluster assembly), the immune-related terms predominate, suggesting the cluster mainly reflects innate immune signaling and cytokine control.","confidence":"Medium","size":11,"edges":13,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0016226","count":2},{"id":"GO:0051612","count":2},{"id":"GO:0098924","count":2},{"id":"GO:1901206","count":2}]},{"hash":"108389395563450931","title":"Embryonic morphogenesis and actin cytoskeleton remodeling","description":"This cluster centers on developmental processes (foregut and axial mesoderm morphogenesis, motor neuron axon guidance) and cytoskeletal organization (actin filament bundle assembly, actomyosin structure organization), suggesting coordinated morphogenesis with cytoskeletal dynamics. Some terms (immune signaling, thyroid hormone response, proteasome assembly) are less cohesive with the core theme, but do not override the dominant development-and-cytoskeleton pattern. Confidence: Medium","confidence":"","size":11,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048617","count":2},{"id":"GO:0008045","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0048319","count":2},{"id":"GO:0050852","count":2}]},{"hash":"1547832886678847595","title":"Retina maintenance and VEGF-driven angiogenesis","description":"This cluster centers on retina homeostasis and vascularization, highlighted by terms for retina health, angiogenesis, VEGF signaling, and endothelial cell chemotaxis, with supporting involvement of ERK and BMP signaling pathways and protein autophosphorylation. While one term references sensory perception of sound, the dominant pattern links retinal maintenance with VEGF- and angiogenesis-related signaling, suggesting a cohesive theme of ocular vascular development and tissue homeostasis.","confidence":"High","size":11,"edges":6,"triangles":1,"max_degree":4,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0050910","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0030513","count":4},{"id":"GO:0001895","count":4},{"id":"GO:0001525","count":4}]},{"hash":"1359314243497388009","title":"Signaling and Gene Regulation","description":"The top GO terms span signaling (Rap signal transduction, NF-kappaB signaling), second messenger production (cyclic nucleotide biosynthesis), and intracellular trafficking (plus-end vesicle transport), alongside regulatory processes affecting chromatin and transcription (miRNA processing, histone ubiquitination, heterochromatin formation, isotype switching). This mix suggests a cluster of proteins involved in signaling networks that influence gene expression and chromatin state, with some immune-related roles evident. Therefore, a label emphasizing both signaling and gene regulation is appropriate.","confidence":"Medium","size":11,"edges":17,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009190","count":4},{"id":"GO:0044810","count":3},{"id":"GO:0032487","count":3},{"id":"GO:0090055","count":3},{"id":"GO:0035196","count":3}]},{"hash":"1488724583988133638","title":"Glycosylation and glycan metabolism","description":"This cluster is dominated by glycosylation-related GO terms such as N-glycan processing and protein deglycosylation, along with mannose metabolism and rhodopsin biosynthetic context, pointing to glycoprotein maturation and glycan remodeling. Some terms appear obsolete or peripheral (tRNA wobble uridine modification, histone methylation), but the core signal is glycosylation pathways.","confidence":"Medium","size":11,"edges":19,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0006491","count":2},{"id":"GO:0006486","count":2},{"id":"GO:0016063","count":2},{"id":"GO:0035010","count":2}]},{"hash":"1578751952849045022","title":"Golgi-ER and endosomal vesicle trafficking","description":"This cluster centers on vesicle transport processes, especially Golgi\u2013ER and ER\u2013Golgi traffic, endocytosis, and endosome\u2013Golgi/vacuolar targeting, as well as Golgi-to-plasma membrane routes. The top GO terms (GO:0006890, GO:0006888, GO:0006897, GO:0006623, GO:0042147) support a cohesive intracellular trafficking theme, with a few developmental terms likely representing collateral annotations.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":9},{"id":"GO:0006888","count":9},{"id":"GO:0006897","count":7},{"id":"GO:0006623","count":7},{"id":"GO:0048490","count":5}]},{"hash":"1753606397764551591","title":"Transcription Initiation and Chromatin Regulation","description":"This cluster centers on transcriptional control, with multiple GO terms highlighting RNA polymerase II preinitiation complex assembly and DNA-templated transcription initiation, along with histone-related modification signals. The presence of box C/D snoRNP assembly suggests RNA processing involvement, and transcriptional regulation in a developmental (Notch target) context strengthens the theme of gene expression control. Some terms (development and replication-associated processes) may reflect connected cellular states rather than a single function, but the core signal is transcription initiation and chromatin regulation.","confidence":"Medium","size":11,"edges":52,"triangles":141,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":7},{"id":"GO:0051123","count":5},{"id":"GO:0060760","count":5},{"id":"GO:0030307","count":5},{"id":"GO:0006352","count":5}]},{"hash":"1705074899330483216","title":"Embryonic craniofacial and organ morphogenesis","description":"The top GO terms cluster around developmental morphogenesis across facial structures (face development, epidermis development, embryonic cranial skeleton morphogenesis), neural tube closure, cochlea morphogenesis, and lung morphogenesis, with supporting roles in desmosome organization and Rho signaling. This indicates a coherent theme of embryonic tissue morphogenesis and cell adhesion/cytoskeletal regulation, justifying a label focused on craniofacial and organ morphogenesis.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0044030","count":3},{"id":"GO:0060324","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0002934","count":2},{"id":"GO:0008544","count":2}]},{"hash":"1239299625941395024","title":"Actin cytoskeleton remodeling and trafficking","description":"This cluster centers on cytoskeleton dynamics, with multiple terms tied to actin structure formation (lamellipodium morphogenesis, actin filament bundle assembly, podosome assembly, terminal web) and associated membrane trafficking (ER-to-Golgi transport). It also includes planarity/centrosome-related regulation and related structural components, suggesting a cohesive theme of coordinated actin-based remodeling with vesicular transport. Some terms (immune/viral-related) may reflect secondary associations rather than core function. ","confidence":"Medium","size":11,"edges":52,"triangles":140,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:2000394","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0045347","count":3},{"id":"GO:1904780","count":3},{"id":"GO:0044829","count":3}]},{"hash":"325101238091481557","title":"RNA processing and translation regulation","description":"This cluster is enriched for post-transcriptional gene expression terms, including regulation of translation initiation and preinitiation complex formation, mRNA splicing and export, and regulatory ncRNA-mediated gene silencing, indicating a group of proteins involved in RNA maturation and control of protein synthesis; some terms are obsolete or peripheral, but the core theme centers on RNA processing and translation control.","confidence":"Medium","size":11,"edges":33,"triangles":56,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901536","count":4},{"id":"GO:0006446","count":3},{"id":"GO:1900363","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0031047","count":3}]},{"hash":"311107437260724704","title":"Neural development and axon guidance","description":"The cluster centers on neuronal development processes, including axon fasciculation, axial mesoderm formation, and receptor clustering, which point to neuronal connectivity and guidance. Additional terms reflect broader signaling and protein turnover (JNK regulation, ubiquitin-proteasome catabolic process, IL-7 response), suggesting overlapping developmental signaling. Overall, the function is best captured by neural development and axon guidance, with medium confidence due to some non-neural terms present.","confidence":"Medium","size":11,"edges":34,"triangles":44,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":11},{"id":"GO:0048320","count":11},{"id":"GO:0097155","count":11},{"id":"GO:0032092","count":11},{"id":"GO:0008542","count":11}]},{"hash":"555767707261317245","title":"G-Protein Signaling in Development","description":"The cluster includes terms related to intracellular signal transduction and the heterotrimeric G-protein cycle, along with developmental processes (lateral root development, eye photoreceptor cell development, gastrulation-related polarity) and responses to various stimuli (catecholamines, prostaglandin). This suggests a cohesive theme where G-protein\u2013mediated signaling pathways regulate development and cellular responses across species, making a development-focused, signaling-oriented label appropriate.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0071870","count":11},{"id":"GO:0048527","count":11},{"id":"GO:0048383","count":11},{"id":"GO:0000750","count":11},{"id":"GO:0003380","count":11}]},{"hash":"1024585839995886879","title":"Wnt-driven cell cycle and telomere regulation","description":"The cluster is characterized by strong signals for Wnt signaling (GO:0016055) and regulation of the cell cycle (GO:0007050), plus telomere maintenance and telomere capping (GO:0032212, GO:1904355) and a note of cell migration (GO:0016477). This suggests a cohesive module linking proliferation control with genome maintenance, with Wnt as a central driver and telomere regulation as a supporting theme.","confidence":"High","size":11,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0016055","count":3}]},{"hash":"787581017585261593","title":"Rho GTPase\u2013driven actin remodeling and migration","description":"The cluster centers on Rho GTPase signaling and actin cytoskeleton remodeling (GTPase regulation, lamellipodium and filament bundle assembly) and cell migration, with related notes on JNK signaling and tissue morphogenesis such as heart development and endothelial barrier formation; overall, it reflects cytoskeletal dynamics governing movement.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0035023","count":8},{"id":"GO:0046328","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0090557","count":7}]},{"hash":"1614464322586201963","title":"Golgi\u2013endosome\u2013lysosome vesicle trafficking","description":"This cluster is dominated by terms describing intracellular transport among the Golgi, endosomes, lysosomes, and related compartments, including clathrin-coated vesicle cargo loading and retrograde Golgi\u2013ER transport. Additional terms reflect endocytosis and receptor internalization, pointing to general vesicle trafficking and cargo sorting within the endomembrane system.","confidence":"High","size":11,"edges":38,"triangles":60,"max_degree":9,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0035646","count":4},{"id":"GO:0006895","count":4},{"id":"GO:0090160","count":4},{"id":"GO:0006886","count":4}]},{"hash":"1647795351492572760","title":"Neural development and neuron fate specification","description":"The terms cluster around neural development and neuron differentiation across CNS and PNS regions (spinal cord, cortex, subpallium, inner ear), with several mentions of cell fate specification. A few terms refer to broader organogenesis or transcriptional regulation, but the dominant theme is neuronal development and fate decisions.","confidence":"High","size":11,"edges":14,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":10},{"id":"GO:0090009","count":10},{"id":"GO:0048935","count":10},{"id":"GO:0021530","count":10},{"id":"GO:0060435","count":10}]},{"hash":"279869350954360839","title":"Chromatin modification and transcriptional regulation","description":"The top GO terms are dominated by histone modifications (H3/H4 methylation and acetylation) and DNA-templated transcription, pointing to chromatin-modifying enzymes and transcriptional regulators as the core of this cluster. The presence of several obsolete histone-related terms likely reflects older annotations, but the central theme remains chromatin state control of gene expression. Additional terms like ribosome biogenesis and neural tube closure may reflect broader regulatory roles or developmental contexts, but they do not override the primary signal of chromatin modification linked to transcription. ","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034729","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051568","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0043984","count":4}]},{"hash":"803450705816084009","title":"Organogenesis and tissue development","description":"The top GO terms cluster around development of specific organs and tissues (heart/cardial muscle, inner ear, trachea, vasculature) and regulation of cell migration, along with signaling and transcriptional regulation that drive developmental programs. While a few terms (like LPS signaling) are less central, the dominant theme is organogenesis and tissue morphogenesis. ","confidence":"High","size":11,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032092","count":2},{"id":"GO:0010800","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0055015","count":2}]},{"hash":"1972652065511662808","title":"Neural development and transcription regulation","description":"Top GO terms cluster around neural development (motor neuron differentiation and migration) and transcriptional control (DNA-templated transcription and negative regulation of RNA Pol II), with actin filament bundle assembly pointing to cytoskeletal remodeling. Despite a few unrelated terms (xenobiotic response, regulation of phosphorylation), the dominant theme is transcriptional regulation in neural development, with supporting cytoskeletal dynamics.","confidence":"Medium","size":11,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":1},{"id":"GO:0042325","count":1},{"id":"GO:1900112","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0000122","count":1}]},{"hash":"126575996004371029","title":"Unknown","description":"The GO terms cover a mix of aging, Golgi protein retention, cell division, organelle inheritance, membrane potential regulation, vesicle trafficking, and stress responses, with no clear common function binding the cluster. The sparse connections (low edges, no triangles) further suggest the proteins do not share a single cohesive role, so a specific, representative label isn\u2019t identifiable.","confidence":"","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":3},{"id":"GO:0045053","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0016185","count":2},{"id":"GO:0000055","count":2}]},{"hash":"963297361907827741","title":"Axon Guidance and Receptor Clustering","description":"The terms point to neural development and neurite organization, notably axon fasciculation and receptor clustering, with supporting signals related to neural development and signaling modulation, making this a coherent theme around axon guidance and cell-surface organization.","confidence":"Medium","size":11,"edges":16,"triangles":6,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":11},{"id":"GO:0048320","count":11},{"id":"GO:0097155","count":11},{"id":"GO:0032092","count":11},{"id":"GO:0008542","count":11}]},{"hash":"635463803851694522","title":"Unknown","description":"The top terms span neural functions (sound perception, tachykinin signaling, myelin maintenance, spermatogenesis) and basic cofactor biosynthesis (riboflavin, FMN/FAD) with little overlap, and the cluster has nearly no connections (edge count 1, no triangles). There isn\u2019t a clear common function tying all terms together, so a single cohesive label isn\u2019t supported.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":3},{"id":"GO:0007283","count":2},{"id":"GO:0019430","count":2},{"id":"GO:0007217","count":2},{"id":"GO:0032287","count":2}]},{"hash":"2063203066803428876","title":"Viral entry and replication cluster","description":"Based on the top GO terms, this cluster is enriched for viral-related processes: virion assembly, viral life cycle, RNA-templated DNA biosynthetic process, and symbiont entry into host, with supporting roles for protein folding/isomerization and lipid droplet organization that viruses often exploit. Leukocyte migration hints at host immune interaction, further aligning with viral infection themes. The sepal formation term appears as an outlier/noise. Overall, the proteins appear connected to viral infection, replication, and virus-host interactions.","confidence":"High","size":11,"edges":44,"triangles":104,"max_degree":9,"top_function":"protein folding","top_go_terms":[{"id":"GO:0030260","count":8},{"id":"GO:0010849","count":8},{"id":"GO:0019068","count":8},{"id":"GO:0006278","count":8},{"id":"GO:0000413","count":8}]},{"hash":"1565890686593370355","title":"Ciliary Hedgehog and PCP signaling in neural development","description":"The cluster centers on ciliary biology (non-motile cilium assembly, opsin transport) and signaling pathways that pattern neural tissue (Smoothened/Hedgehog, Wnt/PCP), with related processes such as neural tube closure and embryonic brain development, indicating a cohesive role in cilia-driven neural patterning and signaling. ","confidence":"High","size":11,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901620","count":3},{"id":"GO:0060563","count":3},{"id":"GO:1905515","count":3},{"id":"GO:0036372","count":3},{"id":"GO:0060030","count":3}]},{"hash":"752141070199046890","title":"Ribosome assembly and RNA modification","description":"The top GO terms are dominated by translation (GO:0006412), ribosomal large subunit assembly (GO:0000027), and various RNA modification/methylation processes (GO:0006400, GO:0017000, GO:0036265, GO:0000154). This pattern points to proteins involved in the translational machinery and ribosome biogenesis, with RNA processing marks as a core theme. A couple of dendrite-related terms appear but are likely incidental rather than defining the cluster\u2019s function. ","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0000154","count":1}]},{"hash":"617922100330758755","title":"Proteoglycan biosynthesis and glycosaminoglycan metabolism","description":"The cluster shows strong representation of proteoglycan biosynthetic processes (chondroitin sulfate and heparan sulfate) and their regulation, pointing to a cohesive theme of proteoglycan/GAG synthesis; other GO terms reflect broader metabolic signaling contexts that accompany this core function.","confidence":"Medium","size":11,"edges":20,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006144","count":3},{"id":"GO:2001311","count":3},{"id":"GO:0016036","count":3},{"id":"GO:0050650","count":3},{"id":"GO:0032958","count":3}]},{"hash":"1145205662948518563","title":"Vesicle trafficking and Rac signaling","description":"The proteins appear to cluster around intracellular transport (ER-to-Golgi trafficking, synaptic vesicle budding) and small GTPase signaling, particularly Rac pathways, which also relate to cytoskeleton dynamics, cell migration, and polarity. While some terms touch on development or reproduction, the strongest common theme is vesicle trafficking coupled with Rac-mediated signaling that governs cytoskeletal organization and cell polarity.","confidence":"Medium","size":11,"edges":50,"triangles":124,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0040027","count":2},{"id":"GO:1990386","count":1},{"id":"GO:1902647","count":1},{"id":"GO:0007264","count":1}]},{"hash":"375597740072362414","title":"Vesicle trafficking and autophagy","description":"These proteins show a cohesive theme around intracellular transport (ER to Golgi and endosome-to-Golgi trafficking) and autophagy, suggesting a shared role in vesicle trafficking and turnover. Other GO terms present (developmental processes, circadian regulation, pregnancy) may reflect broader, pleiotropic roles of trafficking-related proteins rather than a single dedicated function for the cluster. Overall, the vesicle trafficking with autophagy theme best represents the cluster.","confidence":"Medium","size":11,"edges":46,"triangles":97,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0016358","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0034498","count":1}]},{"hash":"292109998116773512","title":"Ephrin signaling and actin-driven migration","description":"The cluster centers on actin cytoskeleton remodeling and cell movement, highlighted by ephrin receptor signaling, small GTPase pathways, podosome and actin bundle assembly, and polarity establishment. The inclusion of immunological synapse formation and heart development suggests roles in dynamic cellular adhesion, migration, and tissue organization across contexts, all tied to actin dynamics.","confidence":"High","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0016477","count":9},{"id":"GO:0048013","count":9},{"id":"GO:0007264","count":9},{"id":"GO:0090162","count":8},{"id":"GO:0043547","count":8}]},{"hash":"164723539504503416","title":"Plant defense signaling & amino acid metabolism","description":"The cluster shows enrichment for plant-specific processes such as systemic acquired resistance (SA-mediated signaling) and fruit ripening, alongside several amino acid biosynthesis and catabolic terms (alanine, tyrosine, aspartate, kynurenine). The presence of Notch signaling appears peripheral or possibly an annotation artifact, but the dominant theme ties plant defense signaling to amino acid metabolism.","confidence":"Medium","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":7},{"id":"GO:0097053","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0033362","count":6},{"id":"GO:0019518","count":6}]},{"hash":"1589536090706071013","title":"Developmental signaling and cytoskeletal dynamics","description":"Top terms show Wnt signaling, lamellipodium assembly, microtubule anchoring, endosome transport, and developmental morphogenesis (lymph vessels, metanephric tubules) with ubiquitination and stress-kinase signaling, indicating a cluster centered on coordinated developmental signaling and cytoskeletal trafficking.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0036303","count":2},{"id":"GO:0006954","count":2},{"id":"GO:0072237","count":2},{"id":"GO:0072287","count":2}]},{"hash":"2086002376164665555","title":"Vesicle Exocytosis and Trafficking Regulation","description":"The cluster is dominated by GO terms on synaptic vesicle exocytosis, vesicle priming, and related regulation, with supporting terms like acrosome reaction and Ras/Rho signaling, suggesting a shared function in regulated vesicle fusion across neural, immune, and reproductive contexts, and even brain development.","confidence":"High","size":11,"edges":29,"triangles":28,"max_degree":10,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":8},{"id":"GO:0016082","count":8},{"id":"GO:0010796","count":8},{"id":"GO:0031384","count":8},{"id":"GO:0035023","count":8}]},{"hash":"2068747369197674871","title":"Cardiac muscle development and vascular remodeling","description":"These proteins cluster around heart and vascular biology: ventricular cardiac muscle cell development, heart contraction, vasodilation, and blood vessel remodeling, with calcium signaling regulation supporting contraction. While a few terms appear less related (nitrogen starvation, xenobiotic response, viral RNA replication), the dominant theme is cardiovascular development and function, justifying this label.","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006995","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0042311","count":4},{"id":"GO:0039689","count":4},{"id":"GO:0051279","count":4}]},{"hash":"1368523506780094942","title":"Developmental signaling and organogenesis","description":"The top terms emphasize growth-factor\u2013driven signaling (IGF receptor and receptor tyrosine kinase pathways), organ induction, and brain development (corpus callosum development) along with extracellular matrix remodeling (collagen fibril organization), pointing to a development and tissue-patterning theme. Immune and apoptotic terms appear but are less central than the development/signaling signals, suggesting the cluster mainly captures developmental pathways with some pleiotropic roles. Confidence: Medium","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0001759","count":3},{"id":"GO:0048009","count":3},{"id":"GO:0060168","count":2},{"id":"GO:0051607","count":2}]},{"hash":"207436113372900538","title":"N-glycan processing and deglycosylation","description":"The cluster\u2019s strongest signals are glycosylation-related: N-glycan processing, protein glycosylation, deglycosylation, and mannose metabolism. A subset links to photoreceptor protein maturation (rhodopsin biosynthetic process, R8 cell development), suggesting involvement in glycoprotein production for visual systems. Additional terms imply endocytosis and broader developmental processes, but the glycosylation theme is dominant and coherent across the set.","confidence":"High","size":11,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006491","count":4},{"id":"GO:0006486","count":4},{"id":"GO:0016063","count":4},{"id":"GO:0035010","count":4},{"id":"GO:0006517","count":4}]},{"hash":"682215554322983042","title":"Vesicle Trafficking and Exocytosis Signaling","description":"These terms center on vesicle lifecycle (priming, maturation) and exocytosis in neurons and secretory cells (insulin release), plus membrane lipid remodeling and cytoskeletal regulation (phospholipid/ phosphatidylserine catabolic processes and Rho signaling). While B cell differentiation and BCR signaling appear, the common thread is membrane trafficking and signaling across neural and immune contexts.","confidence":"Medium","size":11,"edges":22,"triangles":12,"max_degree":8,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0016082","count":4},{"id":"GO:0006660","count":4},{"id":"GO:0002316","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0016188","count":4}]},{"hash":"2133943508610305312","title":"mRNA Processing and Translation Regulation","description":"The cluster's terms center on post-transcriptional control of gene expression: mRNA stability, polyadenylation regulation, splice-site recognition, preinitiation complex formation, translation reinitiation, and miRNA-mediated translational silencing. This coherent collection indicates a single theme of regulating mRNA fate and translation rather than transcriptional events.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":9},{"id":"GO:1901407","count":9},{"id":"GO:0048255","count":8},{"id":"GO:0001825","count":8},{"id":"GO:0010610","count":8}]},{"hash":"585572656284027229","title":"Neural development and sensory signaling","description":"This cluster's top GO terms cluster around nervous system development and function: optic nerve morphogenesis, righting reflex, and heart development; sensory perception of sound; circadian sleep/wake regulation; excitatory synaptic transmission with dopaminergic signaling; and responses to cocaine and ethanol. Taken together, the proteins likely participate in neural development and neurotransmission with sensory processing and behavioral links. The obsolete term is not informative for current interpretation.","confidence":"High","size":11,"edges":20,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":6},{"id":"GO:0050910","count":6},{"id":"GO:0060079","count":6},{"id":"GO:0042220","count":6},{"id":"GO:0071361","count":6}]},{"hash":"1063208607110809002","title":"Neuro-immune development and signaling","description":"This cluster combines strong signals for nervous system development (CNS/PNS, organ induction) with immune cell differentiation and trafficking (dendritic cells, B-1 cells, neutrophil extravasation), plus adhesion and ERK pathway activity, suggesting a theme of coordinated neural and immune development and signaling rather than a single enzymatic function.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2001200","count":5},{"id":"GO:0007157","count":5},{"id":"GO:0007417","count":4},{"id":"GO:2000391","count":4},{"id":"GO:0045765","count":4}]},{"hash":"1065687191170151324","title":"Neural development and synaptic adhesion","description":"The top GO terms show a clear emphasis on nervous system development, neuron cell\u2013cell adhesion, and positive regulation of synapse assembly, pointing to roles in neural development and synapse formation; the presence of both homophilic and heterophilic adhesion supports synaptic connectivity, with a few broader development terms as possible context.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":4},{"id":"GO:0035987","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0007158","count":3},{"id":"GO:0007156","count":3}]},{"hash":"240173610520046073","title":"Unknown","description":"The terms span neural development (neurogenesis, collateral sprouting), immune activation (complement pathways), developmental processes (vagina development, GI epithelium maintenance), apoptosis, signaling (protein kinase activity), and xenobiotic response, with no singular, cohesive function tying all proteins together.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048672","count":6},{"id":"GO:0022008","count":6},{"id":"GO:0006915","count":5},{"id":"GO:0060068","count":5},{"id":"GO:0006958","count":5}]},{"hash":"1956091875132144693","title":"Blood coagulation and extracellular matrix remodeling","description":"The top GO terms cluster around coagulation (Factor XII activation, blood coagulation, plasminogen activation, fibrinolysis) and ECM remodeling (collagen catabolic process, extracellular matrix disassembly), indicating a cohesive role in clotting and matrix breakdown/reconstruction. Amelogenesis and development terms appear less central, likely reflecting broader developmental contexts.","confidence":"High","size":11,"edges":11,"triangles":1,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002542","count":7},{"id":"GO:0030574","count":7},{"id":"GO:0010756","count":7},{"id":"GO:0030194","count":7},{"id":"GO:0022617","count":7}]},{"hash":"1342210186010542707","title":"Neuronal membrane excitability and innervation","description":"The top GO terms cluster around neuronal signaling: excitatory postsynaptic potential, sodium and potassium ion transport across membranes, and membrane depolarization/hyperpolarization, plus innervation. These point to a core theme of neural membrane excitability and synaptic activity, with a few metabolism-related terms appearing as secondary associations.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0051899","count":2},{"id":"GO:0071660","count":2}]},{"hash":"489364269017483945","title":"Mitochondrial apoptosis signaling in lymphoid development","description":"The top terms center on mitochondria-mediated apoptosis (cytochrome c release and intrinsic apoptotic signaling) and immune/lymphoid organ homeostasis (thymus, spleen, B and T cell homeostasis). Additional development terms (ear, kidney, spermatogenesis) suggest a broader role for apoptotic signaling in organ development. This points to a cluster of proteins involved in mitochondria-dependent apoptosis with relevance to immune system and organ maturation.","confidence":"Medium","size":11,"edges":36,"triangles":50,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0090200","count":7},{"id":"GO:0001844","count":7},{"id":"GO:0043029","count":6},{"id":"GO:0048538","count":6},{"id":"GO:0007283","count":6}]},{"hash":"957966707650731385","title":"Visual and Cardiac Development with Neural Signaling","description":"The cluster shows strong signals for visual system terms (visual perception, retina layer formation) as well as cardiac development and contraction, plus neural signaling (synaptic vesicle exocytosis) and NF-kappaB\u2013related regulation, suggesting proteins involved in eye and heart development with neural activity.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0007601","count":5},{"id":"GO:0007507","count":4},{"id":"GO:0043123","count":4},{"id":"GO:2001246","count":3}]},{"hash":"74219583199556229","title":"Ciliary assembly and protein trafficking","description":"This set features explicit ciliogenesis signals (non-motile cilium assembly; localization to the ciliary transition zone) and multiple vesicle-transport processes (ER-Golgi, endosome-to-Golgi retrograde transport). Together they point to a theme of ciliogenesis coupled with intracellular trafficking, with some development terms likely reflecting cilia-mediated signaling in neural tube and digit morphogenesis.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":1},{"id":"GO:0018230","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0021532","count":1},{"id":"GO:0042733","count":1}]},{"hash":"123696378401750923","title":"Wnt signaling and organ morphogenesis","description":"This cluster centers on multicellular development and Wnt signaling, including both calcium-modulating and canonical pathway regulation, with many tissue-specific development terms (lung mesenchyme, heart, myoblast differentiation, vagina development, labyrinthine layer vascular development). The recurring theme is Wnt-regulated organogenesis and tissue morphogenesis across multiple organs, with some secondary immune-related terms. ","confidence":"High","size":11,"edges":51,"triangles":130,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0007223","count":5},{"id":"GO:0060716","count":4},{"id":"GO:0060068","count":4},{"id":"GO:0071374","count":4}]},{"hash":"1982860111205504201","title":"Cross-Tissue Developmental Differentiation","description":"The most represented terms cluster around development and tissue differentiation (neuropeptide signaling, pancreatic B cell development, cartilage morphogenesis), suggesting a broad developmental theme across different tissues. Additional terms reflect general cellular processes or distant associations, indicating diverse roles rather than a single cohesive pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007218","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060536","count":2},{"id":"GO:0072321","count":1},{"id":"GO:0045039","count":1}]},{"hash":"124923054257346752","title":"Small-molecule and nucleotide catabolism","description":"This cluster centers on catabolic processes for diverse small molecules and nucleotides, including N-acetylneuraminate, uracil, creatinine, nicotinamide and nicotinate, plus nucleotide salvage and nitrogen utilization, suggesting a cohesive metabolic theme around breakdown and reuse of substrates; a few terms (e.g., phenazine biosynthesis, filopodium assembly, aging) appear as noise or peripheral functions but do not override the main theme.","confidence":"Medium","size":11,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019262","count":2},{"id":"GO:0006212","count":2},{"id":"GO:1904524","count":2},{"id":"GO:0001302","count":2},{"id":"GO:0019740","count":2}]},{"hash":"1713834422604094363","title":"Immune signaling and antibody processes","description":"The terms cluster around immunoglobulin production and transcytosis, neutrophil homeostasis, NK T cell activation regulation, CCR7 signaling, and response to peptidoglycan, suggesting a humoral/innate immune theme; a few unrelated terms (lens morphogenesis, AV node action potential, fat cell proliferation) appear, indicating some noise but the dominant signal is immune-related.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902414","count":2},{"id":"GO:0070352","count":2},{"id":"GO:0002415","count":2},{"id":"GO:0086016","count":2},{"id":"GO:0001780","count":2}]},{"hash":"1752148653985508975","title":"Developmental ECM signaling and cell adhesion","description":"The top GO terms point to broad developmental roles (skeletal system, CNS, hippocampus) plus extracellular matrix organization (collagen fibril) and growth-factor signaling (FGF stimulus), with accompanying cell adhesion and monocyte aggregation. This suggests a coherent theme of developmental signaling coupled with ECM remodeling and adhesion processes, rather than a single narrow function.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0050728","count":10},{"id":"GO:0001501","count":10},{"id":"GO:0044344","count":10},{"id":"GO:0030199","count":10},{"id":"GO:0007417","count":10}]},{"hash":"1627441532960944348","title":"Neuroimmune-Dopaminergic Signaling","description":"The GO terms cluster around CNS-focused immune modulation and dopaminergic signaling, including negative regulation of inflammation, general immune response, glial/astrocyte-related activities, and dopamine transport and signaling pathways, suggesting proteins that coordinate neuroimmune interactions with dopamine signaling in glial-neuronal contexts.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":11},{"id":"GO:0042493","count":11},{"id":"GO:2000458","count":11},{"id":"GO:1900168","count":11},{"id":"GO:0048245","count":11}]},{"hash":"681234724879167090","title":"Meiotic recombination and DSB repair","description":"This cluster is dominated by GO terms tied to meiotic recombination and double-strand break (DSB) repair, including meiotic recombinase assembly, reciprocal meiotic recombination, replication-born DSB repair via sister chromatid exchange, SDSA-mediated DSB repair, and meiosis I regulation. While there are some related stress-response terms, the core theme points to meiotic DNA processing and repair pathways. Confidence: High","confidence":"","size":10,"edges":39,"triangles":87,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000707","count":3},{"id":"GO:0007131","count":3},{"id":"GO:0090656","count":3},{"id":"GO:0042493","count":3}]},{"hash":"367217062082099885","title":"Neural development and axon guidance","description":"This cluster centers on neural development and connectivity, highlighted by terms like axon fasciculation, receptor clustering, and visual learning, along with supporting processes such as DNA-templated transcription and regulation of signaling and protein turnover that are important for neuronal differentiation and synaptic organization. While there are a few metabolism-related terms, the predominant theme ties to brain development and neural network formation.","confidence":"Medium","size":10,"edges":35,"triangles":77,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:2001275","count":9},{"id":"GO:0048320","count":9},{"id":"GO:0097155","count":9},{"id":"GO:0032092","count":9}]},{"hash":"1612808613862236081","title":"Steroid signaling and prostate development","description":"The top GO terms include steroid hormone receptor complex assembly, prostate gland development, and male sex differentiation, which together point to androgen/steroid signaling governing prostate-associated development. While there are additional terms related to oxidative stress and immune signaling, the strongest shared function across the cluster appears to be steroid hormone signaling linked to male reproductive development.","confidence":"Medium","size":10,"edges":28,"triangles":26,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":4},{"id":"GO:0071353","count":3},{"id":"GO:0033197","count":3},{"id":"GO:0006463","count":3},{"id":"GO:0046661","count":3}]},{"hash":"1242502758618468574","title":"Cell Polarity and Microtubule Transport in Migration","description":"The terms cluster around polarity establishment, the centrosome cycle, and minus-end-directed microtubule transport, with links to Golgi localization, stress granule assembly, and tube formation\u2014reflecting cytoskeletal organization underlying migration and morphogenesis.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":2},{"id":"GO:0001764","count":2},{"id":"GO:0030010","count":2},{"id":"GO:0035148","count":2},{"id":"GO:0072385","count":1}]},{"hash":"610880256322431487","title":"Ubiquitin-Proteasome Regulation of Apoptosis and DNA Repair","description":"This cluster centers on ubiquitin-related processes: K6-linked ubiquitination, neddylation, and enhancement of ubiquitin-protein transferase activity, plus APC/C-dependent proteolysis. The presence of apoptosis and DNA repair terms suggests a functional module coordinating protein turnover with cell-cycle control and DNA damage response. Given these converging themes, the label reflects a coherent ubiquitin-mediated regulation of cell cycle, survival, and repair pathways.","confidence":"High","size":10,"edges":38,"triangles":75,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043524","count":9},{"id":"GO:0006344","count":9},{"id":"GO:0031145","count":9},{"id":"GO:0043951","count":9},{"id":"GO:0085020","count":9}]},{"hash":"1392221563803693625","title":"Ribosome Biogenesis and Chromatin Remodeling","description":"This cluster is dominated by rRNA maturation terms (LSU- and 5.8S rRNA processing) indicating ribosome assembly, alongside chromatin remodeling terms (histone deacetylation, nucleosome mobilization, histone displacement). Together these point to nucleus/nucleolus\u2013associated processes linking ribosome biogenesis with chromatin dynamics; a few terms about meiosis or gland development are less connected and may reflect broader nuclear regulation or annotation noise, but the core signal supports the ribosome/chromatin theme.","confidence":"Medium","size":10,"edges":37,"triangles":70,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035948","count":6},{"id":"GO:0016575","count":5},{"id":"GO:0042766","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000132","count":4}]},{"hash":"281188792714429267","title":"Mitotic cell cycle regulation","description":"The cluster\u2019s GO terms cluster around mitosis and cell cycle control\u2014cell division, mitotic cell cycle phase transitions, regulation of mitotic cycle, and CDK activity\u2014along with traits like cell proliferation and chromatin dynamics, suggesting these proteins coordinately regulate progression through mitosis and proliferation. Hydrogen peroxide response and transcription regulation appear as supplementary contexts rather than core functions.","confidence":"High","size":10,"edges":17,"triangles":10,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0070301","count":3},{"id":"GO:0006357","count":3},{"id":"GO:0044772","count":3},{"id":"GO:0007488","count":3}]},{"hash":"1351384418048068836","title":"Ubiquitin-dependent proteolysis and mitophagy","description":"This cluster centers on ubiquitination events (autoubiquitination and multiple ubiquitin linkages) linked to protein degradation, including mitophagy and ubiquitin-dependent catabolic processes, suggesting a proteostasis and mitochondrial quality-control theme. Some terms point to stress responses and vesicle formation regulation, which can be connected to ubiquitin-mediated turnover and autophagic pathways. Overall, the dominant signal is ubiquitin-driven protein turnover with mitophagy involvement.","confidence":"High","size":10,"edges":35,"triangles":57,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0070979","count":4},{"id":"GO:0085020","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0033132","count":3}]},{"hash":"726587635130755333","title":"Immune signaling and chromatin remodeling","description":"Top GO terms indicate immune signaling pathways (JNK cascade regulation, NF-kappaB activation, V(D)J recombination) alongside chromatin-related processes (histone acetylation/methylation, histone ubiquitination, histone catabolic process). This suggests a cohesive theme of regulating gene expression and signaling in immune contexts through chromatin remodeling and post-translational modifications, rather than a single targeted enzymatic function.","confidence":"High","size":10,"edges":26,"triangles":28,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":5},{"id":"GO:2000620","count":5},{"id":"GO:0070512","count":5},{"id":"GO:0046328","count":5},{"id":"GO:1903762","count":5}]},{"hash":"1214399007966298895","title":"Embryonic and Organ Morphogenesis","description":"The top GO terms cluster around development and tissue shaping across multiple organs (hair follicle, ovarian follicle, prostate gland, heart, eye), including embryonic development and morphogenesis, indicating a shared role in organogenesis rather than a single tissue-specific function.","confidence":"High","size":10,"edges":12,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051798","count":7},{"id":"GO:0001547","count":7},{"id":"GO:0060528","count":7},{"id":"GO:0055010","count":7},{"id":"GO:0001701","count":7}]},{"hash":"473096467128837193","title":"Mitotic spindle and cytokinesis machinery","description":"GO terms center on mitosis-related processes (spindle assembly, midzone assembly, metaphase chromosome recapture, actomyosin ring assembly) with supporting cues from cell junction maintenance and adhesion signaling, suggesting a core cluster of spindle dynamics and cytokinesis proteins that also participate in cytoskeletal organization and morphogenesis.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":9},{"id":"GO:0072092","count":8},{"id":"GO:0048364","count":8},{"id":"GO:0099607","count":8},{"id":"GO:0001560","count":8}]},{"hash":"1538684501573112459","title":"Lipid Biosynthesis and Remodeling","description":"This cluster is dominated by GO terms for the biosynthesis and remodeling of glycerophospholipids and related lipids (cardiolipin, phosphatidylcholine, ether lipids, triglycerides, CDP-diacylglycerol) and includes mitochondrial ATP synthesis linked to lipid metabolism. While a couple of tissue-specific terms appear, the prevailing theme ties to lipid creation/remodeling and its role in mitochondrial membranes and energy production.","confidence":"High","size":10,"edges":23,"triangles":23,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006663","count":5},{"id":"GO:0035965","count":5},{"id":"GO:0036151","count":5},{"id":"GO:0042775","count":4},{"id":"GO:2001246","count":4}]},{"hash":"867780862791485491","title":"RNA splicing and translation regulation","description":"Top GO terms indicate a cohesive group centered on RNA processing and control of protein synthesis: regulation of mRNA splicing via the spliceosome, mRNA stability, regulation of translational initiation, preinitiation complex formation, and translation reinitiation. The presence of regulatory ncRNA-mediated gene silencing further supports RNA-guided control in these proteins. A blastocyst formation term may reflect developmental contexts where these RNA regulatory mechanisms are active, but the dominant signal is RNA maturation and translational regulation.