[{"hash":"647620333916407445","title":"Lung Mesenchyme Development and Cell Migration","description":"This cluster centers on developmental processes with a strong emphasis on mesenchymal tissues and lung development. GO terms include lung-associated mesenchyme development, skeletal and multicellular organism development, and regulation of cell migration, suggesting active morphogenesis and tissue remodeling. Additional hints come from hyaluronan metabolism and actin cytoskeleton regulation by cell\u2013cell adhesion, pointing to extracellular matrix interactions and cytoskeletal remodeling. The negative regulation of canonical Wnt signaling aligns with signaling fine-tuning during tissue formation. Overall, these proteins likely participate in developing lung mesenchyme with migratory and morphogenetic roles.","confidence":"Medium","size":29,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043065","count":6},{"id":"GO:0001501","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0008285","count":5},{"id":"GO:0016477","count":5}]},{"hash":"907607330954724369","title":"Ubiquitination and Proteasome Regulation","description":"The two most enriched terms are protein ubiquitination and proteasome regulatory particle assembly, which together point to proteostasis and degradation machinery as the cluster's core function. Other terms suggest linked signaling or stress-response processes (temperature sensing, responses to capsazepine and vitamin D), but the dominant theme remains ubiquitin-mediated protein turnover and its regulation. Therefore this label captures the cluster's central activity.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":25},{"id":"GO:0070682","count":25},{"id":"GO:0050960","count":25},{"id":"GO:0035556","count":25},{"id":"GO:1901594","count":25}]},{"hash":"1644107604332850792","title":"PNS axon regeneration and collagen remodeling","description":"Based on the prominent GO terms, this cluster centers on peripheral nerve repair and axon regrowth, including regeneration at the neuromuscular junction and PNS axon regeneration, with a strong signal for collagen fibril organization, indicating remodeling of the extracellular matrix during regeneration. Other terms (platelet aggregation, leptin response, triglyceride homeostasis, mesenchymal-epithelial signaling) are present but appear less central to the main theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048692","count":11},{"id":"GO:0030199","count":11},{"id":"GO:0014814","count":11},{"id":"GO:0014012","count":11},{"id":"GO:0070527","count":11}]},{"hash":"1277558737392257874","title":"Neurodevelopmental Transcription Regulators","description":"The cluster\u2019s top GO terms are dominated by DNA-templated transcription and neural/embryonic development (forebrain development, neural tube closure, skeletal system development), suggesting proteins that regulate gene expression during neurodevelopment. The inclusion of mitotic cell cycle terms supports a proliferative developmental context. While a few terms are more general or ancillary, the overall pattern points to transcriptional regulation in neural development.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0030900","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0001403","count":6}]},{"hash":"978451943296246084","title":"mRNA processing and translation initiation","description":"The GO terms show strong signals for both translation initiation (preinitiation complex formation, translation reinitiation, eIF4F complex assembly) and various RNA processing steps (mRNA splicing regulation, splice site recognition, mRNA modification, and ncRNA-mediated silencing). This suggests a coherent cluster of proteins involved in mRNA maturation and its control at the level of translation initiation, hence the label that captures both processes.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":12},{"id":"GO:0002188","count":12},{"id":"GO:0031047","count":11},{"id":"GO:0048026","count":10},{"id":"GO:0006376","count":9}]},{"hash":"303920511574158846","title":"Bacterial core transcription and biosynthesis","description":"This cluster shows enrichment for DNA-templated transcription, fatty acid biosynthesis, cell division, and protein oligomerization/assembly, along with cobalamin biosynthesis. These represent fundamental bacterial growth and housekeeping processes (gene expression, metabolism, and cell proliferation), suggesting a cohesive theme of core cellular functions rather than a single pathway. ","confidence":"Medium","size":29,"edges":378,"triangles":2973,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0019518","count":7},{"id":"GO:0006633","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0051260","count":7}]},{"hash":"1517363869969642355","title":"Vascular Angiogenesis and Blood-Pressure Signaling","description":"Top terms cluster around blood vessel biology: both angiogenesis (and its regulation), vasoconstriction and blood pressure regulation, platelet activation, GPCR signaling and ERK cascade, pointing to a cohesive vascular signaling/angiogenesis module. Electron transport chain and antibiotic response may reflect energy needs or stress responses but do not define the main theme.","confidence":"High","size":29,"edges":7,"triangles":1,"max_degree":3,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0016525","count":7},{"id":"GO:0001525","count":6},{"id":"GO:0045777","count":6},{"id":"GO:0010579","count":6},{"id":"GO:0022900","count":6}]},{"hash":"670325291343404590","title":"Ribosome Biogenesis & Translation","description":"The cluster is dominated by GO terms for ribosome biogenesis, ribosomal subunit biogenesis, nucleolar rRNA transcription, and translational processes (initiation and cytoplasmic translation), indicating a cohesive role in ribosome assembly and protein synthesis. Some cell cycle-related terms likely reflect growth coordination with ribosome production, but the central theme remains ribosome/translation machinery.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0042274","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0010124","count":2}]},{"hash":"615635534422599426","title":"Vascular-immune signaling and angiogenesis","description":"This cluster is enriched for proteins involved in endothelial/vascular signaling and immune modulation, including platelet activation, complement activation, regulation of vascular permeability, angiogenesis suppression, Tie signaling, and receptor tyrosine kinase activity, as well as cell-matrix adhesion and immune-related processes. A single outlier term about synaptic transmission exists, but the dominant themes point to vascular-immune crosstalk and angiogenic regulation. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051968","count":6},{"id":"GO:0002740","count":5},{"id":"GO:0030168","count":5},{"id":"GO:0001867","count":5},{"id":"GO:0043116","count":5}]},{"hash":"2055180833712808492","title":"RNA Splicing and Translational Regulation","description":"The proteins are enriched for RNA-centric processes: mRNA splicing via spliceosome (splicing regulation, splice site recognition), mRNA modification, and regulation of mRNA stability in response to stress, as well as components involved in translation initiation (eIF4F complex assembly, regulation of translational initiation). This points to a cohesive theme of post-transcriptional control of gene expression, spanning both splicing and initiation of translation. A single DNA replication term is present but peripheral; overall the dominant signal is RNA processing and translational regulation.","confidence":"High","size":29,"edges":89,"triangles":183,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":9},{"id":"GO:0031047","count":9},{"id":"GO:1901407","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0006376","count":6}]},{"hash":"145872543512257074","title":"RNA processing and cytoskeletal signaling","description":"The cluster includes terms for RNA splicing and transport (RNA processing) alongside signaling and cytoskeletal regulation (positive regulation of GTPase activity, Arp2/3-mediated actin nucleation, and tyrosine phosphorylation), with additional developmental and stress-related terms (skin and seminiferous tubule development, hypoxia response, aging). This suggests a theme around coordinating gene expression with cytoskeletal dynamics and signaling in development and stress, rather than a single narrow function.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0007568","count":9},{"id":"GO:0000398","count":8},{"id":"GO:0043588","count":8},{"id":"GO:0000278","count":7}]},{"hash":"1546871017578930067","title":"Cell cycle regulation and proteostasis","description":"The terms point to core cell cycle processes (cell division, cell cycle, CDK regulation) coupled with protein turnover pathways (ubiquitination, proteasome assembly, ERAD) and ribosome biogenesis, suggesting a coordinated program linking cell division with proteostasis and growth. Confidence: High","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0007049","count":8},{"id":"GO:0070682","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0051260","count":6}]},{"hash":"1243178526810618855","title":"Neural development and axon guidance signaling","description":"This cluster is dominated by terms related to nervous system development, axon guidance, hippocampus development, and signaling pathways like Roundabout and Smoothened, with ERK cascade modulation and neuron apoptotic regulation. While organ development (heart, kidney) appears, the core theme points to neural development and axon pathfinding via key developmental signals.","confidence":"High","size":29,"edges":58,"triangles":16,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":6},{"id":"GO:0007399","count":5},{"id":"GO:0001822","count":5},{"id":"GO:0035385","count":5},{"id":"GO:0007224","count":5}]},{"hash":"1652980791715502337","title":"Immune signaling and vesicle trafficking proteins","description":"The top GO terms cluster around immune responses (interferon-alpha, interferon-beta, response to biotic stimulus, host-mediated suppression of symbiont invasion) and vesicle trafficking (synaptic vesicle clustering, endosome to plasma membrane protein transport). Some bone development terms appear as well, suggesting multifunctionality. Overall, this cluster seems to group proteins involved in signaling and intracellular transport with immune-related functions, though the diversity indicates heterogeneity rather than a single canonical pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044381","count":2},{"id":"GO:0035455","count":2},{"id":"GO:0009607","count":2},{"id":"GO:0097091","count":2},{"id":"GO:0099638","count":2}]},{"hash":"906842392089539483","title":"Apoptosis and immune signaling","description":"The top GO terms point to apoptotic pathways (extrinsic signaling, necroptosis, T cell death) and immune/inflammatory responses (response to LPS, IL-13 regulation), suggesting a cluster centered on cell fate decisions under stress and immune signaling, despite some unrelated developmental terms that may reflect annotation noise.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006977","count":3},{"id":"GO:0090557","count":3},{"id":"GO:2001241","count":3},{"id":"GO:0003283","count":3},{"id":"GO:0006412","count":2}]},{"hash":"2125417136890468223","title":"Cardiac contraction and heart electrical activity regulation","description":"Top GO terms center on cardiac muscle contraction, calcium handling, and regulation of cardiac action potentials, including SA node and atrial cell electrical activity. This points to a cluster enriched for proteins involved in excitation-contraction coupling and cardiac electrophysiology. While a few terms reference diaphragm contraction, transcription regulation, and insulin secretion, the strongest signal is heart-specific contraction and electrical control.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0043388","count":5},{"id":"GO:0001824","count":5},{"id":"GO:0010881","count":5},{"id":"GO:0060048","count":5}]},{"hash":"357813173836242303","title":"Ubiquitin-Mediated Regulation and NF-kappaB Signaling","description":"The cluster is dominated by ubiquitination-related terms (protein ubiquitination, ubiquitin-dependent ERAD) and NF-kappaB transcription factor activity regulation, suggesting a core theme around ubiquitin-mediated control of signaling pathways, including immune/inflammatory signaling. Other terms hint at broader regulatory roles (GTPase activity, cell cycle) and viral-host interactions, but the strongest signal centers on ubiquitin-related regulation and NF-kappaB pathways.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051092","count":8},{"id":"GO:0016567","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0033280","count":6},{"id":"GO:0043547","count":5}]},{"hash":"1672046761335118731","title":"Multisystem signaling and stress responses","description":"The top GO terms mix immune-regulatory signaling (NF-kappaB regulation, NOD2 signaling, IL-12 production) with processes related to protein localization and mechanical/stretch responses, plus cardiac conduction. This suggests a broad set of regulatory signaling activities and cellular stress responses across different tissues rather than a single cohesive function. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032088","count":13},{"id":"GO:0002268","count":12},{"id":"GO:0086070","count":12},{"id":"GO:0097284","count":12},{"id":"GO:0070431","count":12}]},{"hash":"572345748974544073","title":"Innate immunity and ubiquitin-regulated cell death","description":"Major signals are innate immunity and programmed cell death, with regulation by ubiquitin-proteasome pathways (innate immune response, pyroptotic and apoptotic processes, and protein ubiquitination). Some spindle/cell division terms may reflect broader cellular regulation, but the core theme is immune-triggered cell death linked to ubiquitin-mediated degradation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0045087","count":8},{"id":"GO:0090307","count":6},{"id":"GO:0070269","count":6},{"id":"GO:1990001","count":6},{"id":"GO:0016567","count":5}]},{"hash":"213960694530826491","title":"Neural development and migration regulators","description":"This cluster is dominated by neural-related processes: nervous system development, forebrain development, cell migration, and bipolar cell polarity, with activity in Wnt signaling regulation and apoptotic/differentiation processes, suggesting a cohesive set of proteins guiding neural development and tissue patterning.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016477","count":28},{"id":"GO:0090090","count":28},{"id":"GO:0008285","count":28},{"id":"GO:0043065","count":28},{"id":"GO:2000727","count":27}]},{"hash":"158815410223881648","title":"T Cell Death and Inflammatory Signaling","description":"The top GO terms cluster around activation-induced T cell death, IL-1 signaling, DISC assembly, JNK/NF-\u03baB pathways, and LPS signaling, indicating a coherent theme of immune activation and apoptosis signaling. Some terms are peripheral or obsolete, but the dominant theme supports this label.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0006924","count":5},{"id":"GO:0046330","count":5},{"id":"GO:0006977","count":5},{"id":"GO:0070498","count":5},{"id":"GO:0070926","count":5}]},{"hash":"1365242717718635340","title":"NF-kappaB signaling in innate immunity","description":"The cluster is strongly enriched for innate immune response and canonical NF-kappaB pathway terms, including NF-kappaB activation and signaling, cytokine-mediated pathways (IL-1 and TNF), NF-kappaB-inducing kinase activity, and ubiquitination processes (K63-linked and autoubiquitination) that regulate NF-kappaB. This points to a cohesive module centered on NF-kappaB\u2013driven immune signaling in response to innate stimuli, with downstream links to T cell proliferation. Confidence: High","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":12},{"id":"GO:0032088","count":12},{"id":"GO:0051092","count":9},{"id":"GO:0070534","count":7},{"id":"GO:0051865","count":7}]},{"hash":"2076998328885266178","title":"K63 Ubiquitination-Driven NF-\u03baB Signaling","description":"The terms are dominated by ubiquitination, especially K63-linked ubiquitination and autoubiquitination, coupled with NF-\u03baB pathway activation (I\u03baB phosphorylation, NF-\u03baB\u2013inducing kinase), TNF signaling, and innate immune response, indicating a cluster of proteins functioning in ubiquitin-mediated NF-\u03baB signaling and TNF-driven innate immunity.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0070534","count":15},{"id":"GO:0051865","count":15},{"id":"GO:1903265","count":15},{"id":"GO:0051092","count":14},{"id":"GO:0045087","count":14}]},{"hash":"1945174664389279396","title":"Innate immune signaling and inflammatory response","description":"The GO terms cluster around innate immunity and inflammatory signaling: response to virus, LPS- and peptidoglycan-recognition pathways, innate immune and inflammatory responses, and regulation of TNF and NF-kappaB activity, with associated STAT phosphorylation. A single outlier term about neuron projection is likely noise; overall, the theme is pathogen recognition driving pro-inflammatory signaling.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042511","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0009615","count":3},{"id":"GO:0032760","count":3},{"id":"GO:0061057","count":3}]},{"hash":"1211671287154676628","title":"Developmental signaling and neural differentiation","description":"The terms cluster around neural development and synaptic plasticity (long-term potentiation, neuron projection development) while also spanning broader tissue differentiation (lens fiber, skin, skeletal) and multicellular development. Signaling pathways like ERK cascade and Rho regulation connect these processes, with additional terms pointing to general developmental and cellular machinery (innate immune response, mitotic cohesion). This suggests a cohesion around development driven by conserved signaling modules, though the set is diverse beyond strictly neural functions. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0031175","count":3},{"id":"GO:0070306","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1626345976997289312","title":"Neural development and synapse formation","description":"This cluster is enriched for neural development and synapse-related terms, including positive regulation of synapse assembly, neuron projection development, nervous system development, and axon guidance, suggesting a coordinated role in neural development and synaptic organization. Some terms like heart development and vitamin D3 metabolic process appear but are less central to the main theme. The lack of observed edges does not negate a cohesive developmental function indicated by the GO terms, so a neural development/synapse formation label is most representative.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0070640","count":3},{"id":"GO:0007399","count":3}]},{"hash":"1064747849587490470","title":"Nervous system development and innervation","description":"The top GO terms are centered on nervous system development, innervation, and glial signaling, indicating a cluster enriched for neural development and neural communication. While a few terms relate to inflammatory responses or GI-related processes, the dominant signal points to neural tissue development and signaling. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007417","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006954","count":3},{"id":"GO:0061580","count":3},{"id":"GO:0002063","count":3}]},{"hash":"1292347678415448068","title":"Developmental Differentiation and Regeneration","description":"This cluster shows enrichment for terms related to promoting differentiation across multiple lineages (bone, fat, macrophages, placenta) and tissue regeneration (liver/hepatocytes), suggesting a broad developmental and regenerative program. Additional terms on transcriptional regulation and ER stress response support a coordinated gene-expression program underpinning differentiation and tissue repair, though the mix also includes immune-related and placental processes, indicating a diverse, multi-taceted role rather than a single pathway. ","confidence":"Medium","size":28,"edges":367,"triangles":3006,"max_degree":27,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":13},{"id":"GO:0035470","count":8},{"id":"GO:0045669","count":7},{"id":"GO:0045600","count":7},{"id":"GO:0045348","count":7}]},{"hash":"1290283331988687314","title":"TGF-\u03b2/Wnt/Hippo signaling and transcriptional regulation","description":"The cluster is enriched for major signaling pathway terms (TGF-\u03b2, Wnt, Hippo) and DNA-templated transcription, plus downstream outcomes like apoptosis and differentiation (keratinocyte differentiation). This suggests proteins coordinating cell fate decisions and growth control via these interconnected signaling networks rather than a single function.","confidence":"High","size":28,"edges":285,"triangles":1504,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":13},{"id":"GO:0030512","count":12},{"id":"GO:0006351","count":10},{"id":"GO:0006935","count":9},{"id":"GO:0071560","count":9}]},{"hash":"2256120291753284493","title":"DNA replication and telomere maintenance","description":"The top GO terms cluster around DNA replication, fork progression, and telomere maintenance (including telomerase regulation and DNA repair), indicating a cohesive group of proteins involved in genome replication/stability. Some RNA surveillance terms may be incidental, but the dominant theme is replication and telomere maintenance.","confidence":"High","size":28,"edges":313,"triangles":2053,"max_degree":27,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0032508","count":16},{"id":"GO:0006310","count":9},{"id":"GO:0000184","count":8},{"id":"GO:0044806","count":8},{"id":"GO:1902983","count":7}]},{"hash":"1631776767137955049","title":"Ribosome Biogenesis and Developmental Proteins","description":"Top terms show ribosome biogenesis and ribosomal subunit biogenesis, as well as mitotic cell cycle, alongside forebrain development and CNS neuron axonogenesis, suggesting these proteins link ribosome assembly with developmental programs. While some terms touch immune signaling or ER stress, the dominant signal is a link between growth machinery and development.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0006351","count":3}]},{"hash":"865922568849507835","title":"Immune-coagulation and vascular regulation cluster","description":"The top GO terms cluster around adaptive immune response, complement activation, platelet activation, fibrinolysis, and regulation of vascular permeability, suggesting a cohesive module where immune activation interfaces with coagulation and endothelial barrier control. Additional terms like cell-matrix adhesion and receptor tyrosine kinase signaling support a coordinated response. A few terms (e.g., synaptic transmission) may reflect multifunctional proteins rather than core cluster function.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"wound healing","top_go_terms":[{"id":"GO:0002250","count":6},{"id":"GO:0042730","count":6},{"id":"GO:0051968","count":6},{"id":"GO:0002740","count":5},{"id":"GO:0030168","count":5}]},{"hash":"2173819352227522221","title":"Protein Translation and Membrane Targeting","description":"This cluster is dominated by translation-related GO terms (translation, mitochondrial translation) and both SRP-dependent cotranslational and post-translational targeting to membranes, suggesting a cohesive theme around ribosome-associated protein synthesis and membrane trafficking; tRNA wobble modification also ties into translation. A few other terms appear peripheral and do not define the main function.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0006616","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0032543","count":3}]},{"hash":"97347176356482776","title":"DNA replication, repair, and transposition","description":"The cluster is dominated by GO terms for DNA replication (GO:0006260), base-excision repair (GO:0006284), and DNA transposition (GO:0006313), with a secondary signal for cell division (GO:0051301). While there are some developmental and host-symbiont related terms present, the strongest and most frequent annotations point to DNA metabolism and genome maintenance as the core theme of this cluster.","confidence":"Medium","size":28,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046718","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006313","count":3},{"id":"GO:0007568","count":3}]},{"hash":"1613109337533093339","title":"Apoptosis and adhesion/motility signaling","description":"The cluster features several apoptotic terms (activation-induced T cell death; extrinsic apoptotic signaling; apoptotic process) alongside adhesion and cytoskeletal dynamics terms (cell-matrix adhesion; lamellipodium assembly; regulation of integrin activation; platelet activation), suggesting a core theme of cell death linked to adhesion and motility. Some terms like photosynthesis, vocalization, and fertilization appear as outliers, likely due to annotation breadth or multifunctional proteins. Overall, the apoptosis coupled with adhesion/motility theme best represents the cluster.","confidence":"Medium","size":28,"edges":85,"triangles":47,"max_degree":13,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006924","count":6},{"id":"GO:0033623","count":6},{"id":"GO:0010572","count":6},{"id":"GO:0015979","count":5},{"id":"GO:0071625","count":5}]},{"hash":"2187394889739258809","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0000184","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0007049","count":3}]},{"hash":"152142471627938671","title":"Neurodevelopmental Signaling and Angiogenesis","description":"The top GO terms cluster around nervous system development (including hippocampus development) and axon guidance signaling (Roundabout and Smoothened), with sprouting angiogenesis and related developmental processes, suggesting a cohesive theme of neurodevelopmental signaling coupled with vascular growth.","confidence":"High","size":28,"edges":330,"triangles":2204,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":14},{"id":"GO:0050852","count":13},{"id":"GO:0035385","count":13},{"id":"GO:0021766","count":10},{"id":"GO:0043525","count":10}]},{"hash":"2198782400163999038","title":"Vesicle trafficking and cytoskeletal dynamics","description":"This cluster centers on vesicle trafficking and cytoskeletal remodeling: retrograde Golgi-ER transport, endosome-to-postsynaptic transport, autophagy-related targeting, filopodium assembly, and small GTPase\u2013driven signaling. While some terms touch on development, these processes depend on vesicle traffic and actin/microtubule dynamics, supporting a cohesive functional theme.","confidence":"Medium","size":28,"edges":32,"triangles":1,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043552","count":9},{"id":"GO:0032258","count":8},{"id":"GO:0090307","count":8},{"id":"GO:0006890","count":8},{"id":"GO:1900026","count":8}]},{"hash":"811638718271802907","title":"TNF/NF-kB\u2013driven inflammatory signaling","description":"This cluster centers on GO terms related to TNF and IL-6 responses, positive regulation of canonical NF-kappaB signaling, and necroptosis-related processes (including ripoptosome assembly and negative regulation of necroptotic process), indicating a core theme of inflammatory signaling and cell death regulation. Additional terms about cellular responses to TNF and IL-6 reinforce a cytokine-driven response, while germinal center formation and follicular dendritic cell differentiation hint at involvement in adaptive immune processes within lymphoid tissues. Taken together, the proteins appear to participate in balancing inflammatory signaling and apoptosis/necroptosis in immune contexts.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060546","count":4},{"id":"GO:0043123","count":4},{"id":"GO:0071356","count":3},{"id":"GO:0071354","count":3},{"id":"GO:0002268","count":3}]},{"hash":"421414300940874838","title":"Mitotic Cell Cycle and RNA Processing","description":"This cluster shows enrichment for cell division and DNA replication alongside RNA processing activities (spliceosome-mediated splicing, mRNA export, transcription, and polyadenylation). The co-occurrence of mitotic regulation with RNA maturation/trafficking suggests a module coordinating replication and division with RNA processing; antiviral/innate immune terms may reflect stress-responsive regulation layered onto this core. Confidence: Medium.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006260","count":3}]},{"hash":"2234275621153695366","title":"Growth Factor Signaling and Proteostasis","description":"The cluster is enriched in insulin receptor signaling and insulin-like growth factor signaling, along with ubiquitin-dependent proteolysis, proteasome assembly, translation, and COPII vesicle cargo loading. This combination suggests a coherent theme where growth factor signaling coordinates protein synthesis, degradation, and trafficking to maintain cellular protein homeostasis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0006511","count":2},{"id":"GO:0043248","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0034260","count":2}]},{"hash":"745721215167514526","title":"Cellular stress response and genome maintenance","description":"Most frequent terms indicate cellular stress and immune/xenobiotic responses (response to xenobiotic stimulus, antibiotic, lipopolysaccharide) along with autophagy regulation and DNA maintenance (DNA replication, DNA recombination, X-ray response) and cell-cycle control (CDK activity). This points to a cluster of proteins involved in coping with stress and preserving genome integrity, rather than a single pathway. The compound eye development term appears less related and does not define the core theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042493","count":6},{"id":"GO:0043029","count":6},{"id":"GO:0048749","count":6},{"id":"GO:0046677","count":6},{"id":"GO:0006310","count":5}]},{"hash":"1963493614249378700","title":"Immune signaling regulation and hematopoietic development","description":"The cluster centers on tuning immune pathways (negative regulation of MAPK/ERK signaling and T cell receptor signaling, TLR7 signaling) and blood cell formation (hematopoietic progenitor differentiation, megakaryocyte development), with additional modulation of vascular permeability and stress responses (PERK-mediated UPR) and receptor turnover. This combination suggests a cohesive module of proteins that coordinate immune signaling with hematopoiesis and related barrier and stress pathways.","confidence":"High","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0070373","count":26},{"id":"GO:0000200","count":26},{"id":"GO:0050860","count":26},{"id":"GO:0070445","count":20},{"id":"GO:0002244","count":20}]},{"hash":"2097195755638537962","title":"Lipid catabolism and remodeling","description":"The top GO terms are dominated by phospholipid and triglyceride catabolic processes (phosphatidylethanolamine catabolic process, phosphatidylcholine catabolic process, triglyceride catabolic process, triglyceride mobilization, triglyceride acyl-chain remodeling), pointing to lipid breakdown and remodeling as the core function of this cluster. While there are some protein turnover terms (protein ubiquitination, proteasome regulatory particle assembly), they appear as secondary associations and do not outweigh the lipid-focused signal. Overall, the cluster is best described by lipid catabolism and remodeling.","confidence":"High","size":28,"edges":139,"triangles":14,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0046338","count":15},{"id":"GO:0006642","count":15},{"id":"GO:0010898","count":15},{"id":"GO:2000480","count":15},{"id":"GO:0034638","count":15}]},{"hash":"1727968975430201829","title":"Cardiovascular and Immune Signaling","description":"The GO terms show cardiovascular development and vasoconstriction alongside immune-related processes (B cell homeostasis, IL-4 production, NK T cell differentiation), with additional roles in cell migration and Rho signaling, suggesting a cluster involved in remodeling and signaling at the intersection of cardiovascular and immune functions. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0045907","count":4},{"id":"GO:0007605","count":3},{"id":"GO:0097194","count":3},{"id":"GO:0001782","count":3}]},{"hash":"1377902924672489383","title":"Inflammatory Immune Signaling with Cytoskeletal Remodeling","description":"The top GO terms cluster around inflammatory and immune responses (inflammatory response, response to lipopolysaccharide, regulation of IL-6 production) and cytoskeletal changes (Rac protein signaling, filopodium assembly), suggesting a group of proteins involved in immune activation and actin remodeling. Germinal center formation hints at adaptive immunity, while DNA transposition/integration may be incidental. Overall, they point to immune signaling with cytoskeletal dynamics as the central theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006313","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0002467","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0032675","count":3}]},{"hash":"1515327961855296469","title":"Nucleocytoplasmic transport and nuclear import","description":"Top GO terms include ribosomal protein import into nucleus, NLS-bearing protein import into nucleus, and nuclear pore complex assembly, pointing to a cohesive role in nucleocytoplasmic transport and nuclear import. The presence of NPC assembly and import-related terms supports a label capturing nuclear trafficking of proteins, though a few unrelated terms are present.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006610","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0051292","count":4},{"id":"GO:0000060","count":4}]},{"hash":"136180048932476915","title":"Neural development and neuroimmune signaling","description":"The cluster is enriched for neural-development concepts (synapse assembly, corpus callosum development, axonogenesis) and neuronal signaling (dopamine response, pain behavior), indicating a brain-focused role. It also includes neuroimmune terms (innate immune response, interferon-beta production, LPS signaling), suggesting neuroimmune activity within the same group. An outlier term on telomere maintenance via telomerase is present but less central. Overall, a brain development with neuroimmune signaling theme fits best.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051965","count":7},{"id":"GO:0022038","count":7},{"id":"GO:0045087","count":6},{"id":"GO:0045359","count":5},{"id":"GO:1903351","count":5}]},{"hash":"757571387122398527","title":"Synaptic and acrosomal vesicle exocytosis","description":"This cluster centers on vesicle trafficking and exocytosis, as indicated by GO terms for intracellular protein transport, synaptic vesicle maturation and fusion, regulation of synaptic vesicle exocytosis, and long-term potentiation, with acrosome reaction extending the exocytosis theme to sperm. While a couple terms touch on centrosome/spindle biology, the dominant signal is vesicle-mediated exocytosis at presynaptic and acrosomal sites.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":3},{"id":"GO:0007340","count":3},{"id":"GO:0016188","count":2},{"id":"GO:0031629","count":2},{"id":"GO:0007098","count":2}]},{"hash":"1463332771923425049","title":"Innate Immune NF-\u03baB Signaling","description":"The cluster centers on innate immune response and antiviral defense, with multiple terms for NF-\u03baB signaling (canonical pathways) indicating a core role in immune activation. Supporting signals involve Rho-mediated cytoskeletal regulation and actin localization, which can influence signaling dynamics. Some cardiac-related terms and obsolete annotations appear incidental and do not define the main function of the cluster.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0051770","count":2},{"id":"GO:0051607","count":2}]},{"hash":"951199253353777447","title":"Multisystem Signaling and Development","description":"The top GO terms span metabolic insulin signaling, glucose transport, mechanotransduction (muscle stretch), multiple developmental processes (forebrain and thymus), cardiac signaling, and various immune-related pathways, plus RNA processing. This suggests proteins involved in a broad array of signaling and developmental roles across different tissues rather than a single cohesive pathway, which justifies a \"multisystem signaling and development\" label. The lack of edges indicates no tight network connectivity within the cluster, reinforcing a broad functional grouping rather than a single module.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0030900","count":2},{"id":"GO:0000350","count":2}]},{"hash":"1273506242265542664","title":"NF-kB\u2013driven inflammatory signaling","description":"The cluster is dominated by GO terms tied to canonical and regulatory NF-kappaB signaling, IL-1 and LPS-mediated pathways, and ubiquitination events (including K63-linked ubiquitination and autoubiquitination), pointing to a cohesive NF-kB\u2013mediated inflammatory signaling module with ubiquitin-regulation features.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":3},{"id":"GO:0090557","count":3},{"id":"GO:0032088","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0031666","count":2}]},{"hash":"385197824856600358","title":"Neural synapse formation and axon guidance","description":"This cluster is dominated by neural-related functions: positive regulation of synapse assembly, axonal fasciculation, and regulation of dendritic spine development, with a strong emphasis on Rho signaling pathways that shape neurite outgrowth and synaptic connectivity. Some terms like heart development and B cell affinity maturation seem incidental or reflective of multi-functional proteins, but the prevailing signal points to neural connectivity and synapse formation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":4},{"id":"GO:0007413","count":4},{"id":"GO:0048671","count":4},{"id":"GO:0035023","count":3},{"id":"GO:0002344","count":3}]},{"hash":"1776359887488009726","title":"Intestinal microvilli actin dynamics","description":"The top GO terms converge on actin cytoskeleton organization and microvilli structure: actin filament bundle assembly, depolymerization, and capping, plus regulation of Rho signaling, terminal web assembly, and regulation of microvillus length. This points to a coherent theme of actin-driven organization of intestinal microvilli and their supporting terminal web, which aligns with functions like glucose absorption at the brush border. Minor terms related to rRNA maturation and DNA replication appear less connected to this core theme and may reflect general cellular housekeeping. Overall, the dominant signal is actin-based microvilli dynamics.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0051017","count":2},{"id":"GO:1902896","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0030042","count":2}]},{"hash":"1874047134423786591","title":"Multisystem Development","description":"The top GO terms point to developmental processes across multiple tissues and systems (nervous system development, kidney development, ossification, multicellular organism development, and germinal center formation), with an additional note of immune signaling and cytoskeletal organization. The lack of direct edge connections among proteins suggests this cluster reflects a broad theme of development across systems rather than a single molecular function, making \u201cMultisystem Development\u201d a fitting, concise label.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0050853","count":5},{"id":"GO:0045214","count":5},{"id":"GO:0051260","count":4},{"id":"GO:0007275","count":4}]},{"hash":"612549380102488133","title":"Developmental signaling and differentiation","description":"The GO terms span developmental and differentiation processes across immune, plant, nervous, and muscle systems, with related signaling pathways and protein interaction processes. The lack of a single dominant function points to a broad developmental theme rather than a specific pathway.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002467","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0009911","count":5},{"id":"GO:0050853","count":5},{"id":"GO:0009742","count":5}]},{"hash":"2116628124321006399","title":"Signaling and Gene Expression Regulation","description":"The terms point to a cohesive theme where signal reception (germinal center/ B cell receptor, brassinosteroid signaling) influences gene expression and protein dynamics (transcription, translation initiation, ubiquitin-proteasome\u2013dependent degradation, and protein oligomerization), spanning plant and animal contexts and touching circadian and defense networks.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":3},{"id":"GO:0009911","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0009742","count":3},{"id":"GO:0042752","count":3}]},{"hash":"1422496736121170523","title":"Embryonic Development and Organogenesis","description":"The top GO terms cluster around embryogenesis, patterning, and organ formation (in utero embryonic development, left-right pattern formation, cranial skeletal system development, ureter development, neuronal stem cell maintenance), with supporting growth and cell-cycle signaling (insulin receptor signaling pathway, mitotic G2 checkpoint) and some immune modulation. Together these point to a cohesive theme of developmental programs governing tissue and organ formation, so this label captures the core function of the cluster.","confidence":"High","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":5},{"id":"GO:0001701","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0072189","count":3}]},{"hash":"1225580386150634980","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0043044","count":6},{"id":"GO:0060303","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0043046","count":5}]},{"hash":"1136401608039442275","title":"Anthocyanin and flavonoid glycoside biosynthesis","description":"The strongest signals are flavonoid-related glycoside biosynthesis terms: cyanidin 3-O-glucoside, quercetin- and kaempferol-O-glucoside biosynthesis, and the broader anthocyanin-containing compound biosynthetic process, indicating a cluster focused on flavonoid glycoside production. Some unrelated or obsolete terms (e.g., xenobiotic glucuronidation, estrogen catabolism) may reflect annotation noise or secondary functions, but they do not override the flavonoid biosynthesis signal. ","confidence":"High","size":27,"edges":15,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009718","count":7},{"id":"GO:0030259","count":6},{"id":"GO:0016999","count":6},{"id":"GO:0052696","count":5},{"id":"GO:0052697","count":5}]},{"hash":"2208310201507801326","title":"Unknown","description":"The top GO terms span very divergent processes (platelet activation and IL-6 response in animals; pituitary development; nitrate assimilation and antibiotic biosynthesis in microbes; UV protection; cytokinesis; protein secretion regulation). There isn\u2019t a single coherent biological theme tying these together, suggesting the cluster is heterogeneous or functionally mixed. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030168","count":10},{"id":"GO:0055114","count":8},{"id":"GO:0042128","count":7},{"id":"GO:0009650","count":6},{"id":"GO:0071354","count":6}]},{"hash":"1796755529588105838","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":135,"triangles":483,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0006412","count":5},{"id":"GO:0000466","count":4},{"id":"GO:0006605","count":4},{"id":"GO:0019079","count":4}]},{"hash":"286885000727882294","title":"Neural development and axon guidance","description":"I named it Neural development and axon guidance because the cluster is dominated by terms related to nervous system development, axonogenesis/morphogenesis, and axon guidance pathways (Roundabout, Hedgehog/Smoothened), with strongest representation in neural differentiation and connectivity. A few immune signaling terms are present but do not define the core theme.","confidence":"High","size":27,"edges":310,"triangles":2081,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":11},{"id":"GO:0007224","count":11},{"id":"GO:0050852","count":11},{"id":"GO:0035385","count":11},{"id":"GO:0001822","count":11}]},{"hash":"2201381012357584873","title":"Glutamatergic Synaptic Regulation","description":"This cluster is dominated by terms linked to glutamatergic synaptic transmission and synapse structural plasticity, plus protein localization to the cell surface and cell-matrix adhesion, which together point to neuronal signaling and receptor trafficking components involved in synapse formation and remodeling. The remaining terms touch on immune/vascular processes that can accompany CNS remodeling, but the central theme appears to be synaptic regulation. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051968","count":7},{"id":"GO:0010519","count":6},{"id":"GO:0034394","count":6},{"id":"GO:0051835","count":5},{"id":"GO:0001837","count":5}]},{"hash":"2078565684475931630","title":"RNA splicing and translation regulation","description":"The cluster shows strong signals for post-transcriptional control: mRNA splicing (spliceosome regulation, splice site recognition), mRNA modification, translation initiation regulation (eIF4F assembly, translational initiation control), and stress-related mRNA stability. These together point to a cohesive module governing RNA processing and translation, justifying the label.","confidence":"High","size":27,"edges":187,"triangles":633,"max_degree":26,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0006376","count":6},{"id":"GO:0097010","count":6},{"id":"GO:0010610","count":6}]},{"hash":"164587842234072606","title":"Developmental Signaling and Neural Morphogenesis","description":"Top GO terms indicate involvement in embryonic development and signaling (dorsal closure, axial mesoderm formation; Wnt and tyrosine kinase\u2013mediated pathways) as well as neural morphology (dendritic spine morphogenesis; acetylcholine GPCR signaling) and RNA regulation (mRNA stabilization). This combination suggests a cluster of proteins coordinating developmental signal transduction with neural differentiation and structure.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007394","count":2},{"id":"GO:0061098","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0035176","count":2},{"id":"GO:0048320","count":2}]},{"hash":"2187700292123221933","title":"Ubiquitin-Dependent NF-\u03baB and TNF Signaling Regulation","description":"This cluster is enriched for terms related to protein ubiquitination (including autoubiquitination and K63-linked ubiquitination) and components of NF-\u03baB and TNF signaling, such as activation of IKK and positive regulation of I\u03baB phosphorylation. The ubiquitin-proteasome system appears to regulate NF-\u03baB activity within TNF-mediated pathways, linking these proteins functionally. Therefore, the cluster centers on ubiquitination-driven control of NF-\u03baB/TNF signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0032088","count":8},{"id":"GO:0016567","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0007250","count":7},{"id":"GO:0033209","count":7}]},{"hash":"1992639978667735061","title":"Unknown","description":"The top GO terms span telomere maintenance, fat cell differentiation, cell cycle regulation, mRNA processing, muscle stretch response, cell migration, and even plant/yeast growth terms, with no single unifying function across the cluster. This diversity suggests no clear common theme to name. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0035994","count":10},{"id":"GO:0016477","count":7},{"id":"GO:2001275","count":7},{"id":"GO:0032212","count":7},{"id":"GO:0045444","count":7}]},{"hash":"2120895910979179051","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0007049","count":6},{"id":"GO:0046718","count":5},{"id":"GO:0007059","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0075713","count":4}]},{"hash":"832866311478948978","title":"Neurodevelopmental and Synaptic Signaling","description":"The top terms point to neural development (tangential migration to the olfactory bulb, regulation of neuroblast proliferation) and synaptic function (excitatory postsynaptic potential, regulation of synaptic vesicle exocytosis, Wnt signaling in neural contexts). Additional terms involve signaling cascades (small GTPases, CAMKK\u2013AMPK) and cellular stress/protein turnover that commonly intersect with neuron biology. A single term on osteoclast development is likely a broader pathway overlap, but the dominant theme is neurodevelopment and synaptic regulation.","confidence":"Medium","size":27,"edges":39,"triangles":7,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902236","count":5},{"id":"GO:0060079","count":5},{"id":"GO:1904887","count":4},{"id":"GO:0022028","count":4},{"id":"GO:2000300","count":4}]},{"hash":"2204519895387453821","title":"Ribosome Biogenesis and Cell Division","description":"The top GO terms cluster around fundamental nuclear processes: ribosome biogenesis (including large subunit biogenesis), nucleotide-excision repair, and cell division (including mitotic chromosome alignment). These point to core activities tied to growth, genome maintenance, and proper cell cycle progression. Some outliers (intraciliary transport, mushroom body development) exist but do not override the dominant theme. ","confidence":"Medium","size":27,"edges":8,"triangles":0,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0042273","count":2}]},{"hash":"232317592468243619","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":168,"triangles":827,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0043044","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0071051","count":4}]},{"hash":"585038659914409033","title":"Cell cycle and development regulation","description":"The top GO terms center on regulation of growth, division, and differentiation (mitotic cell cycle, DNA replication, DNA-templated transcription, and multicellular organism development) as well as modulating survival and fate (negative regulation of cell proliferation, positive regulation of apoptosis). Although terms also touch on neural and immune signaling, the overarching theme is broad regulatory control of cell proliferation, differentiation, and development across tissues, rather than a single pathway. ","confidence":"Medium","size":27,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":13},{"id":"GO:0060020","count":12},{"id":"GO:0060079","count":12},{"id":"GO:0050852","count":12},{"id":"GO:0006260","count":12}]},{"hash":"616268820908570625","title":"Unknown","description":"This cluster shows GO terms from widely divergent processes (karyogamy, DNA replication, sporulation, antibiotic biosynthesis/response, metabolism, development, and viral replication) with no evident shared function or interaction network. Given such heterogeneity and no edges, there is no coherent theme to assign; label Unknown.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2}]},{"hash":"1177304945043418074","title":"Nuclear Gene Expression and RNA Processing","description":"The terms cluster around transcription and RNA processing in the nucleus (DNA-templated transcription, splicing, snoRNP assembly, and regulation of nuclear export), with related connections to cell cycle and differentiation and a peripheral link to innate immune transcriptional responses, suggesting a unified theme of nuclear gene expression control.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0032298","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0002062","count":4}]},{"hash":"1213028228392184734","title":"Cerebellar development and glial differentiation","description":"The top GO terms center on cerebellar cortex formation and Bergmann glial cell differentiation, with accompanying neural signaling and axon regeneration processes. This pattern points to a cluster of proteins involved in cerebellar development and glial maturation, with some ancillary signaling terms that may be less central. ","confidence":"High","size":27,"edges":350,"triangles":2900,"max_degree":26,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0000200","count":20},{"id":"GO:0050860","count":20},{"id":"GO:0070373","count":20},{"id":"GO:0008285","count":16},{"id":"GO:0060020","count":16}]},{"hash":"957329375566235773","title":"ER Quality Control and Ubiquitin-Proteostasis","description":"The top GO terms cluster around ER-associated processes: ERAD and maintenance of unfolded proteins, ubiquitin-dependent protein catabolism, deubiquitination, and ER membrane insertion of tail-anchored proteins, with translation and protein modification (sumoylation) also represented. This suggests a coherent module focused on ER protein quality control and ubiquitin-mediated turnover, with some broader immune-related terms appearing as ancillary associations.","confidence":"High","size":27,"edges":20,"triangles":1,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1904378","count":4},{"id":"GO:0016925","count":4},{"id":"GO:1903071","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0043029","count":3}]},{"hash":"771207239799888886","title":"Endothelial remodeling and lipoprotein clearance","description":"This cluster centers on endothelial cell behavior (proliferation, migration) and extracellular matrix remodeling (collagen fibril organization), paired with immune/inflammatory activity (complement activation, inflammatory response) and lipid handling (lipoprotein transport and clearance). Together these terms suggest a cohesive theme of vascular remodeling during inflammatory contexts with lipid clearance, though somite development and protein homotrimerization are less specific and may reflect broader developmental/protein assembly roles within the same context.","confidence":"High","size":27,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":23},{"id":"GO:0006958","count":23},{"id":"GO:0070207","count":23},{"id":"GO:0061053","count":23},{"id":"GO:0042953","count":23}]},{"hash":"369135759509319756","title":"Dopaminergic Synapses and Reward-Related Sensory Processing","description":"Based on enrichment of dopaminergic synaptic transmission, pain perception, and cocaine response, the cluster centers on neural signaling involved in reward and sensory processing. Additional terms like synapse assembly, visual perception/learning, and prostaglandin response suggest broader neuronal plasticity and signaling, with dopamine-mediated pathways as the core theme. Some terms (angiogenesis, macrophage chemotaxis) are peripheral but may reflect tissue remodeling or inflammatory contexts linked to neural environments.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0019233","count":16},{"id":"GO:0051965","count":14},{"id":"GO:0048148","count":13},{"id":"GO:0001963","count":13},{"id":"GO:0007266","count":13}]},{"hash":"54838262707466191","title":"Innate TNF/NF-\u03baB Ubiquitination Signaling","description":"The top GO terms point to innate immune responses with TNF-mediated signaling and activation of NF-\u03baB, driven by ubiquitination events (K63-linked ubiquitination and autoubiquitination) and I\u03baB phosphorylation. This forms a coherent theme of ubiquitin-dependent NF-\u03baB signaling in innate immunity, even though a few outliers exist. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":13},{"id":"GO:0045087","count":12},{"id":"GO:0070534","count":12},{"id":"GO:0033209","count":11},{"id":"GO:1903721","count":11}]},{"hash":"1912486725557975676","title":"Immune-Endocrine Signaling","description":"The top GO terms emphasize immune regulation (positive regulation of interleukin-3 production, mast cell cytokine production, neutrophil clearance, STAT signaling) and endocrine/metabolic pathways (vitamin D3 metabolism, parathyroid hormone secretion), suggesting a shared theme of immune-endocrine crosstalk, with some developmental terms likely peripheral.","confidence":"Medium","size":27,"edges":128,"triangles":162,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0045401","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0070640","count":2},{"id":"GO:0010863","count":2},{"id":"GO:0032762","count":2}]},{"hash":"2030751171491127793","title":"Neural development and signaling","description":"The cluster is dominated by nervous system development terms (nervous system development, forebrain development, bipolar cell polarity) and neural differentiation cues, along with transcriptional regulation (DNA-templated transcription) and signaling pathways (p38MAPK cascade, p53-mediated signaling). This pattern suggests proteins involved in neural development paired with associated stress and signaling processes, making \"Neural development and signaling\" a representative label.","confidence":"High","size":27,"edges":79,"triangles":76,"max_degree":25,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2000727","count":27},{"id":"GO:0007399","count":27},{"id":"GO:0061246","count":27},{"id":"GO:0043433","count":27},{"id":"GO:0030900","count":27}]},{"hash":"384128259711786293","title":"Keratinocyte development and wound healing","description":"Based on the top GO terms, the cluster is enriched for keratinocyte development, epithelial morphogenesis, and wound healing, which together describe epidermal growth and repair. Additional terms like cellular response to mechanical stimulus and regulation of JNK cascade support stress-responsive signaling in skin cells, aligning with wound repair processes. A few terms (bone resorption, synaptic vesicle regulation, ribosomal export) are less obviously connected and may reflect multifunctional proteins or annotation noise, but do not obscure the epidermal/wound-healing theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0003334","count":7},{"id":"GO:0003382","count":7},{"id":"GO:0044319","count":7},{"id":"GO:0034260","count":6},{"id":"GO:0045453","count":6}]},{"hash":"1543245573374343871","title":"Telomere maintenance and ADP-ribosylation","description":"This cluster is dominated by GO terms about telomere maintenance (including telomerase regulation, telomere capping, and telomere localization) and post-translational ADP-ribosylation (poly- and auto-ADP-ribosylation), pointing to a cohesive telomere biology/DNA damage response theme. A few outliers like cell migration or metabolic terms exist but do not offset the core telomere signal. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:1904357","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0070198","count":3},{"id":"GO:0070213","count":3}]},{"hash":"2214767443616630631","title":"TLR4-LPS Innate Immune Signaling","description":"The dominant GO terms point to innate immune sensing of bacterial components: detection of LPS, LPS-mediated signaling, TLR4 signaling, peptidoglycan recognition signaling, and inflammatory response. This suggests a cluster centered on host defense against Gram-negative bacteria and LPS-induced inflammation. A few terms about DNA endoreduplication regulation and organ identity appear incidental to the immune theme, but do not override the clear inflammatory/immunity signal.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032875","count":3},{"id":"GO:0032760","count":2},{"id":"GO:0034142","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0061057","count":2}]},{"hash":"2253210676174143497","title":"Developmental morphogenesis and immune signaling","description":"These terms collectively point to developmental morphogenesis (axon guidance, neuron differentiation, salivary gland boundary specification, hair follicle development) alongside immune signaling (STAT phosphorylation, NF-kappaB regulation, response to lipopolysaccharide, IL-13 regulation, necroptotic signaling, T cell death). This suggests the cluster comprises proteins involved in developmental signaling networks with cross-talk to immune pathways, rather than a single narrowly defined function. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033564","count":3},{"id":"GO:0021859","count":3},{"id":"GO:0007432","count":3},{"id":"GO:0042511","count":3},{"id":"GO:0051092","count":3}]},{"hash":"1714359514011469778","title":"Innate immune and inflammatory signaling","description":"This cluster shows strong enrichment for innate immune response, inflammatory response, TNF production, and pathways sensing bacterial components (LPS, peptidoglycan recognition). Endothelial barrier establishment can relate to inflammation, while neuronal development terms are weaker; overall, the dominant theme is innate immune/inflammatory signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051092","count":6},{"id":"GO:0090557","count":5},{"id":"GO:0032760","count":5},{"id":"GO:0061057","count":5},{"id":"GO:0006954","count":5}]},{"hash":"523222951930206037","title":"Olfactory GPCR-Pheromone Signaling","description":"The Top Terms show strong enrichment for sensory perception of smell (GO:0007608), GPCR signaling (GO:0007186), and response to pheromone (GO:0019236), which together point to olfactory or pheromone-detecting G protein-coupled receptors. While there are a few metabolic or detoxification terms and even innate immune signals in the list, the dominant theme across the highest-frequency terms is olfactory/pheromone signaling via GPCRs, suggesting this cluster mainly comprises olfactory receptor-related proteins. Some non-specific terms may reflect broader annotation noise, but the core signal supports the proposed function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0007608","count":2}]},{"hash":"515537978828130478","title":"Vascular coagulation and angiogenesis signaling","description":"This cluster centers on endothelial-related processes: platelet activation, coagulation pathways, Tie signaling, and regulation of angiogenesis and vascular permeability, plus cell-matrix adhesion. Together these terms point to a cohesive vascular\u2013coagulation signaling module balancing coagulation, vascular integrity, and angiogenesis, with an immune-vascular interface suggested by complement-related terms.","confidence":"High","size":26,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007160","count":24},{"id":"GO:0002740","count":23},{"id":"GO:0030168","count":23},{"id":"GO:0001867","count":23},{"id":"GO:0043116","count":23}]},{"hash":"1174564613719028143","title":"Neuronal vesicle cycling and endosomal transport","description":"This cluster is dominated by GO terms tied to synaptic vesicle exocytosis and endocytosis regulation, along with multiple endosomal trafficking steps (early to late endosome, endosome to Golgi/lysosome) and an autophagy-related Cvt pathway term. The presence of neuronal development (substantia nigra) and excitatory postsynaptic potential terms further supports a neuronal/synaptic context. Overall, the common theme is vesicle cycling and endosomal transport in neurons.","confidence":"High","size":26,"edges":48,"triangles":15,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0060079","count":8},{"id":"GO:0021762","count":8},{"id":"GO:0035690","count":8},{"id":"GO:2000300","count":7}]},{"hash":"1242128699463577509","title":"Ubiquitin\u2011Mediated ERAD and Proteostasis","description":"Top terms cluster around ubiquitin-dependent ERAD, unfolded protein maintenance in the ER, and related post-translational processes (deglycosylation, autoubiquitination). While some terms touch signaling or development, the dominant theme is proteostasis via ubiquitin-mediated ER-associated degradation, suggesting the cluster represents proteins involved in ER quality control and ubiquitination pathways.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0034140","count":5},{"id":"GO:0021762","count":5},{"id":"GO:0043029","count":5},{"id":"GO:0001666","count":4}]},{"hash":"12376614166330338","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":300,"triangles":2136,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":8},{"id":"GO:0042853","count":8},{"id":"GO:0097053","count":8},{"id":"GO:0019878","count":7},{"id":"GO:0009436","count":7}]},{"hash":"522769284807506166","title":"Plant cell wall biosynthesis and pollen exine formation","description":"The cluster is dominated by GO terms for plant-type secondary cell wall biogenesis, glucuronoxylan biosynthetic process, and pollen exine formation, indicating roles in constructing plant cell walls and pollen walls. Some terms like proteoglycan biosynthesis appear, but the overall signal centers on polysaccharide assembly and wall organization in plants.","confidence":"High","size":26,"edges":182,"triangles":551,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":9},{"id":"GO:0009834","count":7},{"id":"GO:0010417","count":7},{"id":"GO:0050651","count":6},{"id":"GO:0050650","count":6}]},{"hash":"1086086154781918032","title":"Developmental regulation and cytoskeletal signaling","description":"This cluster includes GO terms focused on organismal development (forebrain and retina development, multicellular development) and transcriptional processes (DNA-templated transcription), along with cytoskeletal dynamics (stress fiber assembly, positive regulation of GTPase activity) and proteostasis (protein ubiquitination). The combination suggests a theme around developmental gene regulation intertwined with cytoskeletal remodeling, with some stress response elements (cadmium) also present. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0043149","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0030900","count":2}]},{"hash":"2112486477357819170","title":"Intracellular trafficking and nuclear transport","description":"This cluster centers on transport processes: nuclear import (NLS-bearing proteins), mRNA export, ER-to-Golgi and inter-Golgi vesicle trafficking, and proteasome assembly, with regulation by small GTPases. The presence of DNA replication and cell division hints at coordination with the cell cycle, suggesting these proteins are involved in maintaining intracellular trafficking in the context of cell growth. Overall, a label emphasizing intracellular transport with nuclear transport components best fits the set.","confidence":"Medium","size":26,"edges":17,"triangles":3,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006607","count":6},{"id":"GO:0006406","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0015991","count":4}]},{"hash":"1314832624342048802","title":"Lipid biosynthesis and remodeling (ether lipids)","description":"Dominant GO terms indicate lipid metabolism and remodeling, especially ether lipids and glycerophospholipids (PAF biosynthesis, phosphatidylcholine remodeling, cardiolipin remodeling, triglyceride biosynthesis, CDP-diacylglycerol biosynthesis) and mitochondrial energy context (ATP synthesis).","confidence":"High","size":26,"edges":24,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006663","count":5},{"id":"GO:0042775","count":4},{"id":"GO:0035965","count":4},{"id":"GO:0016024","count":4},{"id":"GO:0002071","count":4}]},{"hash":"740951728120914552","title":"Transcription Regulation and Ubiquitination in Cell Cycle","description":"The cluster centers on nuclear regulatory processes, with multiple GO terms for DNA-templated transcription and transcription factor activity (including NF-kappaB), alongside protein ubiquitination (including K11-linked) and histone modification. It also features mitotic cell cycle and developmental growth signals, plus stress-related apoptotic signaling, implying a coordinated regulatory module governing transcription and protein turnover during cell division and response to stress. This combination best fits a label focusing on transcription control and ubiquitin-mediated regulation linked to the cell cycle.","confidence":"High","size":26,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0070979","count":4},{"id":"GO:0070059","count":4}]},{"hash":"697325184816050889","title":"Skeletal development and angiogenesis","description":"This cluster is enriched for ossification and somite development (bone maturation and vertebrate patterning) and endothelial cell proliferation (angiogenesis), pointing to coordinated skeletal and vascular formation. Additional terms on cell adhesion, immune remodeling (complement activation, apoptotic cell clearance, IL-8 regulation) reflect tissue remodeling during development but do not override the core skeletal-vascular theme. Confidence: Medium","confidence":"","size":26,"edges":241,"triangles":1072,"max_degree":23,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":4},{"id":"GO:2000483","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0043931","count":3},{"id":"GO:0043277","count":3}]},{"hash":"1773887573873968299","title":"Sugar-nucleotide and carbohydrate biosynthesis","description":"This cluster shows a clear emphasis on biosynthetic processes related to carbohydrates and nucleotide-sugars (e.g., UDP-D-xylose, ADP-L-glycero-beta-D-manno-heptose, galacturonate biosynthesis), suggesting a coherent theme around carbohydrate metabolism and sugar-nucleotide production, despite some noisy or obsolete terms and unrelated development terms.","confidence":"Medium","size":26,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0001081","count":1},{"id":"GO:0033481","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0006541","count":1}]},{"hash":"2158344859609552484","title":"Rho GTPase Signaling and Cytoskeleton Remodeling","description":"Proteins in this cluster are enriched for small GTPase signaling (Rho family) and actin cytoskeleton remodeling, including GTPase-mediated signal transduction, podosome assembly, and plasma membrane tubulation. These features align with processes that drive cell motility and directional migration, such as the extension of leading processes in radial glia. While a few terms relate to adipose development or cellular fusion, the dominant theme is regulation of GTPase activity and downstream cytoskeletal dynamics.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0021816","count":8},{"id":"GO:0035023","count":8},{"id":"GO:0007264","count":8},{"id":"GO:0045737","count":8}]},{"hash":"279943740172347902","title":"Cardiac mechanotransduction and SA node electrophysiology","description":"The top GO terms cluster around heart function: SA node cell signaling and regulation of action potential, cellular and mechanical responses in cardiac tissue (response to muscle stretch, cellular response to mechanical stimulus, SA node\u2013to\u2013atrial muscle communication). These strongly suggest a theme of cardiac rhythm generation and mechanotransduction influencing electrical signaling, possibly via membrane protein localization and ubiquitination processes that regulate ion-channel trafficking and turnover. Some outlier terms (immune-related, hepatocyte apoptosis) seem less representative of the main pattern.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0035994","count":13},{"id":"GO:0002268","count":12},{"id":"GO:0086070","count":12},{"id":"GO:0097284","count":12},{"id":"GO:0072660","count":12}]},{"hash":"885591932539169754","title":"Diverse stimulus-response and trafficking","description":"The proteins show enrichment for immune/biotic stimulus responses (interferon-alpha/beta, biotic stimulus), metabolic signaling (glucose import in response to insulin), and intracellular trafficking processes (endosome to plasma membrane transport, synaptic vesicle clustering), plus developmental functions (bone formation/morphogenesis) and neuromuscular tasks. This mix points to a broad theme of signal transduction and cellular response to external cues rather than a single cohesive function, so a broad label is appropriate.","confidence":"Low","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044381","count":4},{"id":"GO:0035455","count":4},{"id":"GO:0009607","count":4},{"id":"GO:0097091","count":4},{"id":"GO:0099638","count":4}]},{"hash":"1906457295871464856","title":"Retroviral integration and transposition","description":"This cluster is best named for strong enrichment of GO terms related to proviral latency establishment, DNA transposition, DNA integration, and retrotransposition, pointing to proteins involved in viral integration or transposon-like activity. Some terms about host signaling and axonogenesis may reflect downstream effects of host\u2013virus interactions or annotation noise, but the core theme centers on retroviral/ transpositional mechanisms.","confidence":"High","size":26,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":5},{"id":"GO:0046718","count":5},{"id":"GO:0006313","count":5},{"id":"GO:0015074","count":5},{"id":"GO:0039651","count":5}]},{"hash":"535524610884326230","title":"Vascular-immune signaling and cell adhesion","description":"This cluster centers on vascular and immune-related functions, including blood coagulation, plasminogen activation, complement activation, and vasoconstriction, together with lipoprotein transport and cell adhesion/junction formation. ERK signaling and synapse/junction terms suggest shared extracellular signaling roles in tissue remodeling and communication, implying a vascular-immune axis with adhesion-mediated interactions.","confidence":"Medium","size":26,"edges":27,"triangles":3,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0042953","count":4},{"id":"GO:0006958","count":4},{"id":"GO:0030194","count":3}]},{"hash":"755075159383238003","title":"Neural development and axon guidance","description":"The top GO terms cluster around nervous system development, neuron migration, Roundabout signaling, axon guidance, and neurotransmitter secretion, indicating a neural development and axon guidance theme. Some non-neural terms are present, but the dominant pattern supports a neural development function.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0001764","count":3},{"id":"GO:0035385","count":3},{"id":"GO:0043931","count":3},{"id":"GO:0007269","count":3}]},{"hash":"128260341964101906","title":"Immune signaling and cytoskeletal remodeling","description":"The top GO terms point to innate immune response and B cell signaling, including follicular B cell differentiation, alongside cytoskeletal and signaling processes such as actin filament assembly, cell migration, mechanotransduction, Rho signaling, and IP3 biosynthesis. This pattern suggests a cohesive function where immune signaling pathways intersect with cytoskeletal dynamics to enable immune cell activation, movement, and interaction with the tissue environment (bone development may reflect osteoimmune signaling), justifying the label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":8},{"id":"GO:0060348","count":7},{"id":"GO:0060335","count":6},{"id":"GO:0016477","count":6},{"id":"GO:0051017","count":6}]},{"hash":"1924444741951345491","title":"Cardiac electrophysiology and signaling regulation","description":"The top GO terms strongly point to heart-specific functions: regulation of atrial and SA node action potentials, regulation of cardiac muscle contraction via calcium release, and GPCR\u2013PLC\u2013mediated signaling. This suggests the proteins in this cluster are involved in cardiac electrical activity and excitation-contraction coupling, with additional signaling roles (NF-kappaB, endothelial barrier) that support vascular\u2013cardiac signaling context. The label succinctly captures the dominant cardiac electrophysiology theme with a nod to broader signaling roles. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0007200","count":3},{"id":"GO:0032760","count":3},{"id":"GO:0098910","count":3}]},{"hash":"1087379639224563249","title":"Neuronal development and Kv channel clustering","description":"The set\u2019s top GO terms center on neural development processes\u2014axonogenesis, myelination, and synapse assembly\u2014along with clustering of voltage-gated potassium channels, which points to neuronal differentiation and excitability. While a few terms relate to heart development and angiogenesis, these appear less central, so the strongest theme is neural development and ion-channel organization.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045163","count":2},{"id":"GO:0038095","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0006469","count":2}]},{"hash":"1852011742219595107","title":"Ubiquitin-Proteasome System and Signaling","description":"The presence of GO terms for protein ubiquitination and proteasome regulatory particle assembly suggests a cluster centered on protein degradation via the ubiquitin-proteasome system, with additional signals pointing to intracellular signaling and stress responses that often accompany UPS function. While other terms (temperature sensing, vitamin D response, and immune differentiation) are diverse, the strongest common theme is proteolysis and regulation of signaling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0070682","count":4},{"id":"GO:0050960","count":4},{"id":"GO:0035556","count":4}]},{"hash":"894455239747645259","title":"Necroptosis signaling and inflammatory response","description":"This cluster is dominated by terms for necroptosis (necroptotic signaling pathway, RIPoptosome/DISC assembly) and inflammatory signaling (TNF production, type I interferon signaling), indicating a functional module centered on programmed necrosis and immune responses. A few terms like mRNA processing and cellular response to mechanical stimulus appear but do not define the main theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0006397","count":3},{"id":"GO:1901026","count":3},{"id":"GO:0071550","count":3},{"id":"GO:0097527","count":3}]},{"hash":"1657756125593341696","title":"Cell migration and adhesion cluster","description":"The GO terms are centered on cell movement and cell\u2013cell interactions, including receptor clustering, angiogenesis-related migration, myoblast migration, and heterophilic adhesion, with negative chemotaxis and axonal defasciculation also represented. A couple of terms (endodermal differentiation, pericentric heterochromatin formation) seem less directly tied to migration/adhesion and may be incidental. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043113","count":2},{"id":"GO:0002042","count":2},{"id":"GO:0043277","count":2},{"id":"GO:0007414","count":2},{"id":"GO:0035987","count":2}]},{"hash":"1458894566632826126","title":"Extrinsic apoptotic and immune signaling regulators","description":"The top GO terms are dominated by extrinsic apoptotic signaling regulation via death receptors, including two terms for positive regulation of this pathway. Additional terms point to immune signaling (immunoglobulin production, NF-kappaB activity) and related STAT signaling. A few terms touch development/neural differentiation, but the strongest cohesive thread across the cluster is signaling that promotes or modulates extrinsic apoptosis and immune responses, rather than a single, narrowly defined process.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:2001241","count":5},{"id":"GO:0033564","count":5},{"id":"GO:0021859","count":5},{"id":"GO:0007432","count":5},{"id":"GO:0042511","count":5}]},{"hash":"1882172959073433947","title":"Unknown","description":"The top GO terms are scattered across unrelated processes (mitochondrial targeting, pheromone maturation, lifespan, ubiquitin recycling, viral process, catabolic processes) and include obsolete annotations, with no clear shared function or interaction pattern among the proteins. The lack of edges or a coherent theme prevents a meaningful, specific label.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006627","count":1},{"id":"GO:0071432","count":1},{"id":"GO:0008340","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0016032","count":1}]},{"hash":"1943949616116286441","title":"Developmental signaling and cell migration","description":"This cluster clusters proteins involved in developmental processes and cell movement, including axon guidance, neuron differentiation, angiogenesis, mast cell migration/differentiation, Rho-mediated cytoskeletal dynamics, and cell adhesion. These terms together suggest a cohesive theme of tissue development and coordinated cell migration rather than a single, isolated pathway.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0033564","count":3},{"id":"GO:0002551","count":3},{"id":"GO:0021859","count":3},{"id":"GO:0007432","count":3}]},{"hash":"2085559127025349004","title":"Innate Immune Signaling and Proteostasis","description":"The cluster is enriched for innate immune signaling terms (negative regulation of NF-kappaB transcription factor activity and NOD2 signaling) along with protein turnover processes (protein ubiquitination and proteasome regulatory particle assembly). Additional terms related to hepatocyte apoptosis, cell migration, and cellular response to mechanical stimulus suggest broader cellular stress and movement responses, but the strongest and most coherent themes center on immune signaling and proteostasis. Therefore, Innate Immune Signaling and Proteostasis","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":8},{"id":"GO:0016477","count":7},{"id":"GO:0071260","count":7},{"id":"GO:2001275","count":6},{"id":"GO:0097284","count":6}]},{"hash":"1045824532491119719","title":"Neuronal Development and Synapse Assembly","description":"The cluster is dominated by neuronal-related terms such as positive regulation of synapse assembly, fasciculation of sensory neuron axon, and sensory perception of sound, pointing to roles in neuronal connectivity and synapse formation. Other terms like innate immune response and apoptotic cell clearance appear but are less central to the main theme; ossification-related terms seem ancillary noise. Overall, there is a coherent neuronal development signal with some background functional diversity.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0043277","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1856817602951710375","title":"Steroid Hormone Signaling and Organ Development","description":"This cluster centers on organ development (liver, heart, prostate) and male differentiation, with strong signals of steroid hormone receptor activity (steroid hormone receptor complex assembly, glucocorticoid signaling). While some cell-cycle/metabolism terms appear (cell division, glycogen biosynthesis), the dominant pattern ties hormone signaling to developmental processes across tissues.","confidence":"Medium","size":25,"edges":35,"triangles":16,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001889","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0046661","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0051301","count":4}]},{"hash":"800679451401767405","title":"Cell Cycle and DNA Replication","description":"The top GO terms cluster around DNA-templated transcription, DNA replication, the mitotic cell cycle, and cell division, indicating a cohesive theme of cell proliferation and genome maintenance. Retina-related terms appear (retina vasculature development and visual perception), suggesting possible tissue-specific roles in the retina, but the dominant signal is core nuclear processes driving cell cycle progression. Additional enrichment for stress and immune response terms (cadmium, toxic substance, innate immune response) fits common regulatory layers that modulate proliferation. ","confidence":"High","size":25,"edges":22,"triangles":6,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0061298","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0071276","count":5}]},{"hash":"989368733089295156","title":"Cytoskeleton Remodeling and Cell Migration","description":"The top GO terms cluster around actin filament bundle assembly, cell migration, and spindle assembly, indicating cytoskeletal dynamics as the central theme; neuron projection development aligns with growth driven by the cytoskeleton, while apoptotic mitochondrial changes and apoptosis suggest stress-related remodeling. Overall, the proteins appear to participate in cytoskeleton-mediated movement and division with ancillary stress responses.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1785857583628743206","title":"Vertebrate Embryonic Development and Vasculature","description":"The cluster centers on vertebrate development processes, notably spinal cord and somite formation, endothelial proliferation, and collagen fibril organization, all pointing to tissue and vascular remodeling during embryogenesis. Additional terms like lipoprotein transport and protein homotrimerization support extracellular matrix and lipid-related aspects of developing tissues, while regulation of mRNA stability under stress reflects gene regulation during development. Immune-related terms (complement activation, apoptotic cell clearance) can occur in remodeling contexts in development, making the overall theme embryonic development with vascular/ECM remodeling, with some immune participation.","confidence":"Medium","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0021510","count":6},{"id":"GO:0010610","count":5},{"id":"GO:0007565","count":5},{"id":"GO:0043277","count":5},{"id":"GO:0006958","count":5}]},{"hash":"827109326529389054","title":"Innate Immunity and Immunological Synapse","description":"The cluster is strongly enriched for innate immune processes and immune-cell communication, including innate immune response, immunological synapse formation, complement activation, and apoptotic cell clearance. While there are some developmental terms (heart, somite) and synaptic plasticity signals present, the dominant theme is immune signaling, making this label representative of the cluster\u2019s core function.","confidence":"High","size":25,"edges":16,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":7},{"id":"GO:0001771","count":6},{"id":"GO:0001935","count":5},{"id":"GO:0032332","count":5},{"id":"GO:0043277","count":5}]},{"hash":"1771393639939913815","title":"Neuronal development and synaptic signaling","description":"This cluster is dominated by GO terms related to nervous system development, dopamine signaling, and synaptic activity (excitatory postsynaptic potential) with supportive links to Wnt pathway regulation and membrane trafficking. Together these terms point to proteins involved in neural development and synaptic transmission, particularly dopaminergic signaling and excitatory synapse function, with signaling and endosomal transport features that fit synaptic regulation. Some terms about cell division may reflect multifunctional proteins but do not override the neural theme. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:1903351","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0000186","count":4}]},{"hash":"741782717868207183","title":"Mitochondrial dynamics and cell cycle","description":"This cluster is dominated by GO terms linking mitochondrial processes (mitochondrial membrane fission; mitochondrial genome maintenance) with cell division and cell cycle, suggesting a coordinated role of mitochondrial dynamics in cell proliferation. Other terms appear secondary or pleiotropic and do not override this central theme.","confidence":"High","size":25,"edges":17,"triangles":2,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0007049","count":6},{"id":"GO:0090149","count":6},{"id":"GO:0000002","count":6},{"id":"GO:0061179","count":6}]},{"hash":"1577908101435858691","title":"Unknown","description":"The top GO terms span diverse biological areas\u2014protein autoprocessing, neural/behavioral responses (amphetamine response, memory), angiogenesis, reproductive biology (acrosome reaction, left/right axis determination), embryonic development, insulin processing, surfactant homeostasis, and LDL receptor biosynthesis\u2014showing no single cohesive function or pathway that ties the cluster together. Therefore there isn\u2019t a clear, representative label beyond Unknown, with None confidence.","confidence":"","size":25,"edges":21,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016540","count":3},{"id":"GO:0001975","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0007613","count":2},{"id":"GO:0043129","count":2}]},{"hash":"1843627874038155275","title":"Integrin signaling and lamellipodium dynamics","description":"The terms point to actin-driven protrusions (lamellipodium assembly) and adhesion-dependent spreading, centered on integrin signaling and cytoskeletal remodeling that underlie cell migration. Developmental processes like blood vessel and skin formation fit with adhesion/motility contexts, and related processes such as ectodomain proteolysis and apoptotic cell engulfment further support matrix remodeling and clearance in motile cells. Overall, a cohesive theme of adhesion-mediated cytoskeletal dynamics and signaling.","confidence":"High","size":25,"edges":8,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":2},{"id":"GO:0034446","count":2},{"id":"GO:0051044","count":2},{"id":"GO:2001237","count":2},{"id":"GO:0097062","count":2}]},{"hash":"796829471055518893","title":"Multi-system Developmental and Behavioral Regulators","description":"Top GO terms include bone morphogenesis, female gonad development, cytokine production, leukocyte mediated immunity, locomotory behavior, behavioral response to ethanol, mating behavior, and positive regulation of canonical Wnt signaling. This spread suggests proteins involved in broad regulatory signaling that coordinates development across tissues while also influencing neural and immune-related processes and behavior. There isn\u2019t a single tight functional core, but the common thread is regulatory signaling linking development, immunity, and behavior. ","confidence":"Medium","size":25,"edges":27,"triangles":4,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0060349","count":2},{"id":"GO:0008585","count":2},{"id":"GO:0001816","count":2},{"id":"GO:0007626","count":2}]},{"hash":"388354805958019900","title":"Sensory perception and metabolic regulation in multicellular organisms","description":"The terms point to sensory processes (pain, vision) alongside thermogenic and circadian regulation, and ion transport across membranes, plus development-related terms. Together, they suggest proteins involved in environmental sensing and integrated physiological responses in multicellular organisms, including signaling and membrane transport components. Despite diverse functions, the common thread is sensing stimuli and coordinating metabolic/physiological responses.","confidence":"Medium","size":25,"edges":19,"triangles":0,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":8},{"id":"GO:0007275","count":7},{"id":"GO:0097623","count":6},{"id":"GO:1990573","count":5},{"id":"GO:0098719","count":5}]},{"hash":"597947382954708888","title":"Unknown","description":"The top GO terms are highly diverse, including transcription (DNA-templated transcription), stress responses (response to magnesium ion, response to X-ray), various differentiation/regulation terms (mammary gland, Leydig cell, epithelial differentiation), signaling regulation (insulin receptor signaling), autophagy initiation (ULK1 complex assembly), and even plant-specific processes (stomatal opening). There is no clear, single biological process or pathway tying these proteins together, suggesting a heterogeneous set rather than a cohesive functional cluster.","confidence":"","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0032026","count":6},{"id":"GO:0033601","count":5},{"id":"GO:0030857","count":5},{"id":"GO:0033327","count":5}]},{"hash":"1567206352422571432","title":"Nervous system development and axon guidance","description":"This cluster is dominated by GO terms related to neural development and axon pathfinding, including nervous system development, axon guidance, and multiple signaling pathways (BMP, SHH/Smoothened, Roundabout) that regulate neural patterning and growth, with ERK cascade modulation supporting neural signaling. While there are tangential developmental terms like kidney development and ossification, the core theme centers on neural development and guidance cues.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0030513","count":6},{"id":"GO:0007224","count":5},{"id":"GO:0035385","count":5},{"id":"GO:0007411","count":5}]},{"hash":"1523340792789165654","title":"Cell Signaling and Cytoskeleton Dynamics","description":"This cluster includes GO terms related to immune receptor signaling (B cell receptor), kinase activity (protein autophosphorylation/regulation), and cytoskeletal remodeling activities (myosin II filament disassembly, calcium-dependent adhesion). While the terms span multiple processes, the common thread appears to be signaling events coupled with changes in the cytoskeleton and adhesion, suggesting a general theme of signaling and cytoskeletal dynamics rather than a single coherent pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:1990637","count":2},{"id":"GO:0051262","count":2},{"id":"GO:0071454","count":2},{"id":"GO:0010961","count":2}]},{"hash":"2265638236811287549","title":"Unknown","description":"The top terms are highly diverse, including visual perception, RNA splicing, transcription regulation, ribosomal export, DNA replication initiation, ion transport regulation, and oxidative stress response. This lack of a cohesive functional theme suggests there is no single representative function for the cluster, so a precise label is not apparent.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0000398","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0032298","count":1}]},{"hash":"1059860216986543649","title":"Integrin- and ECM-Mediated Adhesion in Morphogenesis","description":"Top GO terms cluster around cell adhesion and extracellular matrix interactions, especially integrin- and calcium-independent adhesion, as well as cell-matrix and heterophilic cell-cell adhesion. Several terms reference developmental morphogenesis (palatal shelf, ventral spinal cord, coronary vein) and cell migration, indicating a cohesive function in tissue shaping during development. A less central term on synaptic transmission likely reflects adhesion roles at synapses but does not override the dominant adhesion/morphogenesis theme.","confidence":"High","size":25,"edges":35,"triangles":30,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:1990134","count":24},{"id":"GO:0007157","count":22},{"id":"GO:0021517","count":20},{"id":"GO:0033631","count":20},{"id":"GO:0007160","count":20}]},{"hash":"1272188728860693642","title":"Unknown","description":"Top GO terms span circadian regulation, immune signaling, plant development, muscle/nervous system development, and calcium signaling, with no single shared function across the cluster. The diversity suggests no coherent, interpretable theme.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042752","count":9},{"id":"GO:0002467","count":7},{"id":"GO:0051209","count":6},{"id":"GO:0009911","count":6},{"id":"GO:0048741","count":6}]},{"hash":"375426455226889457","title":"SA node signaling and heart development","description":"The cluster is strongly anchored by cardiac-related GO terms: SA node cell communication, regulation of SA node action potential, regulation of cardiac muscle contraction via calcium release, and heart development. While there are some cell-cycle terms, the dominant themes point to pacemaker signaling and cardiac morphogenesis, suggesting these proteins function in heart electrophysiology and development.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0086070","count":4},{"id":"GO:0072660","count":4},{"id":"GO:0098907","count":4},{"id":"GO:0051301","count":3}]},{"hash":"1489737456285984368","title":"Innate immune cell death: pyroptosis and apoptosis","description":"This cluster is characterized by terms for innate immune response and programmed cell death (pyroptosis and apoptosis), with ubiquitination and inflammatory signaling supporting this theme. While a few terms touch on mitosis or adhesion, the dominant pattern points to inflammation-driven cell death within the innate immune system.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0090307","count":11},{"id":"GO:0016567","count":9},{"id":"GO:0070269","count":9},{"id":"GO:0006915","count":9},{"id":"GO:0045087","count":9}]},{"hash":"48716513838359904","title":"Neural development and transcription regulation","description":"The top GO terms cluster around nervous system and forebrain development, bipolar cell polarity, and DNA-templated transcription, pointing to proteins involved in neural differentiation and regulation of gene expression. The presence of DNA replication and p53-related signaling terms suggests coordination with cell proliferation and stress responses in neural progenitors, while other terms reflect broader transcriptional regulation. Overall, the cluster seems to represent neural development with transcriptional control as a unifying theme.","confidence":"Medium","size":25,"edges":130,"triangles":469,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:2000727","count":23},{"id":"GO:0007399","count":23},{"id":"GO:0061246","count":23},{"id":"GO:0043433","count":23}]},{"hash":"2295072276265995616","title":"Biosynthesis and xenobiotic detoxification","description":"The top GO terms cluster around several biosynthetic pathways (antibiotic, biotin, menaquinone, poly-hydroxybutyrate) and RNA/protein modification (tRNA methylation, N-terminal peptidyl-serine trimethylation), with additional terms related to detoxification and xenobiotic response (oxidant detoxification, cellular response to xenobiotic stimulus, response to cocaine). This suggests a theme of metabolic biosynthesis with ancillary mechanisms to cope with foreign compounds, hence this label. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0009102","count":6},{"id":"GO:0009234","count":6},{"id":"GO:0030488","count":5},{"id":"GO:0098869","count":4}]},{"hash":"215593936899840837","title":"Developmental signaling in heart, vasculature, and immunity","description":"This cluster centers on signaling pathways involved in development and immune responses across tissues: heart development, endothelial/vascular barrier formation, neuron projection development, and immune signaling (T cell receptor and TNF pathways), alongside Rho-mediated signaling which governs cytoskeletal dynamics and cell movement essential for development and tissue integrity.