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:0048255","count":8},{"id":"GO:0001825","count":8},{"id":"GO:0010610","count":8}]},{"hash":"2117051191140066851","title":"Post-transcriptional gene expression regulation","description":"The top terms cluster around mRNA export, translation initiation/reinitiation, and miRNA-mediated translational silencing, together with ubiquitination/ERAD for proteostasis. This suggests a cohesive theme of coordinating RNA processing with translation control and protein quality control, with supporting signals related to stress and cell division. A few terms are older or broader, but the core pattern remains clear.","confidence":"High","size":10,"edges":30,"triangles":39,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2}]},{"hash":"2095471454563355828","title":"Interferon-Driven Antiviral and ER Stress Response","description":"The cluster is dominated by GO terms tied to interferon signaling and antiviral defense (cellular response to interferon-alpha, cellular response to type I interferon, defense response to virus) and by ER-stress\u2013related translation regulation, suggesting a cohesive theme of innate immune and cellular stress responses. There are a few terms that are less related (cilium assembly, cytokinin signaling, male differentiation), likely representing annotation noise or broader regulatory links, but the interferon/virus-defense pattern is the strongest signal.","confidence":"Medium","size":10,"edges":19,"triangles":21,"max_degree":7,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006463","count":6},{"id":"GO:1905515","count":6},{"id":"GO:1903071","count":6},{"id":"GO:0009736","count":6},{"id":"GO:0035457","count":6}]},{"hash":"2194553681613131028","title":"Actin Cytoskeleton and Nuclear Dynamics","description":"This cluster is dominated by GO terms tied to actin organization and interactions with the nucleus, including actin crosslink formation, mitotic contractile ring assembly, and structures like the terminal web, plus processes that involve nuclear localization and nuclear membrane anchoring. The presence of karyogamy and ascospore formation hints at fungal cytoskeletal roles during mating and sporulation, while the cardiac and Purkinje cell morphogenesis terms reflect broader cytoskeletal functions in development. Taken together, the common thread is actin-based cytoskeletal dynamics that coordinate cell division, nuclear positioning, and morphogenesis.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051764","count":2},{"id":"GO:0000742","count":2},{"id":"GO:1902896","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0051457","count":2}]},{"hash":"1050203199855775272","title":"Developmental signaling and apoptosis cluster","description":"The proteins are enriched for GO terms related to developmental signaling pathways (Wnt, Hippo), tissue development (forebrain, keratinocyte, muscle), and cell fate processes (apoptosis, DNA damage response), suggesting they collectively regulate growth, differentiation, and survival across tissues.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006977","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0030216","count":2}]},{"hash":"1294502039534491085","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":9,"triangles":2,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0000209","count":4}]},{"hash":"245946480045812059","title":"Neurodevelopment and Forebrain Patterning","description":"This cluster is dominated by GO terms related to neural differentiation and forebrain patterning (visceral motor neuron differentiation, neuronal commitment in the forebrain, cerebral cortex regionalization) as well as transcriptional regulation, which points to a coordinated neural developmental program. While additional terms touch broader embryonic morphogenesis (limbs, digits, heart), the strongest signals center on neural specification and forebrain development, justifying a label focused on neurodevelopment with patterning. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021524","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0021983","count":3},{"id":"GO:0048706","count":3},{"id":"GO:0021902","count":3}]},{"hash":"296552527440877953","title":"DNA replication and genome maintenance","description":"This cluster centers on core genome integrity processes: DNA replication alongside repair pathways (base-excision, nucleotide-excision), plus mitotic controls like sister chromatid separation and spindle assembly checkpoint. Additional meiosis- and RNA quality-control terms fit within broader genome maintenance and expression surveillance during cell division.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0016446","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006286","count":3}]},{"hash":"1934218305351272086","title":"Neural development and synaptic signaling","description":"The top terms converge on neural development and neuron-specific regulation: neural tube closure, visual learning, excitatory postsynaptic potentials, receptor clustering, and DNA-templated transcription tied to neuronal programs, with supporting developmental processes like cell migration. A few terms are general stress responses or imprinting, but the dominant theme is neural development and synaptic activity.","confidence":"Medium","size":10,"edges":4,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0008542","count":3},{"id":"GO:0043113","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0060079","count":3}]},{"hash":"2036803080581432473","title":"Drosophila R8 photoreceptor development and ciliary function","description":"The GO terms primarily point to R8 photoreceptor development and photoreceptor organization, along with regulation of cilium beat frequency and Smoothened (Hedgehog) signaling, collectively highlighting a theme of eye development and ciliary function in Drosophila; other terms such as autophagy and Golgi retention appear as peripheral cellular processes.","confidence":"High","size":10,"edges":10,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":3},{"id":"GO:0016236","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0060296","count":3},{"id":"GO:2000253","count":3}]},{"hash":"165740192773394164","title":"Actin Cytoskeleton Remodeling and Cell Motility","description":"The cluster is enriched for actin-related processes (actin cortical patch assembly, actin filament bundle assembly, lamellipodium assembly) and signaling events (JUN phosphorylation, PDGFR signaling) that drive cytoskeletal remodeling and cell movement, with engulfment of apoptotic cells also relying on actin dynamics; other terms point to related but less central functions like chromatin, osteoblast fate, and fatty acid oxidation.","confidence":"Medium","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:1901076","count":9},{"id":"GO:0007258","count":9},{"id":"GO:0030702","count":8},{"id":"GO:0002051","count":8},{"id":"GO:1990859","count":8}]},{"hash":"406160913878023596","title":"Translation and mitotic cell cycle","description":"The top GO terms show a strong emphasis on translation (protein synthesis) and mitotic cell cycle/cell division, suggesting the cluster centers on core cellular growth and division machinery. A few development and cilium-related terms are present but with lower frequency, implying a mix of roles or annotation noise rather than a single cohesive pathway.","confidence":"Medium","size":10,"edges":28,"triangles":34,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0072189","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1441894506501980499","title":"RNAi and miRNA Processing Machinery","description":"The top GO terms cluster tightly around RNA interference components: RISC complex assembly, miRNA processing, and mRNA silencing, including adenosine-to-inosine editing and mRNA cleavage, suggesting a core function in RNAi/miRNA pathways; a few developmental or proliferative terms may reflect broader roles of these factors but do not outweigh the RNAi signal.","confidence":"High","size":10,"edges":41,"triangles":92,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035087","count":6},{"id":"GO:0035280","count":6},{"id":"GO:0097049","count":6},{"id":"GO:1902033","count":6},{"id":"GO:0045070","count":6}]},{"hash":"936635347932086511","title":"Osteoblast differentiation and bone formation","description":"The cluster is enriched for osteogenesis-related GO terms such as osteoblast fate commitment (GO:0002051), endochondral ossification (GO:0001958), osteoblast development (GO:0002076), and positive regulation of osteoblast differentiation (GO:0045669), indicating proteins involved in bone formation and skeletal development. Additional terms like stem cell differentiation and cell maturation reinforce a developmental trajectory toward osteogenic lineages. A few non-bone terms (eye cone cell differentiation, imaginal disc-derived female genitalia development) may reflect species-specific annotations or broader developmental contexts, but the dominant pattern points to osteoblast biology. Therefore the label Osteoblast differentiation and bone formation captures the cluster's core function.","confidence":"High","size":10,"edges":27,"triangles":35,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0002051","count":8},{"id":"GO:0001958","count":8},{"id":"GO:0042675","count":8},{"id":"GO:0048469","count":8},{"id":"GO:0048863","count":8}]},{"hash":"1768142413509881500","title":"Golgi Trafficking and Organization","description":"The cluster is enriched in Golgi-associated terms such as protein retention in the Golgi, ER-to-Golgi transport, and regulation of Golgi organization, with additional links to related processes like autophagosome maturation and cell division. This pattern suggests a cohesive module centered on Golgi trafficking and organelle maintenance during the cell cycle.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045053","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0035617","count":3},{"id":"GO:0007080","count":3},{"id":"GO:0000278","count":3}]},{"hash":"2225499538315394825","title":"Neural development and synaptic signaling","description":"This cluster's terms mainly indicate nervous system development and neuronal communication: substantia nigra development, peripheral nervous system myelination, and excitatory postsynaptic potentials. Cell\u2013cell adhesion further supports neural tissue organization. Calcium-related terms point to synaptic calcium signaling, though one item is obsolete. A few terms\u2014negative regulation of inflammatory response and sphingomyelin catabolic process\u2014are more peripheral but can intersect neural contexts, and a cardiac hypertrophy term appears unrelated to brain function. Overall, the dominant theme is neural development and synaptic signaling.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006685","count":4},{"id":"GO:0050728","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0060316","count":3},{"id":"GO:0022011","count":3}]},{"hash":"228338366152589757","title":"Osteoclast differentiation and skeletal development signaling","description":"Dominant GO terms include skeletal system development and regulation of osteoclast differentiation, along with IGF receptor signaling, all central to bone formation and remodeling. Supporting terms about Rac/Ral signaling, phosphorylation, and protein localization further align with signaling networks that govern bone cell activity. Together, these terms suggest a cohesive theme of bone remodeling and skeletal development signaling.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":2},{"id":"GO:0010667","count":2},{"id":"GO:0032485","count":1},{"id":"GO:0048009","count":1},{"id":"GO:1902634","count":1}]},{"hash":"1511107378459350423","title":"Deubiquitinases modulating TLR signaling","description":"The top GO terms point to ubiquitin chain-specific deubiquitination (K11, K63, K48) and Toll-like receptor signaling (TLR2/9), with additional notes on downregulation of IL-6 and B cell activation, suggesting a cluster of proteins that regulate innate immune signaling via deubiquitination.","confidence":"High","size":10,"edges":19,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035871","count":3},{"id":"GO:0070536","count":3},{"id":"GO:0071108","count":3},{"id":"GO:0050869","count":2},{"id":"GO:0045947","count":2}]},{"hash":"1146867177181421373","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902035","count":3},{"id":"GO:1903527","count":2},{"id":"GO:0006513","count":2},{"id":"GO:0007276","count":2},{"id":"GO:0006281","count":2}]},{"hash":"606130379881856064","title":"Growth-factor signaling and developmental responses","description":"The terms include insulin receptor signaling, responses to VEGF and prostaglandin stimuli, and negative regulation of JNK, alongside development-related terms such as inner ear development and labyrinthine layer blood vessel development, plus transcription. This suggests a theme of signaling pathways driven by growth factors/hormones that influence developmental processes and gene regulation, though the terms span several related contexts. Therefore, a label focusing on growth-factor\u2013mediated signaling and developmental responses seems most representative, with moderate confidence given term diversity.","confidence":"Medium","size":10,"edges":7,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001275","count":7},{"id":"GO:0032092","count":7},{"id":"GO:0046329","count":7},{"id":"GO:0098761","count":7},{"id":"GO:0006351","count":7}]},{"hash":"543800191955867503","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006311","count":2},{"id":"GO:0010845","count":2},{"id":"GO:2000821","count":1},{"id":"GO:0035418","count":1},{"id":"GO:0048541","count":1}]},{"hash":"897100686467009428","title":"Cytoskeleton remodeling in morphogenesis","description":"The top GO terms point to cytoskeletal organization and remodeling (actin filament bundle assembly; microtubule anchoring at centrosome) and several development-related processes (face morphogenesis, neuron remodeling, spermatid nucleus elongation). This pattern suggests a cohesive theme around cytoskeleton-driven shape changes and morphogenesis, with some noise from unrelated terms (plant signaling, obsolete annotations). Overall, a cytoskeleton-centric morphogenesis label best fits the cluster.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032981","count":1},{"id":"GO:0060325","count":1},{"id":"GO:0032434","count":1},{"id":"GO:0009788","count":1},{"id":"GO:0034454","count":1}]},{"hash":"2280890049003255345","title":"Transcriptional regulation and chromatin modification","description":"The top GO terms cluster around DNA-templated transcription, its positive/negative regulation, and chromatin-level control (histone deubiquitination, RITS complex assembly). A few terms touch on signaling or neural processes, but the predominant theme is transcriptional regulation and chromatin remodeling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007412","count":1},{"id":"GO:0043569","count":1},{"id":"GO:1904802","count":1},{"id":"GO:0043085","count":1}]},{"hash":"1084383719531394320","title":"ER Trafficking and Steroid Biosynthesis","description":"This cluster is dominated by GO terms pointing to endoplasmic reticulum functions, especially retention in the ER lumen and ER-to-Golgi vesicle transport, plus ER-dependent peroxisome organization and steroid biosynthetic processes, suggesting a core role in ER-based protein processing and lipid metabolism. The remaining terms hint at related stress and signaling aspects (redox balance, apoptotic signaling) that can intersect ER function, while a few terms reflect broader developmental or mitochondrial processes that are less central but not mutually exclusive. Overall, the common theme centers on ER-associated protein handling and steroid/lipid biosynthesis.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0018401","count":1},{"id":"GO:0045454","count":1},{"id":"GO:2001238","count":1}]},{"hash":"2206528700095609844","title":"DNA Damage Response and Ubiquitin-Proteasome Regulation","description":"The proteins cluster around nucleotide-excision repair activities (global genome NER, preincision complex stabilization) and DNA damage signaling (G1 checkpoint), together with ubiquitin-dependent proteolysis pathways (SCF-dependent degradation and neddylation) and related turnover via the multivesicular body route. This points to a cohesive theme where DNA repair is coordinated with regulated protein degradation. A couple of terms like viral process and IL-1 response may reflect broader stress signaling overlaps but do not define the core function.","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":2},{"id":"GO:0045116","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0031571","count":2}]},{"hash":"485422277509824731","title":"Transmembrane Ion and Metabolite Transporters","description":"The cluster is dominated by GO terms for transmembrane and ion transport, especially for potassium and sodium, as well as for transport of organic acids like malate, succinate, and citrate. This pattern strongly suggests a group of membrane transporter proteins dedicated to shuttling ions and metabolites across membranes. The cytosine metabolic process and regulation of phosphate transport appear as related metabolic/regulatory connections but do not override the transport-focused theme.","confidence":"High","size":10,"edges":22,"triangles":18,"max_degree":8,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0006813","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0019858","count":3},{"id":"GO:0098656","count":3},{"id":"GO:0015743","count":3}]},{"hash":"459145833660852713","title":"Metabolic and Renal-Vascular Regulation","description":"This cluster centers on metabolic control (gluconeogenesis and triglyceride metabolism) and vascular/renal signaling (renal blood-flow response, renin-angiotensin-related blood pressure regulation, innervation, and smooth muscle behavior), with a minor component of immune-related activity (mast cell immunity). The combination suggests a cohesive theme of energy metabolism intertwined with vascular and renal regulatory processes, despite some heterogeneous terms.","confidence":"Medium","size":10,"edges":7,"triangles":4,"max_degree":4,"top_function":"protein maturation","top_go_terms":[{"id":"GO:0045721","count":8},{"id":"GO:2000098","count":8},{"id":"GO:2001275","count":7},{"id":"GO:0002448","count":7},{"id":"GO:0001999","count":7}]},{"hash":"1618017525714072693","title":"Cardiovascular development and vasculature regulation","description":"The top terms show a clear focus on heart and blood vessel formation, with cardiac muscle tissue development and negative regulation of endothelial differentiation and vasculogenesis indicating a cardiovascular developmental theme. Other terms reflect miscellaneous metabolic processes and occasional outliers, but the vascular-development signals dominate, suggesting the cluster centers on cardiovascular development/regulation.","confidence":"Medium","size":10,"edges":36,"triangles":63,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":2},{"id":"GO:0046944","count":1},{"id":"GO:0006796","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0048738","count":1}]},{"hash":"1118001337009568736","title":"Regulatory Signaling and Adhesion","description":"The terms point to regulation of signaling pathways (including cAMP/PKA-related signaling and extrinsic apoptotic signaling), plus processes like cadherin-mediated cell\u2013cell adhesion, cytokinesis, RNA localization, and oxidative stress responses. The proteins seem to engage in broad regulatory roles spanning signaling modulation, cell\u2013cell interactions, and stress responses rather than a single pathway, supporting a label centered on Regulatory Signaling and Adhesion.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1902490","count":1},{"id":"GO:0019933","count":1},{"id":"GO:0010737","count":1},{"id":"GO:2001240","count":1},{"id":"GO:0051237","count":1}]},{"hash":"1561076512460438274","title":"Rho/Ras signaling and differentiation cues","description":"This cluster centers on modulation of key signal transduction pathways, especially Rho and Ras signaling, with supporting terms like IP3 biosynthesis and phospholipid catabolism, plus downstream processes such as synapse assembly and long-term potentiation. The inclusion of differentiation-related GO terms (follicular B cell differentiation and osteoblast fate commitment) suggests signaling cues influence diverse cell fates, not a single tissue. Together, the terms point to a theme of signaling regulation guiding differentiation and synaptic functions.","confidence":"Medium","size":10,"edges":38,"triangles":85,"max_degree":9,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0002316","count":10},{"id":"GO:0035023","count":10},{"id":"GO:0009395","count":10},{"id":"GO:0032959","count":10},{"id":"GO:0046580","count":10}]},{"hash":"660787867657054352","title":"Amino acid biosynthesis and central carbon metabolism","description":"The top GO terms point to amino acid biosynthesis (L-leucine and L-lysine) and central carbon metabolism (2-oxoglutarate and isocitrate pathways), along with NADPH regeneration, suggesting a cohesive metabolic module for amino acid production and redox/energy balance. There are also a couple of regulatory terms (e.g., responses to nutrients or hormones) that are less central and involve fewer proteins, but the dominant theme is metabolic. ","confidence":"Medium","size":10,"edges":40,"triangles":90,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0009098","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0048545","count":2},{"id":"GO:0006103","count":2}]},{"hash":"914858374537247097","title":"Immune signaling and developmental processes","description":"The GO terms point to immune signaling (B cell receptor signaling pathway, type 2 immune response, pro-T cell differentiation) and to various developmental processes (endocrine system development, left-right pattern formation, skeletal muscle fiber development, circadian rhythm). This suggests the proteins function in immune signaling with broader developmental roles, hence a label capturing both aspects.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":2},{"id":"GO:0045497","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0048741","count":1},{"id":"GO:2000176","count":1}]},{"hash":"2183801620518794623","title":"Cardiac potassium transport and membrane potential regulation","description":"The top GO terms cluster around cardiac electrophysiology and potassium handling, including regulation of resting membrane potential, atrial action potential repolarization, potassium ion transport and homeostasis, and regulation of heart rate via cardiac conduction. These suggest proteins that maintain cardiac membrane potential and drive potassium-linked action potentials, with a secondary note on stress-related cardiac hypertrophy. The touch sensation term appears less connected but does not dominate the cluster\u2019s theme. Overall, this cluster reflects cardiac potassium transport and membrane potential regulation.","confidence":"High","size":10,"edges":11,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060075","count":8},{"id":"GO:0098914","count":8},{"id":"GO:1990573","count":7},{"id":"GO:0086091","count":7},{"id":"GO:0086002","count":7}]},{"hash":"2113871031636879750","title":"Neural development and neuron survival signaling","description":"This cluster centers on nervous system development and neuronal processes, including neuron migration, sympathetic nervous system development, and branchiomeric muscle development, with a strong emphasis on negative regulation of neuron apoptosis. It also features MAPK stress-activated signaling and STAT phosphorylation, suggesting coordinated signaling that supports neural development and neuronal survival; inflammatory and vascular cues appear as contextual co-signals during development. ","confidence":"Medium","size":10,"edges":28,"triangles":35,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0001764","count":5},{"id":"GO:2001240","count":5},{"id":"GO:0048485","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0031098","count":5}]},{"hash":"755126370722042509","title":"Immune and vascular activation","description":"This cluster shows immune system engagement (basophil activation, complement activation, cellular response to fungal origin), platelet activation, and vascular remodeling (lymph vessel morphogenesis, cell adhesion molecule production). The presence of arachidonic acid\u2013related signaling further supports inflammatory mediator production. Together, these terms point to a theme of inflammation coordinating immune responses with hemostasis and vascular changes; a few terms such as mesonephric duct development or senescence may be outliers or reflect broader cross-roles. Therefore this label captures the core pattern of inflammatory-immune and vascular activation present in the cluster.","confidence":"Medium","size":10,"edges":22,"triangles":17,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090403","count":3},{"id":"GO:0072177","count":3},{"id":"GO:0010572","count":3},{"id":"GO:0060355","count":3},{"id":"GO:0051873","count":3}]},{"hash":"2106498403329753621","title":"Cardiac and skeletal muscle development with hypoxia signaling","description":"The top GO terms point to heart development, myoblast differentiation, and intracellular oxygen homeostasis, with related processes like prolyl hydroxylation and ERK/MAPK signaling. This combination suggests a cohesive theme of heart and skeletal muscle development regulated by hypoxia-responsive pathways. Some terms (e.g., xenobiotic response, osteoblast differentiation) appear less central and may reflect broader regulatory roles or annotations, but the core signal emphasizes muscle development linked to oxygen sensing.","confidence":"Medium","size":10,"edges":23,"triangles":21,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0032364","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1901874","count":2},{"id":"GO:0006351","count":2}]},{"hash":"940418394857744655","title":"Neural Development and Sensory Axon Guidance","description":"This cluster shows a clear emphasis on nervous system formation, with recurrent terms like pyramidal neuron development, olfactory lobe development, and fasciculation of sensory neuron axon, indicating roles in neural development and axon guidance. While there are some broader morphogenesis terms present, the strongest and most consistent signal is neural development.","confidence":"Medium","size":10,"edges":40,"triangles":82,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:2000020","count":2},{"id":"GO:0021860","count":2},{"id":"GO:0097155","count":2},{"id":"GO:0014912","count":2},{"id":"GO:0051642","count":2}]},{"hash":"738447305751550124","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning transcription regulation, development (ossification, maternal axis specification), miRNA processing, immune signaling, and learning/locomotion, with several obsolete terms. There is no clear, cohesive function tying the cluster together, so Unknown with None confidence.","confidence":"","size":10,"edges":16,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0001958","count":2},{"id":"GO:0007313","count":2},{"id":"GO:0033280","count":2}]},{"hash":"2261048248406959084","title":"Sperm-Egg Recognition and Fusion","description":"This cluster is dominated by fertilization-related GO terms: sperm-egg recognition, fusion of sperm to the egg plasma membrane during single fertilization, and fertilization itself, suggesting a role in reproductive cell interaction. A few terms such as retina homeostasis and inflammatory response appear as minority annotations and may reflect broader or incidental functions, while the cell wall\u2013related terms are likely noise or cross-species annotations.","confidence":"Medium","size":10,"edges":6,"triangles":0,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0001895","count":9},{"id":"GO:0035036","count":9},{"id":"GO:1903494","count":9},{"id":"GO:0007342","count":9},{"id":"GO:1903496","count":9}]},{"hash":"1086842083575778239","title":"Dopamine/Adrenergic GPCR\u2013cAMP Signaling","description":"These terms indicate GPCR-driven signaling via dopamine/adrenergic receptors that activates cAMP and PLC pathways, with links to heart/skeletal development and sensory phototransduction; thus the cluster likely comprises components of dopaminergic/adrenergic GPCR signaling and downstream effectors.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060158","count":10},{"id":"GO:0043547","count":10},{"id":"GO:0043950","count":10},{"id":"GO:0071880","count":10},{"id":"GO:0007507","count":10}]},{"hash":"2017533098270657390","title":"Diverse small-molecule metabolism","description":"The top GO terms cluster around metabolism of various small molecules, including catabolic (beta-ketoadipate, uracil, prostaglandin) and biosynthetic processes (PHB, alkaloids, antibiotics). This pattern suggests a broad suite of metabolic pathways rather than a single cohesive function, so a concise label like \u201cDiverse small-molecule metabolism\u201d fits best.","confidence":"Medium","size":10,"edges":17,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042952","count":6},{"id":"GO:2000124","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0010223","count":4},{"id":"GO:0055114","count":4}]},{"hash":"6332762403083726","title":"Secretory Vesicle Trafficking","description":"The top GO terms cluster around vesicle transport and secretion (ER to Golgi vesicle transport, protein secretion, vesicle-mediated transport), indicating a group of proteins primarily involved in the secretory pathway. Some terms touch on apoptotic-cell clearance and neural/muscle development, suggesting vesicle-related roles in membrane remodeling and differentiation, but the dominant signal is secretion/vesicle transport.","confidence":"Medium","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0009306","count":1},{"id":"GO:0016192","count":1},{"id":"GO:0043652","count":1},{"id":"GO:0070782","count":1}]},{"hash":"720009179107745455","title":"Inflammatory lipid signaling in macrophages","description":"This cluster centers on macrophage-related inflammatory and lipid pathways: leukotriene biosynthesis, cytokine production (IL-8 and IL-1), foam cell differentiation, and lipid remodeling (phospholipid acyl-chain remodeling) with ERK1/ERK2 cascade activation and positive regulation of phospholipase activity. Together, these terms point to activated macrophage inflammatory responses linked to lipid metabolism, as seen in atherosclerotic contexts. ","confidence":"High","size":10,"edges":33,"triangles":62,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0070374","count":9},{"id":"GO:0019370","count":8},{"id":"GO:0044240","count":8},{"id":"GO:0010518","count":8},{"id":"GO:0045740","count":8}]},{"hash":"49222927302919232","title":"Bacterial metabolite biosynthesis","description":"The cluster includes GO terms for siderophore biosynthesis, menaquinone biosynthesis, lipoteichoic acid biosynthesis, nonribosomal peptide biosynthesis, and other bacterial metabolic processes (pyruvate fermentation to acetate, bile acid metabolism, malonate catabolism, bioluminescence, medium-chain fatty-acyl-CoA metabolism). Taken together, these terms point to a theme of prokaryotic biosynthetic pathways and metabolism, including production of specialized metabolites and cell-wall components, plus energy metabolism. Therefore, the label reflects a coherent bacterial biosynthesis/metabolism cluster.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0008206","count":10},{"id":"GO:0019654","count":10},{"id":"GO:0070395","count":10},{"id":"GO:0043041","count":10},{"id":"GO:1902987","count":10}]},{"hash":"690716645805102085","title":"Photoreceptor Synaptic Signaling","description":"This cluster is dominated by GO terms tied to neural signaling and vision: excitatory postsynaptic potential, visual perception, and regulation of synaptic vesicle exocytosis. Calcium ion transmembrane transport supports Ca2+-dependent signaling in neurons, including photoreceptors, which aligns with a visual system function. A few terms about adipocyte differentiation are present but appear less central to the main theme, so the label focuses on vision-related neuronal communication.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0070588","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007275","count":2}]},{"hash":"768855183223493021","title":"Cardiac Membrane Potential and Potassium Transport","description":"The top GO terms cluster around regulation of resting membrane potential, potassium ion transport/homeostasis, and cardiac action potentials, including heart rate regulation and atrial repolarization, which together point to cardiac electrophysiology and potassium handling. A couple of terms related to neural development or mechanosensory detection appear as peripheral notes, but the core signal is consistent with cardiac membrane potential control and potassium transport.","confidence":"High","size":10,"edges":34,"triangles":66,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0098914","count":10},{"id":"GO:0060075","count":9},{"id":"GO:0050976","count":9},{"id":"GO:0030007","count":8},{"id":"GO:0071805","count":8}]},{"hash":"239246473959569842","title":"Motor neuron development and myelination","description":"The top GO terms cluster around motor neuron differentiation, myelination, axon diameter regulation, and skeletal muscle fiber development, pointing to neuromuscular development and axon\u2013glia interactions. Additional terms about ER-Golgi transport and protein catabolic processes reflect general cellular maintenance that supports these developmental processes. The apoptotic-cell engulfment terms may reflect related developmental clearance activities but are less central. Overall, the dominant signals indicate a neuromuscular development theme.","confidence":"Medium","size":10,"edges":39,"triangles":80,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043652","count":2},{"id":"GO:0070782","count":2},{"id":"GO:0010961","count":2},{"id":"GO:0031133","count":2},{"id":"GO:0042552","count":2}]},{"hash":"1115510985803536687","title":"Yeast pseudohyphal growth and secretory trafficking","description":"This cluster's GO terms cluster around filamentous growth responses to nutrient limitation (invasive growth, pseudohyphal growth) and key components of the secretory pathway (ER exit, Golgi retention, cell surface localization) plus related lipid biosynthesis and septation. These together suggest a yeast/fungal morphogenesis program linked to vesicle trafficking and cell division. ","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0033299","count":2},{"id":"GO:0070863","count":2},{"id":"GO:0007124","count":2},{"id":"GO:0061060","count":2}]},{"hash":"121490322343407519","title":"Phospholipid Biosynthesis and Fatty Acid Transport","description":"This cluster is dominated by GO terms for biosynthesis of membrane phospholipids (phosphatidylserine, phosphatidylethanolamine, and phosphatidylglycerol) and for fatty acid movement related to peroxisomes, indicating a coherent theme around lipid production and lipid-associated transport. A few non-lipid terms appear, but the lipid biosynthesis/transport signal is strong and representative of the cluster's function.","confidence":"High","size":10,"edges":42,"triangles":99,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006659","count":5},{"id":"GO:1905711","count":5},{"id":"GO:0006663","count":5},{"id":"GO:0010512","count":5},{"id":"GO:0070317","count":5}]},{"hash":"999343836256727525","title":"Innate immune signaling and cell adhesion","description":"The top GO terms are dominated by innate immune response and defense against bacteria, with additional enrichment for cell\u2013cell adhesion and signaling pathways (including ROBO signaling and juxtaparanode axon localization). This suggests a theme of signaling and adhesion processes that operate in immune contexts as well as in neural/tissue interactions, rather than a single cohesive pathway. Confidence: Medium","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0042742","count":3},{"id":"GO:0031665","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0014068","count":2}]},{"hash":"1964217188094360312","title":"Yeast nucleophagy and selective autophagy","description":"The top GO terms cluster around selective autophagy processes in yeast, including piecemeal microautophagy of the nucleus, mitophagy, and the cytoplasm-to-vacuole targeting (Cvt) pathway, with mentions of nucleophagy stages. This points to a cohesive theme of nucleus- and organelle-specific autophagy, rather than generic cellular processes. Some additional terms relate to specialized enzyme activities, but they don\u2019t override the central autophagy-focused theme.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034727","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0006501","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0044805","count":2}]},{"hash":"190645431126720036","title":"Synaptic signaling and actin cytoskeleton remodeling","description":"The cluster is driven by GO terms like actin cytoskeleton organization and regulation of Rho GTPase signaling, with protein localization to synapse and receptor signaling pathways indicating neuronal signaling and cytoskeletal remodeling at synapses. Behavioral terms such as grooming and exploration hint at a neural circuit\u2013level role, and serotonin uptake regulation further supports a synaptic neurotransmission focus. Overall, the proteins likely coordinate synaptic signaling with actin dynamics in neurons.","confidence":"High","size":9,"edges":20,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":3},{"id":"GO:0090630","count":3},{"id":"GO:2000821","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0015879","count":2}]},{"hash":"438274641737564528","title":"Unknown","description":"The GO terms here cover a wide range of distinct cellular processes\u2014endocytosis regulation, ER-associated ubiquitin-dependent degradation, DNA repair, innate immune signaling, neurotransmitter release, nuclear pore transport, ribosome assembly, and chromatin methylation. There isn\u2019t a single cohesive theme that ties these functions together, so a specific, intuitive label isn\u2019t justifiable.","confidence":"","size":9,"edges":30,"triangles":49,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1900186","count":8},{"id":"GO:1903071","count":8},{"id":"GO:0070911","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0043433","count":8}]},{"hash":"163592772099560227","title":"Neural development and transcriptional regulation","description":"The terms cluster around neural development and differentiation (neural tube formation, oligodendrocyte differentiation, somatic stem cell maintenance) and transcriptional control (DNA-templated transcription, negative regulation of transcription by RNA Pol II), with supportive signals like Wnt pathway modulation and cell migration. This suggests a module of developmentally regulated gene expression in neural lineages, justifying the label. ","confidence":"Medium","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045819","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0097350","count":4},{"id":"GO:0035019","count":4}]},{"hash":"348444868500837766","title":"Embryonic development and transcriptional regulation","description":"The top GO terms cluster around negative regulation of RNA polymerase II transcription and key developmental processes (in utero embryonic development, ventral cord development, follicle cell of egg chamber stalk formation) with a noticeable stress response (cellular response to hydrogen peroxide). This suggests proteins that coordinate gene expression programs during development, possibly modulated by oxidative stress. Some terms relate to obsolete or more specific pathways, but the central theme appears to be developmental regulation linked to transcriptional control.","confidence":"Medium","size":9,"edges":23,"triangles":25,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0070301","count":6},{"id":"GO:0001701","count":6},{"id":"GO:1901253","count":5},{"id":"GO:0030713","count":5}]},{"hash":"2147180159149371120","title":"Cytoskeletal Regulation and Muscle Function","description":"Most enriched GO terms point to actin cytoskeleton dynamics (actin crosslink formation; cytoskeleton-dependent cytoplasmic transport) and muscle-related processes (regulation of heart contraction; regulation of muscle relaxation). Additional terms touch vesicle trafficking linked to secretion (insulin secretion) and transcription factor localization/regulation, which can be connected to cytoskeletal control of signaling and gene expression. The converging theme is proteins that coordinate the cytoskeleton to drive muscle function and related regulatory pathways.","confidence":"Medium","size":9,"edges":30,"triangles":57,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042994","count":8},{"id":"GO:0098735","count":8},{"id":"GO:0010842","count":8},{"id":"GO:0035774","count":8},{"id":"GO:0035191","count":8}]},{"hash":"1456930573083748123","title":"Neural development and axon guidance","description":"This cluster is dominated by terms associated with neural development and axon pathfinding (fasciculation of sensory neuron axon, axial mesoderm formation, visual learning) and intersects with broader signaling and protein regulation processes (receptor clustering, MAPK/JNK regulation, ubiquitin-dependent degradation). The overarching theme is neural development and axon guidance with ancillary regulatory functions.","confidence":"Medium","size":9,"edges":31,"triangles":56,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":9},{"id":"GO:0048320","count":9},{"id":"GO:0097155","count":9},{"id":"GO:0032092","count":9},{"id":"GO:0008542","count":9}]},{"hash":"893377900809734059","title":"Developmental morphogenesis and organogenesis","description":"The proteins cluster around broad developmental processes across tissues: heart (ventricular septum development), airway/respiratory system morphogenesis, eye development, neural patterning (rhombomere boundary formation), and signaling modulation (BMP sequestration, angiogenesis regulation). The mix of differentiation, morphogenesis, and signaling GO terms suggests a cohesive theme of organ and tissue development rather than a single tissue-specific function.","confidence":"High","size":9,"edges":23,"triangles":22,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0003281","count":8},{"id":"GO:0048754","count":8},{"id":"GO:0003016","count":8},{"id":"GO:0021654","count":8},{"id":"GO:0035582","count":8}]},{"hash":"1859866460454065740","title":"Leukocyte chemotaxis and phagocytosis","description":"This cluster shows strong representation of granulocyte/monocyte chemotaxis, neutrophil clearance, and phagocytosis, pointing to immune cell recruitment and engulfment activities. A few terms related to cytoskeletal dynamics support migration, while some others may be incidental noise (e.g., keratinocyte differentiation, metal ion responses).","confidence":"Medium","size":9,"edges":5,"triangles":1,"max_degree":2,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0031532","count":5},{"id":"GO:0097350","count":4},{"id":"GO:0030216","count":4},{"id":"GO:0071284","count":3},{"id":"GO:0099132","count":3}]},{"hash":"2214811688459764007","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"This cluster centers on actin organization and dynamic remodeling, including cortical actin localization, crosslinking, and protrusive structures like lamellipodia and microspikes, driven by Rho signaling and associated with cell adhesion and polarity. These features collectively point to cytoskeletal rearrangements that enable cell movement and shape changes, making the label representative of the core function despite a few outlier terms.","confidence":"High","size":9,"edges":8,"triangles":4,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051666","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0007155","count":5},{"id":"GO:0071963","count":5},{"id":"GO:1900042","count":5}]},{"hash":"1485211892340643019","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":28,"triangles":42,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034414","count":1},{"id":"GO:0098789","count":1},{"id":"GO:0017001","count":1},{"id":"GO:0034247","count":1},{"id":"GO:0046929","count":1}]},{"hash":"1003225134752404160","title":"Ribosome and translation machinery","description":"The strongest terms are translation and ribosomal small subunit assembly, pointing to proteins involved in protein synthesis and ribosome biogenesis. While a few regulatory or obsolete terms appear, the dominant signal ties to core translation machinery, suggesting this cluster groups ribosomal components or factors supporting translation.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000028","count":4},{"id":"GO:1900186","count":3},{"id":"GO:1903071","count":3},{"id":"GO:0030433","count":3}]},{"hash":"572392030961527789","title":"Immune differentiation and signaling","description":"This cluster is dominated by immune-related functions: B cell receptor signaling, type 2 immune response, and regulation of T cell differentiation and mast cell cytokine production. A few terms refer to circadian rhythm, muscle, and reproductive development, or other processes, which are likely peripheral annotations. Overall, the core signal points to immune cell differentiation and signaling as the defining theme.","confidence":"Medium","size":9,"edges":12,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1900477","count":3},{"id":"GO:0045497","count":2},{"id":"GO:0048741","count":2},{"id":"GO:2000176","count":2},{"id":"GO:0045496","count":2}]},{"hash":"2144696200944032344","title":"Drosophila Development and Morphogenesis","description":"The terms cluster around Drosophila embryonic/larval morphogenesis and tissue patterning, with clear signals from dorsal closure, ring canal formation, wing hair organization, and compound eye photoreceptor development. While there are also broader regulatory terms (centrosome cycle, transport, dephosphorylation, xenobiotic response), the developmental/morphogenetic themes are most prominent.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:1904059","count":2},{"id":"GO:0007391","count":1},{"id":"GO:0030725","count":1},{"id":"GO:0007098","count":1}]},{"hash":"1497191598691418477","title":"Chromatin Regulation & DNA Damage Response","description":"The terms converge on chromatin modification (deneddylation/desumoylation, regulation of chromatin binding) and DNA damage/replication-associated processes (translesion synthesis, kinetochore regulation), with additional signals pointing to development. This suggests a cluster centered on chromatin dynamics connected to DNA damage response and cell cycle control, rather than a single specific pathway. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904333","count":2},{"id":"GO:0032875","count":2},{"id":"GO:0035562","count":2},{"id":"GO:0000338","count":2},{"id":"GO:0090234","count":2}]},{"hash":"710335072363611936","title":"RNA and protein methylation","description":"This cluster is dominated by methylation-related GO terms across substrates: tRNA and rRNA methylation, RNA capping, and protein/peptidyl-arginine methylation, with some histone methylation references. It suggests a cohesive group of methyltransferases and RNA modification pathways.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":5},{"id":"GO:0070476","count":5},{"id":"GO:0006479","count":4},{"id":"GO:0043985","count":3},{"id":"GO:0019919","count":3}]},{"hash":"407894869163315506","title":"Cellular stress response and transport regulation","description":"Top GO terms center on oxidative and light-induced stress (hydrogen peroxide, high light, UV-A, gamma radiation) and on intracellular transport regulation (anterograde axonal transport; negative regulation of intracellular transport), with related growth, aging, and protein oligomerization control. This suggests a theme of stress signaling combined with regulation of intracellular processes rather than a single, cohesive pathway.","confidence":"Medium","size":9,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":7},{"id":"GO:0032355","count":6},{"id":"GO:0009644","count":5},{"id":"GO:0099641","count":5},{"id":"GO:0032463","count":5}]},{"hash":"851179579760392145","title":"Unknown","description":"The GO terms span diverse areas (angiogenesis, chromatin/centromere cohesion, various acetylation and metabolic processes, plant development, and even bacterial biosynthesis), with little coherent overlap to tie all proteins to a single function. While some terms hint at acetylation-related regulation, others are unrelated, so a unified, specific label isn\u2019t supported.","confidence":"","size":9,"edges":14,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":4},{"id":"GO:0006348","count":4},{"id":"GO:0019491","count":3},{"id":"GO:0032920","count":3},{"id":"GO:0030187","count":3}]},{"hash":"1196152776565707427","title":"Ubiquitin-Dependent Proteostasis and Immune Signaling","description":"The cluster is dominated by ubiquitination-related terms (polyubiquitination, K6-linked ubiquitination) and ubiquitin-dependent degradation (ERAD), which point to protein turnover and stress responses including apoptosis. There are immune-related terms (defense response to virus, V(D)J recombination) and some signaling-related processes (Wnt receptor catabolic process), but the strongest link among terms is ubiquitin-mediated proteostasis impacting immune signaling. ","confidence":"Medium","size":9,"edges":5,"triangles":2,"max_degree":3,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0000209","count":5},{"id":"GO:0061087","count":5},{"id":"GO:0034454","count":4},{"id":"GO:0051607","count":4}]},{"hash":"196803791975577144","title":"Auditory synaptic signaling and plasticity","description":"GO terms point to neuronal communication and plasticity in hearing and vocalization (sensory perception of sound, neurotransmitter secretion, dendritic spine morphogenesis, synapse structural plasticity, LTD, and excitatory post-synaptic potential regulation). JNK signaling further supports activity-dependent synaptic changes.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"vesicle-mediated transport","top_go_terms":[{"id":"GO:0007605","count":6},{"id":"GO:0035176","count":5},{"id":"GO:0060292","count":5},{"id":"GO:0043507","count":5},{"id":"GO:2000463","count":5}]},{"hash":"781111734879102957","title":"Centromere Assembly and Mitotic Chromosome Segregation","description":"The dominant GO terms\u2014CENP-A\u2013containing chromatin assembly, mitotic cell cycle, mitotic sister chromatid segregation, and cell division\u2014point to a cohesive set of proteins involved in centromere function and chromosome segregation during mitosis. Other terms like ER transport and photoreceptor development appear ancillary, but do not contradict the main mitotic theme.","confidence":"High","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061641","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0000070","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1053596905069598707","title":"Hormone signaling and development","description":"Many of the top GO terms point to hormone-related biology and developmental processes: regulation of Rap signaling and GTPase activity reflects core signal transduction; insulin secretion and steroid hormone receptor complex assembly indicate endocrine signaling; male sex differentiation, prostate gland development, and ventricular system development reflect developmental outcomes influenced by hormones. A transcriptional (DNA-templated transcription) and immune (type I interferon) components are present but appear secondary to the hormone-development theme.","confidence":"Medium","size":9,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0030073","count":2},{"id":"GO:0071357","count":1}]},{"hash":"1605512592292377849","title":"TGF-\u03b2/BMP Signaling Regulation","description":"This cluster centers on regulation of TGF-\u03b2/BMP-type signaling, including positive/negative regulation of TGF-\u03b2 receptor signaling, BMP signaling, and downstream responses (cellular response to TGF-\u03b2 stimulus, SMAD-related processes). There are also components related to signaling modulation such as peptidyl-threonine dephosphorylation and NF-kappaB regulation, plus developmental contexts (meristem identity, germ-line masculinization) that reflect broader developmental signaling control. Overall, the common theme is modulation of TGF-\u03b2/BMP signaling pathways and their developmental consequences.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0061191","count":6},{"id":"GO:0071560","count":6},{"id":"GO:0010991","count":6},{"id":"GO:0042006","count":6},{"id":"GO:0042347","count":6}]},{"hash":"107574360534168161","title":"Cytoskeletal remodeling and cell migration","description":"This cluster shows a clear emphasis on cytoskeletal organization and movement, with terms like cortical microtubule organization, actin cortical patch assembly, and lamellipodium assembly highlighting cytoskeletal dynamics essential for cell migration. Other terms touch on signaling and development, but the dominant theme ties to how the cytoskeleton is remodeled to drive movement and shape changes. ","confidence":"Medium","size":9,"edges":24,"triangles":36,"max_degree":8,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0002369","count":7},{"id":"GO:0043622","count":7},{"id":"GO:0030702","count":7},{"id":"GO:0015879","count":7},{"id":"GO:0002051","count":7}]},{"hash":"833296744322344091","title":"TLR2-NF-\u03baB Mediated Innate Immune Activation","description":"The top GO terms center on innate immune sensing and signaling: TLR2 signaling, detection of diacylated bacterial lipoproteptides, macrophage activation, defense against virus, and regulation of IL-6 production via the non-canonical NF-\u03baB pathway, indicating a cohesive innate immune\u2013activation cluster. Some terms appear peripheral (e.g., bone morphogenesis, lysosomal pH), likely incidental to the core immune function.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045410","count":9},{"id":"GO:0006469","count":9},{"id":"GO:0042346","count":9},{"id":"GO:0051607","count":9},{"id":"GO:0034134","count":9}]},{"hash":"841456566809468378","title":"Heart development and embryonic morphogenesis","description":"The top GO terms cluster around atrial cardiac muscle morphogenesis and epithelial-to-mesenchymal transition involved in endocardial cushion formation, plus SMAD/TGF-\u03b2 signaling, all pointing to cardiac development and morphogenesis. Additional terms touch on broader embryonic processes like blastocyst formation and follicle growth, suggesting a wider embryogenesis theme; a few terms (dopamine uptake, acrosomal exocytosis) are more peripheral and not central to the main theme. Overall, the cluster seems best described as developmental/morphogenetic processes, especially heart formation.","confidence":"Medium","size":9,"edges":30,"triangles":53,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055009","count":3},{"id":"GO:1905007","count":3},{"id":"GO:0060389","count":3},{"id":"GO:0003198","count":3},{"id":"GO:0051584","count":2}]},{"hash":"2211983194425216230","title":"Nucleotide metabolism and phosphorylation","description":"The top GO terms are dominated by phosphorylation (and dephosphorylation) events and various nucleotide/cofactor biosynthesis pathways (ADP, NAD+, coenzyme A), suggesting a cluster of proteins involved in energy and nucleotide metabolism regulated by phosphorylation. Some terms like DNA repair and viral process appear but are less central to the main theme. Confidence reflects this overall alignment with nucleotide metabolism and phosphorylation rather than a single focused function.","confidence":"Medium","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016310","count":8},{"id":"GO:0015937","count":6},{"id":"GO:0006281","count":5},{"id":"GO:0016032","count":5},{"id":"GO:0016311","count":5}]},{"hash":"1304793864329289804","title":"Complement and Inflammatory Signaling","description":"The cluster is enriched for innate immune and inflammatory pathways: classical and lectin complement activation, Toll signaling regulation, and IL-1\u03b2 production, plus Factor XII activation, indicating coagulation\u2013complement cross-talk. Additional terms like Wnt signaling and angiogenesis point to inflammation-associated vascular remodeling. Atrial natriuretic peptide\u2013related blood pressure regulation is present but peripheral to the main theme. Together, these terms suggest a cohesive group of proteins involved in innate immune activation and inflammatory signaling affecting vascular biology.","confidence":"Medium","size":9,"edges":24,"triangles":21,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":5},{"id":"GO:0001867","count":4},{"id":"GO:0003050","count":4},{"id":"GO:0045766","count":4},{"id":"GO:0042127","count":3}]},{"hash":"1600415802115163180","title":"Neural signaling for movement and circadian regulation","description":"Top GO terms cluster around dopaminergic and acetylcholine-mediated synaptic signaling, action potential generation, and motor-related behaviors (locomotory behavior, righting reflex), with additional ties to nicotine response and circadian regulation of sleep/wake cycles and neural control of respiration. This points to a cohesive set of proteins involved in CNS signaling that coordinates movement and circadian aspects of behavior. ","confidence":"High","size":9,"edges":16,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032226","count":6},{"id":"GO:0045188","count":6},{"id":"GO:0060013","count":6},{"id":"GO:0002087","count":6},{"id":"GO:1901214","count":6}]},{"hash":"505638618955388719","title":"Tissue development and morphogenesis","description":"The top GO terms span development and organ formation across multiple tissues (thymus, lacrimal gland, fat tissue, keratinocytes, fin morphogenesis, brain regions, lung mesenchyme), with several terms referring to proliferation or differentiation rather than a single pathway. This suggests the cluster reflects a broad developmental/differentiation theme rather than a specific process.","confidence":"Medium","size":9,"edges":16,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070858","count":2},{"id":"GO:0043616","count":2},{"id":"GO:0031659","count":2},{"id":"GO:0060128","count":2},{"id":"GO:0070352","count":2}]},{"hash":"574569734154364586","title":"Developmental ECM and EMT signaling proteins","description":"This cluster centers on embryonic development and extracellular matrix organization, highlighted by collagen fibril organization, somite and craniofacial (roof of mouth) development, and epithelial-mensenchymal signaling. While there are a few broader or immune-related terms (e.g., complement pathways, synapse assembly), the dominant theme is developmental processes tied to ECM remodeling and EMT. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":4},{"id":"GO:0061053","count":3},{"id":"GO:0060021","count":3},{"id":"GO:0051965","count":3},{"id":"GO:0008585","count":2}]},{"hash":"782636068583966542","title":"Lipid metabolism and lipoprotein regulation","description":"The top GO terms are dominated by lipid-related processes: triglyceride and diacylglycerol biosynthesis, lipid storage, intracellular lipid homeostasis, and regulation of plasma lipoprotein particle levels, including LDL particle clearance and intestinal lipid absorption. A couple terms (wax biosynthetic process, phytol metabolic process) are less central, but the overall pattern strongly supports a cluster of proteins involved in lipid synthesis, storage, and lipoprotein handling.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010025","count":1},{"id":"GO:0097006","count":1},{"id":"GO:0060613","count":1},{"id":"GO:0034383","count":1},{"id":"GO:0006651","count":1}]},{"hash":"146249970148114131","title":"Opsin GPCR Signaling and Internalization","description":"This cluster is dominated by GO terms for phototransduction, regulation of opsin signaling, and GPCR/internalization, pointing to light-sensing GPCR pathways and receptor trafficking as the common theme. Peripheral terms like stress fiber assembly and fat pad development are less central.","confidence":"Medium","size":9,"edges":19,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043149","count":5},{"id":"GO:0032226","count":3},{"id":"GO:0060613","count":3},{"id":"GO:0002092","count":3},{"id":"GO:0007602","count":3}]},{"hash":"1571445125558978978","title":"Unknown","description":"The top GO terms are very heterogeneous, spanning liver development, proteoglycan biosynthesis, inositol and LBPA metabolism, phosphate starvation and anoxia responses, and neural growth. There isn\u2019t a single, coherent functional theme tying the cluster together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":9,"edges":13,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":2},{"id":"GO:0006144","count":1},{"id":"GO:2001311","count":1},{"id":"GO:0016036","count":1},{"id":"GO:0050650","count":1}]},{"hash":"2053987962823846699","title":"Plant cell wall biogenesis and mucilage glycosylation","description":"Based on the prominent plant-cell-wall\u2013related terms: plant-type secondary cell wall biogenesis, mucilage biosynthetic process, and various polysaccharide biosynthesis (glucuronoxylan, homogalacturonan) along with protein O-linked glycosylation, the proteins appear focused on building and modifying the plant cell wall, especially mucilage-associated components. This supports a cohesive label centered on plant cell wall biosynthesis and mucilage glycosylation.","confidence":"High","size":9,"edges":28,"triangles":42,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0016266","count":3},{"id":"GO:0043403","count":2},{"id":"GO:0035269","count":2},{"id":"GO:0009834","count":2}]},{"hash":"2104138362842290290","title":"Endothelial angiogenesis and signaling","description":"The terms cluster around angiogenesis, hypoxia response, and endothelial cell proliferation, with supporting roles for cytoskeletal remodeling (actin polymerization), junction organization, and signaling pathways (DAG production, PKB/AKT activation). Collectively, these functions point to endothelial-driven vessel formation and proliferative signaling under low-oxygen conditions, justifying a focused label of endothelial angiogenesis and signaling.","confidence":"High","size":9,"edges":11,"triangles":3,"max_degree":6,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0001525","count":8},{"id":"GO:0001666","count":8},{"id":"GO:0001938","count":7},{"id":"GO:0007202","count":7},{"id":"GO:0032148","count":7}]},{"hash":"1222147317459455644","title":"Cardiac and vascular smooth muscle regulation","description":"This cluster is dominated by terms tied to muscle structure and function in heart and vessels, such as sarcomere organization, cardiac muscle contraction, and heart-rate regulation by epinephrine, plus negative regulation of vascular smooth muscle cell migration/proliferation. A few developmental terms appear (axon guidance, epithelial morphogenesis) but are far less represented. Overall, the strongest signal points to sarcomere assembly and regulation of cardiac/vascular muscle activity.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1904753","count":9},{"id":"GO:1904706","count":9},{"id":"GO:0045214","count":9},{"id":"GO:0034609","count":9},{"id":"GO:0060298","count":9}]},{"hash":"1102306837892429656","title":"Taste and Pheromone Sensing via GPCRs","description":"The dominant GO terms point to sensory perception of chemical stimuli (taste and bitter taste) and pheromone detection, coupled with GPCR signaling pathways (including adenylate cyclase-activating GPCR signaling). While a few terms relate to electron transport or blood pressure, the central theme is chemical sensing via GPCR-mediated signaling, justifying this label as representative of the cluster.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007606","count":5},{"id":"GO:0019236","count":5},{"id":"GO:0001580","count":5},{"id":"GO:0050909","count":5},{"id":"GO:0035025","count":4}]},{"hash":"359832236041416678","title":"Cell Cycle Regulation and Differentiation","description":"The terms are dominated by processes governing the cell cycle and its regulation (cell division, regulation of cell cycle, CDK activity) along with differentiation of specific lineages (guard mother cell, multi-ciliated epithelial cells, syncytial blastoderm mitotic cycle). A few outliers (response to leptin or X-ray, host-mediated suppression of viral replication) are present, but the core theme centers on cell-cycle control and developmental differentiation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044321","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0044828","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0010444","count":1}]},{"hash":"149110655516270741","title":"Neuronal signaling and photoreception","description":"This cluster is driven by neural and visual-related functions: visual perception, photoreceptor maintenance, and regulation of AMPA receptors, along with synaptic vesicle transport. GPI anchor biosynthesis may support membrane receptors, while autophagy and apoptotic pathway terms point to cellular stress responses that can intersect neuronal health. The combination suggests a coherent theme around neuronal communication and vision, with some broader cell-stress processes accompanying them.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":3},{"id":"GO:0010506","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0042771","count":2},{"id":"GO:1902230","count":2}]},{"hash":"211422039483751281","title":"Glycosylation and lipoteichoic acid biosynthesis","description":"The top GO terms are dominated by glycosylation-related processes: dolichol-linked oligosaccharide biosynthesis (N-linked glycosylation precursors), lipoteichoic acid biosynthetic process (cell envelope component in Gram-positive bacteria), and glucoside biosynthesis (quercetin and kaempferol O-glucosides), along with broader carbohydrate metabolism and xenobiotic-related glucuronidation. These suggest a cluster of glycosyltransferases and glycosylation pathways tied to cell-wall/lipid components and small-molecule glycosylation, with additional links to antibiotic biosynthesis. Overall, a cohesive theme of glycosylation-related biosynthetic activities.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0030259","count":7},{"id":"GO:0070395","count":7},{"id":"GO:0005975","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0016999","count":7}]},{"hash":"1881724780760163530","title":"Neural memory and synaptic plasticity","description":"This cluster is strongly linked to neural processes, with multiple GO terms about memory (short-term memory, memory) and long-term synaptic potentiation, indicating a learning/plasticity role. While there are some non-neural terms (cardiac contraction regulation, various developmental processes) in the mix, the most frequent and coherent theme centers on neural signaling and synaptic strength modulation.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007614","count":4},{"id":"GO:0007613","count":3},{"id":"GO:0098735","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0071456","count":3}]},{"hash":"740491807416947484","title":"Dopaminergic Neuroimmune Signaling","description":"This cluster merges dopamine-related processes (transport, metabolism, PLC-activated receptor signaling) with immune and glial functions (immune response, astrocyte chemotaxis, eosinophil chemotaxis, neurotrophic factor regulation). The combination suggests a neuroimmune module where dopamine signaling modulates glial activity and inflammatory responses in the nervous system.","confidence":"High","size":9,"edges":19,"triangles":12,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":9},{"id":"GO:0042493","count":9},{"id":"GO:2000458","count":9},{"id":"GO:1900168","count":9},{"id":"GO:0048245","count":9}]},{"hash":"493612775138056100","title":"Flavonoid glycosylation and xenobiotic metabolism","description":"The cluster centers on flavonoid glycosylation (quercetin and kaempferol O-glucosides) and xenobiotic processing (glucuronidation), with broader links to related phenylpropanoid pathways (lignin) and detoxification responses (genistein, estrogen metabolism). This suggests a coherent role in modifying and detoxifying plant secondary metabolites and xenobiotics.","confidence":"Medium","size":8,"edges":7,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030259","count":3},{"id":"GO:0016999","count":3},{"id":"GO:0052697","count":3},{"id":"GO:0033303","count":3},{"id":"GO:0017000","count":3}]},{"hash":"1468723681863136306","title":"Cytoskeleton remodeling and cell migration","description":"This cluster is dominated by GO terms related to actin filament bundle assembly and cell migration, pointing to cytoskeletal dynamics as the core function. While there are also terms for telomere maintenance and cell cycle, the strongest signal ties to cytoskeletal remodeling and motility.","confidence":"Medium","size":8,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0006397","count":4},{"id":"GO:0045444","count":4}]},{"hash":"89811258029837486","title":"Membrane Transport and Xenobiotic Response","description":"The cluster includes GO terms tied to transport across membranes (amino acid transmembrane transport, long-chain fatty acid import into peroxisome, teichoic acid transport, cholesterol efflux, phytosterol absorption regulation) and to responses to xenobiotics (response to antibiotic, response to toxic substance, response to xenobiotic stimulus). The inclusion of a Type I secretion system term further emphasizes membrane-associated export, while abscisic acid transport adds a plant-transport aspect. Together, these terms point to a theme of transport processes linked to detoxification or stress responses.","confidence":"Medium","size":8,"edges":16,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0030253","count":3},{"id":"GO:0080168","count":3},{"id":"GO:0042493","count":3}]},{"hash":"1209733719767904075","title":"Nucleic acid metabolism and signaling pathways","description":"The cluster centers on core gene expression processes\u2014DNA replication, DNA-templated transcription, and mRNA processing\u2014indicating nucleic acid metabolism and transcriptional activity. It is complemented by signaling-related terms, such as cyclic nucleotide biosynthesis, Wnt signaling, and innate immune response, plus microtubule-associated localization, suggesting integration of expression machinery with broader signaling and transport functions.","confidence":"Medium","size":8,"edges":18,"triangles":22,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0009190","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0006397","count":3}]},{"hash":"1343388359647721347","title":"Ubiquitination-Driven Immune Signaling","description":"The top GO term is protein ubiquitination, and the remaining terms cluster around immune/inflammatory signaling (interferon production, IL-4 signaling, leukotriene biosynthesis, endothelin response) with additional growth factor signaling connections (PDGF receptor signaling, growth regulation). This suggests a unifying theme of ubiquitin-regulated signaling in immune/inflammatory contexts, with some overlap into growth-related pathways.","confidence":"Medium","size":8,"edges":23,"triangles":30,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0032481","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0019370","count":4},{"id":"GO:0040014","count":4}]},{"hash":"390542480427489193","title":"Inflammation-Driven Vascular and Cardiac Signaling","description":"The cluster is enriched for inflammatory response terms (cellular response to TGF-beta stimulus; cellular response to lipopolysaccharide; type II interferon production) and vascular permeability regulation, plus terms related to cardiac muscle relaxation/contraction and dopamine metabolism, suggesting an overarching theme of inflammatory signaling influencing vascular and cardiac function, with some peripheral tissue-specific processes (e.g., retinal development). Represents a cohesive inflammatory-cardiovascular signaling cluster, with some dual-role terms.","confidence":"Medium","size":8,"edges":21,"triangles":27,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":3},{"id":"GO:0071222","count":3},{"id":"GO:0043117","count":3},{"id":"GO:0046549","count":2},{"id":"GO:1903206","count":2}]},{"hash":"92958540706655850","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"Proteins in this cluster are enriched for actin cytoskeleton dynamics (lamellipodium assembly; actin reorganization) and cell migration, indicating a shared role in motility. The presence of signaling terms (PDGF receptor, PI3K/AKT) suggests coordinated growth-factor\u2013mediated cytoskeletal changes. Additional terms covering thymus development, IL-7 response, LPS signaling, neurotrophin signaling, and apoptosis imply integration of migration with broader developmental and immune signaling programs. Overall, the core theme is actin-driven cell movement tied to diverse signaling networks.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010641","count":5},{"id":"GO:0030032","count":5},{"id":"GO:2000251","count":5},{"id":"GO:0048538","count":5},{"id":"GO:0016477","count":5}]},{"hash":"174092969160574048","title":"Complement Activation and Immune Regulation","description":"The top terms cluster around the complement system (classical and lectin pathways), its activation and regulation, and related immune processes (leukocyte trafficking, IL-10 production, T cell apoptosis, MAC regulation). Proteolysis ties into complement proteases, supporting a theme of complement-mediated immunity and inflammatory control, with a few outliers likely due to broader roles or annotation noise.","confidence":"High","size":8,"edges":12,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":4},{"id":"GO:0001867","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0045743","count":2},{"id":"GO:0006924","count":2}]},{"hash":"148679286274536908","title":"Craniofacial skeletal development and angiogenesis","description":"The cluster\u2019s top GO terms center on skeletal system development, osteoblast and chondrocyte differentiation, and palate (roof of mouth) development, with BMP signaling and ERK cascades suggesting bone-related growth signaling, plus endothelial migration indicating coordinated vascularization during skeletogenesis. These together point to craniofacial bone formation coupled with angiogenesis.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0070374","count":8},{"id":"GO:0030513","count":8},{"id":"GO:0043536","count":8},{"id":"GO:0010763","count":8},{"id":"GO:0043537","count":8}]},{"hash":"2084374291100893812","title":"Forebrain Neuron Development and Migration","description":"The top GO terms show development of multiple brain regions (striatum, thalamus, olfactory bulb) and neuronal subtypes (pyramidal neurons), plus a tangential migration process from the SVZ to the olfactory bulb, indicating a cluster centered on neuronal development and positioning in the forebrain. Some metabolic terms appear but do not drive the overall theme.","confidence":"High","size":8,"edges":16,"triangles":14,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0021756","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0061034","count":3},{"id":"GO:0072756","count":3},{"id":"GO:0021860","count":3}]},{"hash":"1481986889822874040","title":"Rho-regulated actin cytoskeleton remodeling","description":"The terms cluster around actin dynamics and cytoskeletal organization mediated by Rho signaling, including sarcomere and actin patch assembly, Arp2/3\u2013regulated nucleation, and dendritic spine morphogenesis, pointing to a shared function in actin remodeling across cell types.","confidence":"High","size":8,"edges":6,"triangles":2,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":4},{"id":"GO:0045214","count":4},{"id":"GO:0071364","count":3},{"id":"GO:0000147","count":3},{"id":"GO:0030836","count":3}]},{"hash":"2142504951857452995","title":"Immune cell chemotaxis and phagocytosis with vesicle trafficking","description":"Top GO terms show granulocyte and monocyte chemotaxis, phagocytosis, and membrane trafficking (receptor localization, recycling, exocytosis regulation), indicating a cohesive theme of immune cell migration and engulfment with vesicle dynamics. A few metal ion response terms are present but do not define the core function.","confidence":"High","size":8,"edges":10,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071284","count":2},{"id":"GO:0099132","count":2},{"id":"GO:1905597","count":2},{"id":"GO:0071621","count":2},{"id":"GO:0001921","count":2}]},{"hash":"785055537612738972","title":"Neuronal cytoskeleton dynamics and signaling","description":"The cluster centers on actin cytoskeleton organization and polarity (actin cytoskeleton polarity establishment; dendrite morphogenesis), along with signaling pathways that regulate cytoskeletal remodeling (TORC2 signaling; stress-activated MAP kinase signaling; negative regulation of Ras signaling). Developmental aspects appear (dendrite morphogenesis; substantia nigra development), suggesting a role in neuronal differentiation and morphology. While there is an apoptosis/DNA damage term included, the dominant pattern ties to cytoskeleton-driven signaling in neuronal development.","confidence":"Medium","size":8,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":2},{"id":"GO:0008630","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0090134","count":2},{"id":"GO:0038203","count":2}]},{"hash":"1671429604226217741","title":"Embryonic development and organ morphogenesis","description":"Most GO terms cluster around developmental processes and organ formation, including roof-of-mouth development, left/right patterning, mesoderm development, placental/trophoblast differentiation, hair follicle morphogenesis, and endocrine/pancreatic organ development. A couple of terms relate to general cellular machinery (splicing and ribosomal export) but the dominant theme is embryonic development and morphogenesis.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0060707","count":3},{"id":"GO:0007498","count":3}]},{"hash":"599686612171503021","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (protein folding/isomerization, keratinocyte differentiation, cell cycle, various biosynthetic pathways for pteridines/BH4, tRNA queuosine biosynthesis, neuron apoptosis regulation, and synapse organization) with little cohesion. There is no single unifying function or pathway linking these proteins, so a specific, representative label cannot be inferred.","confidence":"","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000413","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006729","count":1},{"id":"GO:0006728","count":1}]},{"hash":"573256702651740835","title":"Transcription, Proteasomal Degradation, and Mitosis","description":"The cluster\u2019s top terms center on DNA-templated transcription, SCF-dependent proteasomal ubiquitin\u2011dependent protein degradation, and mitotic processes (cell cycle and microtubule-based movement). This suggests a core theme around transcriptional regulation coupled to proteostasis during cell division. Some developmental and defense terms appear but are less cohesive with the main signal, so the label reflects the strongest shared function among the proteins. ","confidence":"Medium","size":8,"edges":7,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0001501","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071276","count":3}]},{"hash":"1974305934081620844","title":"RNA Processing and Translation Machinery","description":"This cluster is enriched for translation-related GO terms (translation, translation initiation, formation of cytoplasmic translation initiation complex) and snoRNA processing/RNase MRP-dependent mRNA decay, pointing to RNA processing and ribosome biogenesis. A few terms relate to chromosome dynamics and protein degradation, suggesting broader cell-cycle and quality-control connections, but the dominant theme is RNA processing together with protein synthesis.","confidence":"Medium","size":8,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000294","count":2},{"id":"GO:0030261","count":2},{"id":"GO:0048235","count":2},{"id":"GO:0034965","count":2}]},{"hash":"255237301409694349","title":"mRNA Stability and Translation Regulation","description":"This cluster is dominated by terms about mRNA processing, stability, and control of translation initiation and silencing by miRNA and ncRNA, plus inclusion of splicing site recognition and translation preinitiation complex formation. The common theme is post-transcriptional regulation of gene expression, rather than transcriptional control, suggesting these proteins work together in mRNA maturation, stabilization, and translation regulation. The blastocyst formation term likely reflects developmental contexts where such regulation is critical; overall, the set points to a cohesive post-transcriptional regulatory module.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":8},{"id":"GO:0001825","count":8},{"id":"GO:0010610","count":8},{"id":"GO:0006446","count":8},{"id":"GO:1900363","count":8}]},{"hash":"229088375256432130","title":"Glutamatergic Synaptic Signaling in Brain","description":"This cluster is dominated by terms related to excitatory synaptic function and neuronal signaling (glutamatergic transmission, excitatory postsynaptic potentials, receptor clustering, and intracellular signaling), with contextual hints of brain development and learning (visual learning, pons maturation). A few terms (e.g., phenylalanine biosynthesis, oocyte maturation) are less aligned and may be annotation noise, but the core signal points to glutamatergic synaptic activity in neural circuits.","confidence":"High","size":8,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008542","count":7},{"id":"GO:0043113","count":7},{"id":"GO:0060079","count":7},{"id":"GO:0035249","count":7},{"id":"GO:0097011","count":7}]},{"hash":"1028011092280450684","title":"Vertebrate Skeletal Development and Growth Signaling","description":"This cluster is dominated by skeletal system development and morphogenesis terms, plus spinal cord development and multicellular growth, pointing to a core theme of vertebrate development and tissue growth. The TORC1 signaling term further supports a link to growth control in developing tissues. Some terms reflect stress responses (ERAD, cadmium) or cellular processes (phagolysosome assembly) that are less central to development, so the label focuses on the main developmental and growth-related signals.","confidence":"Medium","size":8,"edges":20,"triangles":26,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0071276","count":6},{"id":"GO:0035264","count":6},{"id":"GO:0038202","count":6},{"id":"GO:0021510","count":6}]},{"hash":"2080350770989685123","title":"Steroid hormone signaling in ovarian development","description":"The top GO terms point to ovarian development in Drosophila (germarium-derived cyst encapsulation, follicle cell formation) and steroid hormone processes (ecdysone biosynthesis, glucocorticoid response). This suggests a common theme of hormone-regulated reproductive development, despite a few stray terms (mitochondrial import, RNA localization, immune and telomere-related terms). Confidence: Medium","confidence":"Medium","size":8,"edges":17,"triangles":20,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030708","count":2},{"id":"GO:0030713","count":2},{"id":"GO:0006697","count":2},{"id":"GO:0051384","count":2},{"id":"GO:0045041","count":1}]},{"hash":"1715488586320104564","title":"Nuclear transcription and mRNA processing","description":"The top GO terms are dominated by mRNA processing and DNA-templated transcription, with a focus on transcription-coupled repair and mRNA regulatory processes, supporting a nuclear RNA metabolism theme. Some terms (innate immune response, righting reflex, nuclear cortical migration) appear ancillary or annotation noise, but do not redefine the core connection to transcription and RNA processing. Overall, the cluster seems best described by nuclear transcription and RNA processing functions with related post-transcriptional regulation.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0090502","count":2},{"id":"GO:0045087","count":2}]},{"hash":"554805861731000245","title":"Golgi-ER vesicle trafficking and synaptic exocytosis","description":"The cluster is dominated by GO terms related to ER-to-Golgi and intra-Golgi vesicle transport, SNARE complex assembly, and vesicle fusion with the Golgi, plus exocytic insertion of postsynaptic neurotransmitter receptors and links to synaptic potentiation. Together these point to a coherent role in secretory vesicle trafficking and synaptic exocytosis, with additional maturation steps like autophagy and oxidative stress response as ancillary processes. ","confidence":"High","size":8,"edges":25,"triangles":40,"max_degree":7,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0006891","count":5},{"id":"GO:0060291","count":5},{"id":"GO:0098967","count":5},{"id":"GO:0035493","count":5}]},{"hash":"222833531615292479","title":"Mitotic spindle and astral microtubule organization","description":"The GO terms cluster around microtubule-based processes in cell division and nuclear movement, including spindle assembly and metaphase/anaphase transition, astral microtubule organization, and various modes of nuclear migration (pronuclear, interkinetic) as well as dynein arm assembly and related development contexts (spermatid and cortex formation).","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036159","count":1},{"id":"GO:2000574","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0021987","count":1},{"id":"GO:0007091","count":1}]},{"hash":"1770583602666762406","title":"mRNA stability and translation regulation","description":"This cluster is dominated by GO terms tied to post-transcriptional control: mRNA stabilization, stress-related regulation of mRNA stability, regulation of translational initiation, translation preinitiation complex formation, translation reinitiation, splice site recognition, and RNA silencing via miRNA and regulatory ncRNAs. Together, these indicate a cohesive theme of RNA-level regulation of gene expression, spanning processing, stability, and initiation of translation, with silencing mechanisms contributing to translational control.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:0001825","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0006446","count":2},{"id":"GO:1900363","count":2}]},{"hash":"1288167629800258250","title":"Actin Cytoskeleton Dynamics","description":"The cluster is dominated by GO terms related to actin filament polymerization, organization, and the assembly of lamellipodia and filopodia, along with processes like dendritic spine morphogenesis and ruffle formation, pointing to actin cytoskeleton remodeling and protrusive structure formation as the shared function.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030041","count":7},{"id":"GO:0060997","count":7},{"id":"GO:0030032","count":6},{"id":"GO:0051016","count":6},{"id":"GO:0030036","count":6}]},{"hash":"192909433020579368","title":"Mitotic actin ring assembly and centrosome regulation","description":"The top GO terms cluster around mitotic cytoskeleton remodeling and centrosome control, including mitotic contractile ring actin filament bundle assembly, maintenance of centrosome location, and forebrain neuroblast division, suggesting a cohesive theme of cell division tied to cytoskeletal dynamics. Regulation of GTPase activity further supports signaling pathways that govern cytoskeletal organization. Some terms (thrombin receptor signaling, sensory perception of sound) are less directly related and likely peripheral, but the dominant pattern points to mitotic cytoskeleton regulation.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":3},{"id":"GO:0048633","count":2},{"id":"GO:1903477","count":2},{"id":"GO:0045769","count":2},{"id":"GO:0051661","count":2}]},{"hash":"2192559344932967365","title":"RNA Pseudouridine Synthesis","description":"The cluster is dominated by GO terms for pseudouridine synthesis across multiple RNA types (snRNA, rRNA, tRNA, mRNA) and general pseudouridine synthesis, indicating a shared function in RNA modification via pseudouridylation. While other terms (transcription, ER transport, replication) appear, the strongest signal ties to RNA pseudouridylation machinery.","confidence":"High","size":8,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0031120","count":1},{"id":"GO:0000455","count":1},{"id":"GO:1990481","count":1}]},{"hash":"1544531558897751612","title":"Actin Remodeling for Cell Protrusions and Migration","description":"The cluster centers on actin cytoskeleton dynamics, with GO terms highlighting Rac signaling, Arp2/3-mediated actin nucleation, lamellipodium and filopodium assembly, and dendritic spine morphogenesis. These refer to the reorganization of actin to drive membrane protrusions and cell movement across cell types, including immune and neural contexts; related terms about membrane trafficking and development further support a theme of protrusive cytoskeletal remodeling during morphogenesis and migration.","confidence":"High","size":8,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007121","count":4},{"id":"GO:0060997","count":4},{"id":"GO:2000402","count":4},{"id":"GO:1903526","count":4},{"id":"GO:0002625","count":4}]},{"hash":"465150624022030497","title":"Glutamatergic Synapse Regulation","description":"The cluster is driven by GO terms related to excitatory neurotransmission, including NMDA receptor clustering and AMPA receptor activity, along with signaling that modulates dendritic spine structure via Rac/Rho pathways. This points to regulation of glutamatergic synapses and synaptic plasticity, which also connects to behavioral aspects like social behavior and fear responses. Some terms (apoptotic process, endothelial tube extension, LPS-mediated signaling) appear less central and may reflect pleiotropy or annotation noise. Overall, the label captures the core theme of excitatory synaptic signaling and plasticity.