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0051092","count":6},{"id":"GO:0008284","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0032516","count":4}]},{"hash":"1141431776316943516","title":"Vertebrate Embryogenesis and Neural Tube Formation","description":"GO terms are dominated by developmental processes such as forebrain development, multicellular organism development, neural tube closure, and skin development, suggesting these proteins participate in vertebrate embryogenesis and early patterning. The presence of transcription and ribosome biogenesis terms indicates active gene expression and protein synthesis during development, while cell cycle terms reflect proliferative phases. Together they point to a cohesive developmental cluster centered on embryonic growth and neural patterning.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0030900","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0043588","count":4},{"id":"GO:0000278","count":4}]},{"hash":"1726742881909310453","title":"Cardiovascular Development","description":"The terms predominantly point to blood vessel formation and heart-related development (blood vessel lumenization, coronary vasculature development, regulation of NO biosynthesis, and cardiac muscle cell proliferation). While a few terms relate to broader developmental processes in other tissues, the vascular and cardiac themes are the strongest signal in this cluster.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072554","count":3},{"id":"GO:0060045","count":3},{"id":"GO:0007566","count":3},{"id":"GO:0060976","count":3},{"id":"GO:0045429","count":3}]},{"hash":"921756857308001942","title":"Endothelial-immune signaling and angiogenesis","description":"The GO terms cluster around endothelial biology (endothelial cell proliferation, migration, collagen fibril organization, VEGF receptor signaling, and angiogenesis) and immune-related processes (innate immune response, immunological synapse formation, complement activation, apoptotic cell clearance). This suggests a module of cross-talk between vascular/endothelial cells and the immune system with a focus on angiogenic remodeling, justifying a label that reflects both endothelial-immune interactions and angiogenesis.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":4},{"id":"GO:0006958","count":4},{"id":"GO:0001935","count":4},{"id":"GO:0030199","count":4},{"id":"GO:0043542","count":4}]},{"hash":"1474124441042639098","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0016310","count":2}]},{"hash":"413841095431275402","title":"Neuronal signaling, pain perception, and drug response","description":"These terms cluster around nervous system signaling and behavioral responses: pain perception, GPCR signaling, synapse assembly, prostaglandin response, and cocaine-related behavior, with temperature and thermogenesis indicating stress/thermoregulatory pathways. The electron transport chain term suggests energy metabolism supporting neuronal activity. Taken together, they point to neural signaling and pain/drug-response processes as the core theme of this cluster.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":9},{"id":"GO:0045777","count":8},{"id":"GO:0010579","count":8},{"id":"GO:0022900","count":8},{"id":"GO:0048148","count":7}]},{"hash":"82708597187345244","title":"Neural development and synaptic signaling","description":"The cluster\u2019s top GO terms converge on neural development and synaptic communication, including ROBO roundabout signaling (axon guidance), ephrin receptor signaling, Wnt signaling, and ERK/JNK cascades, plus excitatory postsynaptic potentials and regulation of glutamatergic transmission. While there is a mention of T cell receptor signaling, the prevalent themes are neuronal development and synaptic signaling, suggesting proteins involved in neural connectivity and synaptic function.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":7},{"id":"GO:0007399","count":6},{"id":"GO:0035385","count":6},{"id":"GO:0043552","count":6},{"id":"GO:0046330","count":5}]},{"hash":"1626235743101329028","title":"Unknown","description":"The GO terms span highly diverse processes (peroxisomal protein import, ATP export, apoptosis, GTPase regulation, multiple signaling pathways like Wnt, insulin, TGF-beta, angiotensin, and caveolin-mediated endocytosis) with no single shared function linking all members. This scattered set makes it impossible to assign a cohesive, specific label to the cluster beyond Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032091","count":2},{"id":"GO:0016560","count":2},{"id":"GO:1904669","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1068205099738821490","title":"Transcription and Translation Machinery","description":"The cluster is dominated by GO terms tied to core gene expression processes: transcription (DNA-templated transcription), ribosome biogenesis, and translation initiation/reinitiation. While immune and developmental terms appear, the strongest signal ties to the machinery of transcription and translation, suggesting a set of proteins involved in basic expression processes.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":12},{"id":"GO:0007568","count":11},{"id":"GO:0006351","count":11},{"id":"GO:0035264","count":10},{"id":"GO:0042254","count":10}]},{"hash":"823141515738769679","title":"TLR-MyD88 innate immune signaling","description":"The top GO terms strongly point to innate immune and inflammatory pathways, especially MyD88-dependent TLR signaling, defense against virus, inflammatory response, and TNF production, indicating the cluster centers on TLR-driven immune signaling. Some metabolism and transposition terms appear incidental noise but do not define the core theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090180","count":3},{"id":"GO:1903212","count":3},{"id":"GO:2001172","count":3},{"id":"GO:0006313","count":3},{"id":"GO:0032760","count":2}]},{"hash":"608889635278444963","title":"Developmental Transcription Regulation and Apoptosis","description":"This cluster centers on transcriptional control in development and cell fate decisions, with terms like DNA-templated transcription, regulation of gene expression, and cerebral cortex development. It also includes growth and survival signals such as negative regulation of cell proliferation, positive regulation of JNK signaling, and apoptotic processes, suggesting proteins that coordinate development with stress responses and apoptosis. A few terms (e.g., sperm capacitation, imprinting regulation, obsolete notes) appear tangential or exploratory, likely due to annotation noise or multi-functional proteins. Overall, the group seems to represent transcriptional regulators involved in developmental timing and cell fate decisions, including stress-induced pathways.","confidence":"Medium","size":24,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008285","count":7},{"id":"GO:0043433","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0045793","count":5},{"id":"GO:0006915","count":5}]},{"hash":"119536503405928542","title":"Tissue development and morphogenesis","description":"This cluster\u2019s top GO terms largely point to development and morphogenesis across multiple tissues and systems (kidney glomerular development and filtration, CNS development and innervation, colon epithelial migration, chondrocyte development, esophagus smooth muscle function, glial signaling). While a couple terms (lipoteichoic acid biosynthesis, choline biosynthesis) are outliers, the dominant signal is across-tissue developmental processes, suggesting proteins involved in differentiation and tissue formation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070395","count":4},{"id":"GO:0032836","count":4},{"id":"GO:0061580","count":3},{"id":"GO:0002063","count":3},{"id":"GO:0007417","count":3}]},{"hash":"1909381232589579800","title":"Embryonic development and genome maintenance","description":"The top GO terms point to core DNA-centric processes (DNA replication, DNA-templated transcription, DNA repair, mitotic cell cycle) alongside developmental programs (nervous system development, cranial skeleton morphogenesis, bipolar cell polarity). While immune-related signals (lipopolysaccharide response, IL-4 production) appear, the dominant pattern ties embryo development with genome maintenance and cell proliferation, suggesting proteins coordinating growth and differentiation. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":22},{"id":"GO:0048701","count":20},{"id":"GO:0071222","count":19},{"id":"GO:0006351","count":19},{"id":"GO:0000278","count":19}]},{"hash":"596056773244745887","title":"Forebrain Neuronal Development and Signaling","description":"This cluster is dominated by terms tied to neural development and neural differentiation, especially forebrain development and CNS projection neuron axonogenesis, along with signaling pathways (integrin and Wnt) and extracellular matrix interactions (hyaluronan metabolism). These clues point to a cohesive theme of neuronal development and axon guidance, with supportive transcriptional regulation, despite a few outlier terms.","confidence":"High","size":24,"edges":17,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051092","count":7},{"id":"GO:0007229","count":7},{"id":"GO:0030900","count":6},{"id":"GO:0090263","count":6},{"id":"GO:1905050","count":6}]},{"hash":"399908243480473740","title":"Innate Immune Signaling and Clearance","description":"The cluster is dominated by GO terms related to innate immunity (innate immune response, immunological synapse formation, apoptotic cell clearance, host-mediated suppression of symbiont invasion), suggesting a cohesive theme around immune signaling and clearance of cells/foreign entities. Some developmental and nuclear-activity terms appear, but the strongest signal is innate immune function, making this a representative, concise label.","confidence":"High","size":24,"edges":92,"triangles":108,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0021510","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0001771","count":4},{"id":"GO:0043277","count":4}]},{"hash":"324830686059604470","title":"Innate Immune Activation and Immunological Synapse","description":"This cluster is dominated by GO terms related to innate immunity and cell\u2013cell communication in immune responses (innate immune response, immunological synapse formation, complement activation), suggesting a cohesive immune signaling module. While developmental terms (spinal cord and somite development) appear, the strongest and most recurrent signals point to innate immune activation and synapse-mediated signaling as the core theme. Confidence: Medium","confidence":"","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0032332","count":5},{"id":"GO:0021510","count":5},{"id":"GO:0001771","count":5},{"id":"GO:0007565","count":4}]},{"hash":"2198845309780037504","title":"Embryonic Skeletal and Mesoderm Development","description":"The top GO terms cluster around embryonic development and tissue morphogenesis\u2014cranial skeleton morphogenesis, mesoderm formation, chondrocyte differentiation, endoderm development, ventral identity, and transcriptional regulation\u2014pointing to a cohesive program governing skeletal and mesodermal lineage specification and cartilage formation, with regulatory input from transcriptional and SMAD signaling processes.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0048701","count":5},{"id":"GO:0001707","count":5},{"id":"GO:0002062","count":5},{"id":"GO:0007492","count":5}]},{"hash":"1368293018724957470","title":"Developmental signaling and morphogenesis","description":"The top GO terms cluster around developmental signaling (Roundabout/Slit, Hedgehog via Smoothened, nervous system and kidney development) together with processes governing cell polarity, adhesion, and migratory/morphogenetic events (adherens junctions, stress fiber assembly, sprouting angiogenesis). This points to a cohesive role in guiding tissue formation and organization across organs, rather than a single tissue-specific function. ","confidence":"High","size":24,"edges":211,"triangles":926,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":8},{"id":"GO:0035385","count":8},{"id":"GO:0050852","count":7},{"id":"GO:0001822","count":7},{"id":"GO:0007224","count":7}]},{"hash":"1964924555974338971","title":"Receptor Tyrosine Kinase and Adhesion Signaling","description":"The cluster is dominated by GO terms for T cell receptor signaling, ephrin receptor signaling, integrin-mediated signaling, substrate adhesion-dependent spreading, and peptidyl-tyrosine autophosphorylation, all pointing to receptor-driven signaling pathways linked to cell adhesion and movement. Additional terms like cell migration, dendritic spine morphogenesis, and apoptotic processes suggest broader roles in cytoskeletal remodeling and survival, consistent with a module of RTK/adhesion signaling across immune and neuronal contexts.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050852","count":9},{"id":"GO:0034446","count":9},{"id":"GO:0016477","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0038083","count":8}]},{"hash":"945812701606773223","title":"RNA processing and translation initiation factors","description":"Top GO terms point to mRNA splicing regulation and translation initiation/preinitiation complex assembly, with additional signals for mRNA modification and stress-related stability control. This convergence suggests a cohesive group of RNA-processing proteins that also participate in initiating translation, indicating a shared functional theme around RNA processing coupled to translation control.","confidence":"High","size":24,"edges":21,"triangles":1,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":9},{"id":"GO:0001731","count":8},{"id":"GO:0006378","count":8},{"id":"GO:0002188","count":8},{"id":"GO:0006376","count":7}]},{"hash":"312611969333884673","title":"Ribosome biogenesis and translation with cell cycle","description":"The cluster shows strong enrichment for ribosome-related processes: ribosome biogenesis, ribosomal subunit export from nucleus, and cytoplasmic translation, along with cell cycle and cell division terms. This suggests a cohesive module of ribosome assembly and protein synthesis machinery that is coordinated with cell-cycle progression. Minor terms related to stress responses likely reflect regulatory context rather than a different theme.","confidence":"High","size":24,"edges":29,"triangles":6,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0042254","count":7},{"id":"GO:0000747","count":6},{"id":"GO:0002181","count":6},{"id":"GO:0007049","count":5}]},{"hash":"1979074876091490619","title":"Cell cycle and ciliogenesis regulators","description":"This cluster is enriched for mitotic cell cycle, spindle assembly, and cell polarity-related terms, with additional hints of ciliogenesis (non-motile cilium assembly) and exocytic regulation, plus protein localization to the bud neck. The combination points to a group of proteins coordinating cell division with membrane trafficking and ciliary assembly, making the label apt and specific.","confidence":"High","size":24,"edges":51,"triangles":59,"max_degree":15,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0017157","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0051291","count":6},{"id":"GO:0030382","count":6},{"id":"GO:0031175","count":6}]},{"hash":"1284229181884082117","title":"Unknown","description":"Top GO terms span innate immune response, B cell signaling, nervous and skeletal muscle development, RNA processing, and DNA replication, with no single cohesive function evident across the cluster; the diverse and possibly noisy annotations suggest a heterogeneous set rather than a shared pathway, so Unknown with None confidence. ","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008285","count":4},{"id":"GO:0006813","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0007399","count":3}]},{"hash":"2029397253015111024","title":"TLR/MyD88-Driven Inflammatory Signaling","description":"The cluster is dominated by GO terms related to innate immune activation and inflammation, including lipopolysaccharide-mediated signaling, inflammatory response, MyD88-dependent TLR signaling, IL-1 signaling, and downstream NF-\u03baB/JNK pathways. These themes suggest a coherent module of TLR/IL-1\u2013mediated inflammatory signaling, with a few unrelated terms likely acting as noise (e.g., behavioral or obsolete entries). ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031663","count":6},{"id":"GO:0006954","count":5},{"id":"GO:0002755","count":5},{"id":"GO:0006977","count":4},{"id":"GO:0070926","count":4}]},{"hash":"1639618816690708200","title":"Neuronal development and axon guidance","description":"The top GO terms cluster around nervous system development, neuron projection development, and axon guidance (including anterior/posterior guidance and protein localization in axonal regions), with supporting signaling roles (Rho, MAPKKK, calcium) that are typical in neurite outgrowth and guidance. This supports a cohesive theme of neural development and axon pathfinding.","confidence":"High","size":24,"edges":271,"triangles":1921,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0070640","count":2},{"id":"GO:0045663","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0071206","count":2}]},{"hash":"1095177191916476799","title":"Developmental and reproductive processes","description":"These proteins are enriched for GO terms tied to organismal development and germline/sexual maturation (oogenesis, spermatid development, posterior abdomen determination) and developmental signaling (Wnt regulation, lens morphogenesis). While some terms touch on autophagy and DNA repair localization, the overarching theme centers on developmental and reproductive biology rather than a single molecular function. Confidence that this label reflects the cluster's function is Medium.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:1990166","count":2},{"id":"GO:1902902","count":2},{"id":"GO:0007143","count":1},{"id":"GO:0070306","count":1}]},{"hash":"586027274698483196","title":"Wnt-regulated endoderm development and cell cycle control","description":"The terms point to a developmental module focused on endoderm fate specification and morphogenesis, with prominent involvement of Wnt signaling (including negative regulation of canonical Wnt) and links to apoptosis. Additional terms cover cell migration and pseudopodium assembly, supporting migratory behavior during tissue formation, and regulation of the cell cycle, indicating coordination between proliferation and differentiation. Proton transport appears as a peripheral membrane-related aspect but does not define the main theme. ","confidence":"High","size":24,"edges":271,"triangles":1917,"max_degree":23,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0048364","count":14},{"id":"GO:0008285","count":12},{"id":"GO:0043065","count":12},{"id":"GO:0016477","count":12},{"id":"GO:0090090","count":12}]},{"hash":"525089185734591652","title":"Mitochondrial translation and tRNA charging","description":"This cluster is dominated by GO terms related to mitochondrial protein synthesis, especially mitochondrial translation and mitochondrial tRNA aminoacylation (tyrosyl, tryptophanyl, valyl). While angiogenesis-related terms appear, the strongest and most coherent signal is mitochondrial translation, suggesting the proteins primarily participate in mitochondrial protein synthesis and tRNA charging. ","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:1903833","count":4},{"id":"GO:0019284","count":3},{"id":"GO:0019509","count":3},{"id":"GO:0055114","count":3}]},{"hash":"1397146420219496072","title":"Wnt and Hippo Developmental Signaling","description":"The cluster is enriched in positive regulation of canonical Wnt signaling and Hippo signaling, with accompanying terms for apoptosis and development/differentiation across several tissues (forebrain, keratinocytes, cardiac muscle). These together point to a group of proteins involved in developmental signaling and cell fate decisions, despite a few broader terms like potassium transport or amino acid starvation that are less central to the core theme.","confidence":"High","size":24,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0090263","count":18},{"id":"GO:0035329","count":18},{"id":"GO:0006915","count":18},{"id":"GO:0030216","count":18},{"id":"GO:0060044","count":18}]},{"hash":"917533748640930023","title":"Wnt-ERK Developmental Signaling","description":"The cluster centers on positive regulation of canonical Wnt signaling and ERK1/2 cascades, with related developmental terms (forebrain, thymus, multicellular development, angiogenesis). This points to proteins involved in signaling networks that drive development and organogenesis, with broader links to immune-related signaling like LPS pathways. Confidence: High.","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0090263","count":7},{"id":"GO:0051092","count":7},{"id":"GO:0030900","count":6},{"id":"GO:0031663","count":6},{"id":"GO:0043547","count":5}]},{"hash":"1549052488530237910","title":"Chloroplast ribosome biogenesis and translation","description":"The top GO terms are dominated by ribosome biogenesis, cytoplasmic translation, and tRNA modification, indicating a cluster centered on protein synthesis machinery. The presence of protein targeting to chloroplast suggests plastid-associated ribosomes, aligning with chloroplast-specific translation. Other terms like cell cycle and cell septum assembly are peripheral and do not override the core translation theme.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042274","count":16},{"id":"GO:0090529","count":16},{"id":"GO:0006007","count":16},{"id":"GO:1903833","count":16},{"id":"GO:0045036","count":16}]},{"hash":"1644903979288850583","title":"Organogenesis and neural development","description":"The top GO terms point to development of multiple organs (thymus, placenta, heart) and neural tissues (forebrain, nervous system development) as well as cell polarity related to neural patterning, suggesting proteins involved in broad organogenesis and neural differentiation. A few immune-related terms (IL-4 production) can be aligned with thymic immune development, reinforcing the developmental theme rather than a single pathway.","confidence":"High","size":24,"edges":235,"triangles":1368,"max_degree":23,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0048538","count":24},{"id":"GO:0000187","count":24},{"id":"GO:0001890","count":24},{"id":"GO:0071276","count":24},{"id":"GO:2000727","count":23}]},{"hash":"198201766213004485","title":"Neural development and transcriptional regulation","description":"The top GO terms center on nervous system and forebrain development, bipolar cell polarity, and DNA-templated transcription, pointing to transcriptional control of neural differentiation as the core theme. While cytokine production terms (IL-4, IFN-\u03b2) and differentiation terms for other tissues appear, the strongest signal is neural development coupled with transcriptional regulation, suggesting these proteins act as transcriptional regulators in neural lineages. Confidence: High","confidence":"","size":24,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2000727","count":23},{"id":"GO:0007399","count":23},{"id":"GO:0061246","count":23},{"id":"GO:0032633","count":23},{"id":"GO:0043433","count":23}]},{"hash":"1694032506697927889","title":"NF-kappaB Ubiquitination in Innate Immunity","description":"This cluster centers on innate immune signaling and NF-kappaB regulation via ubiquitination. Top terms include innate immune response, TNF-mediated signaling, I-kappaB phosphorylation, and multiple ubiquitination processes (protein ubiquitination, K63-linked ubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process), all pointing to NF-kappaB\u2013driven inflammatory signaling modulated by ubiquitin dynamics. A vitamin D response term appears but is less central. Overall, the proteins are connected by immune signaling and ubiquitin-mediated control of NF-kappaB activity.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051092","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0016567","count":6},{"id":"GO:0033209","count":6},{"id":"GO:0070534","count":6}]},{"hash":"42442752601365268","title":"Ubiquitin-Dependent Protein Degradation and NF-\u03baB Signaling","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolism (including SCF-proteasomal pathways and polyubiquitination) and signals that regulate TNF-mediated pathways and I\u03baB phosphorylation, all pointing to the ubiquitin-proteasome system's role in NF-\u03baB signaling. The recurring themes of ubiquitination types and proteasomal degradation, linked to TNF/NF-\u03baB regulation, support a cohesive functional label.","confidence":"High","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0030433","count":10},{"id":"GO:0051865","count":8},{"id":"GO:1903265","count":8},{"id":"GO:0031146","count":8}]},{"hash":"1423922881352374910","title":"Nuclear transcription and DNA repair","description":"The cluster shows strong signals for nuclear functions, including DNA-templated transcription and single-strand DNA break repair, along with chromatin regulation (histone acetylation) and nuclear inheritance. While a few terms touch on centrosome localization and membrane/trafficking, the dominant theme is nuclear genome maintenance and transcription control, justifying a label focused on nuclear processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0048015","count":2},{"id":"GO:0000012","count":2},{"id":"GO:2000617","count":2},{"id":"GO:0090502","count":2}]},{"hash":"1386929083152528279","title":"Proteostasis and Thermoception Signaling","description":"The terms cluster around protein turnover and assembly (protein homooligomerization, ubiquitination, proteasome regulatory particle assembly), pointing to proteostasis. The presence of thermoception-related terms (detection of temperature stimulus) and related signaling suggests a temperature-sensing signaling component, with other terms indicating broader intracellular signaling and migration as possible downstream effects. Overall, the cluster seems to reflect a proteostasis-linked, temperature-responsive signaling module.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0070682","count":4},{"id":"GO:0050960","count":4},{"id":"GO:0035556","count":4}]},{"hash":"703435768971397498","title":"Rho GTPase\u2013driven actin dynamics in neural migration","description":"The cluster\u2019s top terms cluster around cytoskeletal regulation (positive regulation of GTPase activity, regulation of Rho signaling, barbed-end actin filament capping) and a neural development/migration context (extension of a leading process in radial glia), suggesting a theme of actin remodeling driving neural cell movement. Additional terms point to broader signaling pathways (TGF-beta, interferon, IL-4) that modulate these processes, but the core theme remains cytoskeletal regulation linked to neural migration.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0035023","count":4},{"id":"GO:0060335","count":4},{"id":"GO:0051016","count":4},{"id":"GO:0071560","count":4}]},{"hash":"62417565161214107","title":"Rho-Actin Cytoskeleton Signaling","description":"The terms cluster around Rho-family GTPase signaling and actin cytoskeleton dynamics (actin polymerization and regulation of Rho/GTPase activity), paired with processes of cell motility such as leading-process extension in migrating neurons and membrane invagination. While other pathways (insulin receptor, T cell receptor signaling) and ER stress\u2013related regulation appear, the strongest common theme is cytoskeletal remodeling driven by Rho signaling, supporting the label.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0050852","count":3},{"id":"GO:1903898","count":3},{"id":"GO:1902237","count":3},{"id":"GO:0043547","count":3}]},{"hash":"536031743526621226","title":"Signaling and Trafficking in Cardiac and Immune Cells","description":"The terms point to a mix of signaling pathways (including Wnt and GPCR-related signaling), membrane trafficking and maintenance (pinocytosis, protein localization to plasma membrane), mechanotransduction (response to mechanical stimulus), and context-specific processes (SA node signaling in the heart and follicular dendritic cell differentiation). This suggests a broad theme of signaling and membrane trafficking active in both cardiac and immune cell contexts, rather than a single, tightly defined function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0048549","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0002268","count":3},{"id":"GO:0086070","count":3}]},{"hash":"179668325034746456","title":"Nuclear Transport and Mitosis","description":"The top GO terms point to a core theme of nuclear-cytoplasmic transport and mitotic regulation, with tRNA export from the nucleus, protein localization to the nuclear inner membrane, and mitotic nuclear membrane disassembly forming the strongest connections. Other terms (virus transport, immune signaling, hair follicle development, cardiac muscle signaling) are more peripheral, suggesting pleiotropic roles but the dominant pattern centers on nuclear transport and mitosis.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086014","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0006409","count":2},{"id":"GO:0075733","count":2},{"id":"GO:0007077","count":2}]},{"hash":"1183838720355246560","title":"NF-kappaB Regulation and Endosome Trafficking","description":"The top GO terms point to downregulation of NF-kappaB activity alongside intracellular signaling and vesicle trafficking steps, including plasma membrane to endosome transport and regulation of protein localization to the cell surface, with ubiquitination as a regulatory mechanism. This combination suggests a protein cluster involved in modulating signaling cascades (notably NF-kappaB) through endocytic trafficking and post-translational modification. Some terms related to nervous system development may reflect broader roles of signaling proteins. Confidence reflects a coherent theme but limited direct connectivity in the data, hence a Medium confidence.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0048227","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0031384","count":2}]},{"hash":"1006907874395842108","title":"Proteostasis and Stress Signaling","description":"The cluster shows enrichment for protein ubiquitination and proteasome regulatory particle assembly, indicating a focus on protein turnover and proteostasis. It also includes terms related to temperature- and chemical-stimulus responses (thermoception and capsazepine), hinting at stress-responsive signaling, alongside intracellular signal transduction and cell migration. While other terms touch on differentiation and vitamin D response, the proteostasis-related terms are most representative of the cluster\u2019s function. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0050960","count":3},{"id":"GO:0035556","count":3}]},{"hash":"1245226927589446000","title":"Unknown","description":"The listed GO terms span immune signaling (NF-kappaB regulation, NOD2 pathway, IL-12 modulation, dendritic cell differentiation) and also mechanotransduction and non-immunological processes (SA node communication, hepatocyte apoptosis, response to muscle stretch), with no single dominant function tying all proteins together; thus a cohesive label cannot be confidently assigned.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":6},{"id":"GO:0002268","count":5},{"id":"GO:0086070","count":5},{"id":"GO:0097284","count":5},{"id":"GO:0070431","count":5}]},{"hash":"2042484466239012686","title":"Developmental transcriptional regulation","description":"The terms point to embryonic and tissue development across multiple lineages (primitive streak formation, various organ developments) with ongoing transcriptional regulation by RNA Pol II, suggesting a cluster of proteins involved in controlling gene expression during development.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0090009","count":4},{"id":"GO:0048935","count":4},{"id":"GO:0045648","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1816532761222422354","title":"Developmental Signaling and Innervation","description":"This cluster's terms point to diverse developmental processes and signaling pathways, including nervous system development, innervation, chondrocyte development, basement membrane remodeling, and growth-factor signaling regulation, suggesting a general theme of developmental signaling guiding tissue morphogenesis rather than a single tissue type.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002063","count":5},{"id":"GO:0060686","count":5},{"id":"GO:0007417","count":5},{"id":"GO:0040037","count":5},{"id":"GO:0035860","count":5}]},{"hash":"45027073689288753","title":"Bone development and osteogenesis","description":"The top GO terms are dominated by skeletal system development, angiogenesis, and osteoblast differentiation, which together point to bone formation and skeletal growth as the cluster\u2019s core theme. Additional terms like cell-matrix adhesion and axon guidance fit into broader developmental remodeling often seen during morphogenesis. A couple of terms (subtelomeric heterochromatin formation, mycothiol biosynthetic process) are less directly tied to bone biology and may reflect broader functional annotations, but the main signal supports bone development and osteogenesis.","confidence":"Medium","size":23,"edges":17,"triangles":0,"max_degree":7,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0001501","count":7},{"id":"GO:0001525","count":6},{"id":"GO:0006348","count":5},{"id":"GO:0046330","count":4},{"id":"GO:0007160","count":4}]},{"hash":"1471074690501976524","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by translation-related terms (GO:0006412) and ribosome biogenesis (GO:0042254), with additional enrichment for ribosomal subunit export (GO:0000056). This points to proteins involved in ribosome assembly and protein synthesis; other terms like antibiotic biosynthesis or stress responses appear secondary and do not define a distinct module.","confidence":"High","size":23,"edges":99,"triangles":272,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0017000","count":2}]},{"hash":"116824263982032962","title":"Proviral integration and latency","description":"Based on the top GO terms, the cluster is enriched for DNA-level processes (DNA replication, DNA recombination, DNA integration) and a specific retroviral process (establishment of integrated proviral latency). These indicate a theme centered on viral genome integration and latency control. While other terms related to neuron development and erythrocyte differentiation appear, the dominant signal is proviral DNA integration and latency, justifying the label.","confidence":"High","size":23,"edges":16,"triangles":2,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0045648","count":4},{"id":"GO:0010976","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0075713","count":4}]},{"hash":"1668139984794064555","title":"Genome maintenance and gene expression","description":"The cluster shows strong signals for DNA replication, DNA repair, and SOS response (cell division, DNA replication, nucleotide-excision repair), alongside transcription initiation, ribosome biogenesis, and translation initiation, plus mRNA surveillance (nonsense-mediated decay). This combination points to a core set of genome maintenance proteins closely tied to the machinery of gene expression, suggesting a broad, integrative functional theme rather than a single pathway.","confidence":"Medium","size":23,"edges":144,"triangles":448,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006367","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0006289","count":4},{"id":"GO:0000184","count":4}]},{"hash":"1302411018477733749","title":"Calcium Signaling in Muscle and Bone Remodeling","description":"The top GO terms point to mitochondrial calcium ion homeostasis, myoblast migration in skeletal muscle regeneration, and osteoclast development, which together suggest a calcium-dependent signaling axis coordinating muscle regeneration and bone remodeling. Other terms related to stress responses (salt, thyroid hormone) are present but appear secondary to the central role of calcium handling in these tissue remodeling processes. Thus, the cluster is best described as a calcium-centric module governing muscle and bone remodeling.","confidence":"High","size":23,"edges":67,"triangles":88,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0014839","count":2},{"id":"GO:0009651","count":2},{"id":"GO:0051560","count":2},{"id":"GO:0097066","count":2},{"id":"GO:1900138","count":2}]},{"hash":"1361055403416655160","title":"Neural development with adhesion and innate immunity","description":"The top GO terms cluster around nervous system development and synapse assembly, along with cell-cell adhesion (homophilic/heterophilic) and innate immune processes (complement activation, neutrophil clearance). This suggests proteins that participate in neural connectivity and also in adhesion and immune signaling, indicating a theme of neural development intertwined with immune/adhesive roles.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0007156","count":3},{"id":"GO:0043931","count":3}]},{"hash":"2213834976260596581","title":"Glutamatergic Synapse and Neural Development","description":"The top GO terms are dominated by glutamatergic synaptic transmission, regulation of synapse assembly, and nervous system development, with related terms like inner ear development and glial proliferation. This points to proteins linked to neural signaling and neural development, suggesting a coherent theme around synapse formation and nervous system maturation, despite a few outlier immune-related terms. Therefore, a neural-focused label is most representative.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":3},{"id":"GO:0051965","count":2},{"id":"GO:0002315","count":2},{"id":"GO:0048839","count":2},{"id":"GO:0007399","count":2}]},{"hash":"1038536722859353881","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000350","count":1},{"id":"GO:0000389","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0006626","count":1}]},{"hash":"1362282085813532862","title":"RNA Splicing and Translational Initiation","description":"The cluster shows strong representation of mRNA processing and splicing terms (spliceosome, splice site recognition, mRNA modification) alongside translation initiation factors and regulation of translational initiation, indicating a cohesive theme around RNA processing and control of protein synthesis.","confidence":"High","size":23,"edges":250,"triangles":1710,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":14},{"id":"GO:0010610","count":13},{"id":"GO:0048026","count":12},{"id":"GO:0045292","count":12},{"id":"GO:0006376","count":11}]},{"hash":"1104872406830402622","title":"RNA processing and ribosome biogenesis","description":"The proteins are enriched for mRNA splicing, ribosomal subunit biogenesis, rRNA maturation, translation initiation/reinitiation, and RNA methylation, pointing to a core RNA metabolism and ribosome/translation machinery theme. Some development terms may reflect broader roles in developmental gene expression, but the dominant shared function is RNA processing and ribosome biogenesis.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":8},{"id":"GO:0001731","count":8},{"id":"GO:0002188","count":8},{"id":"GO:0042273","count":8},{"id":"GO:0070306","count":7}]},{"hash":"1390446866557560971","title":"Neural development and synaptic signaling","description":"These proteins collectively relate to neural development and synaptic connectivity, including synapse assembly, cortical layer formation, and dopaminergic GPCR signaling (response to cocaine). Rho signaling aligns with cytoskeletal changes for neurite outgrowth; angiogenesis and growth hormone signaling may reflect neurovascular development and systemic regulation during brain formation.","confidence":"Medium","size":23,"edges":20,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":6},{"id":"GO:0042220","count":6},{"id":"GO:0021819","count":6},{"id":"GO:0045777","count":6},{"id":"GO:0010579","count":6}]},{"hash":"1136525722472417040","title":"Lipid and Steroid Biosynthesis","description":"The cluster's prevalent GO terms include sphingolipid, estrogen, retinoic acid, mycolic acid, and 3-keto-sphinganine biosynthesis, plus tetrahydrobiopterin biosynthesis. Together these indicate a core theme of lipid- and steroid-related biosynthetic pathways, with some less-specific biosynthetic terms (e.g., antibiotic biosynthesis) that fall under the same broad category. Therefore, the label Lipid and Steroid Biosynthesis is representative.","confidence":"High","size":23,"edges":232,"triangles":1390,"max_degree":22,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030148","count":23},{"id":"GO:0055114","count":23},{"id":"GO:0006703","count":23},{"id":"GO:0031427","count":23},{"id":"GO:0017000","count":23}]},{"hash":"305305174873105641","title":"Immune Regulation and Cell Adhesion","description":"This cluster centers on immune modulation: GO terms for negative regulation of cytotoxic T cell degranulation, negative regulation of macrophage activation, and negative regulation of NK cell cytotoxicity\u2014indicating suppression of immune effector functions. It also includes multiple cell\u2013cell adhesion terms (homophilic/heterophilic adhesion and synapse assembly), plus tissue-specific adhesion signals (AV node cell adhesion), suggesting roles in intercellular communication and tissue organization. A few terms touch on neuronal projection and even symbiont entry into host cells, implying diverse contexts where adhesion and signaling intersect. Overall, the proteins appear tied to modulating intercellular signaling with an adhesion component.","confidence":"Medium","size":23,"edges":215,"triangles":1106,"max_degree":22,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043318","count":4},{"id":"GO:0051963","count":4},{"id":"GO:0043031","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0086072","count":4}]},{"hash":"1917125231556851799","title":"Unknown","description":"The top terms include glycosylation and proteoglycan biosynthesis (e.g., chondroitin sulfate pathways) but also plant cell wall modification and plasmodesma organization, plus cartilage/ear development terms. The mix across kingdoms and developmental contexts lacks a single coherent biology, so a clear, representative label cannot be confidently assigned.","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":6},{"id":"GO:0006486","count":6},{"id":"GO:0019276","count":6},{"id":"GO:0050650","count":6},{"id":"GO:0009831","count":4}]},{"hash":"795548494510417944","title":"Regulatory signaling and chromatin regulation","description":"These proteins appear to function as cellular regulators across signaling, proliferation control, cell fate decisions, and chromatin modification (histone acetylation). The top terms span endothelial barrier establishment, negative regulation of proliferation, Rho signaling, dendritic cell apoptosis, oligodendrocyte progenitor proliferation, and histone acetylation, suggesting a broad theme of regulatory proteins rather than a single cohesive pathway. The presence of obsolete terms and no interactions (Edges: 0) indicate the connection is high-level and not tightly unified, so the label carries a medium level of confidence.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090557","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0070433","count":3},{"id":"GO:0007205","count":3},{"id":"GO:2001275","count":3}]},{"hash":"940024161580335385","title":"Integrin-mediated adhesion and tissue development","description":"Central GO terms point to cell-matrix adhesion and integrin-mediated signaling as defining features of this cluster, with additional signals related to skin development, amelogenesis, trophoblast migration, and maintenance of organ identity. This pattern suggests a coherent theme of adhesion-driven communication guiding tissue formation and morphogenesis. Other terms like mitochondrial calcium homeostasis and sodium ion import are present but appear secondary to the adhesion\u2013signaling core.","confidence":"Medium","size":23,"edges":64,"triangles":21,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007160","count":3},{"id":"GO:0007229","count":2},{"id":"GO:0051560","count":2},{"id":"GO:0097369","count":2},{"id":"GO:0097186","count":2}]},{"hash":"1138003218809026024","title":"Neural development and transcription regulation","description":"The top GO terms are dominated by nervous system development, forebrain development, and establishment of neuronal polarity, along with DNA-templated transcription and cell cycle/DNA replication, suggesting a cluster of proteins involved in neural differentiation and regulation of gene expression during development. Some immune-related terms appear but are less central to the theme. Confidence: Medium.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000278","count":22},{"id":"GO:0006260","count":22},{"id":"GO:2000727","count":21},{"id":"GO:0007399","count":21},{"id":"GO:0061246","count":21}]},{"hash":"148484603499305033","title":"Immune system development and signaling","description":"The terms point to immune cell development and function, including NK T cell differentiation, B cell affinity maturation, and innate immune response, as well as cytokine-related processes (interleukin-4 production, response to IL-7). Developmental terms like thymus development (and to a lesser extent heart development) appear, alongside signaling pathways (Wnt, insulin receptor signaling), suggesting a coordinated immune-developmental program with regulatory signaling. Overall, this cluster seems to represent immune system development and cytokine signaling programs.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007507","count":8},{"id":"GO:0032633","count":7},{"id":"GO:0048538","count":7},{"id":"GO:0098761","count":7},{"id":"GO:0016477","count":7}]},{"hash":"1066155817672523873","title":"Methylation and Diverse Biosynthesis","description":"This cluster is enriched for both methylation-related processes (RNA guanine-N7 methylation, tRNA methylation, N-terminal peptidyl-serine trimethylation) and a variety of biosynthetic pathways (sterol, biotin, ubiquinone, vitamin E, resorcinol, antibiotic biosynthesis), suggesting a theme of methylation-modulated biosynthesis. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0030488","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0009102","count":4}]},{"hash":"2116835569463074167","title":"Unknown","description":"The GO terms span neural development (axon guidance, neuron differentiation), immune processes (immunoglobulin production, B cell signaling, germinal center formation), and organogenesis (kidney development, cardiac action potential) with no clear single function uniting them. Hence a specific, representative label cannot be confidently assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033564","count":4},{"id":"GO:0021859","count":4},{"id":"GO:0007432","count":4},{"id":"GO:0042511","count":4},{"id":"GO:0002377","count":4}]},{"hash":"2001580658683374744","title":"Developmental Signaling Across Tissues","description":"These terms cover heart development, CNS/hippocampus development, megakaryocyte development, melanocyte migration, and other tissue-specific developmental processes, plus regulation of signaling cascades (calcineurin-NFAT, kinase activity). This points to a general theme of developmental regulation across multiple tissues rather than a single tissue-specific function. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0051531","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0032516","count":2}]},{"hash":"104044506065715632","title":"Inflammation and vascular signaling","description":"The top GO terms point to inflammatory response and endothelial/vascular processes (endothelial barrier establishment, vascular smooth muscle differentiation, Rho signaling), along with signaling pathways (STAT phosphorylation, necroptosis) and lineage-related development (megakaryocytes) and synapse organization. This suggests a broad cluster of proteins involved in signaling crosstalk between inflammatory responses and vascular/ endothelial function, rather than a single, tight pathway, hence a high-level label focused on inflammation-vascular signaling is appropriate.