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0035021","count":2},{"id":"GO:0035024","count":2},{"id":"GO:0031666","count":2},{"id":"GO:0035176","count":2}]},{"hash":"60634519473192496","title":"Unknown","description":"The GO terms span insect cuticle pigmentation, alkaloid metabolism and alkaloid response, neurotransmitter loading, plant defense compounds, reproductive luteinization, thermotaxis, pH changes, and aging, with no single cohesive biological function tying them together.","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042412","count":7},{"id":"GO:0051454","count":7},{"id":"GO:0015842","count":7},{"id":"GO:0048085","count":7},{"id":"GO:0001553","count":7}]},{"hash":"1619408597899815152","title":"Actin Remodeling and Cell Migration in Epithelium and Vasculature","description":"The cluster is driven by GO terms for actin filament bundle assembly and cell migration, and includes terms related to epithelial cell polarity and endothelial cell behavior, pointing to cytoskeletal remodeling guiding movement and tissue architecture in epithelial and vascular contexts. Some telomere-related terms appear unrelated and may be annotation noise, while a term touching cardiac cell excitability hints at broader motility/polarity changes in muscle contexts rather than a core function. Overall, the dominant theme is actin-driven remodeling enabling migration and polarity in multicellular tissues.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0032212","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0016477","count":4}]},{"hash":"488590054793850238","title":"RNA transcription and translation regulation","description":"The cluster shows strong representation of initiation and reinitiation of translation, translation initiation regulation, DNA-templated transcription, and mRNA stability/regulation, pointing to a core theme of gene expression control at both transcriptional and translational levels. A couple of development-related terms appear (skeletal morphogenesis, blastocyst formation, prostate gland development), which may reflect broader roles in development but do not override the primary RNA-centric signal.","confidence":"Medium","size":8,"edges":10,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0048705","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060528","count":2}]},{"hash":"442521900888753447","title":"Post-transcriptional RNA Stability and Translation Control","description":"Proteins cluster around post-transcriptional control: stabilization of mRNA, regulation of translation initiation and reinitiation, and RNA silencing pathways. The GO terms collectively point to control of mRNA life cycle and coupling RNA processing with translation, rather than a single metabolic or signaling process. Therefore, a label emphasizing post-transcriptional RNA stability and translation control fits best.","confidence":"High","size":8,"edges":9,"triangles":3,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":4},{"id":"GO:0001825","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0006446","count":4},{"id":"GO:1900363","count":4}]},{"hash":"940751256076709787","title":"Unknown","description":"The Top Terms span diverse processes\u2014amino acid response, cell cycle regulation, tRNA and ribosomal protein transport, mRNA transport, cytoskeletal (intermediate filament) assembly, cell migration, glial differentiation, and apoptosis\u2014without a single clear shared function. This heterogeneity suggests no cohesive theme binding the cluster, so a specific, representative label cannot be confidently assigned.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0071230","count":3},{"id":"GO:0007050","count":3},{"id":"GO:0070058","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0051028","count":3}]},{"hash":"1000648423337163049","title":"Mitotic spindle and cytokinesis regulation","description":"Based on GO terms such as meiotic spindle disassembly, chromosome passenger complex localization to spindle midzone, and mitotic actomyosin contractile ring maturation, the cluster appears centered on mitosis/cytokinesis machinery. Tyrosine dephosphorylation and regulation of cell growth further support cell-cycle control, while embryonic development themes reflect division during development. Some terms may be broader or secondary, but the core pattern points to spindle function and cytokinetic regulation.","confidence":"High","size":8,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":5},{"id":"GO:0001701","count":5},{"id":"GO:0071470","count":3},{"id":"GO:2000808","count":3},{"id":"GO:0051229","count":3}]},{"hash":"1099836783074294984","title":"Ribosome Biogenesis and RNA Modification","description":"The cluster is dominated by GO terms tied to ribosome production and RNA modification, including translation, ribosome biogenesis, rRNA and snRNA pseudouridine synthesis, and LSU-rRNA maturation. A few signaling and mRNA surveillance terms appear but are much less represented, so the core theme is ribosome assembly and RNA modification.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000185","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0031118","count":1},{"id":"GO:0000470","count":1},{"id":"GO:1904571","count":1}]},{"hash":"1458961717490972753","title":"B Cell Activation and Cytoskeletal Remodeling","description":"The GO terms cluster around B cell receptor signaling, actin filament bundle assembly, cell migration, and signaling cascades (ERK/MAPK, Rho, PI3K/PLC regulation) with IL-10 production, all of which together point to B cell activation coupled with cytoskeletal remodeling and downstream signaling.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0090162","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1189501731058048737","title":"Mitochondrial Translation and Genome Maintenance","description":"This cluster shows strong enrichment for mitochondrial translation-related GO terms (mitochondrial tRNA aminoacylation for proline, threonine, glycine; and general translation) and mitochondrial DNA metabolism and respiratory chain activity, pointing to proteins involved in mitochondrial protein synthesis and upkeep of the mitochondrial genome. Some terms (e.g., embryonic development) are less directly informative, likely reflecting broader GO associations.","confidence":"High","size":8,"edges":8,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0018189","count":2},{"id":"GO:0006433","count":2},{"id":"GO:0070159","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070150","count":2}]},{"hash":"430503251501569284","title":"Organ and tissue development","description":"These proteins are linked to diverse developmental processes across multiple tissues and organs (angiogenesis, neuron and olfactory system development, gonad and myocardium development, morphogenesis). The collection points to a broad developmental role rather than a single pathway, and the network connections support a cohesive group of development-related proteins.","confidence":"Medium","size":8,"edges":17,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0002040","count":3},{"id":"GO:2000020","count":2},{"id":"GO:0021860","count":2},{"id":"GO:0014912","count":2},{"id":"GO:0051642","count":2}]},{"hash":"984095934780948188","title":"Neural Development and Sensory Signaling","description":"The enriched terms converge on neural traits: detection of mechanical stimuli in hearing, axonogenesis, and clustering of voltage-gated potassium channels, indicating neural development and sensory signaling roles. Additional terms point to broader signaling modulation (kinase activity, NF-kappaB) and even heart development, but the strongest, cohesive signal is toward neural development and sensory function rather than a single non-neural process.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050910","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0032516","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0045163","count":3}]},{"hash":"1143432964980549913","title":"Unknown","description":"The terms are a mix of neuronal signaling (membrane hyperpolarization; potassium channel regulation; long-term synaptic depression; circadian sleep/wake cycle) and immune/apoptotic processes (response to LPS; defense against virus; apoptotic process), plus generic transcription. There isn\u2019t a single clear common function uniting all proteins, so a coherent label isn\u2019t discernible.","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0060527","count":2},{"id":"GO:0051607","count":2}]},{"hash":"1739557644094567870","title":"Antiviral innate immune signaling","description":"The cluster\u2019s top GO terms are dominated by innate immune functions, especially cellular responses to dsRNA, activation of type I interferon production, and overall innate immune responses, suggesting a core antiviral signaling role. Calcium-related terms (calcium import and store-operated calcium entry) likely reflect signaling mechanisms that support immune activation, while the other development-related terms may reflect broader, tissue-expressing proteins that participate in multiple processes. Overall, the clearest shared function across the proteins appears to be antiviral innate immune signaling.","confidence":"High","size":8,"edges":9,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0061000","count":2},{"id":"GO:0001822","count":2},{"id":"GO:0048671","count":2},{"id":"GO:0070509","count":2}]},{"hash":"656396261290669382","title":"Neuronal GPCR signaling and remodeling","description":"The cluster is dominated by neural signaling terms: glutamate receptor signaling, dopamine receptor signaling via phospholipase C and GPCR pathways, and GPCR-mediated regulation of cyclic AMP, along with calcium-dependent exocytosis and Rho-mediated signaling tied to neuron remodeling. This points to a cohesive theme of neuronal communication and plasticity. Some terms like epithelial polarity and copper homeostasis are less central to neurons and may reflect broader cellular contexts, but they do not outweigh the neuronal signaling focus. ","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":8},{"id":"GO:0070208","count":8},{"id":"GO:0006878","count":8},{"id":"GO:0060158","count":8},{"id":"GO:0090162","count":8}]},{"hash":"159891586943182804","title":"Mitochondrial apoptosis and ROS signaling","description":"This cluster centers on mitochondrial functions related to apoptosis regulation and energy metabolism, including protein insertion in the inner membrane, electron transport, and proton transport, along with ROS metabolism. The presence of both intrinsic and extrinsic apoptotic signaling terms, plus stress signaling responses (interferon-beta and retinoic acid), suggests a mitochondria-driven stress and apoptosis module.","confidence":"Medium","size":8,"edges":20,"triangles":23,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097191","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0035458","count":1},{"id":"GO:2001243","count":1},{"id":"GO:0072593","count":1}]},{"hash":"1484275240871233848","title":"Retinal development and visual signaling","description":"Top GO terms point to retina/eye-related processes (visual perception, endosome-to-melanosome transport in pigment cells) alongside neuronal signaling and glial/immune development (paranodal junction assembly, microglia development, Notch and receptor signaling). The combination suggests a cluster centered on retinal development and visual-system signaling with associated vesicle trafficking.","confidence":"Medium","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0014005","count":8},{"id":"GO:0030913","count":8},{"id":"GO:2000145","count":8},{"id":"GO:1900746","count":8},{"id":"GO:0035646","count":8}]},{"hash":"1268720516720827293","title":"Angiogenesis and coagulation regulation","description":"These eight proteins cluster around vascular-related processes: coagulation and fibrinolysis (blood coagulation, fibrinolysis), inflammatory/acute-phase responses, and regulation of angiogenesis (including sprouting angiogenesis). The presence of small GTPase signaling and IGF receptor pathways supports a broader signaling/network remodeling role in vascular contexts. Together, these terms point to a theme of coordinated regulation of blood vessels during inflammation and remodeling rather than a single enzymatic function.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":2},{"id":"GO:0007596","count":2},{"id":"GO:1903779","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0006953","count":2}]},{"hash":"759697238310335700","title":"Embryonic tissue development","description":"This cluster shows GO terms across several developing tissues\u2014nervous system, skeletal muscle/chondrocyte differentiation, bone mineralization, lung alveolus development, and embryonic digestive tract development\u2014suggesting a broad developmental/differentiation theme rather than a single tissue-specific function. A couple of terms (Golgi transport regulation and tRNA splicing) relate to cellular processes and are less central to development, but the dominant pattern supports a general embryonic development label.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0032332","count":1},{"id":"GO:0042997","count":1},{"id":"GO:0048286","count":1}]},{"hash":"910289371927792142","title":"Insect Stress and Development Signaling","description":"This cluster includes GO terms for responses to multiple stresses (hydrogen peroxide, xenobiotic stimuli, lipopolysaccharide, nicotine) alongside developmental and growth-related processes (Hippo signaling, syncytial blastoderm development, compound eye development). The presence of both stress/immunity and developmental signaling terms suggests proteins that participate in broad insect developmental and stress-response networks rather than a single, cohesive pathway. The connection is plausible but not tightly specific, hence a Medium confidence.","confidence":"Medium","size":8,"edges":25,"triangles":39,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":4},{"id":"GO:0042493","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0035329","count":2},{"id":"GO:0035094","count":2}]},{"hash":"553752987677141282","title":"Dopaminergic GPCR trafficking and endocytosis","description":"The top GO terms indicate a focus on endocytosis, clathrin coat assembly, and receptor recycling, with a clear thread of dopamine GPCR signaling and neurotransmitter receptor transport from endosomes to the postsynaptic membrane. While a couple of terms (lung alveolus development, chondrocyte differentiation) are unrelated, the dominant theme centers on trafficking and regulated endocytosis of dopaminergic receptors. This supports a label around dopaminergic receptor trafficking and endocytosis with moderate confidence.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904808","count":2},{"id":"GO:0032461","count":2},{"id":"GO:0048268","count":1},{"id":"GO:0001921","count":1},{"id":"GO:0098887","count":1}]},{"hash":"685320250854616836","title":"ER-Golgi Secretory Pathway","description":"This cluster is dominated by GO terms related to vesicle trafficking between the ER and Golgi (COPI vesicle budding, ER-to-Golgi transport, and protein exit from the ER) and to Wnt secretion, pointing to involvement in the secretory pathway. Some development-related terms appear as secondary associations but do not define the core function. The strong signaling for ER-Golgi trafficking justifies this label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061357","count":1},{"id":"GO:0035964","count":1},{"id":"GO:0070863","count":1},{"id":"GO:1902003","count":1},{"id":"GO:0002121","count":1}]},{"hash":"1415640194297822932","title":"Developmental signaling and immune modulation","description":"The top GO terms cluster around broad developmental processes (skeletal system, heart, nervous system development, angiogenesis, synapse assembly) alongside signaling (positive regulation of STAT phosphorylation) and immune-related activities (chemokine production, neutrophil clearance, complement activation, cell adhesion). This suggests proteins involved in developmental tissue formation with concurrent immune signaling and modulation, possibly coordinating neural and vascular development with immune functions. Confidence in this cohesive theme is moderate due to the mix of development and immune terms, but they plausibly reflect a shared regulatory context.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051965","count":6},{"id":"GO:0001501","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0001525","count":5}]},{"hash":"1321685950593119579","title":"Proteoglycan Biosynthesis & Skeletal Development","description":"The dominant GO terms center on chondroitin sulfate proteoglycan biosynthesis (and chain elongation), plus endochondral ossification and ossification, pointing to extracellular matrix proteoglycan production driving skeletal development. Development-associated terms like Hedgehog signaling regulation and mammary gland development suggest broader tissue morphogenesis roles. Some entries are obsolete or less connected, but the core theme is proteoglycan synthesis in the ECM linked to bone/cartilage formation.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050650","count":3},{"id":"GO:0030206","count":3},{"id":"GO:0075015","count":3},{"id":"GO:0006486","count":3},{"id":"GO:0045880","count":2}]},{"hash":"534979768290878992","title":"Sphingolipid and Phospholipid Metabolism","description":"The top GO terms indicate a focus on lipid handling and signaling, with multiple entries for sphingosine/sphinganine-1-phosphate metabolism, sphingolipid signaling, phospholipid dephosphorylation, and phosphatidylglycerol biosynthesis, suggesting a cluster centered on membrane lipid remodeling and related signaling; while glucose-6-phosphate transport and oxidative detoxification appear, they are secondary to the lipid-centric terms.","confidence":"Medium","size":8,"edges":24,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015760","count":3},{"id":"GO:0009395","count":3},{"id":"GO:0044328","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0006670","count":3}]},{"hash":"448791614563140037","title":"Embryonic Development and Tissue Morphogenesis","description":"These proteins appear linked to broad developmental processes across tissues, with prominent terms for mesonephric duct and metanephric kidney development, cartilage condensation, and endochondral ossification, suggesting tissue formation and differentiation. Additional terms related to skin cornified envelope assembly, PDGF signaling regulation, and oxidative stress detection point to regulatory and stress-response roles during morphogenesis. Overall, the cluster seems to reflect embryonic tissue development rather than a single, narrow pathway.","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903575","count":2},{"id":"GO:0006958","count":2},{"id":"GO:0071230","count":1},{"id":"GO:0070208","count":1},{"id":"GO:0072177","count":1}]},{"hash":"2114540004724883411","title":"Unknown","description":"The GO terms for this cluster span very diverse processes\u2014from light perception to viral release, neuronal signaling, fungal morphogenesis, bacterial cell wall catabolism, lysosomal secretion, and ER export\u2014showing no single cohesive biological theme. This heterogeneity suggests there isn't a well-supported shared function tying the proteins together, so a concise, representative label cannot be assigned with confidence.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050908","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0051966","count":2},{"id":"GO:0016998","count":2},{"id":"GO:0009253","count":2}]},{"hash":"1328811529114827367","title":"Axon guidance and neural development","description":"This cluster is dominated by GO terms related to nervous system development, axon guidance, dendrite self-avoidance, and neuron projection extension, including semaphorin-plexin signaling and branchiomotor neuron axon guidance, indicating core involvement in neural development and neural pathfinding.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003350","count":4},{"id":"GO:0007413","count":4},{"id":"GO:0070593","count":4},{"id":"GO:0097490","count":4},{"id":"GO:0014068","count":4}]},{"hash":"1854682382822473688","title":"Antiviral and Inflammatory Immune Signaling","description":"This cluster centers on immune defense and inflammatory signaling: terms like defense response to virus, T cell homeostasis, and IL-17\u2013mediated signaling point to antiviral immunity and adaptive immune regulation. Additional terms involve LPS signaling and nitric-oxide synthase regulation, suggesting coordinated inflammatory responses. A couple of older/obsolete terms and a DNA repair-related entry appear as background connections but do not define the main theme. Overall, the proteins seem to participate in antiviral defense and inflammatory signaling.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":2},{"id":"GO:0070911","count":2},{"id":"GO:0060546","count":2},{"id":"GO:0050999","count":2},{"id":"GO:0043029","count":2}]},{"hash":"2022929501597060077","title":"Immune Regulation and Complement Pathways","description":"Most terms cluster around immune system modulation: complement activation (classical and alternative), regulation of membrane attack complex, leukocyte adhesion and rolling, IL-10 production, and apoptotic signaling. Together they point to a functional group focused on immune signaling and regulation of inflammatory responses, with complement pathways as a central thread. The presence of an anomalous term like vocalization behavior is likely an annotation noise rather than a core function of the cluster.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006924","count":8},{"id":"GO:0045959","count":8},{"id":"GO:0032613","count":8},{"id":"GO:0050901","count":8},{"id":"GO:0001970","count":8}]},{"hash":"2272020037511552177","title":"Membrane signaling in inflammation and tissue remodeling","description":"The proteins show enrichment for membrane-associated inflammatory signaling (TLR4 pathway activation, TNF production regulation, NF-kB activity) together with extracellular matrix remodeling processes (ECM disassembly, regulation of cell adhesion/spreading) and links to osteoblast differentiation and transport. Although retina homeostasis appears in the terms, the cohesive theme is signaling at the membrane that drives inflammatory responses and structural remodeling, suggesting a cluster centered on inflammation-linked tissue remodeling.","confidence":"Medium","size":8,"edges":7,"triangles":4,"max_degree":3,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0001895","count":4},{"id":"GO:0006881","count":4},{"id":"GO:0090091","count":4},{"id":"GO:0032680","count":4},{"id":"GO:1900229","count":4}]},{"hash":"559980466425519480","title":"Telomere maintenance and chromatin regulation","description":"This cluster is best linked by terms focusing on telomere biology and chromatin state: positive regulation of shelterin complex assembly, subtelomeric heterochromatin formation, replication-born double-strand break repair via sister chromatid exchange, and regulation of protein localization to telomeres, all pointing to telomere maintenance and chromatin regulation. Some terms appear noisy or unrelated (plant signaling, metabolism), but the telomere/chromatin theme is the dominant signal.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0072362","count":2},{"id":"GO:1990414","count":2},{"id":"GO:1904792","count":2}]},{"hash":"930872572021558280","title":"Immune-related transcriptional regulation","description":"This cluster is driven by transcription-oriented GO terms (DNA-templated transcription, RNA polymerase II transcription, miRNA transcription) indicating a shared role in gene expression control. The presence of immune and tissue-remodeling terms (positive regulation of MHC class II biosynthetic process, microglial cell activation, vascular wound healing, fibroblast proliferation) suggests coordinated transcriptional regulation of immune responses and tissue repair processes. While a few terms are obsolete, the overall pattern points to an immune-associated transcriptional program. ","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045348","count":4},{"id":"GO:0035470","count":4},{"id":"GO:0006366","count":4},{"id":"GO:0045872","count":3}]},{"hash":"199266448935981763","title":"Muscle contractile apparatus and sarcomere assembly","description":"This cluster centers on the muscle contractile machinery and sarcomere organization, as shown by terms like sarcomere organization, sarcomerogenesis, filament sliding, and myosin filament assembly, along with T-tubule organization and cardiac/skeletal muscle development. The set suggests proteins involved in assembly of the contractile apparatus and muscle stretch sensing in both cardiac and skeletal muscle.","confidence":"High","size":7,"edges":19,"triangles":25,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0033292","count":1},{"id":"GO:0060047","count":1},{"id":"GO:0048769","count":1},{"id":"GO:0030049","count":1},{"id":"GO:0045214","count":1}]},{"hash":"1858945274662855592","title":"Unknown","description":"The GO terms span mitochondrial protein import, nuclear RNA processing (scaRNA localization), B cell cytokine production, telomere maintenance, cell division, virion assembly, and protein quality control, with several terms marked obsolete. There is no clear shared function or pathway tying these terms together, suggesting the cluster is heterogeneous rather than a single coherent biological process. Therefore I cannot assign a specific, representative label.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":6},{"id":"GO:0090666","count":6},{"id":"GO:0002368","count":6},{"id":"GO:0032212","count":6},{"id":"GO:0051973","count":6}]},{"hash":"799551011312762686","title":"Autophagy and metal ion response","description":"The cluster includes multiple autophagy-related GO terms (autophagosome maturation, targeting to vacuole in autophagy, reticulophagy, piecemeal microautophagy of the nucleus, autophagy of mitochondrion) and responses to metal ions (lead, iron(II), copper), suggesting coordinated roles in organelle turnover and metal-stress handling. Dauer larval development and apoptotic process terms are present but secondary to the autophagy focus.","confidence":"High","size":7,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097352","count":3},{"id":"GO:0040024","count":3},{"id":"GO:0071211","count":3},{"id":"GO:0010288","count":3},{"id":"GO:0010040","count":3}]},{"hash":"1420521184521454491","title":"Mammary gland transcription and lactation regulation","description":"Top GO terms indicate RNA polymerase II\u2013driven transcription and mRNA processing, together with mammary-specific processes such as lactation, mammary epithelial cell proliferation, and response to leptin. This suggests a cluster of transcriptional regulators and effectors governing mammary gland development and lactation.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0006367","count":3},{"id":"GO:0006397","count":2},{"id":"GO:0007595","count":2}]},{"hash":"2149911546125075883","title":"Cohesin-driven chromosome cohesion and HR repair","description":"The cluster\u2019s top GO terms center on cohesin-related processes (mitotic sister chromatid cohesion, maintenance of cohesion, chromosome condensation) and DNA repair via homologous recombination, including meiotic regulation of double-strand breaks. These together point to a cohesive theme of maintaining chromosome structure during cell division and repairing DSBs, with a few peripheral terms (like tRNA gene clustering) not core to this function.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0061780","count":5},{"id":"GO:1903342","count":5},{"id":"GO:0000724","count":5},{"id":"GO:0071960","count":5},{"id":"GO:0007064","count":5}]},{"hash":"2097794122335727601","title":"Nuclear transcription control and ribosome biogenesis","description":"The cluster\u2019s top terms are centered on transcription regulation by RNA polymerase II and ribosome biogenesis/maturation (ribosomal small subunit assembly and SSU rRNA processing), which suggests a nucleus-focused gene expression module. Some other terms (endocytosis, ubiquitin pathways, TLR signaling) appear peripheral or obsolete, but do not override the main theme. ","confidence":"Medium","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:1900186","count":5},{"id":"GO:1903071","count":5},{"id":"GO:1904049","count":5},{"id":"GO:0000028","count":5}]},{"hash":"1153741612274644247","title":"Mammary gland differentiation and epigenetic regulation","description":"This cluster centers on mammary gland epithelial differentiation and involution, including regulation of mammary cell proliferation, with supporting signals from broader developmental processes (angioblast, macrophage, mesoderm differentiation) and epigenetic control through CpG methylation and miRNA transcription.","confidence":"Medium","size":7,"edges":15,"triangles":14,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0035779","count":5},{"id":"GO:0061614","count":5},{"id":"GO:0035019","count":5},{"id":"GO:0044027","count":5},{"id":"GO:0060644","count":5}]},{"hash":"1465550234499037089","title":"Immune cytokine signaling and NF-kB regulation","description":"The GO terms cluster around immune signaling and inflammation: regulation of inflammatory response, cytokine and TNF production, NF-kB/JNK signaling, STAT phosphorylation, PI3K/AKT signaling, and immunoglobulin production, with a couple broader terms like development and circadian temperature homeostasis that are less central. This points to a coherent immune modulation program.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050728","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0042511","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0060086","count":2}]},{"hash":"369485493510198123","title":"Rho GTPase Signaling and Actin Remodeling","description":"The cluster centers on Rho protein signal transduction and actin cytoskeleton organization, with activation of GTPase activity and regulation of Rho pathways prominently represented. These terms point to cytoskeletal dynamics and signaling as the core theme. Apoptosis-related terms appear but are less dominant, suggesting a supportive or cross-talk context rather than a primary function.","confidence":"Medium","size":7,"edges":11,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097194","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0035234","count":2},{"id":"GO:0042098","count":2},{"id":"GO:0032094","count":2}]},{"hash":"1567900779723695232","title":"Endosome-lysosome trafficking","description":"The cluster is dominated by GO terms for lysosome and endosome organization and transport between endosomes and lysosomes, indicating a cohesive vesicular trafficking/maturation function. A few RNA-related terms appear but do not define the primary activity. ","confidence":"High","size":7,"edges":8,"triangles":0,"max_degree":4,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0007040","count":3},{"id":"GO:0007032","count":3},{"id":"GO:0045022","count":3},{"id":"GO:0008333","count":3},{"id":"GO:0031047","count":2}]},{"hash":"592731332697210566","title":"Muscle development and regeneration","description":"The strongest signals come from GO terms tied to muscle biology\u2014cardiac muscle tissue regeneration, skeletal muscle fiber development, and skeletal muscle cell differentiation\u2014suggesting the cluster centers on muscle development and differentiation. Some other terms (microtubule-based movement, spindle-related localization, circadian regulation, plant signaling, and viral latency) appear as broader or incidental annotations but do not override the muscle-focused pattern.","confidence":"Medium","size":7,"edges":13,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0061026","count":1},{"id":"GO:0007018","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0019046","count":1},{"id":"GO:0009742","count":1}]},{"hash":"1272409108354125596","title":"Detox and redox stress response","description":"The cluster\u2019s notable terms include response to xenobiotic stimulus and cell redox homeostasis, which point to a detoxification and oxidative stress response program. Additional terms related to peptide hormone signaling and DNA metabolism appear, suggesting ancillary roles in signaling and DNA processing rather than a single developmental pathway. Overall, the core theme seems to be cellular stress response and detoxification rather than a specific tissue developmental process.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0006308","count":2},{"id":"GO:2000327","count":2},{"id":"GO:0042493","count":2}]},{"hash":"904371503950583840","title":"Embryogenesis and placental development","description":"The GO terms cluster around embryonic development and extraembryonic/placental contexts (trophoblast differentiation, placenta development, left-right patterning, endocrine/pancreatic development, cartilage morphogenesis, EMT in heart structures). A small subset corresponds to innate immune signaling, which are less central to the cluster\u2019s main theme. Overall, the dominant pattern is embryogenesis and placental/organ development.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0003323","count":1}]},{"hash":"2079700344135066431","title":"Unknown","description":"The GO terms cover very different processes (steroid receptor assembly, non-motile cilium assembly, cytokinin signaling, lipopolysaccharide metabolism, interferon response, lipid biosynthesis regulation, viral genome replication regulation, sex differentiation, and cell division) with no clear common theme. There isn\u2019t a unifying function or pathway that ties these proteins together, so a specific, representative label isn\u2019t justifiable.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006463","count":1},{"id":"GO:1903071","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0008653","count":1}]},{"hash":"953474999245465271","title":"DNA Damage Response and Repair","description":"The cluster is dominated by GO terms for DNA damage checkpoints (mitotic intra-S, meiotic, and DNA replication), DNA repair, and cellular responses to ionizing radiation, along with meiotic cell cycle and apoptotic signaling in response to DNA damage. This points to a coherent DNA damage response and repair function, incorporating checkpoint control and apoptosis regulation. A few terms (autophosphorylation, growth regulation, visual learning) appear less directly related and may reflect broader or incidental annotations.","confidence":"High","size":7,"edges":12,"triangles":11,"max_degree":5,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0031573","count":3},{"id":"GO:0051598","count":3},{"id":"GO:0000076","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0051321","count":3}]},{"hash":"808534002360691771","title":"RNA processing and transcription regulation","description":"Enriched GO terms cluster around transcription control (DNA-templated transcription, termination/antitermination) and RNA processing/stability (pre-miRNA processing, miRNA catabolic process, CRD-mediated mRNA stabilization). Some translation regulation terms appear, but the dominant theme is RNA metabolism linked to transcriptional regulation.","confidence":"Medium","size":7,"edges":13,"triangles":11,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031564","count":4},{"id":"GO:0031054","count":4},{"id":"GO:0060567","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0070934","count":4}]},{"hash":"1572501013636723749","title":"MAPK-Driven Innate Immune Signaling","description":"This cluster centers on MAP kinase pathways (JNK and ERK cascades) and lipopolysaccharide-triggered innate immune signaling, with related defense responses and cytoskeletal remodeling, suggesting a coherent module of immune signaling and actin dynamics.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0033138","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0071333","count":4},{"id":"GO:0050830","count":4}]},{"hash":"2048333419674643565","title":"Nuclear import and meiotic DNA replication regulation","description":"The top GO terms concentrate on nuclear protein import (NLS-bearing and ribosomal protein import into nucleus), regulation of DNA replication and chromatin assembly, and meiotic processes (female meiotic nuclear division, sister chromatid cohesion). These together suggest a cluster focused on nuclear transport coupled with replication/meiotic control, with a few peripheral terms (amino acid stimulus, mRNA transport, GTPase activity) that are less central to the core theme.","confidence":"Medium","size":7,"edges":11,"triangles":5,"max_degree":6,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0071230","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0006610","count":5},{"id":"GO:0006335","count":5},{"id":"GO:0097711","count":5}]},{"hash":"1217867988556710870","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":9,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035773","count":1},{"id":"GO:0031016","count":1},{"id":"GO:0034198","count":1},{"id":"GO:0010507","count":1},{"id":"GO:0002192","count":1}]},{"hash":"1672801726254503327","title":"Stress-responsive signaling and cytoskeletal remodeling","description":"The Top Terms include cellular responses to various stimuli (anoxia, brain-derived neurotrophic factor, prolactin) and stress-related processes (necroptosis), along with signaling-related activities (protein autophosphorylation/regulation) and cytoskeletal dynamics (myosin II filament disassembly, calcium-dependent adhesion). This mix suggests a general theme of signaling in response to stress cues that is coupled with cytoskeletal remodeling, rather than a single cohesive pathway. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":1},{"id":"GO:0071454","count":1},{"id":"GO:1990416","count":1},{"id":"GO:1990637","count":1},{"id":"GO:0070266","count":1}]},{"hash":"513919231676471177","title":"Rap GTPase signaling and intracellular transport","description":"This cluster\u2019s top GO terms center on Rap signal transduction, activation of GTPase, and intracellular/nuclear transport processes (microtubule localization, protein export from nucleus), with ancillary links to NMDA receptor activity and broader signaling pathways such as Hippo and angiogenesis. The shared theme appears to be small GTPase\u2013mediated signaling coordinating intracellular trafficking and gene-regulatory processes, rather than a single tightly defined pathway.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032486","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006886","count":2},{"id":"GO:2000310","count":2},{"id":"GO:0090630","count":2}]},{"hash":"1622763948389934952","title":"Macrophage Innate Immune Activation","description":"The top GO terms cluster around defense response to virus, response to lipopolysaccharide, TLR2 signaling, macrophage activation, TNF signaling, and NLRP3 inflammasome assembly, pointing to a macrophage-driven innate immune and inflammatory program. Some terms like aging and glucose homeostasis are less central, but the dominant theme is antiviral/innate immune response and inflammasome regulation, justifying this label.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0032496","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0071356","count":2}]},{"hash":"1749012450101762935","title":"Plant telomere maintenance and chromatin regulation","description":"The cluster's top GO terms cluster around telomere biology and chromatin control in plants: positive regulation of shelterin complex assembly, subtelomeric heterochromatin formation, and regulation of protein localization to telomeres, plus chromatin-related histone H2A deubiquitination and replication-associated DNA repair near telomeres. While some terms touch on broader plant processes such as hormone signaling and flavonoid biosynthesis, the strongest cohesive signal is telomere maintenance and chromatin regulation in a plant context.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035522","count":4},{"id":"GO:0009736","count":2},{"id":"GO:0072362","count":2},{"id":"GO:1990414","count":2},{"id":"GO:1904792","count":2}]},{"hash":"1503617793404662770","title":"Redox balance and cofactor metabolism","description":"The set centers on redox homeostasis and cofactor-related metabolism (tetrahydrofolate, lipoate) and membrane potential regulation, pointing to a cohesive theme of redox-balanced energy metabolism; several unrelated terms (gastrulation, sperm capacitation) appear as background noise but do not outweigh the redox/cofactor signal.","confidence":"Medium","size":7,"edges":9,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007369","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0019383","count":3}]},{"hash":"446302224248539921","title":"Carbohydrate and amino acid metabolism with ion transport","description":"The top GO terms point to central metabolism (carbohydrate metabolic process; L-serine and homocysteine catabolic processes; related cysteine biosynthesis note) and membrane transport of Mg2+ and K+, suggesting a cluster of proteins involved in energy/carbon metabolism linked to ion homeostasis. A retina development term appears but is likely annotation noise; overall the shared theme is metabolic pathways coupled to ion transport and maybe signaling (activation of protein kinase activity). ","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0060041","count":4},{"id":"GO:0006565","count":3},{"id":"GO:0045722","count":3},{"id":"GO:1903830","count":3},{"id":"GO:0045794","count":3}]},{"hash":"1601459706837786875","title":"Unknown","description":"The GO terms are diverse, spanning neural development (axial mesoderm formation, fasciculation of sensory neuron axon), neural signaling and receptor organization (receptor clustering), metabolism (glycogen regulation, insulin response), protein turnover (proteasomal ubiquitin-dependent degradation), and even immune signaling (interleukin-7 response). This lack of a single cohesive biological theme makes it not possible to assign a specific, representative label to the cluster. The presence of an obsolete GO term also suggests annotation noise. ","confidence":"","size":7,"edges":16,"triangles":15,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":7},{"id":"GO:0048320","count":7},{"id":"GO:0097155","count":7},{"id":"GO:0032092","count":7},{"id":"GO:0008542","count":7}]},{"hash":"2010864026581906326","title":"Autophagy and vesicle trafficking","description":"The proteins are enriched for autophagy-related GO terms (glycophagy, autophagy of mitochondrion, piecemeal microautophagy of the nucleus, Cvt pathway) and vesicle transport (ER to Golgi), suggesting a core function in intracellular turnover and vesicle dynamics. Developmental and cell fate terms like forebrain development and programmed cell death further support a context where autophagy intersects with growth and differentiation. This makes \u201cAutophagy and vesicle trafficking\u201d a specific and representative cluster label.","confidence":"High","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":"cytokinesis","top_go_terms":[{"id":"GO:0000910","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0060271","count":2},{"id":"GO:0034727","count":2},{"id":"GO:0008283","count":2}]},{"hash":"1567030680724096591","title":"Prenylation and Neuromuscular Signaling","description":"The cluster is driven by explicit post-translational lipid modification terms: protein farnesylation and geranylgeranylation, which are prenylation processes. This lipidation supports signaling involved in neuromuscular junction development, suggesting the proteins may coordinate synaptic maturation and related signaling pathways. Other terms like response to cytokine and deacetylase regulation are present but less defining, so the prenylation-centric theme best captures the core function of this cluster.","confidence":"Medium","size":7,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045213","count":1},{"id":"GO:0014070","count":1},{"id":"GO:0051770","count":1},{"id":"GO:0007323","count":1},{"id":"GO:0018344","count":1}]},{"hash":"1589366532009960996","title":"Vertebrate embryonic development and morphogenesis","description":"The top GO terms center on embryonic development and morphogenesis across brain ventricles, neural tube closure, axis specification (somites), and early structures like blastocysts, with additional nudges toward mammary gland development and spermatid-related processes. Despite a few terms related to RNA turnover or post-translational modification, the overall theme is vertebrate development and tissue patterning.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021678","count":6},{"id":"GO:0021592","count":6},{"id":"GO:0021555","count":5},{"id":"GO:0001825","count":5},{"id":"GO:0021993","count":5}]},{"hash":"759037837222453183","title":"Neuronal excitability and heart rhythm regulation","description":"This cluster centers on GO terms tied to electrical activity and signaling in neurons and heart tissue: neuronal action potentials, membrane hyperpolarization, potassium channel regulation, and heart rate modulation via cardiac conduction and atrial repolarization. Additional terms about long-term synaptic depression and Rho signaling reflect modulation of signaling pathways that influence excitability, while touch detection and circadian sleep regulation point to broader sensory\u2013neural regulation. Overall, the common theme is cellular excitability and rhythmic control in nervous and cardiac systems.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045188","count":4},{"id":"GO:0060081","count":4},{"id":"GO:1900454","count":4},{"id":"GO:1902260","count":4},{"id":"GO:0086091","count":4}]},{"hash":"580043096866193688","title":"Kidney development and renal function","description":"This cluster shows strong enrichment for kidney-related processes, notably renal sodium ion absorption and branching morphogenesis of the ureteric bud, suggesting a focus on kidney development and renal transport. Other terms (circadian regulation, pregnancy, respiratory system) are broader or ancillary annotations, but the dominant signal is kidney development/function, supporting a Medium confidence level.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0070294","count":4},{"id":"GO:0032922","count":3},{"id":"GO:0007565","count":3},{"id":"GO:0090190","count":3},{"id":"GO:0003016","count":3}]},{"hash":"988208710782918684","title":"Golgi\u2013plasma membrane vesicle trafficking","description":"This cluster is dominated by GO terms for transport between the Golgi, plasma membrane, and endosomes, pointing to a shared function in vesicle trafficking within the secretory/endocytic pathway. Other terms appear more tangential (nerve signaling, transcription regulation, and ion transport), but the clearest common theme is membrane trafficking.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0070525","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0000722","count":1}]},{"hash":"1102128843182037076","title":"Signaling and metabolic stress response","description":"The GO terms span insulin and TGF-beta signaling, hypoxia detection, chaperone-mediated assembly, cell division, and metabolic regulation, suggesting a broad theme around signaling, proteostasis, and stress-adaptive metabolism rather than a single precise function.","confidence":"Low","size":7,"edges":12,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":3},{"id":"GO:0008286","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0032516","count":2},{"id":"GO:0019062","count":2}]},{"hash":"1066634965867830314","title":"Retroviral life cycle and proviral integration","description":"The top GO terms cluster around steps of retroviral infection: entry into host cells, penetration into the nucleus, integration of viral DNA and establishment of proviral latency, and DNA replication; these collectively define the retroviral life cycle and genome integration rather than generic host processes. The presence of RNAi-related modulation further supports viral interaction with host defenses. ","confidence":"High","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":1},{"id":"GO:0075732","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0019058","count":1},{"id":"GO:0090502","count":1}]},{"hash":"1277548030579342658","title":"Embryonic morphogenesis and neural cell migration","description":"This cluster centers on developmental processes: ectoderm formation, female gonad and uterine epithelium development, and motor neuron differentiation/migration, along with cytoskeletal remodeling (actin bundle and lamellipodium assembly) that drives cell movement during morphogenesis. The dominant pattern is embryonic tissue formation and neural cell movement, with some outliers (obsolete term, sulfur oxidation) that do not shift the core theme.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010735","count":5},{"id":"GO:0072283","count":5},{"id":"GO:0097477","count":5},{"id":"GO:0021526","count":5},{"id":"GO:0051017","count":5}]},{"hash":"76037622198345713","title":"Calcium signaling in muscle and neural development","description":"This cluster features terms tied to calcium regulation in the sarcoplasmic reticulum, control of cardiac muscle contraction, myoblast fusion, and actin cortex assembly, all pointing to calcium-dependent muscle development and cytoskeletal dynamics. It also includes axonogenesis and retinal cone development, suggesting concurrent neural/eye development. Additional terms for epinephrine/xenobiotic response and kinase activity regulation reflect signaling and stress-responsive modulation that can intersect calcium signaling. Overall, the shared thread is calcium-mediated signaling coordinating muscle and neural developmental processes.","confidence":"Medium","size":7,"edges":9,"triangles":5,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0007409","count":5},{"id":"GO:0010880","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0086004","count":5}]},{"hash":"1629732090111535990","title":"Immune cell degranulation and vesicle transport","description":"The cluster shows multiple degranulation terms across NK cells, neutrophils, eosinophils, and mast cells (e.g., natural killer cell degranulation, neutrophil/eosinophil degranulation, histamine secretion by mast cells) together with vesicle trafficking processes between Golgi, ER, and endosomes, and general protein transport. This indicates a cohesive module focused on regulated secretion and vesicle trafficking in immune cells.","confidence":"High","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043320","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0043312","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0015031","count":2}]},{"hash":"2244375000352231525","title":"Actin Cytoskeleton Remodeling and Lamellipodium Assembly","description":"These proteins cluster around actin dynamics, with multiple terms for actin nucleation, bundle assembly, and lamellipodium formation, plus related processes like synaptic depression. This suggests a shared role in actin-driven cytoskeletal remodeling governing cell shape and migration, with possible links to synaptic plasticity.","confidence":"High","size":7,"edges":13,"triangles":11,"max_degree":6,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2000251","count":5},{"id":"GO:0060292","count":5},{"id":"GO:0051660","count":5},{"id":"GO:0060065","count":4},{"id":"GO:0045087","count":4}]},{"hash":"2033931027343798813","title":"Neural development and signaling","description":"GO terms cluster around neural signaling and development (receptor guanylyl cyclase signaling, intracellular signal transduction, pons maturation, anterior lateral line development, visual learning, rhythmic excitation), with additional links to respiratory regulation. A single metabolic term (L-phenylalanine biosynthetic process) and an obsolete cAMP term introduce noise, but the overall theme points to neural signal transduction and development.","confidence":"Medium","size":7,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009094","count":2},{"id":"GO:0021586","count":2},{"id":"GO:0007168","count":2},{"id":"GO:0035556","count":2},{"id":"GO:1900194","count":2}]},{"hash":"1744624165968208878","title":"Redox Stress and Xenobiotic Response","description":"The set centers on redox/homeostatic processes (oxidation-reduction, redox homeostasis) and responses to xenobiotic stimuli, with an accompanying apoptotic signal; development terms and other outliers likely reflect annotation noise. This suggests a cohesive theme around cellular stress responses and apoptosis rather than a single developmental pathway.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042493","count":5},{"id":"GO:0007369","count":5},{"id":"GO:0021762","count":5},{"id":"GO:0045454","count":5}]},{"hash":"2206913011255682689","title":"Sphingolipid metabolism and phospholipid turnover","description":"The top terms are strongly lipid-centric, with sphingosine metabolism, regulation of sphingolipid signaling, and phospholipid catabolic/dephosphorylation processes forming a coherent lipid metabolism theme. Some transport and detox/ER-related terms are present but appear ancillary, making the lipid-focused label the most representative for the cluster.","confidence":"Medium","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0030970","count":2},{"id":"GO:0015760","count":2},{"id":"GO:0009395","count":2}]},{"hash":"2217556675969226215","title":"Axon guidance and neuronal migration","description":"The terms cluster around neural development, especially axon growth/guidance (axonal fasciculation, negative regulation of axon extension, nerve branching) and cerebral cortex radial glia-guided migration, with supporting organelle organization processes often linked to neuronal development.","confidence":"Medium","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":3},{"id":"GO:0060317","count":2},{"id":"GO:0032581","count":2},{"id":"GO:0006694","count":2},{"id":"GO:0007413","count":2}]},{"hash":"2089490162644171408","title":"Vesicle trafficking and Rab GTPase signaling","description":"This cluster centers on GO terms for synaptic vesicle endocytosis, endocytic recycling, and Rab GTPase signaling (including regulation of GTPase activity and Rab signal transduction) plus cadherin-mediated adhesion turnover, all pointing to vesicle trafficking and membrane remodeling as the core function. Some terms related to nervous system development and other processes appear, but the dominant theme is Rab-dependent trafficking and endocytosis.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097194","count":2},{"id":"GO:0048488","count":2},{"id":"GO:0043087","count":2},{"id":"GO:2000049","count":2},{"id":"GO:0035745","count":2}]},{"hash":"1925551886342246507","title":"Metanephros morphogenesis","description":"The top GO term is metanephros morphogenesis (kidney development) with a single instance, and there are no edges or additional annotations to reinforce a shared function among all seven proteins. This suggests a weak or incidental link to kidney development rather than a robust, cohesive theme for the cluster.","confidence":"Low","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003338","count":1}]},{"hash":"288735217244980950","title":"Deubiquitinases (DUBs)","description":"The proteins show multiple GO terms tied to ubiquitin removal and deubiquitination, including K11- and K29-linked deubiquitination, monoubiquitinated protein deubiquitination, and general deubiquitinase activity, plus a term on free ubiquitin chain depolymerization. A transcription-related term is present but can be a downstream effect of DUB activity. The strongest common thread is deubiquitination by ubiquitin-specific proteases, suggesting a cohesive function around DUB activity rather than disparate processes.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060013","count":1},{"id":"GO:0035192","count":1},{"id":"GO:0010995","count":1},{"id":"GO:0010606","count":1},{"id":"GO:0035871","count":1}]},{"hash":"1062702156547165509","title":"Peroxisome protein import and microtubule transport","description":"The top GO terms cluster around importing proteins into the peroxisome matrix (docking, translocation, substrate release) and general protein targeting to peroxisomes, plus transport along microtubules and microtubule anchoring. These together point to a coherent theme of peroxisomal protein import machinery and its trafficking along the cytoskeleton, despite a few stray terms. ","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034453","count":3},{"id":"GO:0036250","count":3},{"id":"GO:1901094","count":3},{"id":"GO:0032091","count":3},{"id":"GO:0016560","count":3}]},{"hash":"1831602518335802631","title":"Nucleotide and Small Molecule Metabolism","description":"The proteins cluster around catabolic and biosynthetic processes of small molecules and nucleotides (coenzyme A, folic acid, IPP/FPP, dGTP, nucleobase-containing compounds), suggesting a metabolic coherence. A few RNA processing and DNA repair terms are present but do not define the core function, so the overall theme is nucleotide/SM metabolism.","confidence":"Medium","size":7,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015938","count":1},{"id":"GO:0046656","count":1},{"id":"GO:0009240","count":1},{"id":"GO:0045337","count":1},{"id":"GO:1901639","count":1}]},{"hash":"624685085197977119","title":"Unknown","description":"The top GO terms show a mix of very different biological themes (intracellular calcium homeostasis and actin filament depolymerization alongside serine and carbohydrate metabolism, dephosphorylation, and specific bacterial biosynthetic processes like ADP-L-glycero-beta-D-manno-heptose and N-acetylneuraminate). There is no clear, unifying function or pathway linking these terms, suggesting the cluster spans disparate processes or contains annotations from different contexts. Therefore a single, coherent label is not apparent.","confidence":"","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006874","count":5},{"id":"GO:0006564","count":4},{"id":"GO:0030836","count":4},{"id":"GO:0005975","count":4},{"id":"GO:0016311","count":4}]},{"hash":"1035611921281070629","title":"Neuro-immune Signaling","description":"The cluster centers on neuropeptide signaling and responses linked to the nervous system (neuropeptide signaling, auditory stimulus response, ERK/MAPK cascade regulation, GPCR signaling), while also including immune-related terms (eosinophil chemotaxis, helper T cell extravasation, IL-13 response) and digestion. This suggests a shared theme of cross-talk between neural and immune pathways, potentially with gut-associated neuro-immune interactions, rather than a single narrow function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070374","count":2},{"id":"GO:0010996","count":2},{"id":"GO:0007218","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0007189","count":2}]},{"hash":"127033564571492419","title":"Fucosylation and Lewis antigen biosynthesis","description":"The top GO terms cluster around fucose-containing glycosylation: L-fucose catabolic process, Lewis a epitope biosynthetic process, and glycosylation-related terms (including obsolete glycosylation terms). These point to a shared function in the synthesis and modification of fucosylated glycans, i.e., Lewis antigen biosynthesis. Some immune and neuronal development terms appear, but they are less strongly connected to the main glycosylation theme. Therefore, a glycosylation/fucose biosynthesis label best captures the cluster.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":2},{"id":"GO:0042355","count":1},{"id":"GO:0010493","count":1},{"id":"GO:0097150","count":1},{"id":"GO:0002522","count":1}]},{"hash":"320708136938749814","title":"Diverse Transmembrane Transporters","description":"The top GO terms point to a broad set of transmembrane transport activities, spanning xenobiotic, nutrient (sugar and nitrate/nitrite), and neurotransmitter vesicular loading. This diversity suggests the cluster comprises membrane transporter proteins rather than a single substrate class, justifying a label of broad transmembrane transport capability rather than a narrower function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0098700","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0042128","count":2}]},{"hash":"972603483236050696","title":"Embryonic development and tissue differentiation","description":"The top GO terms cluster around development across multiple tissues (neuron differentiation, ectoderm formation, uterine epithelium and gland development, and organogenesis like ureteric bud). There are also general cellular processes (palmitoylation, vacuole fusion) that are broadly relevant to development. Overall, the common theme is developmental processes across various tissues, supporting a label focused on embryonic development and tissue differentiation.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0018230","count":2},{"id":"GO:0048733","count":2},{"id":"GO:0021526","count":1},{"id":"GO:0060677","count":1}]},{"hash":"848569757231459861","title":"Osteogenesis and Osteoblast Differentiation","description":"The cluster's frequent GO terms center on bone development (GO:0060348) and osteoblast fate commitment, suggesting a shared role in bone formation. Additional terms point to developmental processes and cell motility/polarity, which can accompany tissue morphogenesis and osteoblast differentiation. Overall, the group seems best described by bone formation and osteoblast differentiation activity, with supporting roles in related developmental pathways.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060348","count":2},{"id":"GO:0005975","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0002051","count":1}]},{"hash":"594650529609693468","title":"Dopaminergic neuroimmune signaling and glial regulation","description":"The cluster links dopamine-related processes (dopamine transport, regulation of dopamine metabolism, PLC-activating dopamine receptor signaling) with immune and glial-related terms (immune response, negative regulation of inflammatory response, astrocyte chemotaxis, GDNF production, eosinophil chemotaxis, xenobiotic response), suggesting a cohesive theme of neuroimmune modulation involving glial cells and dopaminergic signaling.","confidence":"Medium","size":7,"edges":14,"triangles":8,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":6},{"id":"GO:0042493","count":6},{"id":"GO:2000458","count":6},{"id":"GO:1900168","count":6},{"id":"GO:0048245","count":6}]},{"hash":"2134289885217307309","title":"Dopaminergic neuroimmune signaling in glia","description":"This cluster's proteins show a pattern where dopamine-related functions (transport and signaling) coincide with immune and glial processes (immune response, astrocyte chemotaxis, glial-derived neurotrophic factor regulation). The combination suggests a theme of dopaminergic signaling intertwined with glial/immune modulation, including xenobiotic responses. Therefore the label captures the core intersection of dopamine biology with neuroimmune/glial activity.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":7},{"id":"GO:0042493","count":7},{"id":"GO:2000458","count":7},{"id":"GO:1900168","count":7},{"id":"GO:0048245","count":7}]},{"hash":"939922280255095353","title":"Chromatin methylation and developmental regulation","description":"The top GO terms center on epigenetic control via histone H3-K9 methylation and heterochromatin formation, with additional signals of glucocorticoid (dexamethasone) response and various developmental processes (neuronal/gliogenesis, myotube development). This suggests a theme where chromatin modification governs developmental gene programs and stress-hormone signaling.","confidence":"Medium","size":6,"edges":10,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090309","count":3},{"id":"GO:0051567","count":3},{"id":"GO:0071549","count":3},{"id":"GO:1900006","count":2},{"id":"GO:0042127","count":2}]},{"hash":"1088877934062611760","title":"Neural axon guidance and synapse development","description":"The top GO terms are dominated by neural development and connectivity (axon guidance, axonogenesis, fasciculation of sensory neuron axons, optic nerve morphogenesis, retinal ganglion cell axon guidance, and trans-synaptic signaling), suggesting a coherent role in establishing neural circuits. A few outliers like vaginal development or mesoderm formation exist but do not outweigh the central neural-focus terms. ","confidence":"High","size":6,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048320","count":4},{"id":"GO:0031290","count":4},{"id":"GO:0097155","count":4},{"id":"GO:0001779","count":4},{"id":"GO:0021952","count":4}]},{"hash":"1444937767772514449","title":"Unknown","description":"The terms span development (neuron differentiation, Notch signaling, hematopoietic differentiation), metabolism (iron-sulfur cluster assembly), protein targeting, and basic processes like DNA replication and stress responses. The set lacks a cohesive, single-function theme, and several terms are obsolete, so a specific, representative label cannot be inferred.","confidence":"","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045665","count":1},{"id":"GO:0045747","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0031204","count":1},{"id":"GO:1902037","count":1}]},{"hash":"43570836577834533","title":"Immune Signaling and Development","description":"The cluster shows strong signals for innate immune response and T cell receptor signaling, with supporting developmental terms (thymus morphogenesis, cranial skeletal development) and related signaling processes (endosome localization, axon guidance). This pattern suggests a theme where immune signaling intersects with developmental pathways, justifying the label \u201cImmune Signaling and Development.\u201d","confidence":"Medium","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":4},{"id":"GO:0097536","count":3},{"id":"GO:0000122","count":3},{"id":"GO:2000637","count":3},{"id":"GO:0045087","count":3}]},{"hash":"1781829951640504821","title":"Aminoacyl-tRNA Synthetases and Translation","description":"Terms point to translation and protein synthesis, including multiple aminoacyl-tRNA synthetases (glutaminyl-, prolyl-, valyl-tRNA aminoacylation) and both cytosolic and mitochondrial translation. While angiogenesis terms appear, the dominant signal is translation machinery. Therefore this label best reflects the cluster\u2019s core function.","confidence":"High","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045765","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0006425","count":1},{"id":"GO:0030154","count":1}]},{"hash":"1936434970373437109","title":"Nuclear import and meiotic chromosome regulation","description":"The top GO terms cluster around nuclear import (NLS-bearing and ribosomal protein import into nucleus), regulation of DNA replication, chromatin assembly during replication, and meiotic nuclear events (female meiotic division, sister chromatid cohesion). Together these point to a core function in nuclear transport and chromosome/meiotic regulation, with ancillary signals from mRNA transport and GTPase activity. ","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071230","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0006610","count":2},{"id":"GO:0006335","count":2},{"id":"GO:0097711","count":2}]},{"hash":"1706055717225118167","title":"Ribosome biogenesis and nuclear transport","description":"The terms spike around ribosomal small subunit assembly and localization to the nuclear pore, suggesting a theme of ribosome maturation with nucleocytoplasmic transport; other terms are more peripheral (endocytosis, signaling, DNA repair), so a ribosome/transport focus is the best cohesive label.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1900186","count":5},{"id":"GO:1903071","count":5},{"id":"GO:0031117","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0030433","count":5}]},{"hash":"1156417610404472816","title":"Nuclear transcription and RNA processing","description":"The top GO terms cluster around nuclear gene expression and RNA metabolism: transcription initiation and regulation (DNA-templated transcription, positive regulation of transcription by RNA Pol II), chromatin remodeling/histone modification (H2B ubiquitination, DNA topological changes), RNA processing events (prespliceosome assembly, nuclear polyadenylation-dependent rRNA catabolism), and DNA repair coordination (transcription-coupled nucleotide-excision repair). A few terms also touch on stress-related RNA localization, supporting a broader RNA-processing/nucleus-centric function. Overall, these proteins appear to participate in nuclear transcription control and RNA processing with links to chromatin state and genome maintenance.","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0071894","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070934","count":2},{"id":"GO:0006283","count":2}]},{"hash":"1651537638426958301","title":"Unknown","description":"The top terms are very diverse, including nervous system and muscle development, reproductive development, circadian rhythm, immune differentiation, cell-cycle spindle localization, plant hormone signaling, and viral latency, plus some likely annotation noise (e.g., atypical terms). There isn\u2019t a single cohesive function or pathway tying these proteins together, so a stable, intuitive cluster label isn\u2019t identifiable. ","confidence":"","size":6,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045497","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0019046","count":3},{"id":"GO:0009742","count":3},{"id":"GO:0048741","count":3}]},{"hash":"43096179550531997","title":"LPS-triggered immune activation and lymphocyte apoptosis","description":"The top GO terms indicate a focus on response to lipopolysaccharide, regulation of B cell proliferation, and apoptotic pathways (including TRAIL signaling and activation-induced T cell death), with additional terms on inflammatory regulation and cytokine production. This combination points to a cluster of proteins involved in LPS-driven immune activation, lymphocyte proliferation control, and programmed cell death, justifying a label centered on immune activation and lymphocyte apoptosis.","confidence":"High","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0030890","count":2},{"id":"GO:0051044","count":2},{"id":"GO:0050728","count":1},{"id":"GO:0006925","count":1}]},{"hash":"1224954783432308785","title":"Motile cilia assembly and left-right development","description":"The cluster is dominated by GO terms for motile cilium/axoneme assembly and left-right symmetry determination, with heart development and related developmental processes likely reflecting cilia-driven signaling in embryogenesis. While there are additional gonad-related terms, they do not override the strong ciliogenesis and left-right patterning signal, making this a coherent, specific theme for the group.","confidence":"High","size":6,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007368","count":2},{"id":"GO:0070286","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0044458","count":2}]},{"hash":"1884892073114276535","title":"Cerebellar development and neuronal migration","description":"Most top GO terms cluster around cerebellar development and neuronal migration, including cerebellum structural organization, radial glia-guided migration of Purkinje cells, and lateral motor column neuron migration. Additional terms touch on neurodevelopmental signaling and differentiation, which fit a developmental context. The dominant theme is cerebellar brain development and neuronal migration, with related synaptic and signaling roles supporting this core function.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":1},{"id":"GO:0097477","count":1},{"id":"GO:0030511","count":1},{"id":"GO:0007268","count":1},{"id":"GO:0060766","count":1}]},{"hash":"149006572151113172","title":"Insect Neurotransmission and Cuticle Development","description":"The cluster centers on neuronal and neuroendocrine functions (aminergic neurotransmitter loading into synaptic vesicles; serotonin biosynthesis) and insect-specific traits (regulation of adult chitin-containing cuticle pigmentation; mating behavior; tracheal system-related processes), suggesting a cohesive theme around insect nervous system activity coupled with cuticle biology. A few terms like ossification/bone remodeling appear as outliers or cross-species signals. ","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030279","count":1},{"id":"GO:2000274","count":1},{"id":"GO:0015842","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0055114","count":1}]},{"hash":"919657654393458626","title":"Lipid Metabolism and Lipoprotein Transport","description":"The top GO terms are dominated by lipid-related processes (leukotriene biosynthesis, reverse cholesterol transport, regulation of lipoprotein metabolic process, lipid digestion), suggesting a lipid metabolism and transport-focused cluster. The developmental terms (mesonephric duct development, metanephric limb development, and cartilage condensation) may reflect broader roles of lipid signaling genes in development or incidental associations, but the primary signal centers on lipid metabolism and transport.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019370","count":2},{"id":"GO:0072177","count":2},{"id":"GO:0043691","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0042994","count":2}]},{"hash":"605668084353730551","title":"P-body mRNA processing and translational control","description":"The top GO terms cluster around cytoplasmic mRNA processing bodies (P-bodies), including P-body assembly, deadenylation-dependent decapping, and negative regulation of translational initiation, indicating a module focused on mRNA metabolism and translational control. While a few chromatin-related terms appear, they are far less represented, suggesting the primary function is mRNA processing rather than chromatin regulation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045190","count":2},{"id":"GO:0033962","count":2},{"id":"GO:0010607","count":2},{"id":"GO:0000290","count":2},{"id":"GO:0045947","count":2}]},{"hash":"2179794680439460567","title":"Golgi\u2013ER and Synaptic Vesicle Trafficking","description":"The top GO terms cluster around vesicle transport involving the Golgi and endomembrane system (ER to Golgi, Golgi to ER, Golgi to vacuole), along with synaptic vesicle processes (budding and anterograde transport) and Golgi inheritance. This points to a coherent theme of intracellular trafficking centered on the Golgi/endomembrane network, with a neuronal/synaptic component. Some brain-related terms appear, but they align with the neuronal trafficking theme rather than indicating a separate function.","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0048490","count":5},{"id":"GO:0006896","count":4},{"id":"GO:0021691","count":4}]},{"hash":"1443181028366034970","title":"Transmembrane sugar and organic substrate transport","description":"The top GO terms are dominated by diverse transmembrane transport activities for sugars (glucose, galactose, fructose), organic anions/cations, phosphate, and xenobiotics, suggesting a shared function of transporting small molecules across membranes; the tissue-related term about intestinal epithelial structure maintenance fits a contextual role but does not alter the core transport theme.","confidence":"High","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043252","count":3},{"id":"GO:1904659","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0070715","count":3},{"id":"GO:1900754","count":3}]},{"hash":"1173582516135028141","title":"Multiorgan development and morphogenesis","description":"Top GO terms point to tissue-specific development and morphogenesis across multiple organs (heart, nervous system, Malpighian tubule, kidney, reproductive tract). The cluster seems cohesively about developmental differentiation rather than a single signaling pathway, justifying a broad label that captures the shared theme without overstretching specificity.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0033627","count":6},{"id":"GO:0021750","count":6},{"id":"GO:0003259","count":6},{"id":"GO:0061382","count":6},{"id":"GO:0003053","count":6}]},{"hash":"688356151454938587","title":"Unknown","description":"The terms are spread across synaptic signaling, vesicle trafficking, signaling cascades, transcription regulation, and development, with no evident cohesive theme and no edges linking proteins, making it hard to assign a specific function to the cluster. Confidence: None","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":3},{"id":"GO:0051036","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0034968","count":2}]},{"hash":"1064151689719447034","title":"Developmental Morphogenesis Across Tissues","description":"The top GO terms point to morphogenesis and differentiation in diverse tissues (thymus, anther tapetum) and cell lineages (spermatid differentiation, thymocyte migration), indicating a shared theme of developmental processes rather than a single specific pathway. Although some terms are obsolete and span different organs, the overarching pattern is tissue morphogenesis and differentiation. Therefore, this cluster can be labeled as Developmental Morphogenesis Across Tissues with moderate confidence.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097536","count":5},{"id":"GO:0007289","count":4},{"id":"GO:0051573","count":4},{"id":"GO:0051571","count":4},{"id":"GO:2000791","count":4}]},{"hash":"2218049664203531777","title":"Sugar Transport and Metabolism","description":"The Top Terms show multiple GO terms about import of glucose/fructose across the plasma membrane, fructose metabolic process, carbohydrate phosphorylation, and D-glucose import regulation, plus pyruvate fermentation, all pointing to carbohydrate uptake and energy metabolism. Some terms like lactation, stomatal closure, and response to ketamine are broader or peripheral annotations. Overall, the core signal is carbohydrate transport and metabolism, so the label reflects that theme.","confidence":"Medium","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007595","count":3},{"id":"GO:0090332","count":3},{"id":"GO:0046324","count":3},{"id":"GO:0019660","count":3},{"id":"GO:1901986","count":3}]},{"hash":"1003454882749415225","title":"Neural development and brain maturation","description":"This cluster centers on neural development with terms like neuron maturation, substantia nigra development, and regulation of synaptic vesicle exocytosis, plus developmental pathways such as canonical Wnt signaling and in utero embryonic development. The presence of endothelial barrier establishment and epithelial polarity also fits broader developmental processes linked to brain vasculature and tissue organization. Together, these terms point to a cohesive theme of neural development and maturation, including brain region-specific growth and synaptic regulation.","confidence":"High","size":6,"edges":7,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035264","count":5},{"id":"GO:0043124","count":5},{"id":"GO:0008283","count":4},{"id":"GO:0042551","count":3},{"id":"GO:0001701","count":3}]},{"hash":"216666820653400441","title":"Mitotic spindle assembly and adherens junctions","description":"The Top Terms cluster around mitotic machinery (spindle assembly, kinetochore attachments, spindle midzone, metaphase chromosome recapture) and cell\u2013cell junctions (zonula adherens maintenance, actomyosin contractile ring). This points to proteins involved in organizing the mitotic spindle and coordinating cytokinesis with adherens junction dynamics during morphogenesis or tissue remodeling. A couple of developmental terms appear, but they likely reflect broader roles in development rather than changing the core theme.","confidence":"High","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0072092","count":4},{"id":"GO:0048364","count":4},{"id":"GO:0099607","count":4},{"id":"GO:0001560","count":4},{"id":"GO:0051255","count":4}]},{"hash":"201579597740681999","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0071166","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0048254","count":2},{"id":"GO:0000244","count":2}]},{"hash":"303731986289113726","title":"Unknown","description":"The top GO terms cover embryonic processes (gastrulation polarity, mesectoderm development), plant development (lateral root development, auxin transport), and diverse signaling responses (dopamine receptor signaling, catecholamine response, prostaglandin response) plus membrane transport. There is no clear, single function tying these terms together, so a coherent cluster label cannot be confidently assigned.","confidence":"","size":6,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0003380","count":2},{"id":"GO:0031684","count":2},{"id":"GO:0007191","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0071870","count":1}]},{"hash":"1251073237894914409","title":"Neural signaling and synaptic vesicle exocytosis","description":"This cluster centers on neural communication and synaptic vesicle regulation, with terms for neurotransmitter secretion and synaptic vesicle exocytosis as top signals, plus neural-development terms like substantia nigra and retina. Some terms are obsolete or peripheral (e.g., myoblast fusion), but the core theme suggests neural signaling. ","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007269","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0016061","count":3},{"id":"GO:0007520","count":3},{"id":"GO:0006469","count":3}]},{"hash":"1620670726255740116","title":"Embryonic organogenesis and morphogenesis","description":"The proteins are tied to early development and tissue formation, with top GO terms spanning in utero embryonic development, embryonic eye morphogenesis, ovarian follicle growth, and cardiac muscle tissue morphogenesis/proliferation. This suggests a cohesive theme of embryonic organogenesis and tissue differentiation, with supportive regulatory roles in inflammation and metabolism that commonly accompany developmental programs.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001547","count":5},{"id":"GO:0060528","count":5},{"id":"GO:0055010","count":5},{"id":"GO:0001701","count":5},{"id":"GO:0060038","count":5}]},{"hash":"1114912348450004816","title":"Calcium-Dependent Signaling Across Tissues","description":"The top terms cluster around calcium handling and signaling in diverse contexts: SR-mediated Ca release and regulation of cardiac muscle contraction/relaxation point to calcium dynamics in muscle; regulation of dopamine metabolism and cone cell development hint at neural and retinal signaling; interferon production and monocyte differentiation reflect immune signaling, which can also involve calcium flux. This suggests a unifying theme of calcium-dependent signaling operating across tissues, hence the chosen label.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046549","count":6},{"id":"GO:1903206","count":6},{"id":"GO:0032729","count":6},{"id":"GO:0055119","count":6},{"id":"GO:0042053","count":6}]},{"hash":"647533838475863242","title":"Glutathione-mediated oxidative stress and cadmium detox","description":"The cluster shows a coherent theme of glutathione metabolism and oxidative stress response, including glutathione biosynthesis and transport, phytochelatin biosynthesis for heavy metal chelation, and cadmium-related detoxification, along with response to hydrogen peroxide and proteasomal degradation of damaged proteins. While some hormone-related terms appear, they seem incidental; the dominant pattern supports a glutathione-driven defense against oxidative stress and cadmium toxicity.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":3},{"id":"GO:0034635","count":2},{"id":"GO:0071372","count":2},{"id":"GO:0046938","count":2},{"id":"GO:0032436","count":2}]},{"hash":"1510169191662231854","title":"Unknown","description":"These proteins show both immune-related terms (innate immune response and B cell homeostasis) and a variety of metabolic processes (CoA catabolic, folic acid and isoprenoid biosynthesis, nucleotide turnover, and RNA editing). The terms do not point to a single coherent function or pathway tying the cluster together, so a specific, intuitive label cannot be confidently assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0001782","count":2},{"id":"GO:0015938","count":1},{"id":"GO:0046656","count":1},{"id":"GO:0009240","count":1}]},{"hash":"734876435439964193","title":"Actin-driven cytoskeleton remodeling & signaling","description":"The top GO terms emphasize actin cytoskeleton assembly (cortical patch, filament bundles, lamellipodium) and signaling pathways that regulate this remodeling (PDGF receptor signaling, endothelin response, p38 MAPK regulation). This suggests a core theme of cytoskeletal dynamics interconnected with growth-factor and vascular signaling, even though some other terms in the set may reflect broader roles. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030702","count":6},{"id":"GO:0002051","count":6},{"id":"GO:1990859","count":6},{"id":"GO:0000147","count":6},{"id":"GO:0051017","count":6}]},{"hash":"150363901638305382","title":"Neuronal cytoskeleton and synaptic adhesion dynamics","description":"These terms cluster around neuronal cytoskeletal remodeling, junction assembly, and synaptic regulation, including actin dynamics (actin filament bundle, lamellipodium), adherens/tight junction localization, Rho signaling, and pathways like JNK, all of which underpin synaptic plasticity and neuron\u2013glia interfaces. The inclusion of social behavior and myelin-associated localization supports a neuronal context for these processes.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051017","count":6},{"id":"GO:0030032","count":6},{"id":"GO:0035176","count":6},{"id":"GO:0035750","count":6},{"id":"GO:0070830","count":6}]},{"hash":"1424135522979853036","title":"Chromatin remodeling and nucleosome dynamics","description":"The cluster centers on chromatin-related processes: histone acetylation regulation (H3-K9/K14), nucleosome assembly/disassembly, and chromatin decondensation, with supplementary links to microtubule dynamics and cell division (stem cell division, budding). This suggests a cohesive theme of chromatin remodeling coordinated with cell-cycle processes. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031116","count":3},{"id":"GO:2000617","count":3},{"id":"GO:0007117","count":3},{"id":"GO:2000035","count":3},{"id":"GO:0006337","count":3}]},{"hash":"1468279533674636140","title":"Skeletal Development and Morphogenesis","description":"The top GO terms are dominated by skeletal system development (3) and skeletal system morphogenesis (2), with gastrulation also present (2). This pattern points to a developmental role focused on tissue and skeletal formation, suggesting the proteins contribute to morphogenetic processes. Some terms like DNA repair and mRNA transport are less directly related, but the strongest signal centers on skeletal development.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0000724","count":3},{"id":"GO:0007205","count":2},{"id":"GO:0048705","count":2}]},{"hash":"13094337010270665","title":"Ubiquitin-regulated mitosis and cytoskeleton","description":"The terms show a clear emphasis on K11-linked ubiquitination and mitotic cell cycle control, including negative regulation of mitotic DNA replication, alongside cytoskeletal processes such as stress fiber assembly and Rho signaling. While there are outliers related to development and morphogenesis, the strongest, most coherent signal ties ubiquitin-mediated regulation to mitosis and cytoskeleton dynamics, justifying a label focused on these processes.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0035019","count":1},{"id":"GO:0031286","count":1},{"id":"GO:0045773","count":1}]},{"hash":"95494674071839981","title":"Developmental signaling and cytoskeletal organization","description":"This cluster centers on cell signaling interfaces, adhesion, and cytoskeletal remodeling that underlie tissue morphogenesis (receptor clustering, lamellipodium assembly, epithelial polarity, and synapse organization). Thymus development and osteoblast fate commitment suggest broader developmental contexts, and endothelin signaling plus MAPK regulation fit into signaling responses. The common thread is developmental signaling coordinating cell structure and connections, though a few terms are more distal.","confidence":"Medium","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015879","count":5},{"id":"GO:0002051","count":5},{"id":"GO:1990859","count":5},{"id":"GO:0030032","count":5},{"id":"GO:0051612","count":5}]},{"hash":"2005164723489518259","title":"Immune signaling and cell adhesion regulation","description":"The cluster centers on immune-related processes such as natural killer cell cytotoxicity and interferon production, while also encompassing regulation of cell\u2013cell interactions (adherens junction organization, epithelial migration) and signaling pathway modulation (p38 MAPK, EGFR). Although a couple terms hint at neuronal structures (axon regeneration, dendritic spine development), the dominant theme is modulation of immune signaling and cell adhesion. ","confidence":"Medium","size":6,"edges":10,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042267","count":5},{"id":"GO:2001275","count":4},{"id":"GO:0048679","count":4},{"id":"GO:0010633","count":4},{"id":"GO:1903753","count":4}]},{"hash":"607457128828352099","title":"Organogenesis and patterning","description":"These proteins are mainly linked to developmental patterning and organ formation across tissues (left/right patterning; alveolar and lung development; skeletal muscle and mesenchymal proliferation; ovarian ovulation; prostate morphogenesis). While a few terms are broader, the dominant theme is developmental morphogenesis, supporting this label.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060972","count":5},{"id":"GO:0008286","count":5},{"id":"GO:0001542","count":4},{"id":"GO:0002074","count":4},{"id":"GO:0060741","count":4}]},{"hash":"1444141624219506217","title":"Actin Cytoskeleton Assembly and Motility","description":"Dominant terms center on actin patch/bundle/lamellipodium assembly and related signaling (PDGFR, endothelin) implying cytoskeleton remodeling and cell movement; other terms are less directly connected but may reflect broader regulatory roles.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030702","count":6},{"id":"GO:0002051","count":6},{"id":"GO:1990859","count":6},{"id":"GO:0000147","count":6},{"id":"GO:0051017","count":6}]},{"hash":"787948414599138826","title":"Chromatin organization and transcription regulation","description":"This cluster centers on nucleosome assembly, heterochromatin organization, and histone modification, pointing to a chromatin-associated nuclear function. While there are some RNA processing and transcription termination-related terms, the dominant theme ties to chromatin structure and the regulation of transcription. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097298","count":1},{"id":"GO:0016584","count":1},{"id":"GO:0098532","count":1},{"id":"GO:0070828","count":1},{"id":"GO:0006334","count":1}]},{"hash":"966161719476989711","title":"Osteogenesis and ECM Regulation","description":"The cluster\u2019s GO terms are dominated by bone-related processes: positive regulation of osteoblast differentiation, osteoblast fate commitment, positive regulation of extracellular matrix (ECM) assembly, and positive regulation of TGF-\u03b2 receptor signaling, suggesting a cohesive module for osteogenesis and ECM remodeling. The presence of negative regulation of ossification adds a balancing nuance common in bone development. A few terms tied to morphogenesis appear, but the core signal points to bone formation and matrix regulation rather than general development. ","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045669","count":3},{"id":"GO:0035725","count":2},{"id":"GO:0071805","count":2},{"id":"GO:1901203","count":2},{"id":"GO:0030511","count":2}]},{"hash":"1603574118647014679","title":"Chemokine signaling and immune cell chemotaxis","description":"The top terms are dominated by immune cell chemotaxis across several cell types (eosinophils, macrophages, neutrophils, T cells) and chemokine-mediated signaling, with ERK cascade regulation indicating signaling activation. A term about insulin secretion is likely incidental. This suggests a core function in chemokine-driven immune cell migration.","confidence":"High","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0048245","count":5},{"id":"GO:0006955","count":5},{"id":"GO:0010759","count":5},{"id":"GO:0070374","count":5},{"id":"GO:0051930","count":5}]},{"hash":"1692627474062058097","title":"Cholesterol Transport and Lipid Homeostasis","description":"This cluster is dominated by GO terms related to cholesterol transport and lipid metabolism, including intracellular cholesterol transport, cholesterol efflux, cholesterol homeostasis, and lipid storage, supported by ganglioside catabolism as a related lipid-processing process. While a couple of terms touch on neural functions, the strongest common theme ties to cholesterol handling and lipid regulation in cells.