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0090557","count":3},{"id":"GO:0042511","count":3},{"id":"GO:0050808","count":3},{"id":"GO:0006954","count":3},{"id":"GO:0007224","count":3}]},{"hash":"960071282656797278","title":"TLR4-Mediated Innate Inflammation","description":"The cluster is dominated by GO terms for inflammatory response, response to virus, LPS/TLR4 and TNF signaling, and necroptosis, indicating innate immune activation and inflammatory signaling. Lipid metabolism terms are present but appear secondary to the core immune-related functions.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":9},{"id":"GO:0009615","count":8},{"id":"GO:0019915","count":8},{"id":"GO:0050885","count":8},{"id":"GO:0051345","count":8}]},{"hash":"1797184773926166737","title":"Immune signaling and cytoskeletal remodeling","description":"The dominant GO terms point to both innate and adaptive immune activation (innate/adaptive immune response, B cell receptor signaling, IL-2 production, and adaptive immune response) and to cytoskeletal dynamics (actin filament bundle assembly, regulation of Rho signaling, and cell migration), suggesting a cluster centered on immune cell activation coupled with actin remodeling that supports migration and adhesion. The presence of JNK cascade regulation also fits immune signaling processes. The epithelial polarity term is less central but may reflect tissue-context interactions; overall, the theme is coherent around immune signaling with cytoskeletal changes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045087","count":9},{"id":"GO:0016477","count":7},{"id":"GO:0051017","count":7},{"id":"GO:0090162","count":7},{"id":"GO:0035023","count":6}]},{"hash":"1406544359203946909","title":"Rab-regulated endocytosis and TLR signaling","description":"The cluster combines Rab GTPase\u2013regulated trafficking (Rab signaling regulation, endocytic recycling, vesicle endocytosis) with innate immune pathways (MyD88-dependent TLR signaling, inflammatory response). This points to a cohesive theme where vesicle trafficking is connected to immune signaling; additional terms like apoptosis and mechanical stimulus response appear auxiliary. The label reflects the core shared functions without overreach.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":2},{"id":"GO:0035745","count":2},{"id":"GO:0048488","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0032456","count":2}]},{"hash":"2264965162536211192","title":"Unknown","description":"The GO terms span diverse biological processes with little cohesive overlap. Neural-related terms (regulation of NMDA receptor activity, midbrain morphogenesis, cerebellar granule cell differentiation) exist alongside endothelial barrier formation, T cell apoptosis, viral mRNA export, transcription, rRNA maturation, Rho signaling, and insulin secretion, making a single unifying function unlikely. Therefore, no confident, representative label can be assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2000310","count":3},{"id":"GO:0090557","count":3},{"id":"GO:0006924","count":3},{"id":"GO:0046784","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1527549051396532131","title":"Polarity Establishment and Rho-Signaling Regulators","description":"The strongest signals are for regulation of establishment of cell polarity and regulation of Rho protein signal transduction, with additional cues for astral microtubule organization and protein localization to the plasma membrane. Together these terms imply a cluster of proteins that coordinate cell polarity and cytoskeletal dynamics through Rho pathways, with some peripheral associations to cell adhesion and membrane processing.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000114","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0090004","count":1},{"id":"GO:0030953","count":1},{"id":"GO:0030826","count":1}]},{"hash":"1480078023802059900","title":"Translation and Translational Fidelity","description":"The strongest signals are translation (GO:0006412) and regulation of translational fidelity (GO:0006450), suggesting a cluster centered on protein synthesis and its accuracy. There are additional signals for glucose metabolism and for cell-matrix adhesion/platelet aggregation, but these are less dominant and may reflect broader cellular states or context-specific roles. Overall, the cluster appears best characterized by translation and its regulation.","confidence":"Medium","size":22,"edges":21,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:1902042","count":3},{"id":"GO:0007160","count":3},{"id":"GO:0070527","count":3},{"id":"GO:0055114","count":3}]},{"hash":"1794426486854859752","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by protein synthesis-related GO terms: translation, cytoplasmic translation, and both general and small subunit ribosome biogenesis. The antibiotic response term also fits the theme, as antibiotics commonly target ribosomal function. A few terms like cell cycle or conjugation appear but are secondary to the core translation/ribosome theme.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":3},{"id":"GO:1901407","count":2},{"id":"GO:0042274","count":2}]},{"hash":"459320484328185158","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (fatty acid response, mitochondrial inheritance, CNS myelin maintenance, sphingolipid metabolism, sebaceous gland differentiation, osmotic stress response, protein oligomerization, kidney development, aerobic respiration) with no single cohesive functional theme binding the cluster. Therefore a representative, specific label cannot be confidently assigned.","confidence":"","size":22,"edges":13,"triangles":8,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070542","count":7},{"id":"GO:0000001","count":5},{"id":"GO:0032286","count":4},{"id":"GO:0006675","count":4},{"id":"GO:0001949","count":4}]},{"hash":"1389393994494313098","title":"NF-\u03baB and TNF inflammatory signaling with ubiquitination","description":"The proteins cluster around TNF-mediated signaling and NF-\u03baB activation, with strong links to ubiquitination (including K63-linked ubiquitination and autoubiquitination), I\u03baB phosphorylation, and innate immune response, indicating a cohesive NF-\u03baB\u2013driven inflammatory module.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0090073","count":13},{"id":"GO:0033209","count":12},{"id":"GO:0051865","count":12},{"id":"GO:1903721","count":12},{"id":"GO:0007250","count":12}]},{"hash":"916317744120625009","title":"Neural Migration and Axonogenesis","description":"The cluster is dominated by neural development terms: medial/lateral motor column neuron differentiation, forebrain regionalization, peripheral nervous system neuron axonogenesis, and neuronal migration. Supporting terms like lamellipodium assembly and cell-matrix adhesion point to cytoskeletal remodeling and adhesion needed for neuron movement and axon outgrowth. A couple of terms (platelet aggregation, sulfur oxidation) appear less connected and likely represent noise, but the core signal is neural development and axon guidance.","confidence":"High","size":22,"edges":214,"triangles":1235,"max_degree":21,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0070527","count":6},{"id":"GO:0097477","count":6},{"id":"GO:0021526","count":5},{"id":"GO:0050859","count":5},{"id":"GO:0035331","count":5}]},{"hash":"2159566446117587299","title":"Energy metabolism and ribosome maturation","description":"The cluster shows strong representation of energy-producing pathways (glycolytic process and TCA cycle) alongside translation-related processes (translation and maturation of SSU-rRNA), suggesting a link between cellular energy state and ribosome biogenesis. The presence of porphyrin/heme and thiamine biosynthesis, plus oxidant detoxification and apoptotic processes, further supports a mitochondria-associated metabolic and stress-response theme.","confidence":"Medium","size":22,"edges":208,"triangles":1261,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0006782","count":2}]},{"hash":"218179454368114676","title":"Integrin signaling and cell adhesion","description":"Proteins here are enriched for adhesion and migration processes, including integrin-mediated signaling, cell\u2013matrix and cell\u2013cell adhesion, and substrate-dependent migration/extravasation. Hyaluronan metabolism supports ECM remodeling, while other terms like endodermal differentiation and dendrite regeneration suggest broader developmental remodeling. Overall, the cluster centers on integrin-ECM adhesion and associated cell movement. ","confidence":"High","size":22,"edges":19,"triangles":2,"max_degree":6,"top_function":"wound healing","top_go_terms":[{"id":"GO:0034113","count":13},{"id":"GO:0045123","count":13},{"id":"GO:0035987","count":13},{"id":"GO:0007229","count":13},{"id":"GO:0007161","count":13}]},{"hash":"1481142417653093926","title":"Translation machinery and mRNA turnover","description":"Most terms are translation-related (initiation, elongation, termination, cytoplasmic and mitochondrial translation, and selenocysteine incorporation) and include mRNA decay via deadenylation-dependent pathways. The \u201cresponse to antibiotic\u201d term aligns with ribosome-targeting antibiotics, reinforcing the translation-focused theme. A single term for glial cell proliferation is less central. Overall, the cluster captures ribosome/translation machinery and linked RNA processing processes.","confidence":"High","size":22,"edges":224,"triangles":1416,"max_degree":21,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":17},{"id":"GO:0046677","count":9},{"id":"GO:0000288","count":6},{"id":"GO:0006413","count":6},{"id":"GO:0045901","count":6}]},{"hash":"317146529570736904","title":"Neurodevelopment and Neuronal Signaling","description":"The GO terms point to brain development and neuronal processes (hippocampus and substantia nigra development, neuron migration) and neuronal activity (membrane depolarization during action potential), suggesting a neurodevelopmental and signaling-focused cluster. A couple terms reference skin development, which may be annotation noise or broader gene involvement, but the neural theme appears dominant.","confidence":"Medium","size":22,"edges":25,"triangles":4,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":4},{"id":"GO:0003334","count":2},{"id":"GO:0071901","count":2},{"id":"GO:1900740","count":2},{"id":"GO:0021766","count":2}]},{"hash":"656480945198898687","title":"Unknown","description":"The cluster's top GO terms cover immune activation (complement, platelet activation), vascular regulation (angiogenesis, vasoconstriction), developmental signaling (Smoothened/Hedgehog), proteolysis, and even bacterial metabolism (antibiotic biosynthesis). This broad mix lacks a single coherent theme, so a specific functional label cannot be confidently assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042619","count":3},{"id":"GO:0045880","count":3},{"id":"GO:0001867","count":3},{"id":"GO:0007171","count":3}]},{"hash":"735318666157782180","title":"Immune signaling and cytoskeletal remodeling","description":"The cluster combines immune-related terms (innate immune response, activated T cell proliferation, regulation of TLR2 signaling, apoptotic process) with cytoskeleton dynamics (actin filament polymerization, Rho/GTPase signaling, membrane invagination, ephrin signaling, and cell migration-related processes), suggesting a theme of immune signaling coupled to cytoskeletal remodeling and motility.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006915","count":7},{"id":"GO:0050798","count":7},{"id":"GO:0048013","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0043547","count":6}]},{"hash":"750115643433971219","title":"Diverse metabolite transporters","description":"This cluster shows enrichment for transport-related GO terms across a range of metabolites (ascorbic acid, dehydroascorbic acid, glucose, arabinose, selenite) and related transporter activity, suggesting these proteins function as membrane transporters or carriers for nutrients/metabolites. The presence of synaptic plasticity terms may reflect annotation noise or broader cellular roles, but the common theme appears to be transport/metabolite handling. Confidence in the label is Medium.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019852","count":3},{"id":"GO:0060291","count":2},{"id":"GO:0060292","count":2},{"id":"GO:0044381","count":2},{"id":"GO:1900754","count":2}]},{"hash":"2294000406675901227","title":"Transmembrane Transport of Ions and Small Molecules","description":"Based on the top GO terms, this cluster is dominated by transmembrane transport activities across a wide range of substrates (potassium ions, xenobiotics, vitamins, nitrate/nitrite, arabinose, aromatic compounds) and even vesicular neurotransmitter loading, indicating a cohesive theme of membrane transporters handling diverse solutes.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071805","count":14},{"id":"GO:0006855","count":14},{"id":"GO:0035461","count":12},{"id":"GO:0042908","count":9},{"id":"GO:1900754","count":8}]},{"hash":"726340975373022345","title":"Prostaglandin and steroid hormone metabolism in reproduction","description":"This cluster centers on lipid-derived hormone synthesis and reproductive processes, notably prostaglandin biosynthesis, progesterone metabolism, triglyceride metabolism, and uterus-related development/parturition, with some lipid-related responses; a brassinosteroid term may be an annotation artifact but does not undermine the reproductive-hormone theme.","confidence":"High","size":22,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":16},{"id":"GO:0060065","count":16},{"id":"GO:0032094","count":16},{"id":"GO:0034653","count":15},{"id":"GO:0002933","count":15}]},{"hash":"1311286838978466785","title":" Neural development and axon guidance signaling","description":"The top terms converge on nervous system development, neuronal migration, and axon guidance, with signals such as Roundabout (ROBO) and Smoothened pathways, and migratory processes described (e.g., tangential migration in the brain). Additional terms related to learning and cell polarity fit within broader neural tissue organization and signaling regulation. A few terms (like T cell receptor signaling) are less aligned, but do not override the central neural development theme. ","confidence":"Medium","size":22,"edges":27,"triangles":5,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0090051","count":8},{"id":"GO:0022028","count":7},{"id":"GO:0007612","count":7},{"id":"GO:0071260","count":7},{"id":"GO:0045197","count":7}]},{"hash":"709238967902872351","title":"Transmembrane Transporters (ions and metabolites)","description":"The Top Terms are all transmembrane transport GO terms for a wide range of substrates, including ions (K+, Na+, phosphate), xenobiotics, vitamins, sugars, nitrite/nitrate, sialic acid, and other metabolites, indicating a cluster of membrane transporter proteins with diverse substrate specificities.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":6},{"id":"GO:0035725","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0035461","count":4},{"id":"GO:0035435","count":4}]},{"hash":"1322841880012272306","title":"Cardiac pacemaker signaling and protein turnover","description":"The top GO terms indicate SA node communication with atrial cardiac muscle cells and regulation of SA node action potential, pointing to pacemaker/conduction activity. Additional terms about maintaining protein localization in the plasma membrane and components of ubiquitination and proteasome assembly suggest linked protein turnover and membrane trafficking supporting cardiac signaling. While a few generic terms are present, the strongest theme is cardiac conduction paired with protein homeostasis.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":3},{"id":"GO:0072660","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1107338716014736031","title":"RNA Methylation and Cofactor Biosynthesis","description":"This cluster centers on RNA modification (tRNA methylation, tRNA queuosine biosynthesis, rRNA base methylation) and on biosynthesis of various cofactors (biotin, molybdopterin, PQQ, protoporphyrinogen IX), suggesting a role in RNA modification alongside small-molecule cofactor production rather than direct protein\u2013protein interaction networks. The diverse yet related biosynthetic terms indicate a cohesive theme around nucleic acid modification and essential cofactors.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0008616","count":1},{"id":"GO:0018339","count":1}]},{"hash":"817301658227086089","title":"Ubiquitination and Proteasome-Linked Signaling","description":"The top GO terms show a strong emphasis on protein ubiquitination and proteasome regulatory particle assembly, pointing to roles in protein turnover. Additional terms for intracellular signal transduction and various stress/differentiation responses (temperature sensing, capsazepine/vitamin D responses, cell migration, follicular dendritic cell differentiation) suggest these proteins also participate in signaling pathways linked to stress, immune/differentiation processes, and cell movement. Overall, this cluster likely represents ubiquitin-proteasome\u2013associated regulators coupled with responsive signaling functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":9},{"id":"GO:0070682","count":9},{"id":"GO:0050960","count":9},{"id":"GO:0035556","count":9},{"id":"GO:1901594","count":9}]},{"hash":"737563595688021688","title":"Endolysosomal trafficking and autophagy regulation","description":"Top GO terms indicate a strong focus on vesicle transport and lysosomal pathways (endosome-to-lysosome transport, Golgi-to-plasma membrane transport, vesicle docking in exocytosis) and autophagy-related regulation (negative regulation of autophagosome assembly, Cvt pathway targeting). Together, these suggest a coherent cluster centered on endolysosomal trafficking and autophagy control, with occasional links to neuronal and immune contexts where such trafficking is critical. Confidence in this label is Medium.","confidence":"Medium","size":22,"edges":6,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":6},{"id":"GO:0008333","count":6},{"id":"GO:0007399","count":5},{"id":"GO:0032258","count":5},{"id":"GO:0006893","count":5}]},{"hash":"1271826902045204608","title":"Neural development and transcription signaling","description":"This cluster is dominated by GO terms related to nervous system and forebrain development, bipolar cell polarity, DNA-templated transcription, and signaling pathways like the p38MAPK cascade and p53-mediated regulation, indicating a cohesive program of neuronal differentiation and transcriptional control. Some terms (e.g., interferon-beta production) are peripheral but do not override the central neural development theme. Confidence: High.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2000727","count":22},{"id":"GO:0007399","count":22},{"id":"GO:0061246","count":22},{"id":"GO:0043433","count":22},{"id":"GO:0030900","count":22}]},{"hash":"2251659381930406558","title":"NF-\u03baB-TNF signaling and ubiquitination cluster","description":"The top GO terms point to innate immune signaling centered on NF-\u03baB activation: innate immune response, TNF-mediated signaling, and positive regulation of NF-\u03baB pathways, along with regulatory ubiquitination steps (K63-linked ubiquitination, autoubiquitination, I\u03baB phosphorylation). These collectively suggest a cohesive role in NF-\u03baB\u2013driven immune signaling, despite one developmental term appearing as an outlier. Confidence that the label matches the cluster\u2019s function is high.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051092","count":12},{"id":"GO:0045087","count":12},{"id":"GO:0001843","count":11},{"id":"GO:0033209","count":11},{"id":"GO:0070534","count":11}]},{"hash":"1558360913672634180","title":"Golgi- and vesicle trafficking during mitosis","description":"This cluster centers on Golgi organization, endocytic recycling, and membrane trafficking that accompany cell division and cytokinesis. Top terms include Golgi organization, mitotic cell cycle, membrane addition at site of cytokinesis, and endocytic recycling, suggesting proteins coordinating vesicle trafficking and Golgi dynamics during mitosis. Some terms like brain development may reflect broader or incidental roles, but the dominant signal points to intracellular transport processes linked to cell division.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045740","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0032456","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0032258","count":3}]},{"hash":"2135482883006573426","title":"GTPase signaling in immune activation and apoptosis","description":"The terms show a strong emphasis on small GTPase\u2013mediated signaling and its regulation, with concurrent involvement in extrinsic apoptotic pathways (death receptors), T cell activation/death (activation-induced cell death), and immune structures like germinal centers. There are also hints of endothelial barrier context, but the dominant theme ties GTPase signaling to immune activation and apoptosis, making this a concise, representative label for the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0090557","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0034260","count":4},{"id":"GO:0006924","count":4},{"id":"GO:0002467","count":4}]},{"hash":"1891379472596337166","title":"Neural development and innervation","description":"Top GO terms are dominated by nervous system development and neural signaling (e.g., CNS development, innervation, glial-derived neurotrophic factor receptor signaling), suggesting these proteins are involved in neural differentiation and nerve connectivity. While a few terms relate to broader developmental processes (otolith morphogenesis, chondrocyte development, basement membrane development, FGFR signaling regulation), the neural-focused terms are prominent, supporting a label centered on neural development and innervation. Confidence: Medium.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007417","count":5},{"id":"GO:0032836","count":4},{"id":"GO:0032474","count":3},{"id":"GO:0002063","count":3},{"id":"GO:0060686","count":3}]},{"hash":"1070261415148774731","title":"Neuroimmune Regulation of Synapse Development","description":"The GO terms span neural development (positive regulation of synapse assembly; axon guidance; dendritic spine development; myelination) and immune signaling (innate immune response; regulation of TLR9 signaling; interferon production; CD8+ T cell proliferation; granzyme B production). This suggests a coherent theme of immune pathways modulating neural maturation and synaptic remodeling, i.e., neuroimmune cross-talk governing synapse development. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051965","count":5},{"id":"GO:0045087","count":4},{"id":"GO:0034164","count":4},{"id":"GO:0032687","count":4},{"id":"GO:2000566","count":4}]},{"hash":"2141954362712629259","title":"NF-kappaB Activation via K63-Linked Ubiquitination","description":"This cluster is dominated by GO terms linking ubiquitination with NF-kappaB signaling and innate immunity, including TNF-mediated signaling, I-kappaB phosphorylation, and K63-linked ubiquitination. The presence of autoubiquitination and ubiquitin-dependent proteolysis further supports a module focused on regulatory ubiquitin signals that activate NF-kappaB. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":13},{"id":"GO:1903265","count":13},{"id":"GO:0070534","count":12},{"id":"GO:0033209","count":11},{"id":"GO:1903721","count":11}]},{"hash":"1329452882911793527","title":"Neuronal differentiation and thermoception with ubiquitin turnover","description":"Based on the top GO terms, the proteins cluster around neural development (cerebellar granule cell differentiation, cell migration) and intracellular signaling, with a strong emphasis on protein turnover via ubiquitination and proteasome assembly. The presence of thermoception-related terms (detection of temperature stimulus, response to capsazepine) suggests involvement in temperature-responsive neural pathways. While vitamin D response and some transcriptional regulation terms are broad, the cohesive theme centers on neuronal development and temperature-sensitive signaling influenced by ubiquitin-mediated turnover. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021707","count":11},{"id":"GO:0016567","count":10},{"id":"GO:0070682","count":10},{"id":"GO:0050960","count":10},{"id":"GO:0035556","count":10}]},{"hash":"2066228825502779124","title":"Neuronal signaling and synaptic plasticity","description":"This cluster features terms tied to neuronal functions: brain development, long-term synaptic depression, exocytosis and calcium import at the plasma membrane, and regulation of Rho signaling and Wnt pathways, all pointing to activity-dependent synaptic transmission and vesicle trafficking. There is one immune-related term (lipopolysaccharide response) that is less central to neuronal function, but the dominant pattern supports neuronal signaling and plasticity.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0019933","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0060292","count":2},{"id":"GO:2000009","count":2}]},{"hash":"64978853813666826","title":"Unknown","description":"The top terms point to both immune processes (germinal center formation, B cell receptor signaling) and neural processes (nervous system development, excitatory postsynaptic potential, synaptic plasticity). With no obvious shared function across all proteins and several unrelated terms, there isn't a clear single theme, so the cluster is best labeled Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0048172","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0032088","count":2}]},{"hash":"749893674566727129","title":"Ubiquitination and Proteasome-Mediated Proteostasis","description":"The top GO terms emphasize protein ubiquitination and proteasome regulatory particle assembly, pointing to a core proteostasis/degradation function. While there are additional terms related to signaling, temperature response, and differentiation, their presence seems secondary to the central ubiquitin\u2013proteasome machinery, supporting a proteostasis-focused cluster with moderate confidence.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":13},{"id":"GO:0070682","count":13},{"id":"GO:0050960","count":13},{"id":"GO:0035556","count":13},{"id":"GO:1901594","count":13}]},{"hash":"1367957985869281455","title":"Innate immune signaling and inflammation","description":"This cluster\u2019s top GO terms are dominated by immune/inflammatory processes: positive regulation of TNF production, PGRP signaling, NF-kappaB modulation, inflammatory response, and immunoglobulin production. While a few terms touch on neural development or cardiac activity, the strongest and most recurrent theme is innate immune signaling and inflammation, suggesting these proteins broadly participate in immune responses.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032760","count":3},{"id":"GO:0033564","count":3},{"id":"GO:0061057","count":3},{"id":"GO:0021859","count":3},{"id":"GO:0007432","count":3}]},{"hash":"156557667930458835","title":"Immune activation and inflammatory signaling","description":"The cluster is enriched for immune-related processes: NF-kappaB regulation, TNF production, JNK cascade, immunoglobulin-mediated response, germinal center formation, and B/T cell regulation, plus a lipopolysaccharide response. These together point to activation of innate inflammatory signaling and adaptive immune responses.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051092","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0032496","count":4},{"id":"GO:0030889","count":4},{"id":"GO:0045060","count":4}]},{"hash":"305555353933541618","title":"Vesicle trafficking and pigmentation","description":"The GO terms point to broad vesicle trafficking processes (endocytosis, ER\u2013Golgi transport, Golgi inheritance, endosome-to-melanosome transport) and pigmentation (melanosome-related transport, pigmentation), suggesting a cohesive cluster centered on vesicle movement and pigment biology. Some terms like response to virus or cerebellar Purkinje maturation are peripheral, but the dominant signal is vesicle trafficking with pigment transport.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009615","count":1},{"id":"GO:1901998","count":1},{"id":"GO:0021691","count":1},{"id":"GO:0043473","count":1},{"id":"GO:0006897","count":1}]},{"hash":"846690001387198449","title":"NF-kB-driven Innate Immunity and Apoptosis","description":"The cluster's top GO terms point to NF-kappaB signaling and immune responses (positive regulation of canonical NF-kappaB signaling, response to lipopolysaccharide, innate immune response, xenobiotic response) along with apoptosis-related pathways (extrinsic apoptotic signaling, activation-induced T cell death, regulation of B cell proliferation). Together these suggest a cohesive theme of NF-kB\u2013mediated immune activation coupled with programmed cell death; a few vesicle-related terms may reflect general trafficking processes linked to immune signaling. Confidence: High","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":3},{"id":"GO:0032496","count":2},{"id":"GO:0006924","count":2},{"id":"GO:0097192","count":2},{"id":"GO:0030889","count":2}]},{"hash":"897739343098420252","title":"Nuclear gene expression and genome maintenance","description":"This cluster is dominated by GO terms tied to DNA-templated transcription, chromatin organization, ribosomal RNA maturation, and DNA repair (transcription, chromatin, rRNA processing, and repair), pointing to core nuclear processes governing gene expression and genome maintenance. Some terms like defense response and plant-pattern formation appear as outliers, but the strongest signal centers on nuclear functions.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0051260","count":3}]},{"hash":"1871350519269989831","title":"Developmental Signaling, Ciliogenesis, and Germline Processes","description":"These GO terms point to developmental biology across tissues: heart formation, germline stem cell biology, ciliogenesis, and Wnt signaling regulation, plus some mitotic and nuclear transport processes. The cluster seems to reflect diverse developmental and differentiation-related functions rather than a single cohesive pathway, especially given there are no interaction edges. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0008542","count":2},{"id":"GO:0044458","count":1},{"id":"GO:0007084","count":1},{"id":"GO:0060914","count":1}]},{"hash":"1530560994399471987","title":"Unknown","description":"The GO terms are diverse: neural differentiation (cerebellar granule cell differentiation), proteostasis (ubiquitination and proteasome assembly), thermoception and signaling (temperature stimulus detection, capsazepine response, intracellular signal transduction), plus vitamin D response and telomere maintenance. There is no single cohesive function that ties the majority of proteins together, so the cluster is best labeled Unknown with None confidence.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":7},{"id":"GO:0021707","count":7},{"id":"GO:0016567","count":6},{"id":"GO:0070682","count":6},{"id":"GO:0050960","count":6}]},{"hash":"1911330280612726980","title":"RNA processing and translation regulation","description":"The top GO terms point to RNA metabolism and control of gene expression at the RNA level: cytoplasmic translation, deadenylation-dependent and -independent mRNA decay, spliceosomal complex assembly, and mRNA localization. While there are a few stress- or signaling-related terms (response to UV-C, amino acid starvation), the dominant theme is RNA processing and regulation of translation, suggesting a cluster centered on post-transcriptional gene regulation.","confidence":"Medium","size":21,"edges":17,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0000245","count":1},{"id":"GO:0071494","count":1}]},{"hash":"1576758324087879612","title":"RNA and Protein Methylation","description":"The top GO terms show multiple methylation-related processes across RNA (tRNA, rRNA, mRNA capping, guanine-N7 methylation) and a protein methylation term (peptidyl-arginine methylation), indicating a functional theme centered on methyltransferase activities modifying both nucleic acids and proteins. While there are some biosynthetic terms (biotin, cobalamin) present, the dominant signal is methylation. This makes \"RNA and Protein Methylation\" a concise, representative label for the cluster. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0002098","count":6},{"id":"GO:0006370","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0036265","count":5}]},{"hash":"750042780656587372","title":"Cell Cycle Regulation and Proliferation","description":"The top GO terms center on transcriptional control (DNA-templated transcription) and classic cell-cycle progression events (G1/S and G2/M transitions, mitotic spindle dynamics, chromosome condensation, and general cell division), with additional hints of proliferation in mammary epithelium and growth signaling via insulin receptor pathways. Together they suggest a cluster of proteins that coordinate transcriptional regulation with cell-cycle progression to drive cellular proliferation, especially in epithelial contexts.","confidence":"High","size":21,"edges":159,"triangles":607,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0046626","count":8},{"id":"GO:0045737","count":8},{"id":"GO:0000082","count":8},{"id":"GO:0010696","count":8}]},{"hash":"2283786713460340463","title":"Nervous system development and axonogenesis","description":"The cluster is enriched for GO terms centered on nervous system development and axon formation, including central nervous system projection neuron axonogenesis, positive regulation of axonogenesis, optic nerve morphogenesis, and transmission of nerve impulses, as well as synapse assembly. These terms point to a cohesive group of proteins involved in neural development, axon guidance, and synaptic connectivity, with photoreceptor differentiation aligning to neural specification. Therefore, this label captures the dominant functional theme of the cluster. ","confidence":"High","size":21,"edges":209,"triangles":1311,"max_degree":20,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":15},{"id":"GO:0021952","count":15},{"id":"GO:0050772","count":15},{"id":"GO:0021631","count":15},{"id":"GO:0048692","count":15}]},{"hash":"173764423877951374","title":"Nervous system development and myelination","description":"This cluster is dominated by GO terms related to neural development (CNS development, retina morphogenesis), myelination, and axon-domain organization (juxtaparanode protein localization, Kv channel clustering), as well as signaling events (STAT phosphorylation) in neural contexts. While a neutrophil clearance and TLR9 signaling term appear, the strongest signal centers on neural differentiation, axon organization, and myelin-related processes, suggesting a coherent theme of nervous system maturation.","confidence":"High","size":21,"edges":177,"triangles":821,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0097350","count":7},{"id":"GO:0045663","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0071206","count":7},{"id":"GO:0045163","count":7}]},{"hash":"1795748692479069474","title":"Cytoskeletal remodeling and cell adhesion signaling","description":"The top GO terms mainly point to actin-based structures and cell\u2013matrix interactions (filopodium assembly, integrin activation) and signaling that regulates the cytoskeleton (Rho signaling, lens fiber differentiation). While there are roles in protein turnover and oligomerization, the prevalent theme ties to cytoskeletal dynamics and adhesion processes that control cell shape, movement, and differentiation. The lack of network edges suggests a broad set of proteins converging on this shared functional area rather than a single complex. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0045332","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0035023","count":2}]},{"hash":"2019436295730979612","title":"DNA replication and cell division cluster","description":"Top terms are centered on DNA replication, Okazaki fragment processing in mitotic replication, and kinetochore localization, plus general cell division, which together define a mitotic DNA replication/cell division module. While there are ancillary RNA processing and translation initiation terms, the core signal is chromosomal replication and segregation.","confidence":"High","size":21,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0043547","count":3},{"id":"GO:0034501","count":3},{"id":"GO:1903461","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1648663296043768509","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":197,"triangles":1116,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0048026","count":3}]},{"hash":"1427244702702868461","title":"Neurodevelopment and cell-cycle regulation","description":"The top GO terms show a clear emphasis on nervous system development (forebrain development, nervous system development) and related patterning (bipolar cell polarity, cranial skeleton morphogenesis), complemented by strong signals for cell-cycle and DNA replication processes (DNA replication, centrosome cycle, positive regulation of nuclear DNA replication). This combination suggests proteins involved in embryonic development where neural tissue proliferation and differentiation are coordinated, with additional hints of broader developmental programs such as cardiac muscle differentiation. Overall, the cluster appears to represent neurodevelopmental processes coupled with cell-cycle control.","confidence":"High","size":21,"edges":86,"triangles":121,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":21},{"id":"GO:0007098","count":21},{"id":"GO:0006260","count":21},{"id":"GO:0010571","count":21},{"id":"GO:2000727","count":20}]},{"hash":"637985854541520228","title":"Transmembrane Xenobiotic and Nutrient Transport","description":"This cluster is dominated by GO terms for transmembrane transport of xenobiotics (xenobiotic transmembrane transport, xenobiotic transport, doxorubicin transport) and nutrients (vitamin transmembrane transport, branched-chain amino acid transport), plus ion and lipid-related transport (potassium ion transmembrane transport, ceramide translocation). The common thread is transport across membranes for a variety of substrates, suggesting a coherent function in membrane transport.  ","confidence":"High","size":21,"edges":67,"triangles":39,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":20},{"id":"GO:0006855","count":20},{"id":"GO:0071805","count":12},{"id":"GO:0042908","count":12},{"id":"GO:1900753","count":11}]},{"hash":"1897454565105676166","title":"Nucleotide turnover and lipid biosynthesis","description":"This cluster shows enrichment for nucleotide catabolic processes (dADP, dGDP, diadenosine polyphosphates) and adenosine editing, together with lipid biosynthesis pathways (cholesterol and IPP biosynthesis). The combination suggests a broad metabolic module centered on turnover and biosynthesis of nucleotides and lipid precursors, rather than a single specific pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030097","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0009240","count":1},{"id":"GO:0015938","count":1},{"id":"GO:0046057","count":1}]},{"hash":"1659472934644353524","title":"Mitotic chromosome condensation and sister chromatid cohesion","description":"The cluster is dominated by GO terms tied to chromosome architecture during cell division, especially mitotic chromosome condensation and sister chromatid cohesion, with supporting links to DNA replication and repair processes that sustain proper chromosome segregation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":1},{"id":"GO:0000733","count":1},{"id":"GO:0070550","count":1},{"id":"GO:0071960","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1512489018912531003","title":"Mitotic/Cytoskeletal Dynamics in Eye Development","description":"This cluster shows enrichment for mitosis-related processes (mitotic sister chromatid cohesion; Okazaki fragment processing in mitotic DNA replication) alongside actin cytoskeleton remodeling (actin filament depolymerization; regulation of GTPase activity) and ocular development (lens fiber cell differentiation; retina development). The combination suggests proteins involved in coordinating cell division and cytoskeletal changes during eye tissue development, with some obsolete terms present likely reflecting historical annotations. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007568","count":7},{"id":"GO:0007064","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0070306","count":5}]},{"hash":"32655054809647594","title":"Developmental morphogenesis and ECM remodeling","description":"The cluster is enriched for developmental processes across multiple tissues (heart and kidney development, retinal axon guidance, BMP signaling) and for extracellular matrix remodeling (collagen fibril organization). Additional terms on endothelial proliferation/migration point to vascular development, while apoptotic clearance and complement activation may reflect immune remodeling during development. Taken together, these terms suggest coordinated tissue morphogenesis and ECM/vascular dynamics, supporting this label.","confidence":"High","size":21,"edges":207,"triangles":1274,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":4},{"id":"GO:0043277","count":3},{"id":"GO:0001935","count":3},{"id":"GO:0043542","count":3},{"id":"GO:0042698","count":2}]},{"hash":"1361302937020863110","title":"Developmental Regulation and Calcium Signaling","description":"The terms cluster around broad developmental processes across multiple tissues (hair follicle, limb, adrenal gland, spermatogenesis, hematopoietic differentiation, osteoclast regulation) and include regulators of calcium entry and cell adhesion, suggesting a general theme of signaling that guides differentiation and tissue development rather than a single organ. The involvement of TGF-beta signaling modulation and store-operated calcium entry further supports a developmental signaling focus.","confidence":"Medium","size":21,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051798","count":2},{"id":"GO:0002244","count":2},{"id":"GO:0045671","count":2},{"id":"GO:0043252","count":2},{"id":"GO:0007283","count":2}]},{"hash":"1602162393014359207","title":"Mitotic cell cycle and ER-Golgi trafficking","description":"These proteins cluster around core mitotic processes (mitotic cell cycle, cell division, mitotic spindle assembly) and vesicle trafficking between the ER and Golgi (COPII budding and retrograde Golgi-to-ER transport), with supporting signaling connections (GTPase regulation, tyrosine phosphorylation, calcium release, TGF-beta response). The convergence of cell-cycle machinery with membrane trafficking suggests a coordinated role in mitosis and related growth signaling, justifying a combined label.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0051209","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0050731","count":3}]},{"hash":"874440601853217269","title":"Developmental gene regulation and apoptosis","description":"This cluster combines terms tied to gene expression control (translation; chromatin state regulation via histone methylation and rDNA heterochromatin), protein modification (K63-linked ubiquitination), and cell fate decisions (apoptotic signaling, negative regulation of proliferation), plus development-related processes (placenta morphogenesis and endothelial barrier formation). The convergence on gene expression modulation, chromatin dynamics, and apoptosis during development supports a cohesive thematic label.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0061087","count":4},{"id":"GO:0061188","count":4},{"id":"GO:0060669","count":4},{"id":"GO:1901536","count":4}]},{"hash":"1586406429207409945","title":"Cytoskeletal dynamics and RNA processing","description":"This cluster centers on cytoskeletal organization (spindle assembly, actin filament bundle assembly) and protein localization, with supporting signals from protein ubiquitination and mRNA processing, suggesting proteins involved in cytoskeletal function, trafficking, and post-transcriptional regulation. Some heart-specific SA node terms appear as annotation noise and do not define the overall theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":10},{"id":"GO:0016567","count":9},{"id":"GO:0086070","count":9},{"id":"GO:0090501","count":9},{"id":"GO:0032212","count":9}]},{"hash":"2174642113559151924","title":"NF-kappaB\u2013TNF inflammatory signaling and barrier regulation","description":"The top GO terms point to inflammatory signaling (positive regulation of TNF production and canonical NF-kappaB activation) and endothelial intestinal barrier establishment, indicating a cluster centered on inflammation-driven control of barrier function. Other terms about metabolism and chromatin remodeling appear ancillary and do not define the core theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032760","count":2},{"id":"GO:0090557","count":2},{"id":"GO:0043123","count":2},{"id":"GO:2001295","count":1},{"id":"GO:0044268","count":1}]},{"hash":"2185236339321046680","title":"Neddylation and protein turnover","description":"Rationale: The cluster is dominated by terms on protein neddylation and its regulation, plus ubiquitin-protein transferase activity and protein catabolic processes, indicating a module focused on post-translational modification and protein degradation. Endocytosis and nervous system development appear as peripheral associations, making the core theme centered on neddylation and turnover.","confidence":"Medium","size":21,"edges":44,"triangles":20,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010332","count":2},{"id":"GO:0010225","count":2},{"id":"GO:0045116","count":2},{"id":"GO:0051443","count":2},{"id":"GO:2000436","count":2}]},{"hash":"846579182667390484","title":"Rho-Actin Remodeling and Immune Signaling","description":"The proteins are enriched for Rho GTPase regulation and actin dynamics (positive regulation of GTPase activity, regulation of Rho signaling, barbed-end actin filament capping) and widened to include neural development (radial glia migration) and immune pathways (TGF-beta response, interferon signaling, innate immunity, TLR regulation). This points to a cohesive theme of cytoskeletal remodeling during development that interfaces with immune and growth-factor signaling. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0050731","count":6},{"id":"GO:0051016","count":6},{"id":"GO:0071560","count":6},{"id":"GO:0035023","count":6}]},{"hash":"696254254308059451","title":"Rho GTPase-driven actin remodeling and cell motility","description":"This cluster is characterized by GO terms tied to small GTPase signaling (Rho and general GTPase activity), actin filament dynamics and membrane invagination, and processes related to cell movement and adhesion; the migration-related term for leading process extension supports cytoskeletal remodeling driving motility. Immune signaling terms appear secondary but do not define the core theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0021816","count":8},{"id":"GO:0007264","count":8},{"id":"GO:0035023","count":7},{"id":"GO:0034136","count":7}]},{"hash":"784010509673250118","title":"Actin Dynamics and ER-Golgi Vesicle Transport","description":"The cluster centers on actin filament dynamics (capping, polymerization, nucleation, severing, bundling) and lamellipodium morphogenesis, with supporting vesicle-traffic terms from the ER to Golgi (COPII cargo loading, ER-Golgi transport). This suggests a cohesive theme where actin remodeling drives vesicle trafficking in the early secretory pathway.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051016","count":3},{"id":"GO:0030041","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0090110","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2226483840826676012","title":"SA node and atrial electrophysiology","description":"The top GO terms cluster around SA node cell communication and action potentials, atrial cardiac muscle cell action potential, and responses to mechanical stretch, pointing to cardiac electrical signaling and mechanotransduction in the atria. Some terms are unrelated (immune/hepatocyte processes), but the dominant theme is atrial/SA node electrophysiology.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0002268","count":5},{"id":"GO:0086070","count":5},{"id":"GO:0097284","count":5},{"id":"GO:0072660","count":5},{"id":"GO:0098907","count":5}]},{"hash":"1116798336980702260","title":"Neural Development and Synapse Formation","description":"The top GO terms cluster around brain development and synaptic wiring\u2014corpus callosum development, CNS projection neuron axonogenesis, optic nerve morphogenesis, dendritic spine morphogenesis, trans-synaptic signaling, and positive regulation of synapse assembly\u2014indicating a group of proteins involved in CNS formation and synapse maturation. While a few terms touch on apoptosis or immune signaling, the dominant pattern is neural development and synaptic organization.