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006689","count":1},{"id":"GO:0032367","count":1},{"id":"GO:0033344","count":1},{"id":"GO:0032760","count":1},{"id":"GO:0019915","count":1}]},{"hash":"2076163025456310032","title":"Antiviral autophagy and immune signaling","description":"The GO terms point to a cohesive immune-focused module: antiviral defense, autophagy regulation, and inflammatory signaling. Terms like positive regulation of autophagy, defense response to virus, T cell homeostasis, and IL-17 signaling indicate coordinated immune responses, while regulation of nitric-oxide synthase activity suggests modulation of inflammatory mediators. Some obsolete/outlier terms are present, but the core theme ties autophagy and immune signaling to antiviral defense.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000653","count":1},{"id":"GO:1901253","count":1},{"id":"GO:0010508","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0060546","count":1}]},{"hash":"805396251662094168","title":"Spermatogenesis and placental development with immune links","description":"The cluster\u2019s top GO terms center on reproductive development, notably spermatogenesis and chorionic trophoblast differentiation, with related processes like acrosome reaction regulation and BDNF signaling modulation. The presence of immune/modulatory terms (blood coagulation and membrane attack complex activation) suggests additional immune involvement in pregnancy-related tissues, indicating a theme of reproductive development with immune interactions.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043113","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0043252","count":2},{"id":"GO:0031549","count":2},{"id":"GO:0060718","count":2}]},{"hash":"1131583398781751304","title":"Diverse biosynthetic pathways","description":"The cluster shows a mix of biosynthetic and catabolic processes across small molecules and cofactors (fatty acid elongation, phylloquinone and tetrahydrobiopterin biosynthesis, poly-hydroxybutyrate biosynthesis) plus antibiotic-related processes and sporulation, suggesting enzymes involved in various metabolic pathways rather than a single, unified function. Confidence: Medium","confidence":"","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":6},{"id":"GO:0030497","count":5},{"id":"GO:0006704","count":5},{"id":"GO:0042376","count":5},{"id":"GO:0042619","count":5}]},{"hash":"264671165462779937","title":"Plant Cell Wall Biogenesis and Glycosylation","description":"Most terms point to plant-specific cell wall construction and polysaccharide modification (secondary cell wall biogenesis, mucilage/glucuronoxylan/homogalacturonan biosynthesis) and related carbohydrate metabolism, alongside protein O-linked glycosylation. An outlier term about skeletal muscle regeneration appears unrelated. Overall, the cluster reflects plant cell wall polysaccharide biosynthesis and glycosylation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043403","count":1},{"id":"GO:0016266","count":1},{"id":"GO:0035269","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0009834","count":1}]},{"hash":"2150619845593070455","title":"Neural development and synaptic maturation","description":"The top GO terms cluster around neural development and synaptic assembly/function: axon guidance, gephyrin clustering at postsynaptic density, protein complex assembly for synapse maturation, neurotransmitter secretion and chemical synaptic transmission, and even vocalization/learning, which points to brain circuits governing communication. Neural tube closure also fits into early neural development, supporting a developmental-to-synaptic maturation theme. Confidence: High","confidence":"","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071625","count":3},{"id":"GO:2000821","count":2},{"id":"GO:0007411","count":2},{"id":"GO:0007268","count":2},{"id":"GO:0097116","count":2}]},{"hash":"1196619141214135670","title":"Palatal and craniofacial development with ECM remodeling","description":"The top GO terms point to palatogenesis (roof of mouth development), craniofacial morphogenesis, and extracellular matrix organization (collagen fibril organization), together with epithelial-to-mesenchymal transition and chondrocyte differentiation. While some terms touch broader embryogenesis (somite and aorta development) the strongest shared theme is craniofacial development tied to ECM remodeling and EMT-driven tissue morphogenesis, suggesting a coordinated role in facial structure formation and cartilage formation. Confidence in this being the core function is Moderate.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":2},{"id":"GO:0030199","count":2},{"id":"GO:0061053","count":1},{"id":"GO:0001837","count":1},{"id":"GO:0018057","count":1}]},{"hash":"300105860476444738","title":"Plant lipid catabolism and secondary metabolism","description":"Top GO terms indicate strong enrichment for lipid catabolic processes (lipid catabolic, triglyceride catabolic) with several other catabolic and secondary metabolism terms (alkaloid metabolism, beta-ketoadipate pathway, uracil catabolic, poly-hydroxybutyrate biosynthetic). The presence of plant-specific terms (secondary shoot formation, defense response to insect) suggests a plant context. Taken together, the cluster seems to group proteins involved in breakdown of lipids and other carbon sources, along with pathways tied to secondary metabolism and defense. Therefore, a concise label reflecting lipid catabolism with plant secondary metabolism is appropriate.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0019433","count":5},{"id":"GO:2000124","count":4},{"id":"GO:0016042","count":4},{"id":"GO:0042952","count":4}]},{"hash":"1649770583114243367","title":"Neural Development and ERK Signaling","description":"These proteins show enrichment in neuron migration, axonal fasciculation, synapse assembly, and homophilic cell\u2013cell adhesion, together with positive regulation of the ERK1/2 cascade, pointing to roles in neural development and connectivity with ERK signaling as a central pathway. While terms like angiogenesis and heart development appear, they do not override the neural-focused terms, making this label a good overall representation.","confidence":"High","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0070374","count":5},{"id":"GO:0001764","count":5},{"id":"GO:0043031","count":5},{"id":"GO:0007413","count":5},{"id":"GO:0007507","count":5}]},{"hash":"600302984910869047","title":"RNA stability and translation regulation","description":"The cluster is dominated by GO terms related to post-transcriptional control of gene expression, including mRNA stability, stress-responsive mRNA regulation, translational initiation, formation of the preinitiation complex, translation reinitiation, and miRNA/ncRNA-mediated gene silencing. These consistently point to coordinated regulation at the RNA level rather than a single enzyme or pathway, supporting a cohesive theme of RNA stability and translation control.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":3},{"id":"GO:0001825","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0006446","count":3},{"id":"GO:1900363","count":3}]},{"hash":"1093859935923700937","title":"Neural development and axon guidance","description":"The top GO terms cluster around neural development and axon navigation: neural precursor cell proliferation, retinal ganglion cell axon guidance, fasciculation of sensory neuron axons, and protein localization in axon regions, with PI3K/AKT signaling supporting neuronal growth. Although a few terms touch on immune regulation and endothelial migration, the dominant theme is neuronal development and axon pathfinding, justifying a label focused on neural development and axon guidance.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043491","count":5},{"id":"GO:2000525","count":4},{"id":"GO:0061351","count":4},{"id":"GO:0048320","count":4},{"id":"GO:0048692","count":4}]},{"hash":"579640489196350023","title":"Drosophila development and transcription regulation","description":"The cluster shows terms tied to developmental processes in Drosophila (sensory organ precursor fate, imaginal disc formation, axial mesoderm formation) and transcriptional regulation, with chromatin modification (histone acetylation) hints. This combination suggests proteins coordinating development through transcription regulation, possibly via chromatin-level control.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016360","count":2},{"id":"GO:0046529","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0045652","count":2},{"id":"GO:0043983","count":2}]},{"hash":"1663698003429284212","title":"Neural and muscle development with vesicle trafficking","description":"The top terms point to development of both muscle (skeletal muscle fiber development, mesoderm development) and neural/sensory structures (retina layer formation, substantia nigra development), suggesting coordinated formation of neural and muscular tissues. Additional terms about endoplasmic reticulum to Golgi vesicle transport, regulation of synaptic vesicle exocytosis, and calcium signaling support cellular trafficking and communication crucial for developing neurons and muscle cells. This combination indicates a theme centered on neural and muscular development with associated vesicle trafficking processes.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0010288","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0007498","count":2}]},{"hash":"365264200744238441","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around ribosome biogenesis (large and small subunit biogenesis), export of ribosomal subunits, and tRNA modification, with several translation- and RNA-processing related terms. While there are a couple of cell division terms present, the dominant signal ties to ribosome assembly and RNA metabolism, suggesting these proteins function together in ribosome production and translation-related processes.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1694410489386451086","title":"DNA replication and damage repair","description":"This cluster is dominated by GO terms related to DNA replication (initiation, strand elongation) and DNA repair (UV-damage excision repair, translesion synthesis, RNA-templated DNA biosynthesis), indicating a genome maintenance function. Some metabolic terms appear, but the DNA replication/repair signals are the strongest theme.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006749","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0070988","count":1},{"id":"GO:0006270","count":1},{"id":"GO:0042276","count":1}]},{"hash":"643495818603660692","title":"Chromatin/heterochromatin formation and histone deacetylation","description":"The top GO terms cluster around chromatin organization, mainly pericentric heterochromatin formation, heterochromatin maintenance, and peptidyl-lysine deacetylation, with localization to nucleolar rDNA repeats supporting a chromatin/nucleolar function.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030702","count":3},{"id":"GO:0000117","count":3},{"id":"GO:0010870","count":3},{"id":"GO:0045128","count":3},{"id":"GO:0034503","count":3}]},{"hash":"1095752162823045094","title":"Telomere maintenance and nuclear organization","description":"The top terms cluster around telomere biology (shelterin complex assembly, subtelomeric heterochromatin formation, protein localization to telomere) and nuclear structure/processes (nuclear migration, nuclear inner membrane organization) with additional links to DNA repair, suggesting a theme of genome stability within the nucleus. Some terms related to plant signaling and metabolism may be incidental annotations, not central to this cluster.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007097","count":2},{"id":"GO:0071765","count":2},{"id":"GO:0010761","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0072362","count":2}]},{"hash":"2101810825360379803","title":"Heart development and angiogenesis","description":"The GO terms show strong signals for heart development and angiogenesis, with additional multicellular development terms, suggesting a cardiovascular development theme. Other terms point to signaling and endocytic regulation that may support development in cardiac or vascular contexts, but the dominant theme centers on heart and vessel formation.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0030100","count":2},{"id":"GO:0038095","count":2},{"id":"GO:0032516","count":2},{"id":"GO:0035023","count":2}]},{"hash":"444096268077693806","title":"Neural development and synaptic morphogenesis","description":"The GO terms point to nervous system development, dendritic spine morphogenesis, receptor clustering, and protein localization to the synapse. Rho signaling and axon midline recognition support cytoskeletal dynamics and guidance during neural development, while visual learning and collateral sprouting suggest activity-dependent synaptic remodeling. Together, these indicate a cluster of proteins involved in neural development, synapse formation, and plasticity.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0008542","count":2},{"id":"GO:0043113","count":2},{"id":"GO:0035418","count":2},{"id":"GO:0008285","count":2}]},{"hash":"529228825018426633","title":"Developmental transcriptional regulation under stress","description":"Many top GO terms point to developmental processes (lens fiber differentiation, seminiferous tubule and skeletal system development) and to transcriptional control (DNA-templated transcription, chromatin organization). The inclusion of stress-related responses (hypoxia, ER stress\u2013induced and other apoptotic signaling, cadmium response) suggests a cluster of proteins involved in coordinating development with cellular stress responses and apoptosis.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070306","count":3},{"id":"GO:0072520","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0071456","count":3}]},{"hash":"2121252542644615516","title":"Cytoskeleton Dynamics and Cell Migration Regulation","description":"The cluster centers on terms like positive regulation of stress fiber assembly, fibroblast migration, and response to mechanical stimulus, highlighting cytoskeletal remodeling and cell movement. Other terms point to trafficking and protein turnover (endocytosis, nuclear export, proteasomal degradation) that modulate these processes, suggesting a cohesive theme of how the cytoskeleton and membrane trafficking are regulated during migration and mechanotransduction.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":2},{"id":"GO:0010763","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0071364","count":1}]},{"hash":"682379344763067695","title":"Spermatogenesis with cytoskeletal and GTPase signaling","description":"The cluster is dominated by terms related to sperm development (spermatid nucleus differentiation; sperm mitochondrion organization) and cytoskeletal/GTPase regulation (regulation of Rho signaling; activation of GTPase activity; spindle assembly), suggesting a cohesive theme around meiosis/cytoskeletal dynamics during spermatogenesis. Some other terms (osmotic stress, endothelial apoptosis) may reflect broader signaling roles or incidental associations, but the main pattern points to sperm development and cytoskeletal control.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0007289","count":2},{"id":"GO:0045792","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0090630","count":2}]},{"hash":"87712425689446613","title":"Skeletal development and embryogenesis","description":"This cluster is named for the strong presence of skeletal system development and morphogenesis terms (GO:0001501, GO:0048705) and gastrulation (GO:0007369), which point to roles in skeletal formation and early embryonic processes. Other items like cilium assembly, mRNA transport, and mitochondrial-nuclear signaling suggest accompanying cellular and developmental functions that often accompany tissue formation, but the central theme remains skeletal development and embryogenesis.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":2},{"id":"GO:0048705","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0000348","count":2},{"id":"GO:0031930","count":2}]},{"hash":"1954245827005897371","title":"Oocyte mRNA localization and translational control","description":"This cluster centers on oocyte development and early embryogenesis, highlighted by oskar mRNA localization to the pole plasm and regulation of mRNA stability and translation (including initiation and polyadenylation), together supporting axis specification and blastocyst formation.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071230","count":3},{"id":"GO:0048255","count":2},{"id":"GO:0007310","count":2},{"id":"GO:1900248","count":2},{"id":"GO:0001825","count":2}]},{"hash":"628597856055455739","title":"Multitissue development and morphogenesis","description":"Many top terms point to development and morphogenesis across tissues (lung, ovary, prostate, muscle, mesenchyme). The presence of insulin signaling and a cell-cycle checkpoint term suggests growth regulation during development, but there is no single pathway dominating. Overall, the proteins appear linked to tissue formation and organ development rather than a specific signaling axis.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0007095","count":2},{"id":"GO:0001542","count":1},{"id":"GO:0002074","count":1},{"id":"GO:0060741","count":1}]},{"hash":"506626272999139930","title":"Cell Signaling and Cytoskeletal Remodeling","description":"The top GO terms point to multiple signaling pathways (Ral, GPCR, JNK) and processes tied to actin dynamics (lamellipodium assembly) and cell adhesion, with vascular and apoptotic context (thrombin signaling, blood vessel development, apoptosis). Together these suggest a cluster of proteins coordinating signal transduction with cytoskeletal remodeling and cellular movement, rather than a single specific pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097194","count":3},{"id":"GO:2001275","count":2},{"id":"GO:0032485","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0046329","count":2}]},{"hash":"2295927085645525830","title":"Mitotic spindle dynamics and adherens junctions in development","description":"The cluster centers on mitotic machinery (mitotic spindle assembly, kinetochore\u2013microtubule attachments, spindle midzone, metaphase chromosome recapture) and on cell\u2013cell junctions (actomyosin contractile ring, zonula adherens maintenance), suggesting proteins involved in chromosome segregation and junction remodeling during development. A few terms reference broader developmental contexts (ureteric bud invasion, root development), but the core theme remains mitosis plus adherens junction dynamics in developmental settings.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0072092","count":3},{"id":"GO:0048364","count":3},{"id":"GO:0099607","count":3},{"id":"GO:0001560","count":3}]},{"hash":"1365104547290496704","title":"Actin Cytoskeleton Organization and Nucleation","description":"The top terms are dominated by actin cytoskeleton\u2013related functions, including actin nucleation, cortical actin organization, formin-nucleated actin cable assembly, and regulation of bleb formation, pointing to a cohesive theme of actin filament assembly and cortex remodeling across the proteins in this cluster. Some developmental terms are present but do not outweigh the strong actin remodeling signal.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072092","count":1},{"id":"GO:0007292","count":1},{"id":"GO:0035320","count":1},{"id":"GO:0051279","count":1},{"id":"GO:2000251","count":1}]},{"hash":"745040651392154585","title":"Neuronal development and axon guidance","description":"This cluster centers on neural development and axon guidance: terms such as pyramidal neuron development, optic vesicle formation, branchiomotor neuron axon guidance, trigeminal nerve organization, and semaphorin-plexin signaling point to neuronal growth and pathwayfinding. Additional terms like carbohydrate metabolism and regulation of GTPase activity are supportive rather than core. Thus the label reflects neural development and axon guidance.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0021860","count":2},{"id":"GO:0005975","count":2},{"id":"GO:1902287","count":2},{"id":"GO:0003403","count":2},{"id":"GO:0021785","count":2}]},{"hash":"348196786780561576","title":"Neural Development and Transcriptional Regulation","description":"The cluster is dominated by GO terms tied to neural and multicellular development (forebrain development, neural tube closure, skeletal system development, multicellular organism development) and transcriptional control (DNA-templated transcription, regulation of gene expression). While there are a few less related terms (cadmium response, defense to Gram-positive bacteria), the central theme points to developmental gene regulation, especially in neural contexts.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":5},{"id":"GO:0001501","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0001403","count":4}]},{"hash":"590012380975243153","title":"Cardiac development and contraction","description":"The strongest signals are heart development and cardiac muscle contraction, suggesting these proteins share roles in cardiac structure and function. Additional terms reflect broader signaling regulation and cell cycle processes, indicating potentially pleiotropic roles, while some terms like visual perception and excitatory postsynaptic potential point to broader tissue distribution. Overall, the cardiac theme is the most representative for this cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0060048","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0043065","count":2}]},{"hash":"174013443851288716","title":"Ran-regulated nuclear transport and microtubule organization","description":"This cluster centers on GO terms linked to Ran signaling, nuclear-cytoplasmic transport (ribosomal subunit export from the nucleus), and microtubule-based processes involved in mitosis (astral microtubule organization and regulation of centrosome duplication). These terms together suggest a theme of nucleocytoplasmic transport coupled with spindle/microtubule organization rather than a single, cohesive pathway; the presence of other diverse terms (neural transmission, xenobiotic response, desumoylation, protein catabolism) is more peripheral and does not strongly redefine the core theme.","confidence":"Medium","size":5,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031291","count":1},{"id":"GO:0060188","count":1},{"id":"GO:0042176","count":1},{"id":"GO:0042493","count":1},{"id":"GO:0007270","count":1}]},{"hash":"302660003570488184","title":"Gametogenesis and Meiosis","description":"This cluster is dominated by terms tied to meiosis and germ cell development (spermatogenesis, sperm mitochondrion organization, spindle assembly in meiosis) along with general cell division and cellular organization terms. The mix suggests a cohesive theme around germ cell formation and meiotic processes, with a few more general processes adding context. Confidence: Medium","confidence":"","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030382","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0007056","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1650324798157734161","title":"Nuclear transcription and RNA processing","description":"The top GO terms are dominated by DNA-templated transcription and mRNA processing, including regulation of poly(A) tail shortening, all pointing to nuclear gene-expression functions. While a few terms touch on cell cycle and protein trafficking, the strongest shared function across the cluster appears to be transcriptional activity and RNA maturation within the nucleus.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0060211","count":2},{"id":"GO:0045053","count":1}]},{"hash":"1856508254656319020","title":"Synaptic vesicle release regulation and receptor clustering","description":"This cluster is dominated by GO terms related to neurotransmitter receptor clustering (glycine and GABA receptors) and the negative regulation of SNARE complex assembly, pointing to regulation of synaptic transmission and vesicle fusion; the metabolic GO terms (cysteine/glutathione biosynthesis, molybdopterin cofactor biosynthesis) appear as supporting pathways but do not define a single cohesive synaptic function, so the label emphasizes synaptic signaling. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":2},{"id":"GO:0019344","count":2},{"id":"GO:0070814","count":2},{"id":"GO:0072579","count":2},{"id":"GO:0019379","count":2}]},{"hash":"215415003201254070","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000736","count":1},{"id":"GO:0000712","count":1},{"id":"GO:0000727","count":1},{"id":"GO:0072429","count":1},{"id":"GO:1905768","count":1}]},{"hash":"1638561782223378285","title":"Neuronal cytoskeleton dynamics and microtubule transport","description":"The cluster shows enrichment for microtubule-based movement, regulation of cytoskeleton organization, and neuron-specific processes such as neuron projection morphogenesis and nervous system development, suggesting a core role in cytoskeletal dynamics supporting neural structure and intracellular transport (including viral material/protein movement along microtubules). This combination points to a cohesive function in neuronal cytoskeleton regulation and microtubule-driven transport.","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0075521","count":1},{"id":"GO:0043087","count":1},{"id":"GO:0051493","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0019060","count":1}]},{"hash":"1189901185465349917","title":"Developmental morphogenesis and axon growth","description":"The GO terms point to development and morphogenesis (nervous system development, trophectodermal morphogenesis, photomorphogenesis) coupled with cytoskeletal regulation (stress fiber assembly, Rho signaling) and axon extension. This suggests a cluster of proteins involved in developmental morphogenesis with neural differentiation and cytoskeletal remodeling. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0035019","count":3},{"id":"GO:0031286","count":3},{"id":"GO:0045773","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0035024","count":3}]},{"hash":"1418595625654280473","title":"Pore Formation and Pyroptosis","description":"The cluster is dominated by GO terms for pore formation in membranes, pore complex assembly, and pyroptotic inflammatory response, pointing to a module centered on pore-mediated inflammatory cell death. The inclusion of positive regulation of intrinsic apoptotic signaling and defense against Gram-positive bacteria supports an immune/inflammatory theme. Several terms describe ectodermal development (eye, skin structures) but these appear ancillary; the primary signal across the top terms is pore formation and pyroptosis.","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035915","count":3},{"id":"GO:0070269","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0036331","count":3},{"id":"GO:2001244","count":3}]},{"hash":"2219193143272636351","title":"Meiosis-linked nuclear transport and replication","description":"This cluster centers on nuclear processes: import of proteins into the nucleus (NLS-bearing; ribosomal protein import), mRNA transport, and regulation of DNA replication with chromatin assembly. The presence of meiotic terms (meiotic sister chromatid cohesion, female meiotic nuclear division) further links this set to meiosis. A weaker tie to ciliary basal body docking and GTPase regulation is present but secondary. Overall, the proteins likely participate in nuclear transport and replication control during meiosis.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071230","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0006610","count":4},{"id":"GO:0006335","count":4},{"id":"GO:0097711","count":4}]},{"hash":"1715689548891863503","title":"GABAergic Synaptic Transmission","description":"Most of the top GO terms point to GABA-related signaling and regulation at synapses (regulation of synaptic transmission GABAergic; gamma-aminobutyric acid signaling pathway; regulation of GPCR signaling in the context of neural transmission), suggesting the cluster centers on inhibitory neurotransmission in the nervous system. Some terms appear as outliers from other species or processes, likely reflecting annotation noise, but the core theme is GABAergic synaptic signaling.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032228","count":1},{"id":"GO:0050966","count":1},{"id":"GO:0008277","count":1},{"id":"GO:0007214","count":1},{"id":"GO:0007399","count":1}]},{"hash":"722112592439031746","title":"Endosome dynamics and receptor trafficking","description":"These proteins cluster around endosome biology and membrane trafficking: regulation of endosome size, receptor recycling, and Rho signaling that governs cytoskeletal changes needed for trafficking, with a note that some terms relate to transcription or older annotations, but the dominant pattern supports endosome-mediated receptor trafficking and signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0051036","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0034968","count":3},{"id":"GO:0060316","count":3}]},{"hash":"483121647002381037","title":"Cytoskeletal Dynamics and Cell Migration","description":"The top GO terms include actin filament bundle assembly, cell migration, and establishment of epithelial cell polarity, which together point to cytoskeletal remodeling and movement as a shared theme. Some other terms (telomere maintenance/capping and cardiac action potential regulation) seem unrelated, suggesting the cluster may contain multifunctional proteins with diverse roles. Thus, this label captures the strongest, common signal, but confidence is Low due to outlier terms.","confidence":"Low","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0032212","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0016477","count":1}]},{"hash":"545389120118169394","title":"Immune Signaling and LPS Response","description":"The cluster is dominated by immune-related terms, notably cellular response to lipopolysaccharide, T cell receptor signaling, and GM-CSF stimulus response, suggesting a core function in immune activation and signaling. The other GO terms appear as less connected metabolic or plant-specific processes, likely noise relative to the main immune theme.","confidence":"Medium","size":5,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0030643","count":1},{"id":"GO:0034478","count":1}]},{"hash":"454996072298160720","title":"Embryonic development and cartilage formation","description":"These proteins cluster around early developmental processes and skeletal tissue formation. Core terms such as gastrulation, mesoderm formation, and BMP signaling point to embryogenesis, while chondroitin sulfate proteoglycan biosynthetic process and embryonic skeletal joint development indicate cartilage/ ECM formation. Additional terms like embryonic fin morphogenesis and multicellular organism growth reinforce a developmental theme. A couple of terms (arabinan biosynthetic process, salicylic acid mediated signaling pathway) seem less directly related, likely reflecting annotation noise, but do not negate the central connection.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007369","count":3},{"id":"GO:0035264","count":2},{"id":"GO:0072498","count":2},{"id":"GO:0050650","count":2},{"id":"GO:0008101","count":2}]},{"hash":"326442454159241797","title":"Arterial endothelial signaling and vascular homeostasis","description":"The terms point to endothelial biology, especially arterial fate decisions (Notch signaling in arterial endothelial cells), mechanotransduction via shear stress, and routes governing blood pressure and coagulation, along with inflammatory signaling (NF-kappaB) and receptor clustering. While a few terms relate to broader development processes, the dominant theme is arterial endothelium signaling and vascular maintenance.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042346","count":4},{"id":"GO:0031622","count":4},{"id":"GO:0043113","count":4},{"id":"GO:0021654","count":4},{"id":"GO:0071498","count":4}]},{"hash":"1534088442063462883","title":"Immune cell adhesion and migration signaling","description":"The top terms cluster around cell movement and adhesion signaling (cell migration, integrin-mediated signaling, actin filament bundle assembly), with immune-specific pathways (B cell receptor signaling, thymus development, cellular responses to IL-7) also prominent. This suggests a cohesive theme of immune cell adhesion, motility, and associated signal transduction, supported by cytoskeletal remodeling and integrin signaling; a few terms on polarity and regulation indicate broader cellular organization but do not override the immune-migration core. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0007229","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0051017","count":2},{"id":"GO:0010641","count":2}]},{"hash":"785548734539706180","title":"N-linked glycosylation proteins","description":"The top terms are dominated by protein N-linked glycosylation (including an obsolete N-linked glycosylation via asparagine term), indicating the shared function is adding N-linked glycans to proteins. The remaining terms (encapsulation of foreign target, unidimensional cell growth) are weak or unrelated annotations and likely noise. Overall, glycosylation is the clearest common theme within this cluster.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":3},{"id":"GO:0035010","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0009826","count":1}]},{"hash":"350278998501533908","title":"Osteoblast differentiation via actin remodeling and WNT signaling","description":"This cluster centers on osteoblast fate commitment and actin cytoskeleton dynamics (ruffle assembly, actin patch/bundle assembly) coupled with signaling pathways (positive regulation of canonical WNT signaling, JNK regulation, GTPase activity). The strongest signals are WNT-driven differentiation and actin remodeling, suggesting a cohesive module of osteogenic signaling linked to cytoskeletal changes; some terms like apoptotic process and heterochromatin formation may reflect broader cellular contexts but are less central to the core theme.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0046328","count":5},{"id":"GO:0097178","count":5}]},{"hash":"1726609657968873831","title":"Endosome-lysosome trafficking and autophagy","description":"The top GO terms indicate vesicle trafficking between endosomes, lysosomes, and the Golgi, plus microtubule-based transport and autophagosome maturation, pointing to a cohesive set of proteins involved in endomembrane system trafficking and autophagy regulation; while a few terms touch on broader signaling, the dominant theme is endosome\u2013lysosome transport and autophagy-related processes.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034499","count":3},{"id":"GO:1903527","count":3},{"id":"GO:0032486","count":2},{"id":"GO:0032418","count":2},{"id":"GO:0035556","count":2}]},{"hash":"1133820328667108448","title":"Ciliary trafficking and morphogenesis","description":"The proteins show enrichment in cilium localization, vesicle transport between endosomes and lysosomes, and regulators of cell polarity and morphology, all pointing to roles in ciliary trafficking and cellular shape changes. Some terms (osteoblast fate, histamine release, ascospore membrane formation) appear less connected and may reflect broader or noisy annotations, but the dominant signal supports a function in ciliary transport and morphogenesis.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0061512","count":2},{"id":"GO:0002051","count":2},{"id":"GO:0032005","count":2}]},{"hash":"1728826119473479455","title":"Coagulation and ECM remodeling","description":"This cluster shows strong signals for blood clot formation and breakdown (Factor XII activation; positive regulation of coagulation and fibrinolysis) plus extracellular matrix turnover (collagen catabolic process; proteolysis), with embryo implantation reflecting tissue remodeling. Hypoxia and misfolded protein responses may reflect stress but do not outweigh the core coagulation/ECM theme.","confidence":"High","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":4},{"id":"GO:0051788","count":4},{"id":"GO:0030574","count":4},{"id":"GO:0002542","count":4},{"id":"GO:0010756","count":4}]},{"hash":"170819442332180667","title":"Unknown","description":"The GO terms include bacterial secretion (Type II secretion and Sec transport) alongside plant photoreception/circadian signals and chromatin organization, showing no clear shared function among the proteins. With no interactions detected (no edges/triangles), there isn't a cohesive theme to unite these proteins, so a specific label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015628","count":1},{"id":"GO:1901529","count":1},{"id":"GO:0052051","count":1},{"id":"GO:1903237","count":1},{"id":"GO:0090314","count":1}]},{"hash":"498169920602261146","title":"Embryonic development and organogenesis","description":"Our terms are dominated by developmental processes such as trophoblast giant cell differentiation, placental and endocrine system development, left-right pattern formation, and cartilage/pancreatic organogenesis, suggesting a cluster tied to embryonic development and organ formation. A few housekeeping terms (splicing, ribosomal export) appear but do not define the cluster\u2019s main theme. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0060536","count":2},{"id":"GO:0060806","count":2}]},{"hash":"514568403216194105","title":"Lipid Catabolism and Remodeling","description":"The top GO terms are dominated by triglyceride metabolism and phospholipid catabolism/remodeling (triglyceride mobilization/catabolic process, triglyceride acyl-chain remodeling, phosphatidylethanolamine/phosphatidylcholine catabolic processes). This suggests a functional cluster centered on lipid breakdown and remodeling, with a few regulatory or peripheral terms (negative regulation of PKA, xenobiotic response) that are less central to the core theme.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006642","count":3},{"id":"GO:2000480","count":3},{"id":"GO:0010898","count":3},{"id":"GO:0046338","count":3},{"id":"GO:0036153","count":3}]},{"hash":"873039194518611483","title":"Oxidative Stress Response and Protein Maintenance","description":"The cluster shows enrichment for GO terms related to cellular oxidant detoxification, response to oxidative stress, and response to hydrogen peroxide, indicating a focus on oxidative stress defense. Additional terms like protein repair and protein modification suggest maintenance of the proteome under stress, while ubiquinone biosynthesis and metabolic pathways hint at redox-related metabolism supporting these processes. Some terms are obsolete, but the core theme appears to be oxidative stress defense combined with protein maintenance.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0098869","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0042952","count":1}]},{"hash":"275391679514905878","title":"Embryogenesis and vascular morphogenesis","description":"The cluster centers on embryonic development processes: embryo implantation, endodermal differentiation, and skeletal morphogenesis, with strong signals for angiogenesis and hypoxia response, suggesting a cohesive program of developmental tissue formation and vascularization (also reflected by neural extension signals). Confidence in this label is High.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"wound healing","top_go_terms":[{"id":"GO:0007566","count":4},{"id":"GO:0001666","count":4},{"id":"GO:0048705","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0071230","count":3}]},{"hash":"1235033470840785802","title":"Hedgehog signaling in neural tube development","description":"The set of GO terms centers on Smoothened (Smo) signaling, dorsal-ventral neural tube patterning, neural tube closure, and embryonic brain development, with supportive terms for ciliogenesis and PCP/Wnt interactions. This points to a shared role of Hedgehog signaling and ciliary processes driving neural tube morphogenesis. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901620","count":1},{"id":"GO:0060563","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0036372","count":1},{"id":"GO:0060030","count":1}]},{"hash":"1786415241091463485","title":"Lipid and small-molecule biosynthesis","description":"This cluster is driven by lipid-related biosynthetic terms (fatty acid elongation; sphingolipid biosynthesis) and several other small-molecule biosynthetic or metabolic processes (glucocorticoid biosynthesis, tetrahydrobiopterin biosynthesis, poly-hydroxybutyrate biosynthesis, phylloquinone catabolic/antibiotic biosynthetic processes). The pattern points to a general theme of biosynthesis and metabolism of diverse metabolites, with lipids being a prominent subset, rather than a single, narrowly defined pathway. ","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030497","count":3},{"id":"GO:0006704","count":3},{"id":"GO:0042376","count":3},{"id":"GO:0030148","count":3},{"id":"GO:0042619","count":3}]},{"hash":"1590353285722109480","title":"Heme and cofactor biosynthesis","description":"This cluster is characterized by strong representation of biosynthetic pathways for heme and related cofactors (heme and protoporphyrinogen IX biosynthesis) and vitamin biosynthesis (biotin), suggesting a cohesive theme around production of essential cofactors and their precursors. Some xenobiotic/nutrient response terms and central metabolite mentions are present but do not define the core theme. ","confidence":"Medium","size":5,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006107","count":2},{"id":"GO:0019878","count":2}]},{"hash":"1116807838722612595","title":"Dopamine and Adrenergic GPCR Signaling","description":"This cluster centers on GPCR signaling pathways triggered by dopamine and adrenergic receptors, including PLC-activating and adenylate cyclase\u2013activating routes (GO:0060158, GO:0007191, GO:0071880, GO:0043547). The presence of heart development (GO:0007507) suggests a cardiovascular signaling context, consistent with GPCR-mediated modulation of cardiac function through both PLC and cAMP cascades. Although a few terms like phototransduction and xenobiotic response appear, the dominant theme is receptor-mediated signaling via dopamine/adrenergic pathways and their downstream second messengers. Overall, a coherent dopamine/adrenergic GPCR signaling module is implied. ","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0060158","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0043950","count":4},{"id":"GO:0071880","count":4},{"id":"GO:0007507","count":4}]},{"hash":"1766617797600507426","title":"Neuronal mitochondrial dynamics and synaptic adhesion","description":"The cluster centers on mitochondrial processes (stress-induced fusion, inner membrane organization, inheritance) and neuronal/synaptic functions (dopaminergic transmission) with membrane/cell-adhesion components (raft localization, cadherin-mediated adhesion), suggesting a theme of mitochondria-related regulation at neuronal synapses and adhesion sites.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045541","count":1},{"id":"GO:0032226","count":1},{"id":"GO:1990046","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0060355","count":1}]},{"hash":"289155331595752338","title":"Neuroimmune signaling and glial chemotaxis","description":"The cluster centers on neural-immune communication and glial-related signaling: immune response terms, eosinophil chemotaxis, and regulation of astrocyte chemotaxis, alongside dopamine transport and neurotrophic factor-related production. Xenobiotic response also aligns with brain stress/detox pathways, suggesting a cohesive theme of neural-immune and glial interactions rather than unrelated processes.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0050728","count":4},{"id":"GO:0042493","count":4},{"id":"GO:2000458","count":4}]},{"hash":"1801577055819407128","title":"Complement activation and immune regulation","description":"The terms cluster around complement activation via classical and lectin pathways, membrane attack complex formation and regulation, plus leukocyte adhesion and anti-inflammatory signals (IL-10) and T cell regulation, with plasminogen activation indicating coagulation-immune cross-talk. This suggests proteins coordinating complement-triggered immune responses and leukocyte interactions.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":4},{"id":"GO:0001867","count":3},{"id":"GO:0031639","count":3},{"id":"GO:0007157","count":3},{"id":"GO:0006924","count":2}]},{"hash":"990501564149163890","title":"Kidney and lymphatic development with immune signaling","description":"The cluster is enriched for kidney development terms (mesonephric duct development, metanephric ascending thin limb development) and lymphatic vessel morphogenesis, alongside immune-related processes (leukocyte tethering/rolling, lectin receptor signaling, complement activation, NK cell chemotaxis regulation, and platelet activation). This suggests the proteins may function at the intersection of organogenesis with vascular-immune signaling pathways, tying kidney/lymphatic development to immune system modulation.","confidence":"Medium","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0072177","count":3},{"id":"GO:0001502","count":3},{"id":"GO:0072218","count":3},{"id":"GO:0060355","count":3},{"id":"GO:0050901","count":3}]},{"hash":"424721879690531035","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060149","count":2},{"id":"GO:0043630","count":2},{"id":"GO:0016973","count":2},{"id":"GO:0034476","count":2},{"id":"GO:0000467","count":2}]},{"hash":"1116588563834291647","title":"ER stress and ubiquitin-mediated signaling","description":"This cluster centers on ubiquitination-related processes (autoubiquitination, ubiquitin chain formation, ERAD) linked to ER-associated protein quality control, ER-to-cytosol retrograde transport, and ER stress\u2013induced apoptotic signaling, with additional connections to interferon signaling. Together these terms suggest a cohesive ER stress/UPR and ubiquitin-response module that can intersect antiviral signaling. ","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0010994","count":4},{"id":"GO:0070911","count":4},{"id":"GO:1904153","count":4}]},{"hash":"1619109670773937500","title":"Neurodevelopment and Morphogenesis","description":"The main terms emphasize nervous system development and axon extension, with supporting themes in stem cell maintenance, morphogenesis, cytoskeletal organization (stress fiber assembly), and regulation of Rho signaling. While some terms originate from non-neural contexts (photomorphogenesis, trophectodermal morphogenesis), the shared thread is developmental regulation and cellular remodeling pertinent to neural structure formation.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0035019","count":3},{"id":"GO:0031286","count":3},{"id":"GO:0045773","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0035024","count":3}]},{"hash":"271775707956152080","title":"Inflammation and immune signaling","description":"The GO terms point to inflammatory processes and immune cell activity (e.g., chronic inflammatory response to antigenic stimulus, monocyte chemotaxis) with modulation by glucocorticoids and involvement of nitric oxide biosynthesis, suggesting a cluster centered on inflammatory/immune regulation and signaling.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045429","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0051384","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0008285","count":2}]},{"hash":"1899251420287579412","title":"Unknown","description":"The terms span neural development (axial mesoderm formation, fasciculation of sensory neuron axons, receptor clustering), learning, immune signaling, and metabolic regulation, with no single cohesive function tying all four proteins together, so a concise, representative label cannot be confidently assigned.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0048320","count":4},{"id":"GO:0097155","count":4},{"id":"GO:0032092","count":4},{"id":"GO:0008542","count":4}]},{"hash":"1710389209041440238","title":"Unknown","description":"The GO terms are highly diverse, spanning skeletal muscle development and sarcomere organization alongside plant brassinosteroid signaling, flower development, nervous system development, circadian rhythm regulation, and even viral latency release. This mix suggests no single cohesive function or theme linking the proteins, making a specific, representative label unlikely.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0007399","count":2},{"id":"GO:0019046","count":2},{"id":"GO:0009742","count":2},{"id":"GO:0048741","count":2}]},{"hash":"942296449586309964","title":"Spindle and Cytokinesis Machinery","description":"Most terms cluster around mitotic spindle function, chromosome passenger complex localization to the spindle midzone, and cytokinesis (actomyosin ring maturation, septation signaling). A few terms reference stress or apoptosis and are less central. Overall, this cluster reflects cell division machinery.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071470","count":2},{"id":"GO:2000808","count":2},{"id":"GO:0051229","count":2},{"id":"GO:0035853","count":2},{"id":"GO:1902310","count":2}]},{"hash":"1468452514114667296","title":"Histone Acetylation and Transcription Regulation","description":"Most top GO terms point to transcriptional control (regulation of DNA-templated transcription) and histone acetylation (H3/H4 acetylation), with a few development-related terms related to cell fate and morphogenesis. This pattern suggests the proteins cluster around chromatin modification that governs gene expression during development. Confidence is Moderate.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016360","count":1},{"id":"GO:0046529","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0045652","count":1},{"id":"GO:0043983","count":1}]},{"hash":"1925162066449234078","title":"Mitotic spindle assembly and cytokinesis","description":"Many GO terms highlight mitosis and spindle apparatus functions (spindle assembly, kinetochore\u2013microtubule attachments, spindle midzone, metaphase chromosome handling, and actomyosin contractile ring assembly), pointing to cell division machinery as the cluster\u2019s core. A few terms relate to development and stress responses, which may reflect multifunctional proteins or annotation noise, but the dominant signal is mitotic apparatus.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":4},{"id":"GO:0072092","count":3},{"id":"GO:0048364","count":3},{"id":"GO:0099607","count":3},{"id":"GO:0001560","count":3}]},{"hash":"1697913455443616756","title":"Organ development and tissue patterning","description":"The top GO terms cluster around developmental processes such as skeletal system development, organ induction, and lung-associated mesenchyme development, with an additional emphasis on pattern formation (including chitin-based cuticle). This points to a common theme of developmental patterning and organogenesis, with supporting signaling activity (e.g., autophosphorylation). Some terms are broader (chemokine regulation, synapse organization), but the dominant signal is developmental patterning and organ formation.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":2},{"id":"GO:0035018","count":2},{"id":"GO:1905065","count":2},{"id":"GO:0060484","count":2},{"id":"GO:0046777","count":2}]},{"hash":"1209975076280166206","title":"Muscle development and morphogenesis","description":"This cluster is dominated by GO terms for muscle tissue development and differentiation, including ventricular cardiac muscle morphogenesis, cardiac muscle cell differentiation, skeletal muscle tissue development, and extraocular skeletal muscle development. Together these point to a core theme of muscle morphogenesis across heart and skeletal muscles. A few outliers (neuronal stem cell maintenance, immune-related regulation) are present but do not define the main theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048294","count":2},{"id":"GO:0055010","count":2},{"id":"GO:0055007","count":2},{"id":"GO:0097150","count":2},{"id":"GO:0007519","count":2}]},{"hash":"736546709358681949","title":"Osteoblast and cardiac differentiation with angiogenesis","description":"The GO terms cluster around differentiation of osteoblasts and cardiac muscle cells, alongside angiogenesis, cell migration, and regulatory signaling (Wnt/PI3K) with apoptotic modulation. This points to a theme of developmentally coordinated differentiation and vascular remodeling, with some supporting or context-dependent immune signals. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045667","count":2},{"id":"GO:2000727","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0008285","count":2}]},{"hash":"296123857277389876","title":"Nervous System Development and Autonomic Regulation","description":"The terms cluster around nervous system development (cerebellum and ventricular system development) and autonomic control of organ function (catecholamine secretion, respiration regulation by the nervous system, blood pressure regulation), suggesting a shared theme of CNS maturation with autonomic physiological control. Some outliers and obsolete terms appear, likely due to annotation noise, but the central signal supports this label.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021591","count":1},{"id":"GO:0007585","count":1},{"id":"GO:0050432","count":1},{"id":"GO:0002087","count":1},{"id":"GO:0072325","count":1}]},{"hash":"1731916054823359753","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":2},{"id":"GO:0000398","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0000350","count":1},{"id":"GO:0000389","count":1}]},{"hash":"1557651698592975573","title":"Mitotic spindle and cytokinesis machinery","description":"Dominant GO terms in this cluster are centered on cell division processes: mitotic spindle assembly, spindle midzone assembly, kinetochore\u2013microtubule interactions, and actomyosin contractile ring assembly, all pointing to chromosome segregation and cytokinesis. While there are a few development-related terms, the strongest and most coherent signal is mitosis/cytokinesis machinery, making this label representative of the cluster\u2019s function.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0072092","count":2},{"id":"GO:0048364","count":2},{"id":"GO:0099607","count":2},{"id":"GO:0001560","count":2}]},{"hash":"2029784931762908777","title":"Skeletal development and morphogenesis","description":"The cluster\u2019s top GO terms are dominated by skeletal system development and skeletal system morphogenesis, indicating a shared role in bone formation and related developmental processes. While there are also terms touching on cilium assembly and cellular transport, the strongest and most frequent signals point to skeletal development as the core theme. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":4},{"id":"GO:0048705","count":4},{"id":"GO:0070208","count":4},{"id":"GO:0000348","count":4},{"id":"GO:0031930","count":4}]},{"hash":"955191505924172111","title":"Actin cytoskeleton and cell polarity","description":"The cluster is driven by terms related to actin filament bundle assembly, cell migration, and establishment of epithelial cell polarity, which together point to cytoskeleton organization and polarity dynamics. A few telomere maintenance and other older/obsolete GO terms appear among the top terms, suggesting some annotation noise rather than a cohesive signal beyond cytoskeletal remodeling. The small cluster size and low edge count support a localized, cytoskeleton/polarity-focused grouping rather than a broader pathway.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":3},{"id":"GO:2001275","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0032212","count":2},{"id":"GO:1904355","count":2}]},{"hash":"1504150912649922246","title":"Unknown","description":"The top terms are varied across innate immunity, cytoskeletal/microtubule localization, neural development, and learning-related processes, with no clear single biological theme linking all four proteins. This diversity makes a coherent, specific label unreliable.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051092","count":4},{"id":"GO:0035372","count":4},{"id":"GO:0045087","count":4},{"id":"GO:2001275","count":3},{"id":"GO:0048320","count":3}]},{"hash":"978609758807447781","title":"Unknown","description":"The GO terms are highly diverse (muscle-related terms such as skeletal muscle fiber development, skeletal muscle cell differentiation, and sarcomere organization appear alongside nervous system development, plant brassinosteroid signaling, viral latency release, circadian rhythm regulation, and other unrelated processes), and there are no edges linking the proteins. This lack of a coherent shared function makes it impossible to assign a meaningful label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0007399","count":1},{"id":"GO:0019046","count":1},{"id":"GO:0009742","count":1},{"id":"GO:0035853","count":1}]},{"hash":"701493775461415090","title":"Epigenetic Regulation of Gene Expression","description":"The cluster\u2019s GO terms repeatedly point to histone modifications (H3K27, H3K4) and DNA methylation regulation, along with negative regulation of transcription by RNA polymerase II. This suggests a cohesive theme centered on chromatin state control and epigenetic mechanisms that modulate gene expression.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901674","count":2},{"id":"GO:0010216","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0080182","count":2},{"id":"GO:2001040","count":2}]},{"hash":"751918132824055039","title":"Differentiation and cell cycle regulation","description":"The cluster centers on regulatory processes that govern cell fate and division, including differentiation of adipocytes and trophoblasts, development-related axis specification, and negative regulation of cytokinesis, with supporting post-transcriptional control via mRNA stabilization. While a plant metabolism term appears unrelated, the dominant theme is proteins involved in controlling differentiation and cell cycle progression.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048255","count":4},{"id":"GO:0045599","count":4},{"id":"GO:0060718","count":4},{"id":"GO:0006884","count":4},{"id":"GO:0071930","count":4}]},{"hash":"1172049852422136005","title":"RNA pseudouridylation and translation machinery","description":"The top GO terms cluster around pseudouridine synthesis across snRNA, rRNA, mRNA, and tRNA, plus tRNA aminoacylation and translation, pointing to a shared role in RNA modification and protein synthesis. Some angiogenesis/vasculogenesis terms are likely less connected to this core function. Therefore this label captures the dominant theme.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031120","count":1},{"id":"GO:0000455","count":1},{"id":"GO:1990481","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0006438","count":1}]},{"hash":"1943852790304500686","title":"RNA methylation and tRNA modification","description":"The top GO terms cluster around RNA modification and capping activities (tRNA wobble uridine modification, tRNA methylation, and 7-methylguanosine mRNA capping), suggesting a shared function in RNA processing. Other high-scoring terms (cobalamin biosynthetic process, antibiotic biosynthetic process, chlorophyll biosynthetic process, nodulation, and response to tellurium ion) may reflect methyltransferase activities across diverse pathways or annotation noise, but the dominant signal is RNA methylation/modification.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0019919","count":3},{"id":"GO:0017000","count":3},{"id":"GO:1901052","count":3}]},{"hash":"974267639474441158","title":"Unknown","description":"The top terms cover highly diverse processes ( xenobiotic response, virion attachment, TGF-beta signaling, hypoxia detection, metabolism to acetyl-CoA, proteasome regulation, and plant ethylene signaling), with no clear unifying biological function across the proteins. This scattered mix suggests there isn\u2019t a coherent functional theme for the cluster, so I label it Unknown. ","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0032516","count":2},{"id":"GO:0019062","count":2},{"id":"GO:0030511","count":2},{"id":"GO:0010510","count":2}]},{"hash":"2062831568089490956","title":"Embryonic Development and Cell Cycle Regulation","description":"The terms cluster around development and growth control: various developmental processes (root and organ development), and multiple regulators of the cell cycle and proliferation (negative regulation of proliferation, regulation of the cell cycle, and mitotic control), plus Wnt signaling modulation and cell migration, suggesting a coordinated development/growth control theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0045976","count":1}]},{"hash":"1513452965259857314","title":"Chloroplast ribosome biogenesis and protein targeting","description":"The cluster is dominated by GO terms related to ribosome biogenesis (both small and large subunits), ribosomal subunit export, and protein targeting to chloroplasts, suggesting a shared role in chloroplast ribosome assembly and import of ribosome-related components. A few outlier terms (cell division/conjugation, obsolete pore formation) may reflect noise or broader cellular processes, but the core signal centers on ribosome biogenesis and chloroplast targeting.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045036","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1212824370245860663","title":"Aromatic metabolite biosynthesis and catabolism","description":"The top GO terms cluster around aromatic metabolite pathways: cobalamin biosynthesis and methylation point to one-carbon chemistry; coumarin and lignin biosynthesis reflect plant/aromatic secondary metabolite production; and dopamine/catecholamine catabolic processes show metabolism of aromatic amines. Together these suggest a general theme of aromatic metabolite processing, rather than a single tight pathway, though some terms appear noisy or cross-species. Confidence: Medium","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0032259","count":3},{"id":"GO:0009805","count":2},{"id":"GO:0060117","count":2},{"id":"GO:0006584","count":2}]},{"hash":"1404264285158446338","title":"Rho/Rac GTPase signaling and cytoskeleton remodeling","description":"The cluster\u2019s GO terms center on small GTPase\u2013mediated signaling, notably Rac regulation, and processes dependent on cytoskeletal dynamics such as cell migration and cytokinesis (mitotic cleavage furrow ingression). Additional terms for vesicle budding and endosome\u2013lysosome transport suggest coordination between actin-driven remodeling and membrane trafficking. Together, these indicate a coherent theme of Rac/Rho-mediated control of cytoskeleton and trafficking.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990386","count":4},{"id":"GO:1902647","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0035021","count":4},{"id":"GO:0070142","count":4}]},{"hash":"1697283890212489070","title":"Actin cytoskeleton remodeling and lamellipodium formation","description":"This cluster is dominated by GO terms for actin filament bundle assembly, lamellipodium assembly, and actin cortical patch assembly, pointing to cytoskeletal remodeling and protrusive structures involved in cell migration. Some terms touch on signaling and differentiation (PDGF signaling, osteoblast fate), but the strongest shared signal is actin-driven structural dynamics.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030702","count":4},{"id":"GO:0002051","count":4},{"id":"GO:1990859","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0000147","count":4}]},{"hash":"619855978306419242","title":"Mitochondrial dynamics and neuronal adhesion signaling","description":"The terms cluster around mitochondrial dynamics (stress-induced fusion, inner membrane organization, inheritance) and neuronal signaling (dopaminergic synaptic transmission), with supporting membrane-associated processes (lipid rafts, cell adhesion molecule production, cadherin-mediated adhesion) and membrane cholesterol regulation. This suggests a theme where mitochondrial function and dynamics intersect with neuronal synaptic signaling and membrane adhesion contexts.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045541","count":1},{"id":"GO:0032226","count":1},{"id":"GO:1990046","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0060355","count":1}]},{"hash":"116739924794410872","title":"Mitotic spindle assembly and cytokinesis","description":"The cluster's top GO terms are dominated by mitosis-related processes\u2014spindle assembly, kinetochore attachment, midzone formation, mitotic spindle assembly, and actomyosin contractile ring assembly\u2014indicating core cell-division machinery. A few terms touch on apoptosis or development, but they are not the main signal. Therefore, the proteins most likely participate in mitosis and cytokinesis.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0072092","count":1},{"id":"GO:0048364","count":1},{"id":"GO:0099607","count":1},{"id":"GO:0001560","count":1}]},{"hash":"2093234325979120547","title":"Developmental morphogenesis and mitosis","description":"The cluster features GO terms tied to organ/embryonic development (ureteric bud invasion, root development, regulation of cell growth by extracellular stimulus) alongside core mitotic processes (spindle assembly, kinetochore-microtubule attachment, spindle midzone, actomyosin ring/cytokinesis, and adherens junction maintenance). This mix suggests proteins coordinating tissue morphogenesis with cell division and cell\u2013cell adhesion, typical of developmental growth contexts. Rap signaling regulation also fits growth control during development.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0072092","count":4},{"id":"GO:0048364","count":4},{"id":"GO:0099607","count":4},{"id":"GO:0001560","count":4},{"id":"GO:0051255","count":4}]},{"hash":"916367302929122638","title":"Nuclear receptor signaling and metabolic regulation","description":"Top GO terms suggest a core of transcriptional control intertwined with nuclear hormone receptor pathways (thyroid hormone receptor and retinoic acid receptor signaling) and metabolism (glucose and bile acid processes), with supporting roles in inflammatory regulation and developmental timing. This points to a cohesive theme of gene expression control in response to hormonal/metabolic cues, across both metabolic and developmental contexts.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0050728","count":3},{"id":"GO:0010906","count":3},{"id":"GO:0002155","count":3},{"id":"GO:0008206","count":3}]},{"hash":"2244146605399902949","title":"Unknown","description":"The GO terms span fertilization and ovulation alongside immune-cell related processes like thymocyte migration, T cell differentiation, macrophage fusion, and ROBO signaling, plus miscellaneous developmental and signaling terms. There isn't a single cohesive function that clearly binds all four proteins, making a precise, concise label unsupported. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":4},{"id":"GO:2000415","count":3},{"id":"GO:0031659","count":3},{"id":"GO:0035386","count":3},{"id":"GO:0001542","count":3}]},{"hash":"510205388181441591","title":"DNA replication machinery","description":"The top GO terms strongly point to DNA replication processes\u2014initiation, mitotic replication, strand elongation, and the overall replication process, along with GINS complex assembly\u2014suggesting proteins in this cluster participate in replication machinery. Although some developmental terms appear, they are less representative of the core signal dominated by replication-related functions.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090660","count":1},{"id":"GO:0072114","count":1},{"id":"GO:0048858","count":1},{"id":"GO:0006270","count":1},{"id":"GO:0001833","count":1}]},{"hash":"2038373945759516192","title":"RNA pseudouridine synthesis enzymes","description":"The top GO terms are dominated by pseudouridine synthesis in snRNA, mRNA, and tRNA, pointing to RNA modification enzymes as the core function of this cluster. While other signals (signaling/regulation and cytoskeleton-related terms) appear, they are likely incidental, and the shared function is RNA pseudouridylation activity. This suggests the proteins work together in RNA modification processes.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031120","count":1},{"id":"GO:1990481","count":1},{"id":"GO:0031119","count":1},{"id":"GO:2001275","count":1},{"id":"GO:0032485","count":1}]},{"hash":"2151652510121600668","title":"ER\u2013Golgi Vesicle Transport and Melanosome Assembly","description":"The top GO terms center on vesicle trafficking in the early secretory pathway: COPII vesicle coating, ER-to-Golgi and intra-Golgi transport, and protein retention in Golgi, with positive regulation of GTPase activity likely reflecting Rab/ARF regulators. The presence of pigmentation and melanosome assembly terms suggests the cluster proteins act in pigment granule formation as well. Taken together, the cluster seems to represent ER\u2013Golgi vesicle trafficking with a role in pigment/melanosome assembly.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0042338","count":1},{"id":"GO:0048208","count":1}]},{"hash":"1782468773923840704","title":"Skeletal Development and Protein Complex Assembly","description":"The top GO terms show a clear emphasis on skeletal system development and morphogenesis (GO:0001501, GO:0048705), complemented by protein complex formation processes (GO:0051260, GO:0070208). This suggests the proteins may participate in assembling complexes and signaling pathways relevant to skeletal tissue development, with some additional developmental processes (gastrulation, mitochondria-nucleus signaling) that fit a broader developmental role. Confidence: Medium","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0001501","count":2},{"id":"GO:0048705","count":2},{"id":"GO:0070208","count":2}]},{"hash":"177107798929247883","title":"Neurodevelopment and innate immune signaling","description":"The terms show both neural development/axon guidance (ROBO signaling, retinal ganglion axon guidance, Sertoli development) and innate immune signaling (TLR2 pathway, diacyl lipopeptide detection, IL-6 production, NF-kB signaling, antiviral defense), suggesting a cluster of proteins involved in developmental signaling intersecting with immune responses.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060009","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0035385","count":1},{"id":"GO:0031290","count":1},{"id":"GO:0006469","count":1}]},{"hash":"2299159513079752411","title":"Guard Cell Metabolism and Lipid Processes","description":"This cluster is driven by a mix of plant-specific and lipid-related metabolism GO terms: guard cell morphogenesis alongside glycerol metabolic process, phosphatidylglycerol catabolic process, and phosphate ion homeostasis. The combination suggests a theme around plant cell metabolism with an emphasis on guard cells and lipid/phospholipid turnover, rather than a single universal pathway.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030643","count":3},{"id":"GO:0034478","count":3},{"id":"GO:0006071","count":3},{"id":"GO:0010442","count":3},{"id":"GO:0030497","count":1}]},{"hash":"1813021762908497413","title":"Cytoskeletal dynamics and cell adhesion","description":"The GO terms converge on cytoskeletal organization and cell\u2013cell/ECM adhesion, including microtubule anchoring, lamellipodium/adhesion complex assembly, and Rho/integrin signaling. Terms like epithelial cell\u2013cell adhesion, zonula adherens maintenance, and neutrophil chemotaxis point to coordinated movement and junction remodeling, while neuron projection development reflects cytoskeletal-driven outgrowth. Together these terms describe a cluster of proteins involved in cytoskeleton-driven migration and adhesion.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034453","count":1},{"id":"GO:0030593","count":1},{"id":"GO:0045218","count":1},{"id":"GO:0031175","count":1},{"id":"GO:0043552","count":1}]},{"hash":"916436226704609756","title":"Unknown","description":"The top GO terms span retinal cone development, cardiac/muscle calcium handling, dopamine metabolism, immune signaling, and generic regulatory processes, with no clear, single shared function tying all proteins together. This makes it inappropriate to assign a confident, cohesive label to the cluster.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046549","count":4},{"id":"GO:1903206","count":4},{"id":"GO:0032729","count":4},{"id":"GO:0055119","count":4},{"id":"GO:0042053","count":4}]},{"hash":"51697470299433562","title":"Protein deglutamylation processes","description":"The cluster shows multiple GO terms specifically about deglutamylation\u2014side chain, branching point, and C-terminal deglutamylation\u2014pointing to a core theme of removing glutamyl residues from proteins. Other terms present (Purkinje cell differentiation, bradykinin catabolic process, liver regeneration, ECM secretion) likely reflect broader biological contexts in which deglutamylation-related enzymes act, but the recurring deglutamylation terms provide the main through-line.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021702","count":3},{"id":"GO:0035610","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0035611","count":3},{"id":"GO:0071333","count":3}]},{"hash":"1377802440073384019","title":"Neuronal signaling and sensory perception","description":"The proteins share multiple nervous system\u2013related GO terms, including auditory stimulus detection, dopaminergic and acetylcholine signaling, action potentials, reflexes, circadian regulation, and regulation of respiratory function by neural processes, indicating a cohesive theme of neural signaling and sensory processing.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050910","count":2},{"id":"GO:0032226","count":1},{"id":"GO:0045188","count":1},{"id":"GO:0060013","count":1},{"id":"GO:0002087","count":1}]},{"hash":"2242725232812437847","title":"Embryonic Skeletal Development and Chondrocyte Formation","description":"The prominent GO terms point to skeletal formation processes\u2014endomembranous (endochondral) ossification, chondrocyte proliferation, and embryonic cranial skeleton morphogenesis\u2014indicating a cluster focused on cartilage and bone development during embryogenesis. Additional terms related to cell adhesion and broader tissue morphogenesis support this theme, while a few terms may reflect general cellular processes or noise. Confidence: Medium","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071230","count":2},{"id":"GO:1905523","count":2},{"id":"GO:0042756","count":2},{"id":"GO:0044331","count":2},{"id":"GO:1904807","count":2}]},{"hash":"89958788039233314","title":"Mitochondrial Respiratory Chain & Complex III Assembly","description":"The GO terms point to mitochondrial electron transport (NADH to ubiquinone; ubiquinol to cytochrome c), proton transmembrane transport, and assembly of the respiratory chain Complex III, indicating a role in oxidative phosphorylation and aerobic respiration. Some peripheral terms may be incidental, but the core signal is mitochondrial energy production.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":1},{"id":"GO:0006122","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0034551","count":1},{"id":"GO:0009060","count":1}]},{"hash":"1985614855074465164","title":"Neuronal development and axon pathfinding","description":"The top GO terms point to neural development and axon guidance (hippocampus development, axon fasciculation, receptor clustering, and learning-related processes), indicating proteins likely participate in neural circuit formation. Some terms are broader or developmental, but the dominant theme is neuronal development and axon pathfinding.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":2},{"id":"GO:2001275","count":1},{"id":"GO:0048320","count":1},{"id":"GO:0097155","count":1},{"id":"GO:0032092","count":1}]},{"hash":"1578205222896324085","title":"Neural crest\u2013driven craniofacial and cardiac morphogenesis","description":"This cluster centers on neural crest\u2013mediated morphogenesis affecting craniofacial skeletal development, neural tube closure, pharyngeal arch artery formation, and heart development, with Hedgehog signaling (Smoothened pathway) and folate-related transport/response linking to developmental patterning. A few taste-receptor regulatory terms may reflect broader developmental expression but do not define the core theme. ","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048705","count":2},{"id":"GO:0061713","count":2},{"id":"GO:0071231","count":2},{"id":"GO:1904657","count":2},{"id":"GO:1904661","count":2}]},{"hash":"1201112752037595163","title":"Monocyte chemotaxis and PI3K/ERK signaling","description":"The terms show a clear emphasis on monocyte movement (monocyte chemotaxis) and key signaling pathways (PI3K/AKT and ERK cascades) that regulate cell migration and activation, with additional links to angiogenesis and immune cell trafficking (T cell extravasation). This suggests the cluster groups proteins involved in immune cell recruitment and the associated signaling networks that drive migration and vascular remodeling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002548","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0014911","count":2}]},{"hash":"504506434210864518","title":"Unknown","description":"The GO terms span diverse developmental processes across multiple organs (embryonic digestive tract, lung alveolus, bone/cartilage, cardiac muscle development) plus DNA repair and stress responses, with no single unifying function or pathway evident for the cluster. Hence a cohesive, specific label isn't supported. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048566","count":2},{"id":"GO:0010212","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0032332","count":1},{"id":"GO:0042997","count":1}]},{"hash":"1310621124712870821","title":"Vertebrate embryonic morphogenesis","description":"The terms cluster around embryonic development and patterning in vertebrates, including neural tube closure, notochord and somite morphogenesis, midbrain-hindbrain boundary formation, ventricle development, and early blastocyst formation, with a supporting Wnt calcium-modulating pathway; a lysyl-hydroxylation term may relate to extracellular matrix changes during morphogenesis. This suggests a cohesive theme of vertebrate embryonic structure formation.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061038","count":2},{"id":"GO:0048570","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0007223","count":2},{"id":"GO:0021678","count":1}]},{"hash":"430117004668877261","title":"Vacuolar acidification and ion homeostasis","description":"Most terms point to vacuolar function and ion balance: vacuolar acidification, vacuole organization, protein targeting to vacuole, and various ion transport terms (protons, sodium, copper). This pattern suggests a cluster focused on vacuolar processes that regulate pH and ion homeostasis, likely involving V-ATPase activity and vacuolar trafficking.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":3},{"id":"GO:0007035","count":3},{"id":"GO:0006878","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0006814","count":2}]},{"hash":"289529823591126762","title":"Actin Cytoskeleton Remodeling in Vascular Signaling","description":"Most terms center on actin-related structures and assembly (actin cortical patch, actin filament bundle, lamellipodium), indicating cytoskeletal remodeling involved in cell migration. Supporting terms involve PDGF receptor signaling and endothelin response, linking cytoskeletal dynamics to vascular signaling and smooth muscle behavior. A couple of terms (pericentric heterochromatin formation, osteoblast fate commitment) are less aligned, but the predominant theme ties to actin-driven motility in vascular contexts.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030702","count":1},{"id":"GO:0002051","count":1},{"id":"GO:1990859","count":1},{"id":"GO:0000147","count":1},{"id":"GO:0051017","count":1}]},{"hash":"583697836378399466","title":"Cellular stress signaling and survival","description":"The cluster's top GO terms cluster around stress-activated signaling cascades (MAPK), PI3K/AKT signaling, and regulation of apoptosis and receptor signaling via JAK-STAT, which together point to proteins involved in cellular stress responses and survival pathways. A couple of terms about catabolic processes (D-xylose, naphthalene) seem unrelated or noisy annotations, but the dominant theme is stress signaling and apoptosis regulation.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":4},{"id":"GO:0042843","count":4},{"id":"GO:0031098","count":4},{"id":"GO:0046427","count":4},{"id":"GO:0043066","count":4}]},{"hash":"1783191896366542863","title":"Unknown","description":"Top terms span neural dopamine signaling, astrocyte chemotaxis, eosinophil chemotaxis, immune defense, and cardiovascular/epithelial transport, with no single cohesive function tying all terms together. This heterogeneity suggests no clear unifying theme for the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:2000458","count":4},{"id":"GO:0042346","count":4},{"id":"GO:0048245","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0008542","count":4}]},{"hash":"2189359446450821320","title":"Protease-Driven Vascular and Metabolic Regulation","description":"The GO terms point to proteolytic cascades (proteolysis, kallikrein-kinin), vascular remodeling (endothelial migration, angiogenesis in wound healing, blood pressure regulation), and metabolic balance (energy and glucose homeostasis, ROS metabolism). Together these suggest a cluster where proteolytic signaling modulates vascular function alongside metabolic homeostasis, with a few terms likely reflecting noise or misannotation (lipoteichoic acid biosynthesis).","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":1},{"id":"GO:0002155","count":1},{"id":"GO:0043535","count":1},{"id":"GO:0002353","count":1},{"id":"GO:0097009","count":1}]},{"hash":"270918882134957593","title":"Sulfur amino acid and carbohydrate metabolism","description":"The top GO terms cluster around sulfur-containing amino acid metabolism (L-serine, homocysteine, cysteine/cystathionine, hydrogen sulfide biosynthesis) and general carbohydrate metabolism (carbohydrate metabolic process, gluconeogenesis regulation). A few terms hint at metal ion homeostasis, but the dominant signal is metabolic pathways, especially sulfur amino acids and carbon metabolism. Confidence in a cohesive functional label is Medium.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006565","count":1},{"id":"GO:0045722","count":1},{"id":"GO:1903830","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0032147","count":1}]},{"hash":"920823021235637903","title":"Bacterial antibiotic biosynthesis and NRPS pathways","description":"The cluster is enriched for antibiotic-related processes (GO:0017000 antibiotic biosynthetic process; GO:0046677 response to antibiotic) and nonribosomal peptide biosynthesis (GO:0043041, via amino acid activation for NRPS), plus lipoteichoic acid biosynthesis and related bacterial biosynthetic activities (e.g., ubiquinone biosynthesis from tyrosine). While retinal-related terms appear as outliers, the dominant theme across the proteins points to bacterial secondary metabolism and cell-wall biosynthesis, suggesting a coherent cluster of antibiotic production and NRPS-associated pathways.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0042574","count":4},{"id":"GO:0042572","count":4},{"id":"GO:0048384","count":3}]},{"hash":"1082852513895109582","title":"Cardiac calcium handling and contraction regulation","description":"This cluster centers on calcium release from the sarcoplasmic reticulum via RyR channels, calcium signaling that drives cardiac muscle contraction, and regulation of heart force. Supporting terms include ventricular heart tissue morphogenesis and muscle-related processes, reinforcing a cardiac-muscle theme. Some obsolete terms are present, but the core signals point to calcium-driven cardiac contraction control.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0014808","count":3},{"id":"GO:0055010","count":3},{"id":"GO:0097274","count":3},{"id":"GO:0060315","count":3},{"id":"GO:0016061","count":2}]},{"hash":"1535683902798515207","title":"Adaptive Immune Activation and Leukocyte Chemotaxis","description":"This cluster is dominated by immune-related functions: T and B cell trafficking (helper T cell extravasation, B cell chemotaxis), leukocyte chemotaxis including eosinophils, IL-13 response, virus defense, and cytotoxic/granzyme activity, all pointing to adaptive immune signaling and recruitment of immune cells; non-canonical NF-kappaB signaling and occasional cell cycle regulation fit with immune cell activation and proliferation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"wound healing","top_go_terms":[{"id":"GO:0035962","count":4},{"id":"GO:0035684","count":4},{"id":"GO:0007050","count":4},{"id":"GO:0042346","count":4},{"id":"GO:0048245","count":4}]},{"hash":"1364609698004299061","title":"Unknown","description":"The terms present a mix of antimicrobial/bacterial cell wall\u2013related processes (defense response to bacterium, peptidoglycan catabolic process, cytolysis, cell wall macromolecule catabolic process) alongside unrelated functions (electron transport chain, locomotory behavior, pain regulation, viral release, and signaling). There is no single cohesive theme tying all terms together, so a specific label isn\u2019t warranted; Unknown is most appropriate.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":4},{"id":"GO:0007626","count":4},{"id":"GO:0051482","count":4},{"id":"GO:0019835","count":4},{"id":"GO:0051930","count":4}]},{"hash":"604946049389542308","title":"Heart and muscle development with ECM signaling","description":"This cluster highlights developmental signaling, ECM interactions, and muscle structure, linking heart development with cell migration cues and sarcomere organization.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"wound healing","top_go_terms":[{"id":"GO:0035385","count":4},{"id":"GO:0030199","count":4},{"id":"GO:0030513","count":4},{"id":"GO:0001764","count":4},{"id":"GO:0010763","count":4}]},{"hash":"780697754553898246","title":"Immune Cell Apoptosis and Inflammation Regulation","description":"Based on the top GO terms, the proteins are linked to dampening inflammatory responses (negative regulation of inflammatory response) and to apoptotic signaling and death programs in immune cells (activation-induced T cell death, TRAIL pathway, T cell apoptotic process). There are also terms for regulating cytokine production and fever, which fit inflammatory signaling. Taken together, these terms suggest a function in coordinating immune cell survival/apoptosis with inflammatory signaling rather than a single metabolic or structural role. Therefore the cluster is best described as Immune Cell Apoptosis and Inflammation Regulation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":3},{"id":"GO:0006925","count":3},{"id":"GO:0006924","count":3},{"id":"GO:0009786","count":3},{"id":"GO:0036462","count":3}]},{"hash":"2175039575452247781","title":"Developmental Regulation and Cell Cycle Control","description":"This cluster centers on GO terms related to development (root development, neural plate development, renal outer medulla development, chitin-based larval cuticle pattern formation) and on cell cycle control (negative regulation of mitotic cell cycle, regulation of cell cycle, cytokinesis) along with chromatin remodeling. The combination suggests proteins involved in coordinating development with cell division via chromatin-mediated transcription, rather than a single tissue-specific function. Confidence: Medium","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045976","count":2},{"id":"GO:0048364","count":2},{"id":"GO:0072054","count":2},{"id":"GO:0007050","count":2},{"id":"GO:0032467","count":2}]},{"hash":"1120923790397539659","title":"Ribosome Biogenesis and tRNA Modification","description":"The top GO terms cluster around ribosome assembly and processing, including ribosome biogenesis, small and large subunit biogenesis, and tRNA modification, with an annotation for nuclear export of ribosomal subunits. While a few terms relate to unrelated processes, the dominant signal points to a shared function in ribosome maturation and translation readiness.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090529","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0055072","count":1},{"id":"GO:0042254","count":1}]},{"hash":"949070336986635907","title":"ER-Golgi trafficking and cytoskeleton dynamics","description":"Named for the strongest GO signals in the cluster: ER-to-Golgi vesicle transport, microtubule anchoring at centrosome, and actin filament bundle assembly. Together these terms indicate intracellular trafficking coupled with cytoskeletal organization, which fits a group of proteins involved in vesicle movement and structural remodeling. Other terms (transcription, spermatogenesis, etc.) are likely ancillary or older annotations, but do not override the central trafficking/cytoskeleton theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0034454","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0035071","count":2},{"id":"GO:1900740","count":2}]},{"hash":"1164866885409936881","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034414","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0001825","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0006446","count":2}]},{"hash":"461686594979012020","title":"Keratinocyte differentiation and hair follicle morphogenesis","description":"This cluster is dominated by epidermal-related terms: keratinization, keratinocyte migration, and hair follicle morphogenesis, indicating a core function in skin/epidermal development and hair follicle formation. Some neural or other tissue terms appear as peripheral associations, but the prevailing signal points to keratinocyte biology and skin appendage development.