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022038","count":3},{"id":"GO:0021952","count":3},{"id":"GO:0021631","count":3},{"id":"GO:0071372","count":3},{"id":"GO:0048320","count":3}]},{"hash":"102538634000253085","title":"Innate immune and inflammatory signaling","description":"This cluster is dominated by GO terms related to innate immunity and inflammation\u2014such as inflammatory response, innate immune response, peptidoglycan recognition protein signaling, lipopolysaccharide signaling, TNF production regulation, and antiviral response\u2014indicating a cohesive theme of immune signaling. A few terms like learning/memory or lipid storage are less central to the cluster\u2019s core function but do not override the strong immune/inflammatory signal. Confidence: High","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032760","count":5},{"id":"GO:0061057","count":4},{"id":"GO:0006954","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0007611","count":4}]},{"hash":"412753845965196345","title":"Metabolic signaling with telomere regulation and immune activity","description":"The cluster shows strong signals for metabolic/adipose-related processes (fat cell differentiation, triglyceride catabolism, insulin response) and general intracellular signaling, plus immune-related functions (apoptotic cell clearance, complement activation) and telomere maintenance/capping. This suggests a broad signaling/metabolic-immune profile with an unusual link to telomere regulation, hence the chosen label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035994","count":5},{"id":"GO:0035556","count":4},{"id":"GO:0016477","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0010898","count":4}]},{"hash":"297414082370406120","title":"SA Node signaling and cardiac cell communication","description":"The top GO terms strongly point to regulation of SA node action potential and communication between SA node and atrial cardiac muscle cells, indicating a focus on cardiac pacemaker signaling and intercellular cardiac communication. Additional terms about membrane protein localization and mechano-sensing fit with membrane-associated signaling in cardiac cells, while some unrelated terms may reflect background noise. Overall, the cluster represents cardiac electrical signaling and cell-cell communication.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":11},{"id":"GO:0002268","count":10},{"id":"GO:0086070","count":10},{"id":"GO:0097284","count":10},{"id":"GO:0072660","count":10}]},{"hash":"536215901436589389","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning immune processes (germinal center formation, defense response to bacterium), multiple signaling pathways (smoothened signaling, ERK cascade, NF-kappaB regulation), development (anterior/posterior axon guidance), and catabolic processes for cell walls, with no single unifying function connecting them. With no edges and diverse functions, there isn\u2019t a coherent theme to assign a meaningful label beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":2},{"id":"GO:0007224","count":2},{"id":"GO:0009253","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0016998","count":2}]},{"hash":"2128714386914979216","title":"Intestinal barrier immune signaling","description":"Top GO terms are dominated by processes related to the intestinal endothelial barrier and innate immune signaling (establishment of endothelial intestinal barrier; MyD93-dependent toll-like receptor signaling; lipopolysaccharide-mediated signaling; inflammatory and defense responses), suggesting a cohesive function in gut barrier immunity. A few translation-related terms appear but appear incidental rather than defining the cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090557","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0050830","count":2}]},{"hash":"378290658836136983","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":7,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0000466","count":3}]},{"hash":"1064087308194602185","title":"Chromatin Remodeling and Heterochromatin Formation","description":"The top GO terms cluster around chromatin organization, heterochromatin formation, and transcription-coupled chromatin remodeling, indicating the proteins share a role in chromatin packaging, genome maintenance, and gene regulation.","confidence":"High","size":20,"edges":103,"triangles":287,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":12},{"id":"GO:0045815","count":11},{"id":"GO:0006335","count":11},{"id":"GO:0051290","count":11},{"id":"GO:0000183","count":11}]},{"hash":"352890095592237111","title":"Developmental Differentiation and Neurogenesis","description":"This cluster centers on development and differentiation across lineages, with notable neural development signals such as neuron maturation, neural precursor cell proliferation, and dopamine metabolism, alongside gastrulation and megakaryocyte differentiation. The presence of adhesion (integrin-mediated) and proteolysis terms also supports a broader developmental/ morphological context rather than a single pathway. Overall, the proteins appear to participate in multi-lineage developmental processes, especially neural development.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006508","count":3},{"id":"GO:0033631","count":3},{"id":"GO:1902987","count":3},{"id":"GO:0032496","count":2}]},{"hash":"509971436672148677","title":"Post-transcriptional RNA processing and translation control","description":"The top GO terms point toward mRNA splicing and spliceosome activity, mRNA modification and stability, and regulation of translational initiation, including eIF4F complex assembly and IRES-dependent translation, all of which indicate a cluster of proteins involved in post-transcriptional processing and control of translation, especially under stress.","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":3},{"id":"GO:0097010","count":3},{"id":"GO:0010610","count":3},{"id":"GO:1905663","count":3},{"id":"GO:0048026","count":3}]},{"hash":"1284283659866704510","title":"ERAD-Linked Ubiquitin/SUMO Protein Quality Control","description":"The cluster\u2019s top terms highlight ubiquitin deubiquitination and sumoylation, ER-associated protein handling (including tail-anchored membrane insertion into the ER), ERAD-related quality control, and regulation of proteasomal degradation, all pointing to protein homeostasis pathways that manage folding, modification, and turnover in the ER. A few terms about cell morphogenesis and spindle functions are less central but may reflect shared trafficking or regulatory connections, so the overall theme remains protein quality control in the secretory pathway.","confidence":"Medium","size":20,"edges":188,"triangles":1105,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":18},{"id":"GO:0016925","count":13},{"id":"GO:0071816","count":11},{"id":"GO:0006412","count":11},{"id":"GO:0033132","count":11}]},{"hash":"2305545173752241487","title":"NF-kB\u2013driven immune regulation via ubiquitination","description":"This set centers on immune signaling and ubiquitin-related regulation: it includes terms about NF-kappaB transcription factor activity, B and T cell homeostasis, and regulation of T cell proliferation, pointing to modulation of adaptive immunity. It also highlights ubiquitin pathways (K63-linked ubiquitination, ubiquitin-dependent protein catabolic processes, ERAD), suggesting a coordinated role of ubiquitination in signaling and protein turnover within immune cells. Overall, the cluster appears to represent immune regulation through ubiquitin-mediated signaling, with emphasis on NF-kB pathways.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051092","count":7},{"id":"GO:0001782","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0007568","count":5},{"id":"GO:0008283","count":5}]},{"hash":"1058642767004318659","title":"Cilium-Linked Signaling and Vision","description":"This cluster is dominated by terms related to cilium assembly and visual perception, pointing to ciliary signaling and photoreceptor-related processes. Additional terms like Ran protein signal transduction and GTPase activity suggest broader signaling roles that often accompany ciliary and neuronal functions. While there are other outliers (e.g., mitotic cell cycle, tRNA modification), the clearest cohesive theme is cilium-associated signaling with vision-related activity.","confidence":"Medium","size":20,"edges":126,"triangles":409,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":17},{"id":"GO:0019236","count":16},{"id":"GO:0031291","count":16},{"id":"GO:1905608","count":16},{"id":"GO:0002098","count":16}]},{"hash":"1492767012683019381","title":"Unknown","description":"The top GO terms are highly heterogeneous, including bacterial lipopolysaccharide biosynthesis, amino acid biosynthesis, plant/stilbene metabolism, hormone response, calcium homeostasis, P450 pathways, and metal transport, with several obsolete terms. There\u2019s no cohesive, single function tying these proteins together, so a meaningful label cannot be assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0009103","count":5},{"id":"GO:0006564","count":4},{"id":"GO:0046272","count":3},{"id":"GO:0046839","count":3}]},{"hash":"583644652046446920","title":"Unknown","description":"The terms span DNA replication, multiple ubiquitin/ERAD-related deubiquitination terms, and disparate processes like fear behavior, hearing, LPS response, Wnt signaling, and complement activation. There is no single cohesive function tying all proteins together, so a specific, representative label cannot be determined.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0035523","count":3},{"id":"GO:1904378","count":3},{"id":"GO:1903070","count":3},{"id":"GO:0044313","count":3}]},{"hash":"353601092044205796","title":"Proteostasis and Stress Signaling","description":"The cluster is dominated by ubiquitination and proteasome assembly terms, pointing to protein quality control, i.e., proteostasis. Additional terms touch on stress and signaling (temperature sensing, response to capsazepine, intracellular signaling), suggesting a broader but diffuse stress-response/theme. However, several terms (vitamin D response, telomere maintenance, cell migration) are more peripheral, making a tight cohesive theme unlikely. Overall, the connection exists but is not strong, so confidence is Low.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010745","count":15},{"id":"GO:0016567","count":14},{"id":"GO:0070682","count":14},{"id":"GO:0050960","count":14},{"id":"GO:0035556","count":14}]},{"hash":"1084594438624926821","title":"ECM remodeling, EMT, and innate immunity","description":"Top terms point to extracellular matrix remodeling (collagen fibril organization, integrin signaling) and developmental processes (epithelial-to-mesenchymal transition, somite development, endothelial proliferation) with concurrent innate immune activity (innate immune response, classical complement activation). This suggests a cluster of proteins involved in ECM dynamics during development, with immune modulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001046","count":13},{"id":"GO:0045087","count":12},{"id":"GO:0030199","count":11},{"id":"GO:0001837","count":11},{"id":"GO:0043277","count":10}]},{"hash":"805840942690574176","title":"Ubiquitin-Proteasome\u2013Mediated Proteolysis","description":"The top GO terms cluster around ubiquitin-dependent protein catabolic processes, including SCF- and APC/C-mediated proteolysis, various ubiquitin linkages (K11, K48), autoubiquitination, and ERAD, pointing to a cohesive role in tagging substrates for degradation by the proteasome, with connections to cell division and DNA repair pathways.","confidence":"High","size":20,"edges":119,"triangles":298,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0051865","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0070979","count":8}]},{"hash":"1082895744651300963","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":67,"triangles":89,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0048026","count":8},{"id":"GO:0031047","count":8},{"id":"GO:0000184","count":7},{"id":"GO:0071035","count":7}]},{"hash":"246492796297500340","title":"Spliceosome-driven mRNA splicing and processing","description":"This cluster is dominated by spliceosome-centered RNA processing: mRNA splicing via the spliceosome, cis-splicing, splice site recognition, and regulation of mRNA stability in response to stress. The presence of eIF4F complex assembly and regulatory ncRNA-mediated gene silencing suggests a broader tie between RNA maturation and translation control.","confidence":"High","size":20,"edges":26,"triangles":30,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000398","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0048026","count":4},{"id":"GO:1901407","count":4}]},{"hash":"854017072598963059","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030206","count":5},{"id":"GO:0015012","count":5},{"id":"GO:0050427","count":5},{"id":"GO:0048702","count":5},{"id":"GO:0042403","count":5}]},{"hash":"360527292785302774","title":"Membrane Protein Targeting and ER Stress Response","description":"The cluster is dominated by GO terms for SRP-dependent cotranslational targeting to membranes and related membrane targeting processes, along with terms describing cellular responses to unfolded proteins and ER stress. This points to a common theme of directing nascent proteins to membranes and maintaining ER proteostasis, with additional terms like iron-sulfur cluster assembly and DNA replication appearing as less central or outlier connections. Overall, the proteins seem enriched for membrane targeting and ER quality control functions rather than a single tight pathway.","confidence":"Medium","size":20,"edges":184,"triangles":1042,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0031204","count":8},{"id":"GO:0006880","count":8},{"id":"GO:0000742","count":8},{"id":"GO:0006616","count":8}]},{"hash":"414742686050167900","title":"Cardiovascular signaling and hormonal regulation","description":"These proteins cluster around regulatory signaling processes that control vascular physiology and hormone-related functions. The most represented terms indicate blood pressure regulation and GPCR/Rho-GTPase signaling, together with hormone secretion and platelet activation, central to cardiovascular and endocrine homeostasis. While terms like lipopolysaccharide response and circadian rhythm appear, the dominant theme is signaling networks that modulate vascular tone, coagulation, and hormone release.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045777","count":6},{"id":"GO:0010579","count":6},{"id":"GO:0035025","count":6},{"id":"GO:0022900","count":6},{"id":"GO:0043547","count":5}]},{"hash":"451543601485176140","title":"Broad Signaling in Development and Differentiation","description":"These proteins appear to participate in a variety of signaling pathways (Wnt, Hippo, TCR, Ephrin) and differentiation-related processes (keratinocyte differentiation), along with apoptosis and cytoskeletal dynamics. The Top Terms span multiple, diverse signaling networks rather than a single pathway, indicating a broad role in coordinating signaling across developmental and cellular contexts rather than a specific, unified function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":13},{"id":"GO:0035329","count":12},{"id":"GO:0006915","count":12},{"id":"GO:0030216","count":12},{"id":"GO:0060044","count":12}]},{"hash":"1099586092497785778","title":"Cofactor Biosynthesis and Methylation","description":"The cluster is dominated by GO terms for biosynthesis of cofactors/vitamins (menaquinone, cobalamin, biotin) and RNA/protein methylation (rRNA methylation, peptidyl-glutamine methylation), suggesting a core role in cofactor production and related modifications. There are also xenobiotic and stress-related terms, but the strongest signal centers on vitamin/cofactor biosynthesis and methylation activities. Confidence: Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0009236","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0018364","count":4}]},{"hash":"654761975313176434","title":"Ubiquitin-Proteasome Signaling and Thermoception","description":"The cluster is driven by proteins involved in ubiquitination and proteasome assembly, pointing to protein turnover as a central theme that modulates signaling, including regulation of GTPases and cell migration. The presence of thermoception-related terms (temperature stimulus detection and response to capsazepine) suggests a thermo-sensing signaling dimension that could be shaped by ubiquitin-proteasome\u2013dependent regulation of signaling components. Vitamin D response and telomere maintenance terms appear peripheral but may reflect broader regulatory networks linked to signaling and genome maintenance.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0034260","count":10},{"id":"GO:0016567","count":9},{"id":"GO:0033280","count":9},{"id":"GO:0070682","count":8},{"id":"GO:0050960","count":8}]},{"hash":"1071407167606103944","title":"Ubiquitin-Proteasome-Mediated Protein Turnover","description":"Dominant terms center on protein ubiquitination and proteasome-related processes (ubiquitin-dependent catabolic process and proteasome regulatory particle assembly), indicating the cluster largely reflects protein tagging and degradation. The remaining terms (thermoception, vitamin D response, and signal transduction) appear peripheral and do not overturn the main theme of ubiquitin-proteasome\u2013driven turnover.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":7},{"id":"GO:0016567","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0070682","count":4},{"id":"GO:0050960","count":4}]},{"hash":"1149455560054215182","title":"Protein folding and cell division control","description":"The cluster includes chaperone-assisted protein refolding, ER-stress\u2013related translation initiation, ubiquitin-mediated regulation, and mitotic progression terms, suggesting a cohesive theme of proteostasis coupled to cell cycle control. Some terms appear peripheral (e.g., cilium assembly, histone modifications), but the dominant signal centers on folding/quality control and mitosis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070389","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0051291","count":5},{"id":"GO:0036494","count":4},{"id":"GO:1905515","count":4}]},{"hash":"1508423706466839689","title":"Lipid and steroid biosynthesis cluster","description":"The top GO terms point to biosynthesis of lipids and lipid-derived metabolites (sphingolipids, mycolic acids, 3-keto-sphinganine) and steroid-related compounds (estrogen biosynthesis, androgen catabolic), with additional signals for retinoic acid biosynthesis. This suggests a cohesive theme around lipid- and steroid-metabolite production, despite a few peripheral terms being more general metabolite biosynthesis.","confidence":"Medium","size":20,"edges":78,"triangles":114,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030148","count":19},{"id":"GO:0055114","count":19},{"id":"GO:0006703","count":19},{"id":"GO:0031427","count":19},{"id":"GO:0017000","count":19}]},{"hash":"675898204255484658","title":"Platelet activation and coagulation signaling in vasculature","description":"These proteins cluster around platelet activation, coagulation pathways, and vascular signaling (including angiogenesis regulation and Tie signaling). The top GO terms suggest roles in hemostasis, vascular permeability control, and cell\u2013matrix interactions, with supporting signals from complement/immune interfaces and related immune modulation. The combination points to a coordinated program governing blood clotting, vessel stability, and immune-vascular cross-talk, rather than a single isolated function. ","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002740","count":7},{"id":"GO:0030168","count":7},{"id":"GO:0001867","count":7},{"id":"GO:0043116","count":7},{"id":"GO:0007160","count":7}]},{"hash":"279161227346900249","title":"Musculoskeletal and cardiac development and adhesion","description":"The cluster shows strong representation of terms related to development of musculoskeletal and cardiac tissues (skeletal system development, heart development, sarcomere organization) and general cell adhesion (cell adhesion, homophilic cell-cell adhesion), with additional signals for multicellular development and some neural-related processes. This suggests a cohesive theme around tissue formation and structural organization, hence the chosen name.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2000391","count":6},{"id":"GO:0007155","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0051965","count":5},{"id":"GO:0001501","count":5}]},{"hash":"1881256713679314050","title":"DNA replication and chromosome maintenance","description":"The cluster is dominated by core genome maintenance and cell cycle processes (DNA replication, cell division, CENP-A chromatin assembly, microtubule severing, translesion synthesis), suggesting a cohesive function in genome replication and chromosome segregation. A few terms related to protein trafficking and host interactions appear as potential ancillary roles or multifunctional proteins.","confidence":"High","size":20,"edges":44,"triangles":43,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0070987","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051013","count":3}]},{"hash":"1964146145089622939","title":"Mitotic Division and Secretory Trafficking","description":"This cluster is enriched for GO terms tied to the cell cycle (mitotic cell cycle, cell division, mitotic spindle assembly) and components of the secretory pathway (COPII-coated vesicle budding, retrograde Golgi-to-ER transport), suggesting a theme around coordinating cell division with vesicle trafficking. Additional terms like growth, signaling, NMDA receptor regulation, and apoptosis reflect broader cellular processes but do not override the core mitotic/secretory pattern.","confidence":"Medium","size":20,"edges":18,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046330","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0035264","count":4},{"id":"GO:2000310","count":3},{"id":"GO:0097284","count":3}]},{"hash":"865894688683030087","title":"Innate antiviral and inflammatory signaling","description":"The top GO terms cluster around host defense: suppression of viral release, viral mRNA export, TNF production, NF-kappaB signaling, and inflammatory response, pointing to innate immune and antiviral responses. A few terms about cardiac electrophysiology appear tangential, likely representing pleiotropic genes or annotation noise rather than a core cardiac function of the cluster. Overall, the dominant theme is host antiviral/inflammatory signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":2},{"id":"GO:0032760","count":2},{"id":"GO:0061057","count":2},{"id":"GO:0098910","count":2},{"id":"GO:0010881","count":2}]},{"hash":"1716322413472991440","title":"Cytoskeletal remodeling in muscle and immune signaling","description":"This cluster is driven by enrichment in Rho-regulated actin cytoskeleton dynamics and sarcomere organization, pointing to cytoskeletal remodeling in muscle contexts (heart development, sarcomere-related terms). The concurrent presence of innate immune response, B cell receptor signaling, IL-2 production, and dendritic spine regulation suggests immune signaling pathways that also involve cytoskeletal organization. Together, these terms indicate a shared theme of cytoskeletal dynamics coordinating muscle/heart function with immune signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0045214","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0007507","count":4},{"id":"GO:1900042","count":4}]},{"hash":"244426760338793474","title":"Ubiquitin-Dependent Innate Immune Signaling","description":"This cluster centers on ubiquitin-dependent proteolysis and innate immune signaling, with multiple terms for ubiquitin-mediated protein catabolism, NF-kappaB activation, innate immunity, defense against viruses, and TNF signaling. While a couple of terms are outliers or obsolete, the dominant pattern ties proteostasis via ubiquitination to innate immune responses, suggesting a coherent functional group.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":12},{"id":"GO:0043547","count":11},{"id":"GO:0007568","count":10},{"id":"GO:0033280","count":9},{"id":"GO:0036205","count":8}]},{"hash":"867092247218726369","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning splicing, chromatin organization, DNA repair, cilium assembly, immune responses, hormone biosynthesis, and development, with no clear single function or pathway tying the 20 proteins together. This makes it inappropriate to assign a specific functional label beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0060271","count":2},{"id":"GO:0051607","count":1},{"id":"GO:0006697","count":1}]},{"hash":"2204487156790502115","title":"Rho-dependent cytoskeleton remodeling during cell migration","description":"The GO terms show a strong emphasis on cell migration and actin dynamics (e.g., cell migration, actin filament bundle assembly), with related signals in Rho pathway regulation, leading process extension in radial glia, ephrin signaling, and epithelial polarity. This points to a cohesive function in cytoskeleton-driven migration, particularly neural/glial migration, with a small, less central contribution from immune signaling terms.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0016477","count":6},{"id":"GO:0051017","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0060670","count":5},{"id":"GO:0048013","count":5}]},{"hash":"539845827371647307","title":"TNF/NF-\u03baB Signaling with K63-Linked Ubiquitination","description":"This cluster is dominated by GO terms for innate immune responses and signaling that converge on NF-kappaB activation, especially via TNF-mediated pathways and K63-linked ubiquitination, including I\u03baB phosphorylation and NIK-related signaling. The strong representation of ubiquitination-related terms and NF-kappaB transcriptional activity indicates a coherent pathway module centered on ubiquitin-dependent TNF/NF-\u03baB signaling in antiviral defense.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045087","count":14},{"id":"GO:0070534","count":13},{"id":"GO:0051865","count":13},{"id":"GO:1903265","count":13},{"id":"GO:0033209","count":12}]},{"hash":"2252964887288638401","title":"Neuronal development and signaling","description":"Based on the top GO terms, the cluster centers on nervous system/brain development and neuronal signaling processes, including regulation of Rho signaling, synaptic vesicle exocytosis, and Hedgehog (Smoothened) pathway activity. Some terms appear non-neural (e.g., mating projection growth, plant ABA signaling), suggesting broad annotations, but the recurrent neural-development and signaling themes dominate the set.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0007399","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0001302","count":3},{"id":"GO:0001501","count":3}]},{"hash":"1300480969301582446","title":"Unknown","description":"The proteins show a mix of neural development terms (axon guidance, neuron differentiation, sympathetic neuron projection) and immune signaling terms (immunoglobulin production, NF-kappaB/STAT signaling, interleukin-3 production, T cell apoptosis) plus a cardiac action potential term. This combination does not point to a single, cohesive function or pathway, making a definite label difficult. Therefore, Unknown with no confidence. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0033564","count":5},{"id":"GO:0021859","count":5},{"id":"GO:0007432","count":5},{"id":"GO:0042511","count":5},{"id":"GO:0002377","count":5}]},{"hash":"2093400710580323121","title":"Cell cycle and Wnt signaling cluster","description":"This cluster is dominated by GO terms for cell cycle and cell division, indicating a proliferative program. The inclusion of the Wnt signaling pathway reinforces a developmental/signaling theme linked to differentiation and polarity, even though other terms (apoptosis, adipogenesis, dendrite and myeloid processes) add diversity. Overall, the core connection appears to be cell-cycle\u2013related signaling with Wnt involvement, rather than a single specialized function. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":7},{"id":"GO:0051301","count":4},{"id":"GO:0035556","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0071260","count":3}]},{"hash":"106101646109929464","title":"Drosophila imaginal disc morphogenesis and behavior","description":"The top GO terms center on imaginal disc development in Drosophila (eye-antennal and leg disc morphogenesis, ventral midline development), suggesting a morphogenesis-focused cluster. There are also neuronal/behavioral terms (larval walking, regulation of postsynaptic potential), indicating broader roles beyond morphogenesis. However, the strongest signal is imaginal disc morphogenesis, with a few outlier terms like ubiquitination and pigmentation, so the overall theme is not exclusively cohesive.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902499","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0090180","count":1},{"id":"GO:0048092","count":1},{"id":"GO:0007478","count":1}]},{"hash":"721565837127427637","title":"Broad Developmental and Innate Immune Functions","description":"The top GO terms point to diverse developmental processes (multicellular organism development, skeletal system development, anterior/posterior axon guidance, pyramidal neuron differentiation, salivary gland boundary specification) as well as components of innate immunity (innate immune response, immunoglobulin production, NF-kappaB signaling, STAT phosphorylation). The lack of edges suggests these proteins act in different contexts or as regulators across tissues rather than a single pathway. Thus, the label reflects a broad theme connecting development with immune-related functions rather than a precise function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0033564","count":3},{"id":"GO:0021859","count":3}]},{"hash":"453757414091359730","title":"B Cell Activation and Germinal Center Formation","description":"Based on the top GO terms, the cluster is enriched for germinal center formation and B cell receptor signaling, pointing to a B-cell\u2013focused activation and germinal center biology theme. While other terms in the list (e.g., ubiquitin-dependent protein catabolic process, cell division, and development terms) are present, they do not define a single cohesive function, so the dominant signal remains immune-related. Overall, the cluster appears centered on B cell processes, with some noise from unrelated pathways.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":7},{"id":"GO:0050853","count":7},{"id":"GO:0051260","count":7},{"id":"GO:0007399","count":6},{"id":"GO:2000312","count":6}]},{"hash":"1160250153419207844","title":"Unknown","description":"The GO terms cover neural development, immune responses, and cardiac-related processes, with no single cohesive function linking them all. This makes it difficult to assign a meaningful, specific label to the cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0033564","count":4},{"id":"GO:0002467","count":4},{"id":"GO:0021859","count":4},{"id":"GO:0007432","count":4},{"id":"GO:0042511","count":4}]},{"hash":"1249425566441424520","title":"Embryonic neural development and differentiation","description":"The cluster\u2019s top GO terms cluster around nervous system development and neuron differentiation (nervous system development, anterior/posterior axon guidance, pyramidal neuron differentiation, dendritic spine regulation/dendritic cell differentiation) with additional embryonic tissue development signals (heart development, salivary gland boundary specification, sarcomere organization). This points to a developmental program with a neural emphasis, rather than a single, narrowly defined function, so the label captures the dominant theme while acknowledging broader tissue differentiation. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0007399","count":2},{"id":"GO:2001200","count":2}]},{"hash":"2167339346086561042","title":"Unknown","description":"The top GO terms cover a broad mix of developmental processes (anterior/posterior axon guidance, pyramidal neuron differentiation, salivary gland boundary specification), signaling pathways (STAT phosphorylation, NF-kappaB regulation), immune-related activities (immunoglobulin production, interleukin-3 production, CD8+ T cell apoptosis), and cardiac function (atrial cardiac muscle cell action potential). There isn't a single cohesive biological theme or pathway linking these terms, so a unified, intuitive label is not reliably assignable.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033564","count":2},{"id":"GO:0021859","count":2},{"id":"GO:0007432","count":2},{"id":"GO:0042511","count":2},{"id":"GO:0002377","count":2}]},{"hash":"219895543742075677","title":"Steroid hormone signaling in development","description":"Reasoning: The top GO terms cluster around steroid hormone receptor complex assembly and developmental processes (male sex differentiation, prostate gland development, striatum development), suggesting a theme of hormone-driven developmental signaling. Other terms like non-motile cilium assembly and cell division can be connected to broader developmental contexts, supporting this theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0046661","count":6},{"id":"GO:0021756","count":6},{"id":"GO:0030850","count":6},{"id":"GO:0006463","count":6}]},{"hash":"1357460723739328542","title":"Neurodevelopment and neuroimmune signaling","description":"This cluster is dominated by nervous system development terms (nervous system development, corpus callosum development, juxtaparanode axon localization, notochord cell development) and tau-related neuronal regulation, suggesting a neural development theme. The presence of immune-related terms (neutrophil clearance, natural killer cell differentiation, negative regulation of T cell cytotoxicity) implies possible pleiotropy or coordinated neuroimmune processes, but the overall signal centers on neural development and axonal organization with a Tau/neuronal signaling context.","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0038161","count":15},{"id":"GO:1902948","count":15},{"id":"GO:0097350","count":15},{"id":"GO:0001915","count":15},{"id":"GO:0045663","count":15}]},{"hash":"1955404145041961263","title":"RNA Splicing and Chromatin Remodeling","description":"This cluster is dominated by RNA-centric processes (mRNA splicing via spliceosome, regulatory ncRNA\u2013mediated gene silencing) and chromatin remodeling, with supporting links to DNA replication context. While a few terms touch on DNA replication and other pathways, the strongest signals are RNA processing and chromatin dynamics, justifying a label centered on those functions.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0006269","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0035640","count":3},{"id":"GO:0006268","count":3}]},{"hash":"2134415795184733728","title":"Bacterial lipid and siderophore biosynthesis","description":"The top GO terms cluster around lipoteichoic acid biosynthesis, fatty acid metabolism, and siderophore biosynthesis, with additional menaquinone and related metabolic processes, suggesting a bacterial program focused on lipid envelope components and iron-chelating metabolite production. A few terms (seed coat development, phenylpropanoid metabolism) are likely annotation noise or cross-species biases.","confidence":"High","size":19,"edges":53,"triangles":37,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0070395","count":7},{"id":"GO:0036112","count":6},{"id":"GO:0001676","count":5},{"id":"GO:0043041","count":5},{"id":"GO:0019290","count":5}]},{"hash":"332160954148835767","title":"Lung morphogenesis and ECM remodeling","description":"This cluster\u2019s strongest signals are lung development-related terms (epithelial tube branching and lung morphogenesis) along with extracellular matrix remodeling processes (collagen catabolic process, basement membrane disassembly, bradykinin catabolic process). These co-occur suggesting a theme of lung branching morphogenesis coupled with ECM turnover. Some other terms (e.g., decidualization, thyroid hormone response) may reflect broader tissue remodeling signals or off-target associations, but the lung morphogenesis/ECM remodeling axis is the most coherent theme.","confidence":"High","size":19,"edges":166,"triangles":887,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":18},{"id":"GO:0050790","count":18},{"id":"GO:0060448","count":18},{"id":"GO:0001913","count":18},{"id":"GO:0010815","count":18}]},{"hash":"1490800432020611085","title":"Immune Signal Transduction and Cytokine Regulation","description":"These terms cluster around immune signaling and cytokine regulation, including LPS response, NK cell cytotoxicity, IL-3 production, JAK/STAT/NFAT and prolactin signaling, collagen receptor signaling, and ubiquitination. Adherens junction organization and LDL particle response reflect associated cell signaling and adhesion roles in inflammatory contexts.","confidence":"Medium","size":19,"edges":28,"triangles":22,"max_degree":8,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0038063","count":11},{"id":"GO:0045401","count":11},{"id":"GO:0032496","count":11},{"id":"GO:0016567","count":11},{"id":"GO:0045954","count":11}]},{"hash":"1405781062978031802","title":"Ribosome biogenesis and translation","description":"This cluster is strongly enriched for translation (GO:0006412) and ribosome biogenesis/assembly terms (GO:0042254, GO:0042273, GO:0042256), with supporting terms on rRNA processing and maturation (GO:0006364, GO:0000463). These indicate a core role in ribosome production and protein synthesis, with some auxiliary terms like translational fidelity and antibiotic response as related contexts. Overall, the main theme is ribosome biogenesis coupled with translation.","confidence":"High","size":19,"edges":147,"triangles":644,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0042254","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0006364","count":2}]},{"hash":"2021841491085962657","title":"Neuronal Spine Morphogenesis and Cytoskeletal Regulation","description":"Top GO terms emphasize brain and hippocampus development, dendritic spine morphogenesis, filopodium assembly, and Rho/Rac signaling, suggesting the proteins function in neuronal development and cytoskeletal remodeling of spines and filopodia.","confidence":"High","size":19,"edges":95,"triangles":181,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":3},{"id":"GO:0051489","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0035023","count":3}]},{"hash":"655244693489652521","title":"Neuronal signaling and synaptic regulation","description":"The cluster centers on neural communication and signaling, with terms for GABAergic synaptic transmission and auditory perception, plus neurotrophic/hormonal responsiveness (BDNF, prolactin). Supporting terms include calcium/magnesium homeostasis, regulation of protein autophosphorylation, and calcium-dependent cell\u2013matrix adhesion, all pointing to modulation of synaptic signaling and neural responsiveness. This suggests a cohesive theme around neuronal signaling and synaptic regulation rather than a broader, non-specific set of functions. ","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046777","count":3},{"id":"GO:0051262","count":3},{"id":"GO:0051932","count":2},{"id":"GO:0007605","count":2},{"id":"GO:1990637","count":2}]},{"hash":"286475752543472854","title":"Developmental signaling and patterning","description":"The top GO terms cluster around broad developmental roles across tissues\u2014nervous system development, kidney development, and multicellular organism development\u2014along with signaling pathways such as Smoothened (Hedgehog) and Roundabout, plus axon guidance and ERK1/2 cascade regulation. This pattern suggests the proteins participate in developmental signaling and tissue patterning rather than a single tissue-specific function.","confidence":"High","size":19,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":3},{"id":"GO:0007399","count":2},{"id":"GO:0007224","count":2},{"id":"GO:0002551","count":2},{"id":"GO:0035385","count":2}]},{"hash":"1501513199284700772","title":"Mitochondrial and peroxisomal quality control","description":"Many top GO terms point to organelle maintenance and protein handling under stress (chaperone-mediated assembly, oxidative stress response, regulation of mitochondrial DNA replication, peroxisomal matrix import) and to turnover via autophagic pathways (late endosomal microautophagy). This combination suggests a cluster focused on quality control of mitochondria and peroxisomes, including their maintenance and degradation, with some broader terms reflecting cellular remodeling contexts. ","confidence":"Medium","size":19,"edges":49,"triangles":43,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051131","count":10},{"id":"GO:0070407","count":10},{"id":"GO:0090296","count":10},{"id":"GO:0034599","count":10},{"id":"GO:0006260","count":10}]},{"hash":"1882406040375599240","title":"B cell activation and actin remodeling","description":"This cluster is enriched for B cell receptor signaling and adaptive immune response, alongside GO terms for actin filament polymerization, Rho GTPase signaling, and ruffle assembly, indicating coordinated B cell activation with cytoskeletal remodeling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0030041","count":3},{"id":"GO:1900029","count":3},{"id":"GO:0030838","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1040420016191668517","title":"Unknown","description":"This cluster shows a broad mix of GO terms (splicing, stress response, synapse assembly, growth hormone secretion, organ development, angiogenesis, cocaine response) with no single unifying function. The lack of a cohesive theme and the presence of outlier terms make a specific label unreliable; thus Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":2},{"id":"GO:0051867","count":1},{"id":"GO:0051965","count":1},{"id":"GO:0060133","count":1},{"id":"GO:0030252","count":1}]},{"hash":"735117362093696595","title":"Metabolic Biosynthesis and Signaling","description":"The cluster centers on several biosynthetic processes (NAD+ biosynthesis, cAMP biosynthesis, oxaloacetate and polyamine biosynthesis, lipoprotein biosynthesis) and on intracellular signal transduction, including receptor signaling pathways, plus ubiquitin-dependent protein catabolic process. This combination suggests proteins involved in general metabolism and coordination of cellular signaling, rather than a single tight complex. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0009435","count":1},{"id":"GO:0006107","count":1},{"id":"GO:0042158","count":1},{"id":"GO:0046686","count":1}]},{"hash":"863401354881440178","title":"T Cell Signaling and Developmental Regulation","description":"This cluster is dominated by the T cell receptor signaling pathway, pointing to immune signaling, with additional terms indicating broader signaling roles in cell proliferation regulation and developmental processes (planar polarity, mesenchymal/lateral mesoderm development, hormone secretion). The overall theme suggests proteins involved in signal transduction that influence immune responses and developmental cell fate, rather than a single narrow function.","confidence":"Medium","size":19,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050852","count":13},{"id":"GO:0008285","count":13},{"id":"GO:0043552","count":13},{"id":"GO:0010863","count":12},{"id":"GO:0060484","count":12}]},{"hash":"1855054611095184966","title":"Unknown","description":"The GO terms span protein ubiquitination and proteasome assembly (proteostasis), intracellular signaling, temperature sensation, responses to chemical stimuli, and immune-related processes (follicular dendritic cell differentiation), with no single dominant function unifying the cluster. This lack of a cohesive theme makes it inappropriate to assign a precise, specific label.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":11},{"id":"GO:0070682","count":11},{"id":"GO:0050960","count":11},{"id":"GO:0035556","count":11},{"id":"GO:1901594","count":11}]},{"hash":"821996291893428064","title":"Adaptive Immune and Angiogenic Signaling","description":"This cluster centers on adaptive immune processes (adaptive immune response, interleukin-4 production, TLR signaling regulation) coupled with vascular remodeling cues (angiogenesis, endothelial cell migration, integrin signaling, adherens junction organization). The repeated involvement of ERK1/2 signaling and protein ubiquitination suggests coordinated signaling regulation that links immune activation with angiogenesis and cell adhesion. Confidence: Medium","confidence":"","size":19,"edges":19,"triangles":14,"max_degree":7,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0002250","count":16},{"id":"GO:0001525","count":16},{"id":"GO:0070374","count":16},{"id":"GO:0043536","count":16},{"id":"GO:0007229","count":14}]},{"hash":"469160562388485995","title":"Protein Ubiquitination and Proteasome Assembly","description":"The cluster shows strong enrichment for ubiquitination and proteasome assembly GO terms, pointing to a core role in protein turnover and proteostasis. Other terms (temperature sensing, signal transduction, and differentiation) appear ancillary, suggesting they may reflect broader cellular contexts rather than defining the cluster\u2019s primary function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":13},{"id":"GO:0070682","count":13},{"id":"GO:0050960","count":13},{"id":"GO:0035556","count":13},{"id":"GO:1901594","count":13}]},{"hash":"1035531156148602403","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0042264","count":1},{"id":"GO:0021678","count":1},{"id":"GO:0034630","count":1}]},{"hash":"858218762619651881","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:1904693","count":2},{"id":"GO:0030033","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0032485","count":2}]},{"hash":"1293628567170305660","title":"DNA replication and cell cycle cluster","description":"This cluster is dominated by GO terms for DNA replication and mitotic cell cycle, with auxiliary themes around telomere maintenance and mRNA processing, suggesting core involvement in nuclear DNA metabolism and cell division. The presence of stress-response terms is secondary to the central cell-cycle/DNA replication signal, supporting the chosen label. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0035994","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0032212","count":3}]},{"hash":"149626396844142848","title":"Unknown","description":"The top terms are highly diverse, spanning somite development, electron transport chain, immune/inflammatory responses (LPS, IL-6, inflammatory regulation), and neural signaling (adrenergic signaling, NMDA receptor activity) along with cocaine-related behavior. With no clear unifying function or interaction pattern (no edges/triangles), there isn\u2019t a coherent theme to label this cluster beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061053","count":2},{"id":"GO:0022900","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0071880","count":2},{"id":"GO:0032675","count":2}]},{"hash":"1416099104517547638","title":"Dendritic spine morphogenesis via Rac signaling","description":"This cluster centers on Rac-mediated signal transduction and neuronal cytoskeletal remodeling, with strong representation of dendritic spine development and morphogenesis, as well as hippocampus development. Actin-structure dynamics like ruffle and lamellipodium assembly further support a theme of Rac-driven spine formation and neuronal maturation, with additional inflammatory signaling and mechanosensory responses providing broader context.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016601","count":3},{"id":"GO:0060999","count":3},{"id":"GO:0061001","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0071356","count":3}]},{"hash":"1598953124770377516","title":"Translation Initiation and Cytoskeletal Signaling","description":"The top GO terms cluster around translation initiation components (formation of translation preinitiation complex, regulation of translational initiation, EIF4F assembly, mRNA export and splicing) and also include regulators of the actin cytoskeleton, Rho signaling, endocytosis, and JNK signaling, suggesting a link between translation machinery and cytoskeletal/trafficking pathways.