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":3},{"id":"GO:0014012","count":3},{"id":"GO:0031069","count":3},{"id":"GO:1904714","count":3},{"id":"GO:0055015","count":3}]},{"hash":"1098993901392720826","title":"Immune development and inflammatory regulation","description":"This cluster centers on immune system-related processes: germinal center formation, thymus development, and response to lipopolysaccharide, with a note of negative regulation of inflammatory response. Additional terms point to immune signaling (peptidyl-serine autophosphorylation) and stress-related processes (protein modification/repair, oxidative stress response). While some terms are broader, the dominant theme ties to immune system development and regulation of inflammation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0006464","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0030091","count":1}]},{"hash":"318298611996068827","title":"Embryogenesis and cell fate regulation","description":"The terms center on embryo development (blastocyst formation, axis elongation, chiasma assembly) and cell fate decisions (apoptosis, autophagy) with supporting roles for protein turnover and chromatin regulation; together they suggest a cluster involved in developmental progression and cellular quality control under stress. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000653","count":1},{"id":"GO:0010508","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0051026","count":1},{"id":"GO:0060028","count":1}]},{"hash":"1700551993841823761","title":"Multisystem Developmental Processes","description":"The top GO terms cover diverse developmental themes across multiple tissues (digestive tract morphogenesis, thymus development, spermatogenesis, melanocyte differentiation) as well as neural-related processes (synaptic vesicle exocytosis, neuron apoptotic regulation). This suggests a broad developmental role rather than a single, specific pathway, so a label reflecting multisystem development is appropriate.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071230","count":2},{"id":"GO:0030279","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0010248","count":2},{"id":"GO:2000302","count":2}]},{"hash":"1883625759044945069","title":"Unknown","description":"The GO terms cover a mix of immune signaling, developmental pathways, and general cellular processes with no single cohesive function linking them all, making a specific, representative cluster label unclear.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0032481","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0048320","count":3},{"id":"GO:0002051","count":3},{"id":"GO:0035771","count":3}]},{"hash":"571603218046951844","title":"Transcriptional Regulation and miRNA Control","description":"The set centers on DNA-templated transcription and regulation of miRNA transcription (both positive and negative) and includes a term on chromatin binding regulation, pointing to a shared role in gene expression control and chromatin state. Additional terms hint at stimulus-responsive transcriptional programs (nicotine, mechanical stimuli) that can be downstream of transcriptional regulators. Overall, the cluster is best described by transcription regulation with chromatin/miRNA modulation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0014904","count":2},{"id":"GO:1902895","count":2},{"id":"GO:1902894","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006967","count":1}]},{"hash":"1837970582171992498","title":"DNA replication and repair","description":"The cluster\u2019s strongest signals are GO:0006260 (DNA replication) and GO:0006281 (DNA repair), both linked to genome maintenance. A response-to-toxic-substance term also fits a DNA-damage context, supporting the idea that these proteins contribute to DNA integrity. The remaining GO terms appear more varied (developmental and neural terms), likely reflecting broader annotations or multifunctionality, but the core theme is DNA maintenance.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006281","count":3},{"id":"GO:2001275","count":2},{"id":"GO:0048320","count":2}]},{"hash":"730907728578779119","title":"Unknown","description":"The top GO terms cover retinal cone cell development, immune responses to LPS, interferon production, monocyte differentiation, dopamine metabolism, and calcium-related cardiac/muscle regulation, a mix suggesting no single cohesive function linking these proteins.  ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046549","count":3},{"id":"GO:0071222","count":3},{"id":"GO:1903206","count":2},{"id":"GO:0032729","count":2},{"id":"GO:0055119","count":2}]},{"hash":"2106939736814942977","title":"DNA replication and genome maintenance","description":"The terms focus on core DNA replication processes (initiation, elongation, templated replication) and genome stability activities (UV-damage repair, translesion synthesis, telomere maintenance). This points to a cluster specialized in coordinating replication with DNA damage response and genome integrity.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006270","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0032877","count":1},{"id":"GO:0000738","count":1},{"id":"GO:0006279","count":1}]},{"hash":"297553679378080165","title":"Neuroinflammatory signaling and neuronal apoptosis","description":"The GO terms point to immune and inflammatory signaling (response to lipopolysaccharide, regulation of IL-6/IL-23 production, negative regulation of inflammatory response) together with neural-specific processes (necroptotic signaling, motor neuron apoptotic process, regulation of myelination) and signaling-related activities (plasma membrane localization, autophosphorylation). This suggests a cluster of proteins involved in neuroinflammation and neuron-specific cell death pathways, rather than a single housekeeping function. Confidence: Medium","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":3},{"id":"GO:0044130","count":3},{"id":"GO:0050728","count":2},{"id":"GO:0036289","count":2},{"id":"GO:0097049","count":2}]},{"hash":"160944515877955218","title":"Innate and Adaptive Immune Signaling","description":"The terms point to immune defense functions spanning innate responses (innate immune response, cellular defense, response to Gram-positive bacteria, LPS) and adaptive immunity (B cell receptor signaling, B cell affinity maturation) with interferon-mediated signaling. This suggests a cohesive immune signaling module involving both branches and interferon pathways.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0002344","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0006968","count":2},{"id":"GO:0060337","count":2}]},{"hash":"932914368014557908","title":"Neural Development and Axon Fasciculation","description":"The top GO terms cluster around neural development and axon fasciculation (fasciculation of sensory neuron axon; nervous system development; cerebellum development; neural tube closure; axial mesoderm formation), suggesting a core role in nervous system formation and axon organization; some terms are peripheral but do not change the main interpretation.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097155","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0021549","count":2},{"id":"GO:0001843","count":2}]},{"hash":"849657847553220051","title":"Unknown","description":"The top GO terms cover a mix of immune signaling (interferon production, IL-4 signaling), metabolic/insulin-related regulation, development (axial mesoderm formation, osteoblast fate), and cell motility/morphogenesis (lamellipodium assembly, axon fasciculation), with no clear shared function tying them together. Therefore a cohesive cluster label cannot be confidently assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0032481","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0048320","count":3},{"id":"GO:0002051","count":3},{"id":"GO:0035771","count":3}]},{"hash":"1439416936764948021","title":"ECM remodeling and cell adhesion","description":"The GO terms cluster around extracellular matrix disassembly regulation, proteolysis, and cell adhesion, suggesting roles in ECM remodeling and cell\u2013ECM interactions. The \u201csymbiont entry into host cell\u201d term can relate to invasion via adhesion/ECM pathways. Other terms are broader, so the main theme is tissue architecture and cell adhesion rather than a single precise pathway.","confidence":"Low","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0010716","count":3},{"id":"GO:0046294","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0060244","count":3},{"id":"GO:0006508","count":3}]},{"hash":"10617482078259057","title":"Spliceosome assembly and RNA decay","description":"Dominant GO terms cluster around RNA processing: spliceosome complex and snRNP assembly, along with mRNA decay pathways (deadenylation-dependent decapping) and P-body formation, plus nuclear import and histone mRNA metabolism. While chromatin and cell-cycle terms appear, the core signal is splicing and RNA turnover, justifying this label.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":3},{"id":"GO:0000387","count":3},{"id":"GO:1990141","count":3},{"id":"GO:0009414","count":3},{"id":"GO:0009737","count":3}]},{"hash":"1074910832011700525","title":"Unknown","description":"The Top Terms are empty, giving no functional signal to tie these proteins together. With only one edge and no triangles, the cluster lacks a shared GO-based function to name.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"1761172152314933509","title":"Neural development and axon guidance","description":"The top GO terms point to neural development (axon fasciculation, axial mesoderm formation) and signaling-related processes (receptor clustering, JNK regulation), suggesting a cohesive theme around neural development and cell signaling. Some terms (immune response, learning, glycogen regulation) are less central or appear as noise, but the neural development signals are the strongest pattern here.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0048320","count":3},{"id":"GO:0097155","count":3},{"id":"GO:0032092","count":3},{"id":"GO:0008542","count":3}]},{"hash":"1059628313290799425","title":"Embryonic development and morphogenesis","description":"The top GO terms are dominated by embryogenesis-related processes like skeletal system development, skeletal system morphogenesis, and gastrulation, which strongly point to embryonic development as the cluster theme. Additional terms such as cilium assembly suggest developmental signaling roles, while mRNA transport and vesicle trafficking reflect cellular processes that support development. Taken together, the cluster appears centered on developmental biology with supportive cellular functions.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":1},{"id":"GO:0048705","count":1},{"id":"GO:0070208","count":1},{"id":"GO:0000348","count":1},{"id":"GO:0031930","count":1}]},{"hash":"69160382970065091","title":"RNA Pol II Transcription Regulation and RNA Processing","description":"The terms mainly describe nuclear transcription control (transcription elongation by RNA Pol II, preinitiation complex assembly, transcription antitermination) and RNA processing/degradation (deadenylation-independent decay, snoRNA splicing) with links to chromatin modification (histone H4 acetylation). A few terms about signaling responses and T cell homeostasis are ancillary, but the core theme is transcription regulation and RNA processing in the nucleus.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0090239","count":1},{"id":"GO:1904628","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0031086","count":1}]},{"hash":"443650224384545628","title":"APC/C-Dependent Mitotic Proteolysis","description":"The cluster\u2019s top GO terms cluster around mitosis and ubiquitin-mediated protein degradation, including mitotic cell cycle, anaphase-promoting complex\u2013dependent catabolic process, cellular division, and K11-linked ubiquitination, indicating a core function in APC/C-driven proteolysis during mitosis. Some terms like DNA-templated transcription are present but do not define the main theme; overall, proteolysis-regulated mitosis best explains the set.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0031145","count":2},{"id":"GO:2001162","count":2}]},{"hash":"1013602233217201468","title":"Actin Cytoskeleton Remodeling and Signaling","description":"The terms with the strongest coherence point to actin organization and remodeling (lamellipodium assembly, actin filament bundle assembly, actin cortical patch assembly), suggesting the cluster centers on cytoskeletal dynamics. There are additional signaling-related terms (PDGF, endothelin, p38MAPK regulation) that may accompany cytoskeletal changes, but the actin-related terms provide the most consistent theme. Overall, the cluster appears to reflect actin cytoskeleton remodeling with linked signaling.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030702","count":2},{"id":"GO:0015879","count":2},{"id":"GO:0002051","count":2},{"id":"GO:1990859","count":2},{"id":"GO:0000147","count":2}]},{"hash":"639702106683932825","title":"Differentiation and migration with cytoskeletal remodeling","description":"The top GO terms center on adipocyte differentiation and foam cell differentiation, together with cell migration, epithelial polarity, endothelial delamination, and actin filament bundle assembly, indicating a theme of differentiation linked to movement and cytoskeletal reorganization; telomere maintenance terms are less central to the cluster. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":3},{"id":"GO:0010745","count":3},{"id":"GO:2001275","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0032212","count":2}]},{"hash":"1929609858147959400","title":"Iron-sulfur cluster assembly and protein quality control","description":"The terms point to iron-sulfur cluster biogenesis and stress-related proteostasis, including iron handling, unfolded protein response, and chaperone-dependent refolding. Even with some unrelated terms, the core theme links maturation of iron-sulfur proteins with protein quality control under stress conditions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1},{"id":"GO:0000902","count":1},{"id":"GO:0031204","count":1},{"id":"GO:1902037","count":1},{"id":"GO:0070389","count":1}]},{"hash":"1641464758585537414","title":"Glycogen and Alpha-glucan Catabolism with PRPP Biosynthesis","description":"The top GO terms point to carbohydrate catabolism (glycogen and alpha-glucan breakdown) and a nucleotide precursor pathway (PRPP biosynthesis); necroptosis is present but less central. This suggests the cluster clusters core metabolism rather than a single signaling or death pathway.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006015","count":3},{"id":"GO:0005980","count":3},{"id":"GO:0030980","count":3},{"id":"GO:0070266","count":3}]},{"hash":"2202411316912693251","title":"Cell polarity and vesicle trafficking in development","description":"The proteins show enrichment for establishing cell polarity (epithelial/endothelial), Wnt signaling in development, and vesicle-related processes (exocytosis, phagosome-lysosome fusion) with actin cytoskeleton regulation, suggesting a cohesive role in polarity and trafficking during development and neural function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061028","count":3},{"id":"GO:0060070","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0090162","count":3}]},{"hash":"2245161335056684396","title":"Intracellular membrane trafficking and organelle transport","description":"This cluster is dominated by GO terms related to trafficking between organelles (Golgi, ER, mitochondria), SNARE-mediated vesicle dynamics, autophagosome maturation, and proteasome assembly, suggesting a cohesive theme of intracellular protein transport and membrane dynamics; a couple of outliers (leading strand elongation, viral genome replication) may reflect annotation noise rather than core function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045053","count":3},{"id":"GO:0045041","count":3},{"id":"GO:0006272","count":3},{"id":"GO:0061166","count":3},{"id":"GO:0031117","count":3}]},{"hash":"1812356934691944274","title":"RNA Processing and Translation Regulation","description":"This cluster centers on mRNA stability and transport of translational control, including regulation of mRNA stability under stress, formation of the translation preinitiation complex, initiation and reinitiation of translation, splice site recognition, and ncRNA-mediated gene silencing. Together these GO terms point to a cohesive theme of post-transcriptional RNA processing and control of protein synthesis, with blastocyst formation reflecting a developmental context where such regulation is critical.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:0001825","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0006446","count":2},{"id":"GO:1900363","count":2}]},{"hash":"60276890325353123","title":"Innate antiviral signaling and ubiquitination regulation","description":"The terms converge on dampening antiviral sensing and downstream signaling (negative regulation of RIG-I pathway and JNK cascade) and on ubiquitin-related processes (protein ubiquitination, K6-linked ubiquitination). This points to a cluster of proteins involved in regulating innate immune responses and ubiquitin signaling, with additional hints from chromatin-related regulation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":3},{"id":"GO:2000620","count":3},{"id":"GO:0070512","count":3},{"id":"GO:0039536","count":3},{"id":"GO:0046328","count":3}]},{"hash":"14704193530351953","title":"Sarcomere organization and muscle contraction regulation","description":"This cluster centers on processes that organize sarcomeres and regulate striated (skeletal and cardiac) muscle contraction, including muscle filament sliding and regulation of contraction speed, with associations to cardiac muscle morphogenesis and fiber-type transitions. The combined GO terms point to proteins involved in the structural assembly of muscle fibers and modulation of their contraction.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032780","count":3},{"id":"GO:0014883","count":3},{"id":"GO:0032781","count":3},{"id":"GO:0030049","count":3},{"id":"GO:0045214","count":3}]},{"hash":"1152603245644668770","title":"Plant leaf development and metabolism","description":"The cluster is characterized by plant-specific developmental terms: leaf formation, negative regulation of leaf senescence, and positive regulation of secondary cell wall biogenesis, suggesting a focus on leaf growth and cell wall\u2013related processes. Supporting terms include sucrose catabolic process (a key metabolic activity in leaves) and alternative mRNA splicing via spliceosome (common in plant gene regulation). Some terms are unrelated or obsolete, indicating a mixed signal, but the prominent plant-development signals justify a leaf-development/metabolism theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010569","count":3},{"id":"GO:0051573","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0010338","count":3},{"id":"GO:1900056","count":3}]},{"hash":"960335406363493130","title":"DNA Repair and Recombination","description":"The top terms show strong representation for DNA repair and DNA recombination (GO:0006281 and GO:0006310, each with 2 hits), suggesting the proteins in this cluster primarily participate in genome maintenance. Other terms (immune signaling, metabolism) are much less represented, so the core function is best captured by DNA repair/recombination rather than broader pathways. Confidence: High","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0019889","count":2},{"id":"GO:0006798","count":2},{"id":"GO:0035882","count":1}]},{"hash":"2278986317370601070","title":"Multi-tissue morphogenesis","description":"The cluster's top GO terms are dominated by developmental and morphogenesis processes across multiple tissues (skeletal and smooth muscle, lung alveoli, ovarian/prostate contexts, and neural development like vocal learning), with a few terms related to chromatin regulation and immune signaling that are less central. This suggests a broad developmental theme rather than a single function.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001542","count":3},{"id":"GO:0002074","count":3},{"id":"GO:0060741","count":3},{"id":"GO:0090055","count":3},{"id":"GO:0042297","count":3}]},{"hash":"1032472169897667896","title":"Lamellipodium/Filopodium Assembly","description":"The GO terms are dominated by lamellipodium and filopodium assembly, actin filament network formation, and actin capping at barbed and pointed ends, with regulatory terms for promoting these structures. This pattern points to actin cytoskeleton remodeling that drives protrusive structures like lamellipodia and filopodia, central to cell motility. A mitochondria fission regulation term appears ancillary to the core actin-focused theme.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":3},{"id":"GO:0030046","count":3},{"id":"GO:0051639","count":3},{"id":"GO:0051016","count":3},{"id":"GO:0010592","count":3}]},{"hash":"1253570386798771281","title":"Neuronal development signaling kinases","description":"This cluster is driven by GO terms related to nervous system and neuron projection development, with an additional emphasis on protein autophosphorylation, pointing to kinase signaling roles in neuronal development. Other terms like cellular response to fatty acid and protein complex oligomerization fit within signaling contexts, while occasional nucleotide biosynthesis terms appear incidental. Overall, the set seems best described as neuronal development signaling proteins, likely including kinases.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0051259","count":2},{"id":"GO:0006228","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0006241","count":2}]},{"hash":"1287213090422414063","title":"Unknown","description":"The GO terms are diverse, spanning T cell homeostasis, ERAD pathway, skeletal development/morphogenesis, cell migration, myosin II regulation, and signaling, with no clear single function tying all three proteins together. This lack of a coherent shared theme suggests no reliable, specific cluster label can be assigned. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001501","count":1},{"id":"GO:0048705","count":1},{"id":"GO:0070208","count":1}]},{"hash":"1367398710928848712","title":"Angiogenesis and skin morphogenesis regulators","description":"The cluster is dominated by angiogenesis and its regulation, with skin development cues such as hair follicle placode regulation and Wnt signaling interconnections, suggesting a vascular-development with skin-patterning theme; other terms like digestion and circadian rhythm are present but less central.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0045987","count":2},{"id":"GO:0007623","count":1},{"id":"GO:0045765","count":1},{"id":"GO:0061170","count":1}]},{"hash":"1428205102085210257","title":"Unknown","description":"The top GO terms cover a wide range of tissue-specific developmental morphogenesis (gonad, lacrimal/trachea glands, digestive tract), germline-associated processes (piRNA processing, spermatid differentiation, histone methylation), and even innate immune signaling, with no single unifying function across the cluster. With only three proteins and no shared pathway, there isn\u2019t a coherent theme to label beyond a broad, non-specific category.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000020","count":1},{"id":"GO:0061138","count":1},{"id":"GO:0048546","count":1},{"id":"GO:0034587","count":1},{"id":"GO:0032808","count":1}]},{"hash":"1146504623623594608","title":"ER-Golgi vesicle trafficking (COPII)","description":"Reasoning: Top GO terms center on vesicle transport between the ER and Golgi, specifically COPII budding and retrograde Golgi-ER transport, suggesting ER\u2013Golgi trafficking as the core function of this cluster. The other terms reflect broader proliferative or developmental processes but do not override the trafficking theme.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0090114","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0035264","count":3}]},{"hash":"685166600010813414","title":"Adaptive immunity and angiogenesis","description":"This cluster centers on adaptive immune functions (antigen processing/presentation via MHC I and adaptive immune response) alongside angiogenesis-related processes (angiogenesis, its positive regulation, and related renin-angiotensin activities). The presence of leukotriene biosynthesis and cell signaling supports inflammatory and immune-vascular communication. While there is a term about symbiont entry into host cells, the dominant theme is immune activation coupled with vascular modulation, justifying the label.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0019370","count":2},{"id":"GO:0002005","count":2},{"id":"GO:0045766","count":2}]},{"hash":"1875234376229076794","title":"TLR2-Mediated Innate Immune Signaling","description":"The top GO terms cluster around innate immune sensing and NF-kappaB\u2013dependent responses: detection of diacyl lipopeptides, TLR2 signaling, IL-6 production, and defense responses to viruses, all indicative of TLR2-driven cytokine signaling. Additional terms like non-canonical NF-kappaB signaling and regulation of kinase activity fit this inflammatory signaling network, while a few unrelated terms may reflect background annotations. Overall, this cluster appears to represent a TLR2-driven innate immune response module.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0035882","count":3},{"id":"GO:0045410","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0042346","count":3},{"id":"GO:0051607","count":3}]},{"hash":"1266252615338672465","title":"Unknown","description":"The top GO terms are highly diverse, spanning blood coagulation and platelet activation, neural dendrite regeneration, various transport and metabolic processes, sporulation, and antibiotic biosynthesis. There\u2019s no clear common pathway or function tying these terms together, and the cluster has no edges or triangles to suggest a cohesive interaction. This suggests no single representative function for the group.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007596","count":2},{"id":"GO:0031104","count":2},{"id":"GO:0055114","count":1},{"id":"GO:1901684","count":1},{"id":"GO:0030245","count":1}]},{"hash":"2192153792251987421","title":"Innate immune signaling and actin remodeling","description":"This cluster\u2019s top GO terms cluster around innate immune processes (defense response to virus, innate immune response, regulation of JNK cascade), suggesting a role in immune signaling. In addition, several terms relate to actin cytoskeleton dynamics (actin filament bundle assembly, lamellipodium assembly, actin cortical patch assembly), pointing to coordinated cytoskeletal remodeling often seen with immune cell movement and signaling. Some terms (e.g., heterochromatin formation, osteoblast fate commitment) appear peripheral noise, so the overall theme is best captured as innate immunity coupled with actin dynamics. Confidence is moderate due to the mixed signals.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0030702","count":1},{"id":"GO:0002051","count":1}]},{"hash":"1973980916297602117","title":"Unknown","description":"The top GO terms span spermatogenesis (sperm individualization, sperm axoneme assembly), immune signaling (interferon-beta production), sensory perception (detection of mechanical stimulus involved in hearing), plasmid maintenance, and mitochondrial distribution. There is no single coherent biological process or function tying all terms together, suggesting the proteins may be functionally diverse or represent annotation noise. Therefore, a concise, representative label cannot be determined.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007291","count":1},{"id":"GO:0032608","count":1},{"id":"GO:0007288","count":1},{"id":"GO:0050910","count":1},{"id":"GO:0006276","count":1}]},{"hash":"1419812259328524622","title":"Pyrimidine nucleotide metabolism","description":"The terms cluster around pyrimidine ribonucleotide metabolism, including dUTP/dUMP biosynthesis and catabolic pathways (dUTP and dITP). This suggests a cohesive role in regulating pyrimidine nucleotide flux, spanning both synthesis and breakdown.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006226","count":3},{"id":"GO:0035863","count":3},{"id":"GO:0046081","count":3},{"id":"GO:0006229","count":3},{"id":"GO:0009220","count":3}]},{"hash":"656641849033210937","title":"Cytokine signaling and inflammation regulation","description":"The proteins appear tied to immune signaling and inflammation, with GO terms highlighting interferon production, IL-4\u2013mediated signaling, leukotriene biosynthesis, and anti-inflammatory regulation. Additional terms referencing growth factor receptor signaling and endothelin response suggest broader signaling crosstalk, but the central theme is cytokine-driven immune modulation.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032481","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0019370","count":3},{"id":"GO:0040014","count":3},{"id":"GO:0050728","count":3}]},{"hash":"17110792805285973","title":"Unknown","description":"The GO terms are a patchwork of metal ion transport, various metabolism processes, and unrelated functions, with only a single edge among three proteins and several obsolete terms, so there is no clear, shared function to label the cluster with confidence.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:1901684","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0030168","count":3},{"id":"GO:0042128","count":3}]},{"hash":"1349721790392965848","title":"Rap/GPCR/Wnt Signaling Regulators","description":"This cluster shows a pattern of proteins involved in regulating multiple signaling pathways, including Rap-mediated signal transduction, GPCR-related signaling, and Wnt signaling, as well as related processes like glucagon response and platelet activation. The common theme is modulation of diverse cellular signaling cascades rather than a single specific function, suggesting these proteins act as regulators of signaling pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071377","count":1},{"id":"GO:0045988","count":1},{"id":"GO:0032487","count":1},{"id":"GO:0032486","count":1},{"id":"GO:0030845","count":1}]},{"hash":"1111658925989583054","title":"Isoprenoid and amino acid biosynthesis cluster","description":"The top GO terms are dominated by biosynthetic processes tied to isoprenoid production (mevalonate and MEP pathways; farnesyl diphosphate; cholesterol) and several amino acid biosynthesis terms (L-homoserine, methionine, threonine), with some carbohydrate-related metabolism also represented. This suggests a cluster centered on core metabolic biosynthesis, especially terpenoid/lipid and amino acid pathways, rather than a single, exclusive function. Confidence: Medium","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009092","count":2},{"id":"GO:0019287","count":2},{"id":"GO:0046396","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0019288","count":2}]},{"hash":"518281351855434671","title":"Developmental signaling and stem cell regulation","description":"Based on GO terms such as regulation of asymmetric cell division, stem cell differentiation, thymus development, and positive/negative regulation of signaling pathways (TGF-beta receptor signaling, nodal signaling) as well as receptor clustering, the proteins appear to participate in coordinating developmental signals and stem cell fate decisions. The presence of these terms provides a cohesive theme around development and signaling. Some terms like carnitine transport and visual learning may be incidental annotations, but the dominant pattern supports a developmental signaling/regulatory role.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009786","count":1},{"id":"GO:0015879","count":1},{"id":"GO:1900108","count":1},{"id":"GO:0030511","count":1},{"id":"GO:0051612","count":1}]},{"hash":"1708596928892984096","title":"Immune cell chemotaxis signaling","description":"This cluster centers on immune cell movement and related signaling, with terms for eosinophil, neutrophil, macrophage, and T cell chemotaxis and a general immune response. It also highlights GPCR-mediated signaling components (dopamine receptor pathways) and downstream ERK/MAPK and GTPase activation, suggesting coordinated immune cell trafficking and signal transduction.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060158","count":2},{"id":"GO:0007191","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0048245","count":2},{"id":"GO:0006955","count":2}]},{"hash":"1996638845430772341","title":"Sterol Biosynthesis and Lipid Metabolism","description":"The dominant terms are sterol biosynthesis (cholesterol, ergosterol, brassinosteroid) and lipid metabolic process, pointing to a lipid/sterol biosynthesis theme. The presence of protein import/insertion into mitochondrial and chloroplast membranes reinforces a link to membrane biogenesis and organelle lipid handling, though a few defense/food response terms may reflect annotation noise.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":1},{"id":"GO:0016132","count":1},{"id":"GO:0006696","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0006629","count":1}]},{"hash":"740267090135950359","title":"Nervous system signaling and reflexes","description":"This cluster centers on neural signaling and quick motor/reflex responses. The top GO terms include startle response, dopaminergic synaptic transmission, acetylcholine receptor signaling, action potential, and righting reflex, with related autonomic and circadian functions. Together they point to a module of neurons governing reflexive movements and cholinergic/dopaminergic signaling, possibly modulated by circadian rhythms. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001964","count":2},{"id":"GO:0032226","count":1},{"id":"GO:0045188","count":1},{"id":"GO:0060013","count":1},{"id":"GO:0002087","count":1}]},{"hash":"1483597085864539123","title":"Mitochondrial inner membrane protein insertion","description":"Proteins in this cluster are linked by GO terms about mitochondrial targeting and insertion into the inner membrane, implying a shared role in importing and integrating proteins into the mitochondrial inner membrane. Although some terms are obsolete, the theme of mitochondrial inner-mmembrane insertion remains clear.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072321","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0006626","count":1}]},{"hash":"1937425627202387107","title":"Neuronal signaling and locomotor behavior","description":"Based on the GO terms, the proteins are linked to neural communication (dopaminergic synaptic transmission, acetylcholine receptor signaling, action potential) and motor outputs (righting reflex, locomotory behavior) as well as circadian regulation of sleep/wake cycles, indicating a focus on neuronal signaling and locomotor control.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032226","count":3},{"id":"GO:0045188","count":3},{"id":"GO:0060013","count":3},{"id":"GO:0002087","count":3},{"id":"GO:1901214","count":3}]},{"hash":"914822043018770388","title":"TLR2 signaling and macrophage activation","description":"The top GO terms cluster around innate immune functions, including defense response to virus, Toll-like receptor 2 signaling, and macrophage activation, with supporting hints of actin remodeling linked to cell migration. This suggests a functional theme centered on innate immune signaling and macrophage activity, despite some peripheral terms. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035882","count":1},{"id":"GO:0051607","count":1},{"id":"GO:0030335","count":1},{"id":"GO:0034134","count":1},{"id":"GO:0035751","count":1}]},{"hash":"1368078493132128298","title":"Glutathione metabolism (biosynthesis and catabolism)","description":"This cluster prominently includes both glutathione biosynthetic and catabolic processes (GO:0006750 and GO:0006751), suggesting a core theme of glutathione metabolism. Related terms like response to xenobiotic stimulus and redox-associated processes support a detoxification/oxidative stress context, reinforcing the glutathione-centered interpretation despite other diverse terms. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006751","count":1},{"id":"GO:0006750","count":1},{"id":"GO:0006508","count":1},{"id":"GO:1901750","count":1},{"id":"GO:0002098","count":1}]},{"hash":"1869144633209696525","title":"Potassium Ion Transport and Membrane Potential","description":"This cluster is dominated by GO terms related to potassium ion balance and the electrical properties of membranes: intracellular potassium ion homeostasis, potassium ion transmembrane transport, stabilization of membrane potential, and regulation of resting membrane potential, plus membrane repolarization in atrial cardiac muscle cells. These points converge on a common theme of cellular electrophysiology and ion transport, suggesting proteins in this cluster work to maintain Membrane potential via potassium handling. The other terms about touch sensation and immune responses appear incidental and do not define the core function here.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:0098914","count":2},{"id":"GO:0050976","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0030322","count":2}]},{"hash":"447094843909215006","title":"Complement regulation and inflammatory signaling","description":"The top GO terms cluster around regulation of the complement system (classical and alternative pathways) and membrane attack complex activation, together with inflammatory cytokine production (IL-1\u03b2 and IL-10) and LPS response, indicating innate immune modulation and inflammation; a few generic terms are present but do not override this central theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0045959","count":3},{"id":"GO:0070208","count":3},{"id":"GO:0050720","count":3},{"id":"GO:0032613","count":3},{"id":"GO:0001970","count":3}]},{"hash":"1705595541240916230","title":"Neuronal development and dendrite morphogenesis","description":"The top GO terms are dominated by neural-related processes: ephrin receptor signaling, dendrite development, positive regulation of dendrite morphogenesis, and neuronal stem cell population maintenance, which together point to neural development and dendrite formation as the core theme. A few plant-focused terms appear, likely due to cross-species annotations or noise, but they do not override the central neural theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048013","count":3},{"id":"GO:0009955","count":3},{"id":"GO:1902213","count":3},{"id":"GO:0016358","count":3},{"id":"GO:0097150","count":3}]},{"hash":"1755787747488063109","title":"Multi-tissue Developmental Regulation","description":"The Top Terms show development across diverse tissues (gonads, neurons, smooth muscle, olfactory structures, sympathetic ganglia, limb buds, pharyngeal system, myocardium, etc.), indicating proteins involved in broad developmental regulation rather than a single tissue-specific function. This suggests a general developmental role spanning multiple tissues.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000020","count":2},{"id":"GO:0021860","count":2},{"id":"GO:0014912","count":2},{"id":"GO:0051642","count":2},{"id":"GO:0021988","count":2}]},{"hash":"211599998623582301","title":"Unknown","description":"The three terms span immune regulation (MHC II biosynthesis), virus\u2013host interaction (activation of viral genome replication), and mRNA processing (poly(A) tail shortening). They don\u2019t cohere around a single function or pathway, and with only three proteins, there isn\u2019t a clear common theme to name a specific cluster function.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045347","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0000289","count":1}]},{"hash":"583517726130853206","title":"Phytochelatin synthesis and proteostasis regulation","description":"This cluster combines phytochelatin biosynthesis (detoxification) with themes of enzymatic regulation, proteolysis, and autophagy regulation, pointing to a link between detoxification pathways and cellular protein quality control under stress.","confidence":"Low","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":3},{"id":"GO:0043085","count":3},{"id":"GO:0006508","count":3},{"id":"GO:1904715","count":3}]},{"hash":"1064956036139536855","title":"Guanylyl cyclase/cGMP signaling and vascular tone","description":"The top terms cluster around receptor guanylyl cyclase signaling, vasodilation, and regulation of cGMP metabolism, pointing to cyclic-nucleotide signaling that controls vascular tone and related cardiac functions. While a few unrelated terms appear, the strongest coherent theme is GC\u2013cGMP signaling affecting vasculature and possibly cardiac electrophysiology.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":2},{"id":"GO:0010996","count":2},{"id":"GO:0003418","count":1},{"id":"GO:0042311","count":1},{"id":"GO:0007168","count":1}]},{"hash":"2244570005314669931","title":"Neuromuscular development and synapse formation","description":"This cluster is enriched for terms related to nervous system development, synapse assembly, myoblast fusion, and cell adhesion, suggesting a common role in neuromuscular development and junction formation. While there are a few other terms (e.g., skeletal development), the dominant theme centers on neuron\u2013muscle interface formation and maturation.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0007156","count":2},{"id":"GO:0007157","count":2},{"id":"GO:0051965","count":2}]},{"hash":"2164728508760534967","title":"Complement Activation Regulation and Immune Modulation","description":"The dominant GO terms describe regulation and activation of the complement system (classical and alternative pathways, membrane attack complex) and immune signaling factors (IL-10 production, platelet activation, PKC signaling, T cell death). Although a fertilization term appears, the strongest signal is immune regulation via complement, so the label focuses on complement activation control and related immune modulation.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0045959","count":3},{"id":"GO:0032613","count":3},{"id":"GO:0001970","count":3},{"id":"GO:0006957","count":3},{"id":"GO:0010572","count":3}]},{"hash":"857778427401118245","title":"Macrophage lipid-mediated inflammation","description":"These proteins cluster around lipid metabolism and inflammatory signaling in macrophages: leukotriene biosynthesis and lipid remodeling point to synthesis and remodeling of lipid mediators; production of IL-8 and IL-1 and foam cell differentiation indicate inflammatory activation; phospholipase activity regulation and lipid storage tie lipid signaling to macrophage function. The combination suggests a theme of macrophage-driven inflammatory responses powered by lipid mediators.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019370","count":3},{"id":"GO:0044240","count":3},{"id":"GO:0010518","count":3},{"id":"GO:0045740","count":3},{"id":"GO:0032637","count":3}]},{"hash":"1168974674114651693","title":"Unknown","description":"Top Terms are empty and there are no edges or connectivity among the listed proteins, so no shared functional theme is evident; without GO terms to guide a label, this cluster is best described as Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"993874148565605932","title":"Glial Neuroimmune and Dopaminergic Regulation","description":"This cluster centers on immune/inflammatory processes and glial functions (astrocyte chemotaxis, GDNF production, xenobiotic response) together with dopaminergic signaling (dopamine transport, metabolism, and PLC-activated dopamine receptor pathway), suggesting a cohesive role in glial-mediated neuroimmune regulation linked to dopamine signaling.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050728","count":3},{"id":"GO:0042493","count":3},{"id":"GO:2000458","count":3},{"id":"GO:1900168","count":3},{"id":"GO:0048245","count":3}]},{"hash":"1079727722686937283","title":"Transmembrane Metabolite Transport","description":"The top GO terms point to the transport of various metabolites and cofactors across membranes (thiamine pyrophosphate, phosphate, coenzyme A, glycine, pyridoxal phosphate, and mitochondrial ATP transport, plus the malate-aspartate shuttle), suggesting a shared function in moving small molecules across membranes, including mitochondrial transport. A couple regulatory terms appear peripheral to this core theme. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030974","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0035349","count":3},{"id":"GO:0036233","count":3},{"id":"GO:0043490","count":3}]},{"hash":"356862224909827408","title":"Brain development and neural signaling","description":"The terms strongly point to neural-focused biology: retina layer formation and substantia nigra development highlight neural tissue development, while regulation of synaptic vesicle exocytosis points to neural signaling. Additional terms touch on stress responses and metabolic transport, which are supportive but do not outweigh the neural development/synaptic theme. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016061","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0043490","count":2},{"id":"GO:2000300","count":2}]},{"hash":"410305016380575949","title":"Amino Acid and Carbohydrate Metabolism with Ion Transport","description":"The top GO terms cluster around amino acid catabolic processes (L-serine and L-homocysteine), broader carbohydrate metabolism and gluconeogenesis, plus transmembrane ion transport (magnesium and potassium). This suggests a metabolic module that links amino acid and carbohydrate metabolism with ion transport; the presence of kinase activation and cell volume regulation terms is peripheral rather than defining. Confidence: Medium.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006565","count":3},{"id":"GO:0045722","count":3},{"id":"GO:1903830","count":3},{"id":"GO:0045794","count":3},{"id":"GO:0005975","count":3}]}]