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0043547","count":2}]},{"hash":"106898715052305350","title":"Chloroplast Translation and Biogenesis","description":"The top GO terms cluster around ribosome biogenesis, translation (cytoplasmic translation and tRNA modification), and protein targeting to chloroplast, which together point to chloroplast-associated protein synthesis and organelle biogenesis. Additional terms related to plastid division (cell septum assembly) support a plastid-centric theme, making this a concise, representative label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0006007","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0045036","count":2}]},{"hash":"484481674677825000","title":"LPS-TLR Innate Immune Signaling","description":"This cluster is driven by GO terms related to lipopolysaccharide response, MyD88-dependent TLR signaling, NF-\u03baB activity, inflammatory response, and TNF production, pointing to a cohesive innate immune signaling module activated by LPS. Some apoptosis-related terms appear, but the dominant theme is TLR/LPS-triggered inflammatory signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0071550","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0006954","count":3}]},{"hash":"1886241078691726286","title":"Embryonic Development and Organogenesis","description":"Top terms span left/right pattern formation, placenta/endocrine development, EMT in heart cushion formation, trophoblast and pancreatic cell development, cartilage morphogenesis, chondrocyte proliferation, and calcineurin-NFAT signaling\u2014collectively pointing to embryonic development and organogenesis across tissues. The common thread is differentiation and patterning during development rather than a single tissue-specific function; the lack of edges indicates these proteins are not tightly connected in this network snapshot but still reflect developmental roles.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060972","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0060806","count":1},{"id":"GO:0003198","count":1},{"id":"GO:0060707","count":1}]},{"hash":"1287599300777919424","title":"Cell Cycle and Growth Machinery","description":"Most terms cluster around fundamental proliferation-related processes: cell division, cell cycle, ribosome biogenesis, and protein homooligomerization, which together point to core growth and division machinery. A few terms (development in animals/plant patterning and inflammatory cytokine production) appear less connected or species-specific, suggesting annotation breadth rather than a single cohesive pathway. Overall, the dominant signal supports a label focused on cell growth and division.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0008584","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0042254","count":3}]},{"hash":"2208307157094483085","title":"Actin Filament Assembly and Remodeling","description":"The top GO terms cluster around actin dynamics\u2014barbed-end capping, polymerization, bundling, and positive regulation of nucleation\u2014along with regulation of Rho signaling, indicating a cohesive theme of actin cytoskeleton organization and remodeling. The mention of megakaryocyte and heart development likely reflects broader developmental roles of actin processes; despite no network edges, the functional signature centers on actin filament assembly and remodeling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051016","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0051127","count":2},{"id":"GO:0035023","count":2}]},{"hash":"2072588833145617092","title":"Retina development and innate immune signaling","description":"The top terms include visual perception (GO:0007601) and retina vasculature development in camera-type eye (GO:0061298), both pointing to retina-related functions. Additionally, innate immune processes (GO:0045087, GO:0043277) and complement activation (GO:0006958) appear alongside cell\u2013matrix adhesion and junction assembly terms (GO:0007160, GO:0030913), suggesting a theme of retina structure maintenance linked with local immune surveillance and tissue remodeling rather than a single narrow function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":4},{"id":"GO:2001046","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0061298","count":4}]},{"hash":"1211606551728423468","title":"Inflammatory signaling and immune regulation","description":"The top GO terms cluster around immune and inflammatory processes (response to lipopolysaccharide, TNF production, IL-13/IL-5 regulation) and cell death pathways (necroptotic signaling, T cell apoptosis, motor neuron apoptosis), with additional signals related to tissue remodeling (hyaluronan biosynthesis, hair follicle development). This suggests a cohesive theme of inflammatory signaling intertwined with immune regulation and associated tissue remodeling, hence the label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900127","count":3},{"id":"GO:0032496","count":2},{"id":"GO:2000666","count":2},{"id":"GO:0051798","count":2},{"id":"GO:0097527","count":2}]},{"hash":"1673440252954870728","title":"Adaptive immune activation and leukocyte migration","description":"This cluster is enriched for GO terms tied to adaptive immunity, including positive regulation of T cell differentiation and positive regulation of B cell proliferation, along with negative regulation of leukocyte migration and integrin-mediated cell adhesion. Together these suggest a set of proteins involved in immune cell activation, trafficking, and adhesion, with some peripheral terms that are less central to this theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046638","count":2},{"id":"GO:0006157","count":1},{"id":"GO:0060407","count":1},{"id":"GO:0097009","count":1},{"id":"GO:0002686","count":1}]},{"hash":"2275755478932872847","title":"Neural development and axon guidance","description":"The cluster is enriched for GO terms related to neuronal differentiation and axon guidance (anterior/posterior axon guidance, pyramidal neuron differentiation, neuron projection development, multicellular organism development). While there are also terms tied to other tissues, the strongest and most frequent signals center on neural development and axon pathfinding, justifying this label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033564","count":4},{"id":"GO:0021859","count":4},{"id":"GO:0007432","count":4},{"id":"GO:0042511","count":4},{"id":"GO:0002377","count":4}]},{"hash":"135757068106078114","title":"Spliceosome Assembly and mRNA Splicing Regulation","description":"The top GO terms center on mRNA splicing via the spliceosome, including spliceosomal snRNP assembly and regulation of splicing, indicating a core group of splicing regulators and spliceosome components. Secondary terms like translation initiation and nuclear import align with broader nuclear gene-expression processes but do not outweigh the spliceosome focus.","confidence":"High","size":18,"edges":91,"triangles":297,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:1901407","count":5},{"id":"GO:0070317","count":4},{"id":"GO:0048025","count":4},{"id":"GO:0001731","count":4}]},{"hash":"1957517309809847267","title":"Pregnancy-associated lipid and steroid metabolism","description":"This cluster centers on lipid and steroid hormone processing, with terms such as prostaglandin biosynthesis, triglyceride and progesterone metabolism, retinoic acid catabolism, and lipid hydroxylation, all of which are relevant to pregnancy and parturition. The presence of redox homeostasis and detoxification terms (oxidant detoxification, response to ozone) suggests concurrent oxidative stress management typical in reproductive tissues, supporting a cohesive pregnancy-related metabolic theme.","confidence":"Medium","size":18,"edges":128,"triangles":572,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":8},{"id":"GO:0098869","count":7},{"id":"GO:0006641","count":5},{"id":"GO:0046232","count":5},{"id":"GO:0045454","count":5}]},{"hash":"1719921274057464981","title":"Immune clearance and vascular remodeling","description":"The dominant GO terms point to immune clearance and inflammatory response (apoptotic cell clearance, complement activation, acute inflammatory response) alongside endothelial processes (proliferation, migration) and extracellular matrix organization (collagen fibril organization), suggesting a nexus of immune activity and vascular remodeling. Lipoprotein transport/clearance adds a metabolic/web link to this vascular-immune context, while somite development and protein homotrimerization appear more peripheral. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":17},{"id":"GO:0006958","count":17},{"id":"GO:0070207","count":17},{"id":"GO:0061053","count":17},{"id":"GO:0042953","count":17}]},{"hash":"599118314404222367","title":"Cytoskeleton remodeling and ubiquitin-proteasome signaling","description":"This cluster is dominated by GO terms for actin filament bundle assembly and cell migration, together with ubiquitination and proteasome regulatory particle assembly, plus intracellular signaling and stress-related responses. The co-occurrence of cytoskeletal dynamics with protein turnover and signaling under environmental cues suggests a module in coordinating movement, signaling, and proteostasis.","confidence":"Medium","size":18,"edges":38,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":10},{"id":"GO:0070682","count":10},{"id":"GO:0016567","count":9},{"id":"GO:0050960","count":9},{"id":"GO:0035556","count":9}]},{"hash":"1515232682240355168","title":"RNA processing and ribosome biogenesis","description":"The top GO terms point to RNA maturation and processing (rRNA maturation for SSU/LSU, spliceosome-mediated splicing, regulatory ncRNA-mediated gene silencing) and structural assembly of the ribosome (ribosomal subunit biogenesis). Those jointly define RNA metabolism and ribosome biogenesis as the cluster\u2019s core function; a few terms (DNA replication, embryonic development, viral genome replication) are peripheral annotations and less central to the dominant theme.","confidence":"High","size":18,"edges":142,"triangles":660,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0048568","count":4}]},{"hash":"250060259862006195","title":"Neurodevelopment and Axon Targeting","description":"The top GO terms cluster around nervous system development (nervous system development, corpus callosum development, notochord development) and axonal localization (establishment of protein localization to juxtaparanode region of axon), indicating a neural development and axon-targeting function for this protein group. A few immune-related terms are present, but they do not dominate the signature, so the central theme appears to be neural development with axon-associated processes.","confidence":"Medium","size":18,"edges":150,"triangles":771,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0038161","count":7},{"id":"GO:1902948","count":7},{"id":"GO:0097350","count":7},{"id":"GO:0001915","count":7},{"id":"GO:0045663","count":7}]},{"hash":"2083845776040395784","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":3},{"id":"GO:0034349","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0051402","count":3},{"id":"GO:0000480","count":3}]},{"hash":"1213722510356400104","title":"RNA Splicing and Translation Initiation Regulation","description":"The GO terms cluster around RNA processing and regulation of gene expression at the post-transcriptional level, including spliceosome-mediated splicing (alternative splicing, splice site recognition, preinitiation complex formation), mRNA export, translation initiation (eIF4F complex assembly, translation reinitiation), and mRNA stability under stress, plus regulatory ncRNA-mediated gene silencing. This suggests the proteins collectively participate in coordinating RNA processing with the initiation of translation, rather than transcriptional control alone.","confidence":"High","size":18,"edges":13,"triangles":1,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:1901407","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0006406","count":6}]},{"hash":"328513654455946013","title":"Neuronal tight junctions and vesicle trafficking","description":"This cluster centers on endothelial barrier and cell junction components (tight and adherens junctions) and on vesicle trafficking between the ER and Golgi, with neural-development terms (substantia nigra) suggesting a neural-endothelial junction theme. The combination of junctional organization/establishment with vesicle transport and ubiquitination supports a cohesive role in neural-endothelial barrier integrity and protein trafficking.","confidence":"High","size":18,"edges":55,"triangles":68,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061028","count":15},{"id":"GO:0048169","count":15},{"id":"GO:0021762","count":15},{"id":"GO:0070830","count":15},{"id":"GO:0055108","count":14}]},{"hash":"825472736086512772","title":"Complement-Driven Immune Activation and Developmental Adhesion","description":"This cluster centers on complement system activation (classical, alternative, lectin) with associated cell adhesion and developmental processes (embryonic and neural development, angiogenesis). While many terms point to immune function, several reflect developmental and adhesion roles, so the label captures both themes without overstating a single function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006958","count":4},{"id":"GO:0090050","count":4},{"id":"GO:0007157","count":4},{"id":"GO:0021680","count":4},{"id":"GO:0044332","count":3}]},{"hash":"1052193985297553480","title":"Adaptive immune response and neutrophil function","description":"The cluster shows GO terms dominated by adaptive immunity (B cell affinity maturation, adaptive immune response, T cell proliferation) and neutrophil activity (neutrophil degranulation, neutrophil clearance), indicating a module of immune activation and effector functions. A few terms like heart development and sodium ion transport appear peripheral, so the core theme remains immune-related. ","confidence":"Medium","size":18,"edges":62,"triangles":20,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0032012","count":3},{"id":"GO:0002344","count":3},{"id":"GO:0010765","count":3},{"id":"GO:0007507","count":3}]},{"hash":"771390110496707570","title":"Ribosome Biogenesis and Cell Cycle","description":"The cluster is dominated by GO terms for ribosome biogenesis, including ribosomal small subunit biogenesis, ribosome biogenesis, and the cell cycle, indicating a core function in ribosome assembly and proliferation. Angiogenesis-related terms appear but are less frequent, suggesting incidental association rather than a primary function of the cluster.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042274","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001569","count":2},{"id":"GO:0048010","count":2}]},{"hash":"855143197362995056","title":"Immune Regulation and Development","description":"The cluster shows terms related to immune signaling (positive regulation of IL-3 production, neutrophil clearance, negative regulation of TLR9 signaling) alongside broad developmental processes (nervous system development, multicellular organism development, lung-associated mesenchyme development, parathyroid hormone secretion) and vitamin D3 metabolism, suggesting proteins involved in coordinating immune responses with developmental and endocrine pathways.","confidence":"Medium","size":18,"edges":20,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045401","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0070640","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0010863","count":2}]},{"hash":"632163309695355832","title":"Complement-mediated inflammation and endothelial remodeling","description":"The proteins in this cluster are dominated by GO terms for immune clearance and inflammatory responses (apoptotic cell clearance, classical complement activation, acute inflammatory response). Several terms also indicate vascular biology (endothelial cell proliferation/migration, collagen fibril organization, lipoprotein particle/clearance), suggesting a theme of immune activity intertwined with endothelial dynamics and lipid transport. Some terms (somite development, protein homotrimerization) are less clearly connected, but the strongest signal points to immune clearance linked to vascular remodeling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":18},{"id":"GO:0006958","count":18},{"id":"GO:0070207","count":18},{"id":"GO:0061053","count":18},{"id":"GO:0042953","count":18}]},{"hash":"157661560861777010","title":"Iron-Sulfur Cluster Biogenesis","description":"The top GO terms cluster around [2Fe-2S] cluster assembly and maturation by iron-sulfur clusters, indicating a shared role in Fe-S cluster biogenesis. A translation term appears, which often accompanies general protein synthesis and biogenesis, but the dominant signal is Fe-S cluster assembly/maturation. Other terms (xenobiotic response, vitamin A, liver development) seem ancillary or noisy relative to the core Fe-S biology. Overall, the cluster most plausibly represents iron-sulfur cluster biogenesis and transfer for protein maturation.","confidence":"High","size":18,"edges":16,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0044571","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0051384","count":2}]},{"hash":"1591170310745163751","title":"Developmental transcriptional regulators","description":"This cluster shows GO terms tied to broad developmental processes across multiple tissues (skeletal, forebrain, heart, immune), plus DNA-templated transcription, implying proteins that regulate gene expression during development rather than a single pathway. The mix suggests regulators that coordinate organogenesis and differentiation across systems.","confidence":"Medium","size":18,"edges":22,"triangles":3,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":16},{"id":"GO:0032633","count":14},{"id":"GO:0030900","count":14},{"id":"GO:0006351","count":14},{"id":"GO:0030500","count":14}]},{"hash":"608568838919698316","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":103,"triangles":307,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0030206","count":9},{"id":"GO:0015012","count":9},{"id":"GO:0050427","count":9},{"id":"GO:0048702","count":9},{"id":"GO:0042403","count":9}]},{"hash":"702934844924941397","title":"Lipid Metabolism and Xenobiotic Detox","description":"The cluster\u2019s top GO terms center on lipid metabolism (triglyceride metabolism, lipid hydroxylation, prostaglandin biosynthesis) and xenobiotic processing (carbazole catabolic process), with additional signals related to retinoic acid and vitamin D responses, ozone/oxidative stress, and apoptosis regulation. This suggests a shared theme around lipid-centric metabolism and detoxification/response to environmental signals, rather than a single narrow function, hence a broad label capturing lipid metabolism plus detox pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":5},{"id":"GO:0006641","count":4},{"id":"GO:0010193","count":4},{"id":"GO:0033280","count":4},{"id":"GO:0043065","count":3}]},{"hash":"1998023426184327329","title":"Neuronal development and synaptic signaling","description":"The top terms cluster around neural processes: glutamatergic and GABAergic synaptic transmission, cellular response to dopamine, and tangential migration to the olfactory bulb, indicating neuronal development and neural connectivity. While a few terms are more general, the dominant theme is neural differentiation and synaptic communication.","confidence":"Medium","size":18,"edges":44,"triangles":6,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0000055","count":8},{"id":"GO:0048312","count":7},{"id":"GO:0051966","count":6},{"id":"GO:1902902","count":6}]},{"hash":"475999977495946799","title":"Complement Activation and Leukocyte Adhesion","description":"This cluster is strongly enriched for terms related to the complement system (classical, lectin, and alternative pathway activation) and complement receptor signaling, as well as leukocyte tethering/rolling and heterophilic cell-cell adhesion. Together these suggest a cohesive theme of complement-mediated immune activation and leukocyte recruitment, with secondary mentions of developmental processes that are less central to the observed cluster signature.","confidence":"High","size":18,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002430","count":2},{"id":"GO:0007157","count":2},{"id":"GO:0050901","count":2},{"id":"GO:0006957","count":1},{"id":"GO:0001701","count":1}]},{"hash":"91512557721982656","title":"Actin-based cell protrusion assembly","description":"The cluster is dominated by GO terms for actin cytoskeleton remodeling, including filopodium assembly, lamellipodium assembly, and actin filament bundle assembly, which together point to actin-driven formation of cellular protrusions and motility. While there are additional terms related to neural processes and other functions, the strongest and most representative signal is actin-based cytoskeleton remodeling. Confidence: High","confidence":"","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050885","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0030032","count":2},{"id":"GO:0090334","count":2},{"id":"GO:0051017","count":2}]},{"hash":"1829870310122379909","title":"TNF-mediated necroptosis signaling","description":"The GO terms are dominated by necroptosis-related processes (ripoptosome assembly, necroptotic signaling) and inflammatory signaling (TNF production, LPS response, T cell death, systemic resistance), indicating a functional module centered on inflammatory cell death pathways triggered by TNF/LPS. A few terms like hair follicle development appear ancillary rather than defining the main function.","confidence":"High","size":18,"edges":17,"triangles":0,"max_degree":16,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:1901026","count":6},{"id":"GO:0032496","count":4},{"id":"GO:2000666","count":4},{"id":"GO:0051798","count":4},{"id":"GO:0097527","count":4}]},{"hash":"707901072882625028","title":"Unknown","description":"The listed GO terms are highly diverse (bradykinin catabolic, stilbene catabolic, strigolactone response, menaquinone and antibiotic biosynthesis, phospholipid dephosphorylation, plant shoot formation) and include obsolete terms; with no edges or cohesive functional signal, there is no clear common function tying these proteins together. Therefore the cluster is best labelled Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":2},{"id":"GO:0071432","count":2},{"id":"GO:0046272","count":1},{"id":"GO:1902348","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1929376829178341967","title":"Cerebral cortex development and neuroendocrine signaling","description":"The top GO terms point to neural development (layer formation in the cerebral cortex, synapse assembly) and endocrine functions (growth hormone secretion, somatotropin cell development), suggesting a neuroendocrine program in cortical/prodromal tissue. Additional terms on angiogenesis and blood pressure regulation imply vascular and systemic context, with electron transport chain terms reflecting general cellular metabolism. Overall, the cluster seems centered on brain development intertwined with endocrine signaling and vascular regulation. ","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0051965","count":12},{"id":"GO:0001525","count":12},{"id":"GO:0021819","count":12},{"id":"GO:0045777","count":12},{"id":"GO:0010579","count":12}]},{"hash":"1330694882408608864","title":"Unknown","description":"Top terms cover transcriptional regulation, signaling pathways, and diverse developmental processes across organisms, with no single cohesive function linking the proteins (edges 0, triangles 0). The mixed GO terms (DNA-templated transcription, GTPase regulation, various developmental processes, signaling pathways) suggest no clear common theme, so a specific label cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043087","count":2},{"id":"GO:0034244","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0010449","count":1}]},{"hash":"660075403827779165","title":"TLR-Mediated Innate Immune Signaling","description":"The top GO terms are dominated by innate immunity and Toll-like receptor signaling (TLR3/4/10 and MyD88-dependent pathways) with related regulation of dendritic cell cytokine production, indicating a coherent theme around innate immune activation via TLRs. Some terms (bone development, floral organ specification, brassinosteroid stimulus) appear as outliers, but the strongest signal centers on TLR-driven immune signaling. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0060348","count":4},{"id":"GO:0008286","count":4},{"id":"GO:0002730","count":3},{"id":"GO:0002755","count":3}]},{"hash":"960542419331314003","title":"TLR4-driven Innate Immune Activation and Inflammation","description":"GO terms point to innate immune sensing and inflammatory signaling: response to virus; TLR4 signaling; LPS-mediated signaling; TNF production; and necroptosis. This pattern suggests a cluster of proteins involved in detecting pathogens and triggering inflammation and programmed cell death. Lipid metabolism terms may relate to membrane biology and energy needs of immune signaling. A neuromuscular balance term appears less central but does not negate the dominant immune theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009615","count":2},{"id":"GO:0019915","count":2},{"id":"GO:0050885","count":2},{"id":"GO:0051345","count":2},{"id":"GO:0032760","count":2}]},{"hash":"699682725024196726","title":"Translation Initiation and Ribosome Biogenesis","description":"The dominant GO terms point to the protein synthesis machinery\u2014formation of translation preinitiation complex, translation reinitiation, and ribosome biogenesis\u2014defining a translation-focused cluster. A subset of terms references ubiquitination and innate immune signaling, suggesting regulatory cross-talk, while a couple relate to development and DNA repair, which may reflect multifunctional proteins or annotation noise. Overall, the cluster seems anchored in translation-related processes with some diverse associations.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1595735367768479210","title":"Organogenesis and tissue development","description":"This cluster\u2019s top GO terms center on developmental and differentiation processes across various tissues (forebrain, skeletal system, glomerular basement membrane, prostate glandular epithelium), suggesting a broad organogenesis/differentiation theme. Some terms also touch on vascular-related processes (coagulation) and hypoxia response, which can be involved in developing tissues. The set is diverse but collectively points to development across organs, so \u201cOrganogenesis and tissue development\u201d is a fitting, moderately confident label.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030194","count":3},{"id":"GO:0032836","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1516159235553003561","title":"Inflammation Regulation and Mechanotransduction","description":"The cluster is enriched for immune signaling terms (negative regulation of NF-kappaB, NOD2 signaling, negative regulation of IL-12 production, immune differentiation) together with terms tied to mechanical stimulus responses and muscle stretch, and some cardiac conduction-related terms. This pattern suggests a theme around how inflammatory signaling is modulated in response to mechanical cues, potentially in muscle/heart contexts, with membrane localization involved in signaling. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0032088","count":10},{"id":"GO:0002268","count":9},{"id":"GO:0086070","count":9},{"id":"GO:0097284","count":9},{"id":"GO:0070431","count":9}]},{"hash":"614627257715071851","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071051","count":2},{"id":"GO:0071038","count":2},{"id":"GO:0071035","count":2},{"id":"GO:0043630","count":2},{"id":"GO:0034475","count":2}]},{"hash":"239299176629667607","title":"NF-kB signaling and proteostasis","description":"The GO terms center on regulation of NF-kappaB activity, ubiquitination, and proteasome assembly, tying together signal transduction with protein turnover. Additional terms like NOD2 signaling and intracellular signaling support a immune/signaling theme, while actin dynamics and pinocytosis suggest cytoskeletal involvement in signaling and endocytosis. Temperature-related terms indicate broader stress responses that coexist with these signaling processes. Overall, these terms point to a cluster focused on signaling regulation and protein homeostasis.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":6},{"id":"GO:0051017","count":5},{"id":"GO:0097284","count":5},{"id":"GO:0048549","count":5},{"id":"GO:0070431","count":5}]},{"hash":"1719954937686059105","title":"Membrane Trafficking and Notch Signaling in Development","description":"These proteins cluster around endosomal transport to melanosomes and phospholipid homeostasis, plus regulation of the Notch signaling pathway, pointing to roles in membrane trafficking and signaling. The presence of terms related to macrophage differentiation and defense responses, along with developmental processes like outflow tract morphogenesis and placenta development, suggests both immune and developmental contexts where trafficking and signaling intersect. Since no single function dominates, the label focuses on the shared themes of vesicle trafficking and signaling in development/immune contexts.","confidence":"Medium","size":17,"edges":13,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030225","count":2},{"id":"GO:0042832","count":2},{"id":"GO:0003151","count":2},{"id":"GO:0001892","count":2},{"id":"GO:1903206","count":2}]},{"hash":"2018788206495482838","title":"Pregnancy-Associated Vascular and ECM Remodeling","description":"The top GO terms point to female pregnancy, immune clearance (apoptotic cell clearance and complement activation), vascular processes (endothelial proliferation and migration), and extracellular matrix organization (collagen fibril), all suggesting remodeling of the maternal\u2013fetal interface with changes to blood vessels and the ECM. Additional terms for lipoprotein transport/clearance and somite development add some breadth but the prominent theme is pregnancy-associated vascular and ECM remodeling with immune involvement.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":17},{"id":"GO:0043277","count":17},{"id":"GO:0006958","count":17},{"id":"GO:0070207","count":17},{"id":"GO:0061053","count":17}]},{"hash":"1275812137059378350","title":"Neural Development with Immune Regulation","description":"This cluster shows a mixture of neural development terms (nervous system development, corpus callosum development, notochord development, juxtaparanode axon protein localization) and immune-related processes (neutrophil clearance, NK cell differentiation, negative regulation of T cell cytotoxicity) along with prolactin signaling. The overlap suggests a theme of neural development with accompanying immune signaling/regulation, rather than a single unified pathway.","confidence":"Medium","size":17,"edges":133,"triangles":636,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0038161","count":12},{"id":"GO:1902948","count":12},{"id":"GO:0097350","count":12},{"id":"GO:0001915","count":12},{"id":"GO:0045663","count":12}]},{"hash":"661164943230823508","title":"Amino acid catabolism and central carbon metabolism","description":"The top GO terms cluster around amino acid catabolic processes (alanine, kynurenine, lysine) and core energy metabolism (TCA cycle, glycolysis, 2-oxoglutarate), with additional lipid biosynthesis (malonyl-CoA, long-chain fatty acids). This suggests a metabolic module rather than a single signaling pathway, though Notch signaling is present among the terms but less central.","confidence":"Medium","size":17,"edges":120,"triangles":560,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006099","count":7},{"id":"GO:0042853","count":6},{"id":"GO:0007219","count":5},{"id":"GO:0097053","count":5},{"id":"GO:0033512","count":5}]},{"hash":"1578344304854993339","title":"Embryogenesis and apoptotic signaling","description":"These proteins show strong representation of developmental processes (multicellular organism development; in utero embryonic development) alongside multiple apoptotic pathways (intrinsic and extrinsic signaling; neuron and B cell apoptotic processes). The inclusion of microtubule-based movement and cellular response to mechanical stimulus suggests cytoskeletal dynamics and mechanotransduction linked to morphogenesis. Together, the cluster appears to group proteins involved in embryonic development that also engage in stress- or signal-induced apoptosis.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0007018","count":3},{"id":"GO:0051402","count":3}]},{"hash":"1006750624923037742","title":"Amino acid, porphyrin, and cofactor biosynthesis","description":"The top terms cluster around biosynthetic pathways for amino acids, porphyrin (protoporphyrinogen IX) synthesis, and cofactors (biotin, coenzyme M), along with related central metabolism (oxaloacetate, 2-oxobutyrate, alanine catabolism). Despite some obsolete terms, these share a common theme of anabolic metabolic pathways rather than signaling or transport, supporting a label focused on biosynthesis of amino acids and cofactors.","confidence":"Medium","size":17,"edges":116,"triangles":457,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0006782","count":6},{"id":"GO:0019878","count":6},{"id":"GO:0042853","count":5}]},{"hash":"362603639081781560","title":"Cardiovascular development and mechanotransduction","description":"This cluster is dominated by GO terms related to heart and blood vessel formation\u2014right atrium morphogenesis, venous endothelial differentiation, and aorta development\u2014as well as Notch signaling in heart-field regulation and cellular responses to mechanical stimuli, suggesting a group of proteins tied to cardiovascular morphogenesis and mechanotransduction. Some nucleic acid metabolism terms appear, but they appear ancillary to the main cardiovascular theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0003213","count":2}]},{"hash":"165950227870892768","title":"RNA processing and antiviral signaling cluster","description":"The cluster shows strong representation of RNA metabolism and processing terms (spliceosomal snRNP assembly, stress granule assembly, deadenylation-dependent decay, miRNA regulation) along with innate immune signaling (RIG-I pathway, type I interferon signaling). These together suggest a coordinated role in RNA regulation and antiviral responses, with some auxiliary terms (receptor internalization, synapse plasticity, chaeta development) contributing less to the core theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":2},{"id":"GO:0060965","count":1},{"id":"GO:1904780","count":1},{"id":"GO:0034063","count":1},{"id":"GO:0060340","count":1}]},{"hash":"431150153833663542","title":"Unknown","description":"This cluster\u2019s top GO terms cover neural and muscle development, immune regulation, signaling pathways, cell cycle, and stress responses (unfolded protein response, glucocorticoid signaling), with no single unifying biological process. The diversity suggests a heterogeneous set of functions rather than a cohesive cluster function.","confidence":"","size":17,"edges":112,"triangles":399,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0021762","count":5},{"id":"GO:0048741","count":5},{"id":"GO:2001034","count":4},{"id":"GO:0051531","count":4},{"id":"GO:0014898","count":4}]},{"hash":"2156964863981127097","title":"Developmental signaling and cytoskeletal regulation","description":"This cluster centers on GO terms related to developmental processes (heart, skeletal, nervous system development) alongside signaling and cytoskeletal control (positive regulation of GTPase activity, Rho signaling) and Ca2+-dependent exocytosis, with additional sensory signaling terms (phototransduction, adrenergic receptor signaling). The mixture suggests proteins involved in developmental signaling networks that regulate cytoskeletal dynamics and secretion, rather than a single narrow function.","confidence":"Medium","size":17,"edges":83,"triangles":171,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":11},{"id":"GO:0001501","count":10},{"id":"GO:0043547","count":9},{"id":"GO:0007399","count":9},{"id":"GO:0007124","count":9}]},{"hash":"1292472629535113728","title":"Unknown","description":"The GO terms span GPCR signaling, small GTPase signaling, neuronal development and synapse-related processes, transcription, immune modulation, and apoptosis, showing no single cohesive function to unite the cluster. Therefore a specific, representative label cannot be confidently assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0032094","count":3},{"id":"GO:0097194","count":3}]},{"hash":"2109455424545714393","title":"Fatty acid beta-oxidation and lipid catabolism","description":"Top terms cluster around fatty acid breakdown and beta-oxidation (long-chain FA catabolic, beta-oxidation via oxidase/dehydrogenase) and related lipid-derived metabolism (ascaroside biosynthesis). While a few terms are peripheral (immune and cardiac differentiation), the dominant signal reflects fatty acid metabolism and energy-related processes.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0055007","count":5},{"id":"GO:0035754","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006552","count":3}]},{"hash":"1114413810509501947","title":"Cardiovascular and Immune Signaling","description":"This cluster's top GO terms emphasize heart development, vascular regulation (vasoconstriction, blood coagulation), and extracellular matrix remodeling (hyaluronan metabolism), together with immune signaling (T cell activation) and receptor-driven pathways (G protein-coupled receptor internalization, Rho signaling, prostaglandin response). The convergence of cardiovascular development cues with immune and GPCR-mediated signaling suggests a functionally cohesive group of proteins involved in heart/vascular biology and immune communication. A couple of terms about neuronal synapse development and chaperone refolding appear less central and may reflect broader signaling roles or annotation noise, but the dominant theme remains cardiovascular and immune signaling.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0030212","count":3},{"id":"GO:0002291","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0071380","count":3}]},{"hash":"1849957798610087599","title":"Developmental morphogenesis and ECM signaling","description":"Dominant terms point to embryonic development and extracellular matrix biology, including gastrulation, ossification, skeletal joint development, cell morphogenesis, and heparan sulfate proteoglycan biosynthesis, with a link to FGFR signaling. DNA replication/recombination terms are present but not central, so the core theme is development and ECM/growth factor\u2013mediated signaling.","confidence":"Medium","size":17,"edges":10,"triangles":0,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0000902","count":2},{"id":"GO:0019252","count":2},{"id":"GO:0005978","count":2}]},{"hash":"1110336428528300301","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosome biogenesis (ribosome assembly) and cytoplasmic translation, indicating a core function in making ribosomes and synthesizing proteins. While cell cycle terms (mitotic cell cycle, mitotic cytokinesis, cell cycle) appear, they likely reflect the link between protein synthesis capacity and cell division. Some membrane-related terms are present but less central to the main theme. Overall, the strongest signal ties to ribosome production and translation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042274","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0003257","count":2},{"id":"GO:0097320","count":2},{"id":"GO:0000278","count":2}]},{"hash":"166378992469955510","title":"Ubiquitin-Proteasome\u2013Mediated Signaling","description":"The cluster is dominated by protein ubiquitination and proteasome regulatory particle assembly, indicating a core role in proteostasis and regulation of signaling pathways; additional terms point to intracellular signal transduction and broader cellular responses (including NF-kappaB-related regulation, thermosensation, and cell migration), suggesting the proteins function together in modulating signaling through protein turnover. ","confidence":"Medium","size":17,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":12},{"id":"GO:0016567","count":9},{"id":"GO:0070682","count":9},{"id":"GO:0050960","count":9},{"id":"GO:0035556","count":9}]},{"hash":"1683535464798917638","title":"Insect epidermal morphogenesis and polarity","description":"The cluster is dominated by terms tied to development of insect epidermal structures and organization, including chaeta morphogenesis, antennal morphogenesis, cuticle pattern formation, and establishment of apical/basal cell polarity, along with processes governing cell junctions and the actin/tubulin cytoskeleton, pointing to a cohesive role in epithelial morphogenesis and patterning.","confidence":"Medium","size":17,"edges":16,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0043967","count":2},{"id":"GO:0090043","count":2},{"id":"GO:0002028","count":1},{"id":"GO:0008407","count":1}]},{"hash":"2276888918996874346","title":"Cell signaling and differentiation","description":"The top terms cluster around intracellular signal transduction and various differentiation-related processes, including cell migration, fat cell differentiation, and regulation of synaptic plasticity. While telomere maintenance/capping and mRNA processing appear, they seem peripheral to the main signaling/differentiation theme, suggesting a broad signaling and differentiation focus rather than a single pathway.","confidence":"Medium","size":17,"edges":16,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0016477","count":3},{"id":"GO:2001275","count":3},{"id":"GO:1900383","count":3},{"id":"GO:0032212","count":3}]},{"hash":"1123940014347211149","title":"Cell Cycle and Signaling Regulators","description":"The top GO terms point to cell division and cell cycle processes, complemented by signaling and adhesion/cytoskeletal modulation (JNK cascade regulation, Rac signaling, ubiquitination, and adherens junction organization) and responses to mechanical stimuli. Together these suggest a cohesive group of proteins that coordinate proliferation with signaling and cell\u2013cell interactions, rather than a single narrow pathway.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0046330","count":3},{"id":"GO:0090316","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0071260","count":3}]},{"hash":"1571469357113690729","title":"Neural development and cytoskeletal remodeling","description":"This cluster is enriched for neural development terms (spinal cord development, neural tube closure) and cytoskeletal dynamics (microtubule-based movement, Arp2/3 regulation, GTPase activity, tyrosine phosphorylation). The combination suggests coordinated signaling and cytoskeletal changes during neural development, with TGF-beta-related responses and apoptosis reflecting developmental remodeling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0007018","count":3},{"id":"GO:0050731","count":3}]},{"hash":"2189007758455486461","title":"ER-Golgi Vesicle Traffic and SNARE Assembly","description":"The top GO terms point to ER-to-Golgi and intra-Golgi transport, SNARE complex assembly, and vesicle fusion with the Golgi, indicating a core secretory pathway role. Additional terms on neurotransmitter receptor exocytosis and synaptic potentiation suggest neuronal vesicle trafficking and membrane insertion during plasticity. Together these indicate a unified function in secretory trafficking and SNARE-driven vesicle fusion in both general and neuronal contexts.","confidence":"High","size":17,"edges":60,"triangles":118,"max_degree":13,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":9},{"id":"GO:0090161","count":9},{"id":"GO:0006891","count":9},{"id":"GO:0035493","count":9},{"id":"GO:0060291","count":9}]},{"hash":"1874358584969163430","title":"Ubiquitin-Dependent TNF/NF-kB Regulation","description":"The top GO terms converge on ubiquitination processes (autoubiquitination; K63- and K6-linked ubiquitination; ubiquitin-dependent protein catabolic process) and TNF signaling with I-kappaB phosphorylation, indicating a module of proteins that regulate TNF/NF-kB pathways via ubiquitination, with connections to chromatin turnover (histone catabolic process) and vitamin D responses.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:1903265","count":12},{"id":"GO:0051865","count":11},{"id":"GO:0042787","count":11},{"id":"GO:0033280","count":11},{"id":"GO:0070534","count":10}]},{"hash":"1848749433148737536","title":"Tissue injury response and remodeling","description":"The top GO terms span heart development and wound healing, along with stress/injury signals such as apoptosis, response to X-ray, autophagy regulation, and endothelial activation, plus immune-related terms (response to LPS, B cell homeostasis). This pattern suggests a generalized tissue remodeling and stress-response program active across multiple tissues, rather than a single, specific pathway. The appearance of both developmental and damage-response processes supports labeling as a multi-tissue injury/repair theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0097194","count":5},{"id":"GO:0007605","count":5},{"id":"GO:0001782","count":5},{"id":"GO:0032496","count":4}]},{"hash":"1668945153294877089","title":"NOD2-NF-\u03baB Ubiquitin-Proteasome Signaling","description":"The cluster is dominated by GO terms for NOD2 signaling, NF-\u03baB regulation, protein ubiquitination, and proteasome regulatory particle assembly, suggesting a common theme of innate immune signaling coupled to protein turnover. Some terms related to thermoception and vitamin D response appear, but the core signal appears to be intracellular signaling linked to ubiquitin-proteasome\u2013mediated regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":6},{"id":"GO:0032088","count":6},{"id":"GO:0016567","count":5},{"id":"GO:0070682","count":5},{"id":"GO:0050960","count":5}]},{"hash":"284782293817613670","title":"Endothelial inflammation and ECM remodeling","description":"The cluster\u2019s top GO terms cluster around classical complement activation and acute inflammatory response, alongside endothelial cell proliferation/migration and collagen fibril organization, which together point to immune\u2013vascular interactions and remodeling of the extracellular matrix. Lipoprotein transport/clearance further links lipid handling to vascular processes, and apoptotic cell clearance aligns with immune clearance in inflamed vessels; somite development is less central. Overall, a vascular inflammation with ECM remodeling theme best fits the set.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":5},{"id":"GO:0001935","count":5},{"id":"GO:0030199","count":5},{"id":"GO:0043542","count":5},{"id":"GO:0043277","count":4}]},{"hash":"243633138234952677","title":"Wnt\u2013Rho GTPase\u2013Lamellipodium Signaling","description":"Based on the dominant GO terms, the cluster appears centered on Wnt signaling and small GTPase\u2013mediated signal transduction, with downstream actin remodeling indicated by lamellipodium and ruffle assembly. Positive and negative regulation of GTPase activity point to tight control of cytoskeletal dynamics, aligning with these processes. Some terms such as brood size regulation and blood-nerve barrier establishment may be peripheral or context-specific noise rather than core features. Overall, the cluster most plausibly reflects signaling pathways that coordinate cytoskeletal dynamics and cell migration through Wnt and GTPase activity.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0060378","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0034260","count":2}]},{"hash":"947414615795935016","title":"Cochlear morphogenesis and auditory system development","description":"These proteins cluster around inner ear development and hearing-related functions (cochlea morphogenesis, sensory perception of sound) and broader neural development (central nervous system development). Supporting cellular processes such as actin bundle assembly, exocytosis, tight junction formation, and planar polarity signaling further link them to cochlear morphogenesis and the establishment of auditory structures, with some regulatory roles in gene silencing and tissue repair. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":2},{"id":"GO:0006887","count":2},{"id":"GO:2000637","count":2},{"id":"GO:0007417","count":2},{"id":"GO:0090103","count":2}]},{"hash":"1923892615139931917","title":"Unknown","description":"The GO terms are highly diverse, spanning plant-specific developmental signaling (brassinosteroid signaling, flower development) and mammalian immune signaling (germinal center formation, B cell receptor signaling, IL-6 production), as well as general transcription and circadian regulation. With no edges or functional cohesion among the terms, there isn\u2019t a single thematic function to label the cluster, so a meaningful, concise name cannot be assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":1},{"id":"GO:0009911","count":1},{"id":"GO:0050853","count":1},{"id":"GO:0009742","count":1},{"id":"GO:0042752","count":1}]},{"hash":"2053557407444963374","title":"Cofactor and vitamin biosynthesis","description":"These proteins show strong enrichment for GO terms related to the biosynthesis of cofactors and vitamins (ubiquinone, menaquinone, cobalamin, vitamin E) and related metabolite formation, plus a tRNA wobble uridine modification term, suggesting a theme of assembling essential cofactors and associated metabolites. Some outlier terms (cellular senescence, response to cocaine) appear less central to the core function but do not override the main biosynthetic theme.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0016049","count":10},{"id":"GO:0010189","count":9},{"id":"GO:0006744","count":9},{"id":"GO:1901052","count":9},{"id":"GO:0042220","count":9}]},{"hash":"653025846462500176","title":"Gene expression and chromatin regulation","description":"This cluster centers on core gene-expression processes, including DNA-templated transcription and translation, along with chromatin-related activities (e.g., histone acetylation) and nuclear RNA processing (telomerase RNA localization to Cajal bodies). Additional terms related to mitotic cell cycle and estradiol responsiveness suggest broader nuclear signaling and regulation of gene expression. Overall, the proteins likely function in gene expression control and chromatin dynamics rather than a single specific pathway.","confidence":"Medium","size":16,"edges":50,"triangles":75,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:1903146","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0051260","count":3},{"id":"GO:1904874","count":2}]},{"hash":"2026817312461657130","title":"Immune regulation and hormone signaling","description":"The cluster is enriched for immune-related terms (IL-4 production, Th17 lineage commitment, TLR2 signaling modulation) and hormone-related signaling (estrogen receptor signaling regulation, hormone secretion). Thymus development reinforces an immune-organ context, while ubiquitination and adherens junction organization hint at protein turnover and cell adhesion in immune signaling. Taken together, the terms point to a network integrating immune regulation with endocrine signaling, justifying the label.","confidence":"Medium","size":16,"edges":18,"triangles":4,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016567","count":12},{"id":"GO:0034332","count":12},{"id":"GO:0046887","count":12},{"id":"GO:0034136","count":12},{"id":"GO:0032633","count":12}]},{"hash":"471959297921326279","title":"Retinoid and Hormone Metabolism","description":"Most informative GO terms highlight retinoid metabolism (retinol, retinal) with strong counts, and hormonal signaling/metabolism (response to thyroid hormone, progesterone metabolism, prostaglandin biosynthesis). The presence of related detox and stress signaling terms (glutathione biosynthesis, daunorubicin metabolism, stress-activated MAPK cascade) suggests a broader theme of metabolism of signaling molecules and xenobiotics. Therefore, Retinoid and Hormone Metabolism is a concise, representative label for this cluster.","confidence":"Medium","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":15},{"id":"GO:0042574","count":15},{"id":"GO:0097066","count":13},{"id":"GO:0001516","count":13},{"id":"GO:1900053","count":13}]},{"hash":"705098566484638938","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":9},{"id":"GO:0034975","count":9},{"id":"GO:0045454","count":9},{"id":"GO:0006458","count":8},{"id":"GO:0036494","count":7}]},{"hash":"1101633970938467523","title":"Angiogenesis and vascular permeability regulation","description":"These proteins are enriched for GO terms tied to blood vessel formation and vascular integrity, including angiogenesis, endothelial cell migration, cell-matrix adhesion, and regulation of vascular permeability, along with ERK signaling. Additional terms like insulin receptor signaling and protein localization to the cell surface suggest broader signaling readiness in endothelial contexts, with a note of immune-endothelial interaction via T cell receptor signaling. Overall, the theme centers on endothelial angiogenic signaling and maintenance of vascular barrier function.","confidence":"High","size":16,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043116","count":6},{"id":"GO:0008286","count":5},{"id":"GO:0007160","count":5},{"id":"GO:0045766","count":5},{"id":"GO:0070374","count":5}]},{"hash":"901000004660948136","title":"Viral Entry and Proviral Transposon Integration","description":"The cluster is dominated by terms tied to viral entry into host cells, integration of viral/proviral DNA, and transposon activity (DNA transposition, DNA integration, retrotransposition, proviral latency). These indicate a shared theme of genome integration and movement within host cells, characteristic of viral/retroelement processes, with some non-specific terms likely representing noise. ","confidence":"Medium","size":16,"edges":28,"triangles":4,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000023","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0006313","count":3},{"id":"GO:0015074","count":3}]},{"hash":"566369497965582162","title":"Membrane Targeting and Unfolded Protein Response","description":"These proteins are enriched for GO terms related to targeting nascent polypeptides to membranes, especially SRP-dependent cotranslational targeting to the ER, and for responses to misfolded proteins and ER stress. Together they point to a membrane-targeting / protein quality-control module, rather than a single process like DNA replication. The presence of unfolded protein response and inclusion body assembly terms supports this interpretation. A few terms such as DNA replication or karyogamy may reflect secondary roles or annotation spillover but do not define the core function of the cluster.","confidence":"High","size":16,"edges":9,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031204","count":8},{"id":"GO:0006880","count":8},{"id":"GO:0000742","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0006616","count":8}]},{"hash":"1715365581196255590","title":"Unknown","description":"Top GO terms are highly diverse, spanning meiosis regulation, protein complex stability, plant inflorescence morphogenesis, blood-nerve barrier establishment, megakaryocyte development, heterochromatin formation, foam cell differentiation, muscle cellular homeostasis, tubulin deacetylation, and olfactory nerve organization. With no shared biological process evident and an edge count of zero, there is no coherent functional theme tying these proteins together. Therefore, a reliable single label cannot be assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010520","count":2},{"id":"GO:0061635","count":2},{"id":"GO:0048281","count":2},{"id":"GO:0008065","count":2},{"id":"GO:0035855","count":2}]},{"hash":"907877882031624964","title":"Bacterial metabolism and flagellar motility","description":"This cluster is dominated by metabolic and energy-related GO terms (phenylacetate catabolic process, formate metabolism, pyruvate decarboxylation to acetyl-CoA, electron transport chain) and by transport (sodium ion transport) and flagellar components (bacterial-type flagellum assembly and motility). Although a brain development term appears, the majority of terms reflect bacterial central metabolism and motility machinery, with a few general cellular processes (DNA replication, protein homooligomerization) likely representing housekeeping functions.","confidence":"Medium","size":16,"edges":73,"triangles":149,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010124","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0015942","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0051260","count":3}]},{"hash":"54926384108165366","title":"Neural Development and Synaptic Signaling","description":"This cluster is dominated by terms related to nervous system development, axon guidance (Roundabout/Robo, hedgehog/Smoothened signaling), neurite outgrowth (filopodium regulation), membrane trafficking to support synapses, and GABAergic synaptic transmission, all pointing to neural development and synaptic connectivity; a few terms like spermatid development appear as noise but do not override the main theme.","confidence":"High","size":16,"edges":42,"triangles":21,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0035385","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0006893","count":3},{"id":"GO:0051932","count":3}]},{"hash":"1440352597227920620","title":"Unknown","description":"This cluster lacks any GO term information in the Top Terms, so there is no clear shared function to tie the proteins together. The network characteristics (16 proteins, 55 edges, high clustering) may reflect a general interaction module rather than a single GO-defined process; without terms, a precise label cannot be assigned.","confidence":"","size":16,"edges":55,"triangles":52,"max_degree":11,"top_function":null,"top_go_terms":[]},{"hash":"1840930307114746145","title":"Cell Signaling and Adhesion","description":"This cluster's GO terms cluster around signaling pathways (prolactin signaling, T cell receptor signaling, peptidyl-tyrosine autophosphorylation) and adhesion/cytoskeletal processes (hemidesmosome assembly, substrate adhesion-dependent spreading, Rho signaling), with an additional note on ER-to-Golgi trafficking, suggesting a general theme of signaling coordinating adhesion and trafficking rather than a single specific function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0038161","count":2},{"id":"GO:0038083","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0034446","count":2}]},{"hash":"1248580896330530670","title":"Axon guidance signaling","description":"The cluster is dominated by terms related to neuronal development and axon pathfinding, including axon guidance and ROBO signaling, with associated intracellular signaling cascades (ERK, PI3K) and nervous system development. Some terms (kidney development, germarium-derived cystoblast division) are less directly connected, but the strongest pattern points to neuronal signaling and guidance.","confidence":"Medium","size":16,"edges":84,"triangles":184,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0035556","count":2},{"id":"GO:2000785","count":2},{"id":"GO:0048142","count":2}]},{"hash":"857083959137087545","title":"Redox Homeostasis and Mitochondrial Regulation","description":"The top GO terms cluster around detoxification of oxidants, redox balance, and glutathione metabolism, along with regulation of mitochondrial membrane potential, pointing to a core theme of oxidative stress management and mitochondrial function. Additional terms touching calcium signaling and differentiation suggest broader signaling roles, but the dominant pattern is redox maintenance and mitochondrial regulation.","confidence":"High","size":16,"edges":97,"triangles":316,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0070527","count":4},{"id":"GO:0006749","count":4}]},{"hash":"268931056652135748","title":"Unknown","description":"The top terms span innate and adaptive immune signaling, ubiquitination/ERAD processes, and cardiac muscle development, with only a few terms per category and no clear dominant theme. The lack of edges or connectivity among proteins also suggests this set does not form a cohesive functional cluster, so a single, interpretable function is not evident. Therefore, Unknown with None confidence. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0050853","count":2},{"id":"GO:1902187","count":1},{"id":"GO:0055002","count":1},{"id":"GO:0071313","count":1}]},{"hash":"322076898073436614","title":"Interferon-mediated innate immune signaling","description":"The cluster is enriched for type I interferon signaling and production, along with TLR/LPS\u2011related pathways and immunoglobulin-mediated immune response, pointing to innate immune activation centered on the interferon axis. A few other terms (potassium transport, mechanical stimulus response, transcription) may reflect additional cellular processes but do not negate the dominant interferon/innate immunity theme.","confidence":"High","size":16,"edges":24,"triangles":12,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0071260","count":2},{"id":"GO:0060340","count":2},{"id":"GO:0034122","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1333388858907111182","title":"Peroxisomal Fatty Acid Transport and Oxidation","description":"The top GO terms are dominated by fatty acid transport into peroxisomes and subsequent beta-oxidation, including long-chain fatty acid import into peroxisomes, fatty-acyl-CoA transport, and beta-oxidation of long and very long-chain fatty acids, plus related catabolic processes. A couple of transcription-regulation terms appear as noise, but the prevailing theme points to peroxisomal fatty acid trafficking and degradation, justifying this label.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051571","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0015916","count":1},{"id":"GO:0015910","count":1}]},{"hash":"1674374654924503190","title":"Regulation and localization of signaling proteins","description":"This cluster centers on protein regulation through ubiquitination and pathways that control signaling and receptor localization. Terms include protein ubiquitination, NOD2 signaling, NF-kappaB regulation, receptor localization to synapse, and maintenance of protein location in the plasma membrane, with additional associations to cell cycle, apoptosis, and immune differentiation. The diversity suggests a broad role in regulating signaling and protein trafficking rather than a single module.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0032088","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0002268","count":4},{"id":"GO:0086070","count":4}]},{"hash":"488872948487645460","title":"Osteogenesis and Skeletal Vasculature Remodeling","description":"The proteins show strong links to bone formation and skeletal development (osteoblast differentiation, bone trabecula formation, skeletal system development) together with vascular remodeling and regulation of vessel tone (blood vessel remodeling, vasoconstriction) and cell-matrix interactions, suggesting a coordinated program of bone formation and associated vasculature remodeling. Memory appears incidental and not central to the main theme.","confidence":"High","size":16,"edges":102,"triangles":357,"max_degree":15,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0001974","count":4},{"id":"GO:0007160","count":4},{"id":"GO:0045669","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0048661","count":4}]},{"hash":"1600225155106116116","title":"Bacterial lipid and secondary metabolite biosynthesis","description":"The cluster shows enrichment for lipid-related pathways (fatty acid biosynthesis, long-chain fatty acid metabolism, lipoteichoic acid biosynthesis, menaquinone biosynthesis) alongside secondary metabolite production (siderophore biosynthesis, nonribosomal peptide biosynthetic activation) and bioluminescence. This pattern points to a bacterial module engaged in producing lipids/cofactors and diverse secondary metabolites, including light-emitting capabilities. Therefore, the label \u201cBacterial lipid and secondary metabolite biosynthesis\u201d is a concise, representative name for this cluster. ","confidence":"Medium","size":16,"edges":94,"triangles":280,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":7},{"id":"GO:0008218","count":7},{"id":"GO:0070395","count":7},{"id":"GO:0001676","count":6},{"id":"GO:0043041","count":6}]},{"hash":"2001201014226339997","title":"Immune signaling and migration","description":"The cluster shows strong representation of immune-related processes (interleukin-4 production, cellular response to interleukin-7, NK T cell differentiation, B cell affinity maturation) along with processes tied to cell movement (lamellipodium assembly, cell migration). While some terms (heart development, insulin receptor signaling, Ras pathway regulation) are broader signaling themes, the dominant theme appears to be immune cell signaling and migration, so the label reflects the core function of the cluster. ","confidence":"Medium","size":16,"edges":17,"triangles":3,"max_degree":12,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006915","count":9},{"id":"GO:0032633","count":9},{"id":"GO:0030032","count":9},{"id":"GO:0098761","count":9},{"id":"GO:0016477","count":9}]},{"hash":"463365440607644464","title":"Innate Immunity and Host Interaction","description":"This cluster is driven by GO terms centered on immune defense, including classical complement activation, immunological synapse formation, and innate immune response, with additional signals for apoptotic cell clearance and host\u2013microbe interactions. While a few terms relate to development and vascular processes (somite development, endothelial proliferation, lipoprotein transport), the dominant pattern points to immune recognition, signaling, and clearance activities and host\u2013pathogen interactions.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":7},{"id":"GO:0001771","count":6},{"id":"GO:0045087","count":5},{"id":"GO:0046718","count":4},{"id":"GO:0007565","count":4}]},{"hash":"1998891270351782037","title":"Dopaminergic signaling and sensory perception","description":"This cluster is enriched for nervous-system related GO terms: dopaminergic synaptic transmission, visual perception/learning, pain perception, and responses to temperature and cocaine, indicating a coherent theme of neural signaling and sensory processing. Some terms like heart development or thermogenesis are present but appear less central.","confidence":"High","size":16,"edges":27,"triangles":17,"max_degree":15,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":11},{"id":"GO:0071502","count":9},{"id":"GO:0002024","count":9},{"id":"GO:0048148","count":7},{"id":"GO:0001963","count":7}]},{"hash":"1155984963008201075","title":"Hippocampal neuron development and GABAergic synapses","description":"Most frequent terms center on hippocampus development, GABAergic synaptic transmission, and neural adhesion/receptor trafficking, with mitochondrial and recycling processes supporting neuron function. While cell-cycle and NF-kappaB terms exist, the prevailing theme is neuronal development and synaptic regulation.","confidence":"High","size":16,"edges":19,"triangles":4,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034332","count":11},{"id":"GO:0042832","count":11},{"id":"GO:0051932","count":11},{"id":"GO:0007049","count":11},{"id":"GO:0043124","count":11}]},{"hash":"1313477134892009085","title":"Adaptive immune\u2013angiogenic signaling","description":"The cluster is enriched for GO terms tying immune activation (adaptive immune response, interleukin-4 production, TLR2 signaling regulation) to vascular remodeling processes (integrin signaling, angiogenesis, endothelial cell migration, adherens junction organization, ERK cascade). The inclusion of ubiquitination as a regulatory layer supports post-translational control of these processes, suggesting a cohesive module that coordinates immune responses with angiogenesis and endothelial junction dynamics.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007229","count":15},{"id":"GO:0002250","count":15},{"id":"GO:0001525","count":15},{"id":"GO:0070374","count":15},{"id":"GO:0043536","count":15}]},{"hash":"2253196235967879865","title":"ER proteostasis and ubiquitination regulation","description":"Top terms point to ubiquitin-like modifications (deubiquitination, sumoylation) and ER-associated protein handling, including tail-anchored protein insertion into the ER membrane, unfolded protein management in ERAD, and proteasomal regulation. The cluster also touches vesicle formation and GPCR trafficking, all aspects of protein quality control and trafficking in the secretory pathway.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":11},{"id":"GO:0016925","count":11},{"id":"GO:0071816","count":10},{"id":"GO:0006412","count":10},{"id":"GO:1904378","count":10}]},{"hash":"452156229371326724","title":"Innate Immunity and ECM Organization","description":"The cluster shows strong representation of innate immune processes (innate immune response, immunological synapse formation) and extracellular matrix remodeling components (collagen and fibronectin fibril organization, tight junction assembly), suggesting a functional module tied to immune-ECM interactions and barrier dynamics. Some terms like foam cell differentiation and zymogen activation are related but peripheral, reinforcing the central theme rather than a single narrowly defined function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":9},{"id":"GO:1904274","count":8},{"id":"GO:0010886","count":8},{"id":"GO:0010744","count":8},{"id":"GO:0018277","count":8}]},{"hash":"1884230319282966645","title":"Dopaminergic signaling and cocaine-related behavior","description":"The top GO terms cluster around dopaminergic synaptic transmission, behavioral response to cocaine, visual perception/learning, and ERK signaling, indicating a neuronal signaling theme tied to perception, learning, and reward. Some terms (macrophage chemotaxis, heart development) are peripheral, but the dominant pattern is dopamine-driven neural communication and related signaling pathways.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0048148","count":9},{"id":"GO:0001963","count":9},{"id":"GO:0010759","count":9},{"id":"GO:0008542","count":9},{"id":"GO:0071380","count":9}]},{"hash":"114116914444562101","title":"RNA cap and protein methylation","description":"The top GO terms center on methylation: RNA guanine-N7 methylation and 7-methylguanosine mRNA capping, plus several peptidyl-methylation terms (serine, lysine, glutamine). This points to a cluster enriched for methyltransferase activities affecting both RNA caps and modified amino acids, despite a few metabolism terms appearing in the list.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0035573","count":1},{"id":"GO:0019505","count":1},{"id":"GO:0010189","count":1}]},{"hash":"1835293439928811174","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000294","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0001682","count":1},{"id":"GO:0000447","count":1},{"id":"GO:1905267","count":1}]},{"hash":"1946622207661636477","title":"Unknown","description":"The cluster contains diverse processes\u2014cytoskeletal regulation (Rho signaling, actin remodeling), neuronal signaling, hormone response, developmental pathways, apoptosis and cell clearance, DNA replication, and innate immunity\u2014without a single dominant theme. It is therefore not possible to assign a specific, informative label.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0035249","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0001707","count":2}]},{"hash":"8084247136885564","title":"GTPase-regulated synaptic signaling and plasticity","description":"The top GO terms indicate a core theme of neuronal signaling and synaptic modulation, including long-term potentiation, regulation of synaptic vesicle exocytosis, and neurotransmitter receptor transport to the postsynaptic membrane, together with small GTPase-mediated signaling and regulation of GTPase activity. This suggests a cluster centered on GTPase-driven synaptic signaling and plasticity, with Wnt signaling as a potential regulatory influence. Some immune/vascular terms are present but do not define the cluster\u2019s primary function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0060291","count":3},{"id":"GO:0043314","count":3},{"id":"GO:2000300","count":3}]},{"hash":"1962184597341187765","title":"Brain and Eye Development","description":"The top GO terms point to development of neural tissues and the eye (nervous system development, substantia nigra development, lens fiber cell differentiation), with supporting signals for general proliferation (cell division, mitotic spindle assembly) and vesicle trafficking (COPII budding, viral mRNA export). This suggests a cohesive theme of developmental processes in brain and eye, though some terms are broader or transport-focused, so the confidence is Medium. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0051092","count":3},{"id":"GO:2000249","count":2},{"id":"GO:0050860","count":2}]},{"hash":"456673994958777726","title":"Diverse Transmembrane Transporters","description":"This cluster is defined by a strong presence of transmembrane transport GO terms across substrates (xenobiotics, nitrate/nitrite, arabinose, vitamins, potassium ions, sugars like fucose) and even vesicular neurotransmitter loading, indicating a set of membrane transporter proteins with broad substrate specificity rather than a single, narrow function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:1900754","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0015751","count":3},{"id":"GO:0035461","count":3}]},{"hash":"248121893419213282","title":"Endothelial angiogenesis and migration signaling","description":"This cluster is enriched for GO terms related to vascular endothelial processes, including endothelial tube lumen extension, regulation of cell migration in sprouting angiogenesis, and GTPase-mediated signaling. The presence of negative regulation of extravasation and remodeling supports a role in controlling endothelial cell movement and vessel formation. Some terms like Golgi localization reflect trafficking roles common to small GTPases, aligning with the core theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007264","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0097498","count":2},{"id":"GO:0002692","count":2},{"id":"GO:0090334","count":2}]},{"hash":"1173751775350539783","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:1902187","count":16},{"id":"GO:0010586","count":16},{"id":"GO:0018032","count":16},{"id":"GO:1903886","count":16},{"id":"GO:0007014","count":16}]},{"hash":"1010342366275935833","title":"GPCR signaling with prostaglandin and morphine responses","description":"The top GO terms cluster around GPCR-mediated signaling (GPCR internalization, GTPase activation, GPCR signaling pathway) and responses to prostaglandin E stimuli and morphine, with additional annotations touching on vasoconstriction and heart development, and even sensory perception of sound. This pattern strongly suggests a cohesive function centered on G protein-coupled receptor signaling and its physiological outputs, spanning cardiovascular, sensory, and analgesic-related contexts.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071380","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0002031","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0051262","count":2}]},{"hash":"1491279704461110903","title":"Cytoskeleton Signaling and Cell Adhesion","description":"The terms cluster around Rho/Rac signaling, microtubule organization, EMT, and leukocyte adhesion, all pointing to cytoskeletal dynamics and cell\u2013cell/membrane interactions, despite a few outliers; thus the cluster is best described as cytoskeletal regulation and adhesion-related processes.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010989","count":2},{"id":"GO:0090004","count":1},{"id":"GO:0016601","count":1},{"id":"GO:0010718","count":1},{"id":"GO:0035023","count":1}]},{"hash":"2300314457267031388","title":"Unknown","description":"The top terms are highly diverse, covering morphogenesis, nuclear transport, Rho and GTPase signaling, blood circulation, inflammatory cytokine production, chromatin organization, DNA repair, and glial apoptosis. With no edges or cohesive shared function among the proteins, there is no clear common theme to define a specific biological role for this cluster. Therefore, the label Unknown with no confidence is appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035775","count":1},{"id":"GO:0000060","count":1},{"id":"GO:0035025","count":1},{"id":"GO:0008015","count":1},{"id":"GO:0002534","count":1}]},{"hash":"34161282506257513","title":"Unknown","description":"The top GO terms cover immune signaling (B cell receptor signaling, NK cell cytotoxicity, LPS signaling), lipid and GTPase signaling (diacylglycerol metabolism, Rho signaling), development (anterior midgut invagination), DNA repair regulation, and neural plasticity (synaptic depression). This diversity suggests no single coherent function or pathway linking all 16 proteins, making a specific, representative label inappropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":2},{"id":"GO:0045954","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0045630","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1779133056491534291","title":"GTPase-driven development and cell polarity","description":"Top GO terms indicate broad developmental processes across tissues (nervous system, brain, kidney) and immune signaling, alongside themes of Rho/GTPase signaling and cytoskeletal organization (sarcomere). This suggests a cluster of proteins involved in developmental signaling and cytoskeletal regulation mediated by small GTPases, including establishment of cell polarity. No single dominant function emerges, but the recurring motif is GTPase-mediated signaling linked to development and cytoskeletal dynamics.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0050853","count":4},{"id":"GO:0001822","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0035023","count":3}]},{"hash":"372386475572608764","title":"Epigenetic regulation of muscle and heart development","description":"The cluster contains GO terms pointing to muscle and heart development (myotube development, negative regulation of skeletal muscle tissue development, heart development) along with epigenetic mechanisms (histone methylation, lysine methylation, deubiquitination) and general protein localization and signaling regulation, suggesting a cohesive theme of epigenetic control guiding muscle/heart differentiation, with some broader regulatory processes as context.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036158","count":1},{"id":"GO:0016579","count":1},{"id":"GO:0048642","count":1},{"id":"GO:0018026","count":1},{"id":"GO:0010452","count":1}]},{"hash":"23201257079217055","title":"Steroid and lipid metabolism and transport","description":"The terms predominantly point to lipid and steroid pathways (glucocorticoid metabolism, ceramide transport, bile acid biosynthesis/secretion, cholesterol transport, progesterone biosynthesis), with a few vascular/developmental terms that could be downstream effects of lipid/steroid signaling. This suggests a cohesive theme around lipid and steroid metabolism and trafficking.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008211","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0070859","count":1},{"id":"GO:0097498","count":1},{"id":"GO:0032782","count":1}]},{"hash":"1931378770548204070","title":"Cardiac mechanotransduction and conduction","description":"The top GO terms cluster around SA node cell action potential regulation and communication with atrial cardiac muscle cells, along with cellular responses to mechanical stimulus and muscle stretch, pointing to cardiac electrophysiology and mechanotransduction. Some immune-related or apoptosis terms appear as noise, but the dominant signal supports a cardiac mechanotransduction/conduction theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002268","count":3},{"id":"GO:0086070","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0072660","count":3},{"id":"GO:0098907","count":3}]},{"hash":"1483979991721697301","title":"Neural signaling and protein turnover","description":"The proteins appear to converge on two themes: neural signaling/development (cell migration, cerebellar granule cell differentiation, intracellular signal transduction) and proteostasis (ubiquitination and proteasome regulatory particle assembly). Additional terms related to sensory/stimulus response (thermoception, capsazepine) and broader signaling inputs (vitamin D response) support a signaling-centric cluster with concurrent protein turnover processes. This suggests a cohesive theme around signaling in neural contexts coupled with protein degradation machinery. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":7},{"id":"GO:0021707","count":7},{"id":"GO:0098907","count":7},{"id":"GO:0007205","count":7},{"id":"GO:0016567","count":6}]},{"hash":"104436671649541884","title":"Neural development and synapse maturation","description":"These proteins are associated primarily with nervous system development and neuron differentiation, as reflected by multiple GO terms for nervous system development, regulation of synapse maturation, neuron differentiation timing, and related neural differentiation processes. While a few terms touch on non-neural differentiation (heart rate regulation, myoblast differentiation), the majority point to neural development and synapse formation, supporting a label centered on neural differentiation and synapse maturation.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0090128","count":9},{"id":"GO:0003062","count":9},{"id":"GO:2000974","count":9},{"id":"GO:0061100","count":9}]},{"hash":"1143638008981635217","title":"Wnt signaling regulators and cell cycle","description":"The top GO terms are dominated by regulation of canonical Wnt signaling (both negative and positive), along with DNA replication and the mitotic cell cycle, suggesting proteins that modulate Wnt-driven proliferation and regeneration. Additional terms like hyaluronan metabolism and cyclic nucleotide biosynthesis point to broader metabolic and extracellular matrix-related activities that can accompany signaling and tissue remodeling, including organ regeneration. Together, these indicate a cluster of factors involved in Wnt pathway control linked to cell cycle and regenerative processes.","confidence":"Medium","size":15,"edges":15,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090090","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0030212","count":6},{"id":"GO:0009190","count":6},{"id":"GO:0097350","count":5}]},{"hash":"1994384261644168838","title":"Chromatin regulation and immune signaling","description":"This cluster centers on GO terms tied to chromatin dynamics and transcription (DNA-templated transcription, heterochromatin formation, histone modifications), pointing to epigenetic regulation. It also includes immune-related processes (MHC class II biosynthesis, macrophage apoptosis) and broader signaling paths (HGF receptor signaling, angiogenesis, ROS regulation), suggesting a cohesive theme of gene regulation integrated with immune and vascular signaling. ","confidence":"Medium","size":15,"edges":79,"triangles":210,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0045348","count":7},{"id":"GO:2000111","count":6},{"id":"GO:1990141","count":5},{"id":"GO:0031648","count":5}]},{"hash":"938592730944107965","title":"Angiogenesis and vascular morphogenesis","description":"This cluster centers on angiogenesis and vascular development, including sprouting angiogenesis, dorsal aorta morphogenesis, and Notch signaling in arterial endothelial fate, with additional links to broader morphogenesis in neural and epithelial tissues. The dominant signal is endothelial vessel formation and patterning, with supporting developmental terms. ","confidence":"High","size":15,"edges":7,"triangles":1,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0090051","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0048680","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0021510","count":4}]},{"hash":"419288758385893915","title":"Endothelial inflammation and ECM remodeling","description":"This cluster combines immune/complement activity and apoptotic clearance with vascular and extracellular matrix processes (endothelial proliferation/migration, collagen fibril organization, lipoprotein clearance), suggesting coordinated remodeling of vessels and ECM during inflammatory contexts; somite development and protein homotrimerization may reflect developmental/structural aspects underpinning these processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":15},{"id":"GO:0006958","count":15},{"id":"GO:0070207","count":15},{"id":"GO:0061053","count":15},{"id":"GO:0042953","count":15}]},{"hash":"784850865798893833","title":"Nucleotide Metabolism and RNA Editing","description":"Enriched for nucleotide metabolism and RNA modification (UMP salvage, uridine biosynthesis, deoxycytidine/cytidine/guanine metabolism) and RNA editing (tRNA wobble A-to-I editing, cytidine deamination), with riboflavin biosynthesis as a connected metabolic process, suggesting a core theme of nucleotide turnover and RNA modification.","confidence":"Medium","size":15,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009231","count":6},{"id":"GO:0044206","count":6},{"id":"GO:0002100","count":6},{"id":"GO:0019858","count":6},{"id":"GO:0009972","count":6}]},{"hash":"725783927636431723","title":"DNA packaging and chromatin regulation","description":"Based on the presence of GO terms tied to chromatin modification (histone acetylation, heterochromatin formation), DNA condensation/packaging (sperm DNA condensation, plasmid partitioning), and transcriptional regulation (RNA polymerase II preinitiation complex assembly, Pol I rRNA transcription control), the cluster appears to center on chromatin state and DNA packaging influences on gene expression. Some terms (photomorphogenesis, pro-B cell differentiation) are less connected and thus peripheral, but the core signal is chromatin/DNA organization and transcription control.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":3},{"id":"GO:0030466","count":3},{"id":"GO:0030543","count":2},{"id":"GO:0035093","count":2},{"id":"GO:2000973","count":2}]},{"hash":"1512460260837397429","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000184","count":5},{"id":"GO:0006269","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0045944","count":4}]},{"hash":"950113320476369944","title":"mRNA Splicing and Translation Regulation","description":"The GO terms cluster around spliceosome-mediated mRNA processing (splicing, splice-site recognition, mRNA modification) and control of translation initiation (eIF4F complex assembly, translational initiation regulation), with a stress-related mRNA stability component, indicating a joint module of RNA processing and translation control.","confidence":"High","size":15,"edges":96,"triangles":355,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0006376","count":5},{"id":"GO:0097010","count":5},{"id":"GO:0010610","count":5},{"id":"GO:1905663","count":5}]},{"hash":"2028844560584473082","title":"Developmental Signaling and Kinase Regulation","description":"The proteins appear to function in regulating signaling pathways (GTPase activity, phosphorylation/autophosphorylation) and developmental processes (multicellular development, skin development), with substrates related to cell adhesion and spreading, suggesting a role in developmental signaling and cytoskeletal dynamics. Some terms (mRNA splicing, ubiquitin-related ERAD) indicate broader regulatory processes, but the dominant theme centers on signaling control during development.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006469","count":3},{"id":"GO:1900026","count":2},{"id":"GO:0007275","count":2}]},{"hash":"2096252272351402259","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":2},{"id":"GO:0009399","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006879","count":1}]},{"hash":"551641753421868564","title":"Epigenetic regulation and chromatin remodeling","description":"The Top Terms cluster centers on epigenetic control of gene expression: DNA methylation-dependent heterochromatin formation, histone modifications (H3K27 methylation, H3K4 trimethylation), and histone deacetylase activity. These converge on chromatin state regulation and transcriptional control, which best explains the group of terms present, despite a few obsolete or unrelated entries that may reflect outdated annotations in the dataset.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904388","count":1},{"id":"GO:2000410","count":1},{"id":"GO:0090308","count":1},{"id":"GO:0048655","count":1},{"id":"GO:0061087","count":1}]},{"hash":"1061295218258289229","title":"Unknown","description":"The terms are diverse and spread across cell migration, cardiac signaling, immune differentiation, liver apoptosis, membrane protein localization, and mechanical response, with several obsolete terms. This lack of a single coherent function or pathway makes it hard to assign a precise label. ","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0002268","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0086070","count":3},{"id":"GO:0097284","count":3}]},{"hash":"184647810051393973","title":"Methyltransferase activities (protein and RNA)","description":"The top GO terms cluster around various methylation reactions\u2014peptidyl-glutamine, peptidyl-arginine, peptidyl-lysine, N-terminal glycine methylation, and rRNA methylation\u2014as well as methylation-related steps in biosynthesis (menaquinone and cobalamin). This pattern points to a group of enzymes that transfer methyl groups to proteins and RNA, with connections to vitamin biosynthesis pathways. ","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018364","count":5},{"id":"GO:0090398","count":5},{"id":"GO:0009234","count":5},{"id":"GO:0009236","count":5},{"id":"GO:0031167","count":5}]},{"hash":"640943077036880410","title":"ATP Synthesis Coupled to Electron Transport","description":"The cluster\u2019s top GO term is ATP synthesis coupled to electron transport, indicating involvement in oxidative phosphorylation and energy production. The high edge and triangle counts suggest a tightly connected energy metabolism module, consistent with ETC complexes and ATP synthase components, making this label representative of the cluster.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042773","count":1}]},{"hash":"2001440718147212393","title":"Circadian Hormonal Signaling with Immune and Bone Remodeling","description":"The top GO terms cluster around circadian rhythm and photoreceptor maintenance, along with hormone secretion and its regulation, plus immune and bone-related processes (LPS response, eosinophil regulation, platelet activation, bone remodeling). Together these suggest an integrated neuroendocrine-immune axis modulated by circadian timing, hence this label captures the shared theme.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":13,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0040015","count":6},{"id":"GO:0032496","count":5},{"id":"GO:0022410","count":5},{"id":"GO:0046879","count":5},{"id":"GO:0043547","count":5}]},{"hash":"434180674364135665","title":"NFAT/calcineurin signaling in cardiac hypertrophy","description":"This cluster is enriched for GO terms tied to calcium-dependent NFAT signaling, notably regulation of the calcineurin-NFAT cascade and its positive regulation, together with cardiac muscle hypertrophy in response to stress (including its positive regulation). This suggests a coherent theme of calcium-activated transcriptional signaling driving cardiac hypertrophic responses. Other terms such as regulation of presynaptic calcium concentration and oxidative processes likely reflect related calcium signaling biology but do not define the core function of the cluster.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0042554","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0014898","count":2}]},{"hash":"264151397956597608","title":"Proteostasis and Stress Response","description":"This cluster is dominated by terms tied to maintaining protein quality and managing cellular stress: proteasomal regulation, ubiquitination and sumoylation, aggrephagy, and ER stress\u2013related signaling. Additional terms for response to toxic substances and nucleotide-excision repair suggest broader genomic and cellular-stress safeguards, and spindle pole body duplication hints at coordination with cell-cycle processes. Overall, the cluster seems to group proteins involved in proteostasis and stress-response pathways.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030474","count":14},{"id":"GO:1901799","count":14},{"id":"GO:0051865","count":14},{"id":"GO:0097237","count":14},{"id":"GO:0016925","count":14}]},{"hash":"26234880567151241","title":"Protein Processing and Modification","description":"The cluster is driven by proteolysis and protein deglycosylation, pointing to protein maturation/remodeling, with additional terms hinting at amino acid catabolism and development/immune signaling contexts.","confidence":"Medium","size":15,"edges":78,"triangles":196,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0033345","count":1},{"id":"GO:0006559","count":1},{"id":"GO:0006517","count":1},{"id":"GO:0038161","count":1}]},{"hash":"365165571087783267","title":"Stress-Response and Immune Regulation","description":"The GO terms cluster around stress-responsive processes (unfolded protein response, glucocorticoid signaling, cardiac hypertrophy in response to stress) and immune regulation (T cell homeostasis, negative regulation of T cell cytotoxicity, calcineurin-NFAT signaling). While there is an outlier for lung epithelial differentiation, the dominant theme ties cellular stress responses to immune signaling, suggesting these proteins function in stress- and immune-related pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0043029","count":3},{"id":"GO:2001034","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0014898","count":2}]},{"hash":"1092907066731340026","title":"Cerebellar development and Bergmann glial differentiation","description":"Most terms point to nervous system development, especially cerebellum-specific processes: Bergmann glial cell differentiation and cerebellar cortex formation, along with broader nervous system and multicellular organism development. Although insulin signaling and metabolic terms appear, the cerebellar development signals dominate, suggesting proteins in this cluster function in cerebellar development and Bergmann glial differentiation.","confidence":"High","size":15,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0008285","count":13},{"id":"GO:0060020","count":13},{"id":"GO:0050852","count":13},{"id":"GO:0048679","count":13},{"id":"GO:0008286","count":13}]},{"hash":"789527987113209662","title":"Neural development and cell adhesion","description":"This cluster centers on neural development signals, with GO terms for neuron projection development and forebrain development, plus cell adhesion, which are key for neural patterning and connectivity. Additional terms point to gene regulation (chromatin organization, histone methylation) that underlies developmental programs, and to CNS-associated processes like glial apoptosis and inflammatory cytokine production. Together, the dominant theme is neural development and neuronal/glial interactions, with supporting regulatory mechanisms.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":2},{"id":"GO:0002534","count":1},{"id":"GO:0043547","count":1},{"id":"GO:2000011","count":1},{"id":"GO:0000724","count":1}]},{"hash":"1596362183785847635","title":"Mitochondrial Metabolite Transport","description":"The cluster's top GO terms mainly describe transport of metabolites and cofactors across the mitochondrial membrane (ADP/ATP, CoA, thiamine pyrophosphate, nucleotides, Mn2+), with supporting mitochondrial localization and apoptotic signals, suggesting a cohesive function in mitochondrial transport and metabolism.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":6},{"id":"GO:0035349","count":6},{"id":"GO:0007565","count":6},{"id":"GO:0015709","count":6},{"id":"GO:0006828","count":6}]},{"hash":"676573570547941641","title":"Cell cycle and DNA replication regulation","description":"The top GO terms are dominated by cell division, DNA replication, APC-dependent catabolic processes, and nuclear pore localization, indicating proteins likely coordinating cell cycle progression and replication with nuclear transport. Other terms like JNK regulation and extrinsic apoptotic signaling suggest broader regulatory roles, and viral mRNA export hints at nuclear transport involvement, but the core signal points to cell cycle/DNA replication control. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0086014","count":2},{"id":"GO:0031081","count":2},{"id":"GO:0021915","count":2},{"id":"GO:0070979","count":2}]},{"hash":"828927697467239139","title":"Neuronal signaling and behavior regulation","description":"This cluster centers on neuronal signaling and excitability: potassium ion transport, intracellular signal transduction, GPCR-PLC signaling-related activity, and especially synaptic vesicle fusion regulation. Coupled with behavioral terms such as locomotory behavior, prepulse inhibition, and responses to ethanol and lithium, the proteins likely function in neural signaling and behavior modulation. A single unrelated term (peptidoglycan catabolic process) may reflect noise or mixed annotations but does not override the dominant neural theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0051482","count":3},{"id":"GO:0043488","count":2},{"id":"GO:0060134","count":2}]},{"hash":"2042490071910392352","title":"Neuronal GPCR Signaling and Sensory Perception","description":"The top GO terms point to GPCR-mediated signaling and synaptic regulation in neurons, with notable associations to sensory modalities (vision, taste) and GABA signaling, plus receptor internalization and responses to electrical stimuli, suggesting a cohesive cluster of neural signaling and sensory perception processes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031631","count":2},{"id":"GO:0007196","count":2},{"id":"GO:0038042","count":2},{"id":"GO:0050908","count":2},{"id":"GO:0007214","count":2}]},{"hash":"809183147938617493","title":"Cardiac development","description":"Two top GO terms are outflow tract morphogenesis and endocardial cushion development, which are core to heart formation (cardiogenesis). While other terms in the set cover diverse processes (translation regulation, ubiquitination/deubiquitination, peroxisome fission, stress responses), the strongest enrichment centers on cardiac development, justifying the label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003151","count":2},{"id":"GO:0003197","count":2},{"id":"GO:0045471","count":1},{"id":"GO:0000338","count":1},{"id":"GO:0006446","count":1}]},{"hash":"1407829335713173675","title":"Proteostasis and Developmental Signaling","description":"The cluster centers on protein ubiquitination and proteasome regulatory particle assembly, indicating a proteostasis core. Additional terms point to intracellular signaling and broad developmental processes (including cardiac morphogenesis and immune cell differentiation), suggesting these proteins couple protein turnover to regulatory signaling and tissue development. This theme ties together degradation, signaling, and morphogenesis across tissues.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":8},{"id":"GO:0070682","count":8},{"id":"GO:0050960","count":8},{"id":"GO:0035556","count":8},{"id":"GO:1901594","count":8}]},{"hash":"1574883881647450530","title":"Unknown","description":"The GO terms span immune, plant development, hormonal signaling, circadian regulation, neural development, and miscellaneous cellular processes, with no clear single function unifying the cluster and no edges to suggest a shared pathway; thus there is no coherent theme to name beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":4},{"id":"GO:0009911","count":4},{"id":"GO:0050853","count":4},{"id":"GO:0009742","count":4},{"id":"GO:0042752","count":4}]},{"hash":"1796799144332261333","title":"Unknown","description":"The GO terms are spread across ion homeostasis, immune activity (innate immune response and classical complement activation), and development (oligodendrocyte differentiation, somite development), with only loosely related processes. Because there is no single cohesive functional theme tying the cluster together, it\u2019s best labeled Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006883","count":4},{"id":"GO:0006958","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0048709","count":3}]},{"hash":"2165279012566768456","title":"DNA replication and sister chromatid cohesion","description":"Most terms point to nuclear processes in the cell cycle, notably DNA replication and cohesion of sister chromatids during mitosis (DNA replication; positive regulation of DNA-directed DNA polymerase activity; maintenance of mitotic sister chromatid cohesion). A few terms (germinal center formation, B cell receptor signaling, brassinosteroid signaling, circadian rhythm, flower development) are likely annotations from other contexts and do not fit the core theme, but they do not override the dominant replication/mitosis signal.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":1},{"id":"GO:0009911","count":1},{"id":"GO:0050853","count":1},{"id":"GO:0009742","count":1},{"id":"GO:0042752","count":1}]},{"hash":"1712492790505556248","title":"Presynaptic vesicle trafficking and Golgi transport","description":"This cluster centers on vesicle movement and sorting in neurons, highlighted by terms for endocytosis, anterograde synaptic vesicle transport, synaptic vesicle budding, and Golgi localization/transport. Although a few terms touch on broader neuronal development, the strongest shared theme is presynaptic vesicle recycling and Golgi-to-transport pathways that support synaptic function in neurons such as Purkinje cells.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0009615","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0051645","count":1},{"id":"GO:0048490","count":1}]},{"hash":"359948534817416239","title":"Developmental cell adhesion and Notch signaling","description":"The cluster centers on adhesion-related processes (cell-matrix and cell-cell adhesion, receptor clustering, hemidesmosome assembly, cell spreading) and morphogenesis (palatal shelf, pericardium; endothelial Notch pathway example), indicating a cohesive theme of adhesion-mediated developmental morphogenesis with Notch as a regulatory element.","confidence":"High","size":14,"edges":30,"triangles":45,"max_degree":8,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:1990134","count":7},{"id":"GO:0003344","count":7},{"id":"GO:0045662","count":6},{"id":"GO:0007161","count":6},{"id":"GO:0097150","count":6}]},{"hash":"866541359398219770","title":"Ribosome biogenesis and RNA processing","description":"The cluster is dominated by ribosome-related processes (ribosome biogenesis, small subunit assembly, and rRNA maturation for SSU/LSU/5.8S) and includes translation and mRNA export terms, pointing to a core function in ribosome production and RNA maturation/transport; additional RNA regulatory terms suggest broader RNA processing roles. Confidence: High","confidence":"","size":14,"edges":13,"triangles":2,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000028","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0048026","count":2}]},{"hash":"1744226248165929256","title":"Transcription Regulation with Proteostasis and Microtubule Assembly","description":"This cluster centers on transcription regulation by RNA polymerase II (elongation and DNA-templated transcription) and includes strong signals for protein folding, chaperone-mediated assembly, ubiquitin-proteasome\u2013mediated quality control, and microtubule/cytoskeletal assembly. The co-occurrence of transcription-related terms with proteostasis and tubulin/cytoskeleton organization suggests a connected theme where gene expression regulation is linked to protein homeostasis and cytoskeletal dynamics.","confidence":"Medium","size":14,"edges":11,"triangles":0,"max_degree":5,"top_function":"protein folding","top_go_terms":[{"id":"GO:0032968","count":5},{"id":"GO:0051131","count":5},{"id":"GO:0007021","count":4},{"id":"GO:0006457","count":4},{"id":"GO:0043622","count":4}]},{"hash":"2299858113749243025","title":"Heterochromatin formation and H3K9 methylation","description":"The top GO terms cluster around chromatin state and histone modification, notably pericentric heterochromatin formation and regulation of H3K9 methylation/acetylation, plus related desuccinylation. Other terms (apoptosis, ovulation, etc.) seem incidental, so the core theme is chromatin epigenetic regulation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990141","count":1},{"id":"GO:1900113","count":1},{"id":"GO:2000111","count":1},{"id":"GO:1905555","count":1},{"id":"GO:0001542","count":1}]},{"hash":"1120677333606199453","title":"Proteostasis and Sensory Stress Signaling","description":"This cluster centers on the ubiquitin-proteasome system (ubiquitination, ubiquitin-dependent protein catabolic process, proteasome regulatory particle assembly) and includes GO terms tied to sensory stress such as temperature detection and mechanical stimulus; together with intracellular signaling, suggesting a group of proteins linking protein turnover to physical stress sensing and signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0033280","count":5},{"id":"GO:2001275","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0042787","count":4}]},{"hash":"1530769424429854012","title":"Nucleotide Biosynthesis and RNA Editing","description":"The cluster is dominated by nucleotide-related processes: UMP salvage, uridine biosynthesis, cytidine metabolism, and deoxycytidine catabolic processes, along with tRNA wobble adenosine-to-inosine editing, indicating a core theme of nucleotide metabolism and RNA modification. Some terms like abscisic acid biosynthesis and aluminum ion response suggest broader stress signaling, but they do not define the primary function, which appears to be nucleotide/nucleoside metabolism and RNA editing.","confidence":"Medium","size":14,"edges":81,"triangles":266,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":6},{"id":"GO:0010044","count":6},{"id":"GO:0009231","count":5},{"id":"GO:0044206","count":5},{"id":"GO:0002100","count":5}]},{"hash":"1731067940150986278","title":"ERAD and Proteostasis Regulation","description":"This cluster centers on ER quality control and proteostasis, highlighted by ERAD/ubiquitin pathway components, deubiquitination, and proteasome regulation. Tail-anchored protein insertion into the ER membrane and translation terms further emphasize protein handling in the secretory pathway, with some ancillary processes like cell morphogenesis and spindle-related functions contributing less directly. ","confidence":"Medium","size":14,"edges":86,"triangles":310,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":9},{"id":"GO:0016925","count":7},{"id":"GO:0016579","count":6},{"id":"GO:0071816","count":6},{"id":"GO:0006412","count":6}]},{"hash":"424427773800275785","title":"Cell stress response and apoptosis","description":"Based on the top GO terms, the cluster centers on cellular stress responses across immune and neural contexts (e.g., response to lipopolysaccharide, response to X-ray, wound healing) and programmed cell death processes (glial apoptotic process, ectopic germ cell programmed cell death), with additional links to autophagy regulation and neural development (hippocampus). This suggests a cohesive theme of stress-induced responses and apoptosis, rather than a single strict pathway, capturing both immune-related and neural-associated processes.","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":2,"top_function":"wound healing","top_go_terms":[{"id":"GO:0043029","count":10},{"id":"GO:0032496","count":9},{"id":"GO:0016241","count":9},{"id":"GO:0045736","count":9},{"id":"GO:0010165","count":9}]},{"hash":"2189511443075818920","title":"ECM interactions in neural development","description":"Top GO terms show a strong emphasis on collagen fibril organization and cell-matrix adhesion, together with CNS development and axonogenesis-related terms (optic nerve morphogenesis, central nervous system development, positive/negative regulation of axonogenesis). This pattern suggests proteins involved in extracellular matrix\u2013mediated guidance and remodeling during neural development and axon growth. While some terms relate to immune clearance, the dominant theme is ECM and neural development. ","confidence":"High","size":14,"edges":50,"triangles":72,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":3},{"id":"GO:0007160","count":3},{"id":"GO:0007417","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0043277","count":3}]},{"hash":"623776138760669523","title":"Angiogenesis and vascular integrity signaling","description":"This cluster centers on endothelial signaling and vascular regulation: negative regulation of angiogenesis, vascular permeability, Tie signaling, RTK activation, and cell-matrix adhesion, with supporting immune-related functions like platelet activation and complement/immune activation, suggesting a coordinated angiogenesis-vascular-immune module. The locomotory behavior term is less connected but does not override the vascular/angiogenesis theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035641","count":5},{"id":"GO:0002740","count":3},{"id":"GO:0030168","count":3},{"id":"GO:0001867","count":3},{"id":"GO:0043116","count":3}]},{"hash":"356089801906407591","title":"Vesicle trafficking and GTPase signaling","description":"The top GO terms cluster around small GTPase\u2013mediated signaling and vesicle transport steps (ER\u2013Golgi, Golgi-to-transport, endosome-to-lysosome), plus processes like synaptic vesicle budding and acrosome assembly. This suggests a coherent function in regulating vesicle trafficking via GTPase activity, with broader implications for secretory pathways and membrane dynamics in specialized cell types. ","confidence":"High","size":14,"edges":16,"triangles":6,"max_degree":10,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0033601","count":9},{"id":"GO:0055108","count":9},{"id":"GO:0043547","count":9},{"id":"GO:1902647","count":9},{"id":"GO:0060999","count":9}]},{"hash":"1911953039701596566","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":38,"triangles":53,"max_degree":9,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006260","count":13},{"id":"GO:0006310","count":13},{"id":"GO:0071051","count":12},{"id":"GO:0034476","count":12},{"id":"GO:0010501","count":12}]},{"hash":"228558733986079819","title":"Craniofacial and ocular morphogenesis","description":"These proteins cluster around embryonic development of craniofacial structures, particularly the eye. GO terms like camera-type eye development, optic cup morphogenesis, olfactory pit development, face development, and neural crest cell development all point to coordinated craniofacial/ocular morphogenesis, with neural crest contributing to craniofacial tissues.","confidence":"High","size":14,"edges":51,"triangles":115,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031076","count":11},{"id":"GO:0010133","count":11},{"id":"GO:0050885","count":11},{"id":"GO:0032180","count":11},{"id":"GO:0009447","count":11}]},{"hash":"1937991682742175664","title":"Unknown","description":"The GO terms are highly diverse, spanning bacterial metabolite biosynthesis (mycothiol), plant development (leaf formation, melatonin biosynthesis), chromatin-related processes (heterochromatin formation, sister chromatid cohesion, histone/H4 acetylation), and various acetylation steps. There isn\u2019t a coherent, single biological function tying all proteins together, so a confident, representative label cannot be formulated.","confidence":"","size":14,"edges":10,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":2},{"id":"GO:0071962","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0060358","count":2},{"id":"GO:0043967","count":2}]},{"hash":"112031306580017389","title":"Translation and ribosome assembly","description":"The top GO terms are dominated by core translation processes (initiation, elongation, termination), ribosomal subunit assembly, and selenocysteine incorporation, spanning both cytosolic and mitochondrial translation. This suggests the cluster mainly comprises proteins involved in the protein synthesis machinery, with a few ancillary RNA-processing terms that are less central to the core theme.","confidence":"High","size":14,"edges":88,"triangles":331,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0006415","count":5},{"id":"GO:0000027","count":3},{"id":"GO:0001172","count":2},{"id":"GO:1902802","count":2}]},{"hash":"2013055551822849558","title":"Neural development and axonal protein localization","description":"This cluster is dominated by terms about nervous system development, corpus callosum formation, and targeting of proteins to juxtaparanode regions of axons, pointing to CNS development and precise axonal protein localization as the main theme. Immune-related terms and ECM remodeling appear but are less central to the core function of the cluster.","confidence":"Medium","size":14,"edges":66,"triangles":155,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":9},{"id":"GO:0030199","count":9},{"id":"GO:0038161","count":8},{"id":"GO:1902948","count":8},{"id":"GO:0097350","count":8}]},{"hash":"15673256792039006","title":"Neuronal development and cytoskeletal remodeling","description":"This cluster is enriched for nervous system development and dendrite morphogenesis, plus cytoskeletal and adhesion processes (stress fiber and spindle assembly, epithelial adhesion, cell migration), with signaling pathways such as Roundabout and T cell receptor\u2013related signaling and ApoA-I\u2013mediated signaling. The combination points to developmentally driven cytoskeletal dynamics and cell movement, particularly in neuronal contexts. ","confidence":"Medium","size":14,"edges":48,"triangles":62,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":9},{"id":"GO:0050852","count":9},{"id":"GO:0035385","count":9},{"id":"GO:0090307","count":7},{"id":"GO:0035099","count":7}]},{"hash":"1745713665176448175","title":"Broad-Spectrum Transmembrane Transporters","description":"The cluster is dominated by GO terms for transporting a wide range of solutes across membranes, including nitrate/nitrite, vitamins, xenobiotics, phosphate, sugars, ions, and even neurotransmitter loading into synaptic vesicles. This points to membrane transporter proteins with broad substrate scope rather than a single substrate class, representing diverse transmembrane transport functions.","confidence":"High","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0042128","count":13},{"id":"GO:0035461","count":12},{"id":"GO:0006855","count":12},{"id":"GO:0035435","count":11},{"id":"GO:0015757","count":11}]},{"hash":"1249222541114880580","title":"Ubiquitination and Endosomal Sorting","description":"The top GO terms cluster around ubiquitination and vesicle trafficking pathways: protein ubiquitination, early endosome to late endosome transport, multivesicular body sorting, and melanosome assembly\u2014clearly pointing to ubiquitin-mediated cargo sorting in the endocytic pathway. Adherens junction organization and GPCR signaling further support roles in membrane protein turnover and surface signaling, which fit with trafficking processes. Overall, the theme is ubiquitin-driven endosomal sorting and vesicle trafficking, with melanosome-related context.","confidence":"High","size":14,"edges":32,"triangles":28,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016567","count":14},{"id":"GO:0034332","count":14},{"id":"GO:0032949","count":14},{"id":"GO:0007097","count":14},{"id":"GO:0007399","count":14}]},{"hash":"1036374586050283498","title":"Unknown","description":"The top GO terms cover immune signaling, neuronal projection, vascular development, cardiac conduction, and general signaling, with no single unifying function. This diversity suggests the proteins do not share a cohesive biological role that can be summarized by a single GO-driven theme, so the cluster is best labeled Unknown.","confidence":"","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0045401","count":1},{"id":"GO:1905404","count":1},{"id":"GO:0097490","count":1},{"id":"GO:1905065","count":1},{"id":"GO:0035023","count":1}]},{"hash":"252288226957501858","title":"Histone Modification and Transcription","description":"The dominant GO terms are histone modifications (H3K9 methylation, H3K4 trimethylation/dimethylation, H3K27 trimethylation, H3K27 acetylation regulation) and transcription-related processes (DNA-templated transcription, mRNA splicing). This points to a cluster of proteins involved in chromatin regulation and control of gene expression, with some developmental context (placenta morphogenesis) suggesting broader roles in regulation during development. Despite no observed interactions, the shared epigenetic and transcriptional functions justify this label.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070651","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1689521422157778906","title":"Endosomal Transport and Localization","description":"This cluster is dominated by GO terms for endosome trafficking and localization (early to late endosome transport, Golgi to endosome transport, protein localization to endosome). The convergence of these terms suggests a cohesive role in vesicular transport involving endosomes. Some secondary terms reference cytoskeletal regulation and mitotic processes, which may reflect ancillary roles in cell shape changes and division, but the core signal remains endosomal transport/localization.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045022","count":2},{"id":"GO:0035646","count":2},{"id":"GO:0036010","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0071963","count":2}]},{"hash":"314310282504250912","title":"Vesicle trafficking and exocytosis regulation","description":"This cluster\u2019s top GO terms cluster around the secretory/endomembrane pathway: ER-to-Golgi transport, Golgi organization, and endosome transport/maturation, plus membrane fusion events like synaptic vesicle fusion and the acrosome reaction. Additional terms related to secretion regulation (norepinephrine and immunoglobulin) and membrane lipid metabolism support vesicle dynamics. Together, they suggest a cohesive theme of vesicle trafficking, Golgi function, and regulated exocytosis.","confidence":"Medium","size":14,"edges":21,"triangles":7,"max_degree":10,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0097352","count":5},{"id":"GO:1903358","count":5},{"id":"GO:0031629","count":4},{"id":"GO:0007340","count":4}]},{"hash":"1772663888065281666","title":"Immune clearance and endothelial remodeling","description":"These proteins show strong links to immune clearance (apoptotic cell clearance, complement activation, inflammatory response) alongside endothelial activities (proliferation, migration) and lipoprotein handling, with extracellular matrix organization (collagen fibril) as well. The combination suggests a coordinated program where clearance/immune signaling intersects with vascular/endothelial remodeling and ECM dynamics, potentially in development or inflammatory contexts.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":13},{"id":"GO:0006958","count":13},{"id":"GO:0070207","count":13},{"id":"GO:0061053","count":13},{"id":"GO:0042953","count":13}]},{"hash":"1537180862874427318","title":"Calcium-regulated cardiac and skeletal muscle contraction","description":"This cluster is dominated by GO terms related to calcium ion detection, calcium-mediated regulation of cardiac muscle contraction, and skeletal muscle fiber development, indicating a core theme of calcium signaling governing muscle contraction in heart and skeletal muscle. While some terms touch on broader development and transcriptional regulation, the recurring calcium- and contraction-focused terms strongly bind the proteins into a calcium-signal-to-muscle-contraction cluster.","confidence":"High","size":14,"edges":33,"triangles":28,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0014898","count":6},{"id":"GO:0048708","count":6},{"id":"GO:0010881","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0072221","count":6}]},{"hash":"2300044461706451221","title":"Neural development and neuromuscular function","description":"This cluster highlights terms for spinal cord motor neuron differentiation, neuromuscular processes, and musculoskeletal movement, along with insulin-like growth factor receptor signaling, suggesting a neural development/neuromuscular function theme. Additional terms for translation and rRNA maturation appear less central to the main pattern.","confidence":"Low","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048009","count":2},{"id":"GO:0006412","count":1},{"id":"GO:1903146","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0000466","count":1}]},{"hash":"1176533149969581906","title":"Proteostasis and Carbohydrate Metabolism","description":"The top GO terms point to both protein turnover processes (ubiquitination and proteasome assembly) and carbohydrate-related metabolism (carbohydrate phosphorylation and multiple catabolic pathways). While there are some additional, less cohesive terms, the strongest, recurring themes are proteostasis and energy/ carbohydrate metabolism, suggesting a cluster centered on protein turnover linked to metabolic processing.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046835","count":5},{"id":"GO:0016567","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046365","count":2}]},{"hash":"1095148072295859231","title":"Ciliary/Photoreceptor Assembly and Hormone Signaling","description":"The top GO terms cluster around non-motile cilium assembly and protein localization to the photoreceptor outer segment, alongside male sex differentiation and prostate gland development driven by steroid hormone receptor signaling. This points to a cohesive theme of ciliogenesis and photoreceptor biology intertwined with hormone-mediated reproductive differentiation; a few immune-response terms may reflect broader signaling connections or annotation noise.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046661","count":10},{"id":"GO:0006463","count":10},{"id":"GO:0030850","count":10},{"id":"GO:0071357","count":10},{"id":"GO:1905515","count":9}]},{"hash":"1492117293500948585","title":"Ubiquitin\u2013proteasome system components","description":"This cluster is dominated by GO terms for protein ubiquitination and proteasome regulatory particle assembly, suggesting a core function in protein turnover and regulation. Additional terms point to ubiquitin-regulated signaling affecting temperature sensing, vitamin D and other responses, as well as cell migration and differentiation, implying broader signaling roles tied to ubiquitination. Overall, the central theme is ubiquitin\u2013proteasome\u2013driven regulation of cellular signaling.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":10},{"id":"GO:0070682","count":10},{"id":"GO:0050960","count":10},{"id":"GO:0035556","count":10},{"id":"GO:1901594","count":10}]},{"hash":"92462834719099558","title":"Tyrosine kinase signaling in development","description":"The terms cluster around tyrosine phosphorylation-driven signaling and downstream cascades (autophosphorylation, ERK/ERK1/2, PI3K, STAT), with associations to Schwann cell development, heart development, motor neuron guidance, and related developmental processes, plus a reproductive capacitation link\u2014pointing to a broad developmental signaling theme rather than a single tissue-specific function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0014044","count":6},{"id":"GO:0090314","count":6},{"id":"GO:0038083","count":6},{"id":"GO:0060045","count":6},{"id":"GO:0014068","count":6}]},{"hash":"1854884076451680261","title":"NF-\u03baB Activation and TNF Signaling","description":"The terms indicate activation of NF-\u03baB signaling (IKK activation, I\u03baB phosphorylation), TNF-mediated pathways, and ubiquitination events (K63-linked) regulating NF-\u03baB, all pointing to an NF-\u03baB\u2013driven innate immune response.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":10},{"id":"GO:0007250","count":10},{"id":"GO:0033209","count":10},{"id":"GO:1903721","count":10},{"id":"GO:0090073","count":10}]},{"hash":"316441506538016778","title":"Epithelial development and polarity signaling","description":"This cluster centers on tissues and processes related to epithelial development and organization: skin epidermis development and establishment of planar cell polarity are prominent, with supporting signals and regulatory pathways such as Notch and TGF-beta, plus prostaglandin biosynthesis that can influence epithelial signaling. The presence of oxidative stress and hypoxia-related terms may reflect contextual stress responses in epithelia, but the strongest cohesive theme is epithelial development and polarity signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0045746","count":5},{"id":"GO:0071456","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0030728","count":4}]},{"hash":"1042523024225433753","title":"Unknown","description":"The top terms are highly heterogeneous, spanning metal ion transport/detoxification, osmotic stress responses, and unrelated developmental processes (kidney and eye morphogenesis) along with ascospore formation. With only a few edges and no cohesive functional theme, there isn\u2019t a clear common function for the cluster, so Unknown is appropriate.","confidence":"","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":3},{"id":"GO:0070574","count":2},{"id":"GO:0006882","count":2},{"id":"GO:0010312","count":2},{"id":"GO:0072220","count":2}]},{"hash":"1347878081676735294","title":"Cell cycle control and protein ubiquitination","description":"The top GO terms are dominated by protein ubiquitination and cell cycle processes, with strong signals for intracellular signaling and transcription regulation. Although there are a few differentiation-related terms (oligodendrocyte and follicular dendritic cell differentiation), the recurring theme centers on ubiquitin-mediated regulation of the cell cycle and associated signaling. This suggests the cluster is enriched for proteins involved in cell-cycle control through ubiquitination and related post-translational modifications.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":12},{"id":"GO:0007049","count":12},{"id":"GO:0035556","count":11},{"id":"GO:1901594","count":11},{"id":"GO:0000083","count":11}]},{"hash":"333968281498955903","title":"Unknown","description":"The top GO terms are highly diverse (ribosome biogenesis, ribosomal export, cell division, apoptosis, signaling, sensory perception, cell fusion, etc.), with no single cohesive function tying the members together, and there are no reported edges, making a confident, specific label inappropriate.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:1901998","count":2},{"id":"GO:0048013","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0000055","count":2}]},{"hash":"1703419975695606792","title":"Cross-tissue developmental differentiation with Wnt signaling","description":"Top GO terms reveal differentiation and development across multiple tissues (trophoblast, somite, dentate gyrus, midbrain) with accompanying signaling-related processes, including Wnt pathway mentions. The cluster therefore seems to represent broad embryonic development across tissues rather than a single, cohesive pathway, though Wnt-related signaling is a common thread.","confidence":"Medium","size":14,"edges":21,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060718","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0042666","count":1},{"id":"GO:0061053","count":1},{"id":"GO:0021542","count":1}]},{"hash":"856050075381835825","title":"Ribosome Biogenesis and Cell Cycle","description":"The cluster centers on ribosome production and function, with multiple terms for ribosomal biogenesis, subunit export, cytoplasmic translation, and tRNA modification, plus cell-division related terms (cell cycle, cell division, cell septum assembly). This suggests a cohesive theme of ribosome assembly/translation machinery linked to proliferative processes, with a few stress-regulation or mating-related terms that are less core to the main theme.","confidence":"Medium","size":14,"edges":11,"triangles":0,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0042274","count":3}]},{"hash":"1580880882760441008","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071347","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0010923","count":1}]},{"hash":"959330495930046806","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0031175","count":2}]},{"hash":"1506436511329845299","title":"Mitotic Regulation and Proteostasis","description":"The top GO terms include spindle assembly, DNA replication initiation, ubiquitination and proteasome assembly, and protein modifications like poly-ADP-ribosylation. This combination suggests involvement in cell cycle progression (mitosis), chromatin regulation, and protein turnover. Despite some obsolete terms, the recurring themes center on mitotic control and proteostasis, justifying this label as representative of the cluster's function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":4},{"id":"GO:0016477","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0070212","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1998998070449954640","title":"Unknown","description":"The top terms span vascular, immune, sensory, and gastrointestinal processes, plus some unrelated metabolic and behavioral terms, with no clear shared function or pathway tying the proteins together. Given there are no edges or clusters connecting these terms, there is no coherent theme to define a specific, representative label beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045446","count":1},{"id":"GO:0007605","count":1},{"id":"GO:0042118","count":1},{"id":"GO:0046373","count":1},{"id":"GO:0035889","count":1}]},{"hash":"396744616122474361","title":"Developmental signaling and morphogenesis","description":"The top GO terms cluster around developmental processes across tissues (cardiac morphogenesis, endothelial differentiation, nervous system development) and signaling pathways (Notch, vitamin D response) plus mechanotransduction and even plant flower development, all pointing to regulation of development and morphogenesis rather than metabolism or immediate immune responses. Despite the cross-species mix and lack of direct interactions, the common theme is developmental regulation and tissue formation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":5},{"id":"GO:0003213","count":5},{"id":"GO:0060843","count":5},{"id":"GO:0003270","count":5},{"id":"GO:0071260","count":5}]},{"hash":"1054622190152770021","title":"Cell division and cytoskeleton regulation","description":"The top GO terms center on mitosis (mitotic spindle assembly, cell division) and cytoskeletal/adhesion dynamics (Rac signaling, adherens junctions, axon extension, TORC2 signaling), with a note that vesicle trafficking (COPII) and ubiquitination appear but are secondary. This points to a cohesive theme of coordinating cell division with cytoskeletal remodeling and cell\u2013cell interactions.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0046784","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0090114","count":3},{"id":"GO:1904515","count":3}]},{"hash":"1181301173257014443","title":"Sterol biosynthesis and lipid metabolism","description":"The top GO terms cluster around sterol production and lipid synthesis, including ergosterol and cholesterol biosynthesis, fatty acid and ether lipid metabolism, and sterol oxidation steps, indicating a cohesive theme of lipid/sterol metabolism. Some terms about myelin maintenance and sebaceous gland differentiation reflect lipid-rich contexts but do not disrupt the core lipid/metabolism signal. Therefore, this label accurately represents the cluster's function.","confidence":"High","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0035754","count":1},{"id":"GO:0006696","count":1}]},{"hash":"1704915095288550902","title":"Embryonic extracellular matrix and vascular development","description":"The dominant themes are extracellular matrix organization (collagen fibril organization) and vascular development (endothelial proliferation), with somite development and lipid transport supporting a broad developmental/embryonic context. Immune-related terms like complement activation and apoptotic cell clearance may reflect tissue remodeling during development. Together they suggest a cluster of proteins involved in embryonic connective tissue and blood vessel formation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006883","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0007565","count":2},{"id":"GO:0043277","count":2},{"id":"GO:0006958","count":2}]},{"hash":"663317730354882753","title":"Unknown","description":"The top GO terms span a highly diverse set of processes (cell division, germinal center formation, nervous system development, flower development, renal sodium absorption, wybutosine biosynthesis, ubiquitin-dependent catabolic process), with some obsolete terms and no shared functional theme. The cluster has no edges or cohesive signal, so a single interpretable label isn\u2019t supported.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0002467","count":1},{"id":"GO:0007399","count":1},{"id":"GO:2000312","count":1}]},{"hash":"1975028718657551772","title":"Neural development and embryogenesis","description":"The cluster shows strong representation of neural development terms (cerebral cortex development, neuron maturation, neuron projection development) and in utero embryonic development, suggesting proteins involved in brain development and early embryogenesis. Some other terms about hematopoietic differentiation and RNA/nucleotide metabolism appear, but they seem secondary to the dominant neural-development signal. Overall, the cluster appears tied to neural development and embryogenesis.","confidence":"Medium","size":13,"edges":39,"triangles":45,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":6},{"id":"GO:0042551","count":5},{"id":"GO:0045654","count":5},{"id":"GO:0045648","count":5},{"id":"GO:0016575","count":5}]},{"hash":"1639946055935369788","title":"Innate Immune Activation and Inflammation","description":"The top GO terms point to innate immune sensing and inflammatory signaling, with multiple entries for innate immune response, response to virus, Toll-like receptor 4 signaling, and TNF production, plus apoptotic cell clearance. Integrin signaling and hydrolase regulation hint at immune cell adhesion and enzyme activity during inflammation, while lipid storage and cholesterol homeostasis reflect metabolic aspects of immune activation. Overall, the cluster seems centered on innate immunity and inflammatory responses.","confidence":"Medium","size":13,"edges":14,"triangles":1,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0043277","count":3},{"id":"GO:2001046","count":3},{"id":"GO:0009615","count":3},{"id":"GO:0019915","count":3}]},{"hash":"665853008606801747","title":"ER proteostasis under oxidative stress","description":"The cluster is dominated by GO terms linking ER functions and redox biology: protein folding in the ER, ER stress response, cellular response to oxidative stress and hydrogen peroxide, and redox homeostasis, with related redox-modified processes like deglutathionylation and prolyl hydroxylation. While a viral process term appears, the strong emphasis on ER proteostasis and oxidative stress suggests a cohesive theme of maintaining protein folding and redox balance under stress in the secretory pathway.","confidence":"High","size":13,"edges":37,"triangles":43,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070301","count":8},{"id":"GO:0034975","count":7},{"id":"GO:0045454","count":7},{"id":"GO:0018401","count":6},{"id":"GO:0055114","count":6}]},{"hash":"758961178835472678","title":"DNA replication and genome maintenance","description":"This cluster is dominated by GO terms tied to DNA replication processes (primer synthesis, topological changes, unwinding) and a DNA damage response (SOS response), suggesting a core role in genome integrity. Secondary terms related to mRNA decay and splicing regulation, plus transcription termination events, indicate connected RNA processing activities that often accompany replication stress. Overall, the common theme is maintenance of DNA replication and genome stability, with some RNA processing links.","confidence":"Medium","size":13,"edges":13,"triangles":4,"max_degree":3,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006269","count":6},{"id":"GO:0000184","count":6},{"id":"GO:0009432","count":6},{"id":"GO:0006265","count":6},{"id":"GO:0006268","count":6}]},{"hash":"1552276123843732061","title":"Ubiquitin-Mediated Protein Regulation","description":"This cluster is dominated by ubiquitination-related terms (protein ubiquitination, autoubiquitination, K11-linked ubiquitination, ubiquitin-dependent pathways), pointing to a shared function in tagging proteins for turnover. While there are a few other diverse terms (DNA repair, transcription regulation, ciliary transport, cholesterol homeostasis), the ubiquitination signals are the strongest unifying theme among the top terms. ","confidence":"Medium","size":13,"edges":12,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0051865","count":2},{"id":"GO:0070911","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035735","count":2}]},{"hash":"1420287166343181490","title":"Mitochondrial dynamics and distribution","description":"The top GO terms are dominated by mitochondrial processes: membrane organization, fission, inheritance, and intracellular distribution, with supporting signals from apoptosis and neuronal GABAergic transmission that often depend on mitochondrial function. This consistent theme across terms suggests the proteins cluster around mitochondrial dynamics and inheritance. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006915","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0032456","count":5},{"id":"GO:0007006","count":5}]},{"hash":"1851034362947830944","title":"Neural development and axonal localization","description":"This cluster shows a clear emphasis on nervous system development, with terms like nervous system development, corpus callosum development, and juxtaparanode region localization, suggesting roles in neural tissue formation and axon organization. While there are a few immune-related terms, they appear less central to the core theme, so the label captures the dominant function of the cluster with moderate confidence.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0038161","count":9},{"id":"GO:1902948","count":9},{"id":"GO:0097350","count":9},{"id":"GO:0001915","count":9},{"id":"GO:0045663","count":9}]},{"hash":"617581099396711014","title":"Neural development and transcriptional regulation","description":"The cluster is dominated by terms tied to nervous system development, forebrain development, and bipolar cell polarity, all pointing to neural differentiation and tissue patterning. Coupled with DNA-templated transcription, the proteins likely function as transcriptional regulators coordinating neural development. Some immune/cytokine terms appear but are less central to the primary theme. ","confidence":"Medium","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2000727","count":13},{"id":"GO:0007399","count":13},{"id":"GO:0061246","count":13},{"id":"GO:0032633","count":13},{"id":"GO:0043433","count":13}]},{"hash":"1354454750189965752","title":"Dendritic spine morphogenesis and synapse organization","description":"The top GO terms cluster around neuronal synapse formation and organization, including dendritic spine morphogenesis, synapse assembly/organization, receptor clustering, and Rho-ERK signaling. The nervous system development term supports a role in neural maturation, pointing to a coherent theme of synapse development and spine remodeling.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0060997","count":9},{"id":"GO:0008285","count":8},{"id":"GO:0035418","count":8},{"id":"GO:0007266","count":8},{"id":"GO:0043113","count":8}]},{"hash":"2156182514320462690","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":4},{"id":"GO:0006402","count":3},{"id":"GO:0006203","count":3},{"id":"GO:0042245","count":3},{"id":"GO:0015969","count":3}]},{"hash":"175011589275895554","title":"Hematopoietic and immune signaling cluster","description":"The top GO terms center on hematopoietic progenitor differentiation, megakaryocyte development, and Toll-like receptor signaling (TLR3/7), with additional regulation of vascular permeability and ER stress responses, pointing to a group of proteins involved in immune/hematopoietic development and associated signaling pathways. One term about oligodendrocyte progenitor proliferation is an outlier but does not override the main immune/hematopoietic theme. ","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0070445","count":10},{"id":"GO:0002244","count":10},{"id":"GO:0035855","count":10},{"id":"GO:0043116","count":10},{"id":"GO:1903899","count":10}]},{"hash":"2301794687028732189","title":"Microtubule Dynamics and Cellular Transport","description":"This cluster is enriched for GO terms centered on microtubule-based processes: spindle assembly, centrosome separation, nuclear migration along microtubules, minus-end directed transport, and regulation of microtubule dynamics, along with related transport tasks such as dendritic receptor movement and chloroplast movement, indicating a cohesive theme of microtubule-driven organization and cargo transport in cells.","confidence":"High","size":13,"edges":18,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":11},{"id":"GO:0000742","count":10},{"id":"GO:0009904","count":10},{"id":"GO:0090307","count":10},{"id":"GO:0060404","count":10}]},{"hash":"519188522096594466","title":"Plant cell wall remodeling and plasmodesmata","description":"This cluster shows enrichment in plant-type cell wall modification, cellulose biosynthesis regulation, and plasmodesma organization, pointing to plant cell wall remodeling and intercellular transport. UDP-sugar metabolism terms support polysaccharide synthesis. Other terms (DNA transposition, proviral latency, symbiont entry) seem unrelated noise. Therefore, the name Plant cell wall remodeling and plasmodesmata captures the core theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009831","count":3},{"id":"GO:2001009","count":3},{"id":"GO:0009663","count":3},{"id":"GO:0052573","count":2},{"id":"GO:0006011","count":2}]},{"hash":"488095469853550015","title":"Neural Development and Synaptic Signaling","description":"This cluster is enriched for nervous system\u2013related terms, including Schwann cell development, nervous system development, and excitatory postsynaptic potential, plus a response to cocaine, pointing to neural development and synaptic activity as the primary theme. The presence of cell cycle terms (G1/S transition, DNA replication, meiotic cell cycle) suggests overlap with cell proliferation machinery, which can be active in neural progenitors; however, the dominant signals are neural development and synaptic function. Confidence: Medium","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014044","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0001915","count":2},{"id":"GO:0034501","count":2}]},{"hash":"2056616497550434594","title":"Meiosis DNA Replication and Recombination","description":"The terms cluster around DNA replication and meiotic processes, including oocyte maturation, sister chromatid cohesion during meiosis, meiotic recombination joint molecule formation, reciprocal recombination, and spindle assembly checkpoint regulation, with a note on DNA damage response. This points to a cohesive set of proteins involved in meiotic DNA replication and recombination, as well as chromosome segregation control during meiosis.","confidence":"High","size":13,"edges":66,"triangles":174,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0071897","count":4},{"id":"GO:0001556","count":3},{"id":"GO:0007066","count":3},{"id":"GO:0051106","count":3}]},{"hash":"1744207288815485439","title":"Mitotic spindle assembly and microtubule dynamics","description":"The dominant signals are mitotic processes and microtubule dynamics: mitotic cell cycle, mitotic spindle assembly, and microtubule-based movement appear with the strongest counts, supported by regulators of GTPase activity and serine/threonine kinase/autophosphorylation activity that modulate these steps. These features together suggest a module centered on cell division machinery and cytoskeletal regulation; other terms like development and hypoxia reflect broader cellular context but are not core to the cluster.","confidence":"High","size":13,"edges":26,"triangles":19,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0043547","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0031954","count":6},{"id":"GO:0071902","count":6}]},{"hash":"2144655704302432401","title":"Immune cell development and signaling","description":"These GO terms indicate immune system development and cytokine-mediated signaling, including hemopoiesis, NK T cell differentiation, B cell maturation, and responses to interleukins. The presence of PI3K and NF-kappaB signaling terms suggests downstream pathways governing lymphocyte activation and survival. Although the network has no edges, the shared functional themes point to a cluster of proteins involved in immune cell development and signaling.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0071372","count":2},{"id":"GO:0032633","count":2}]},{"hash":"1716806859118309028","title":"Neuronal development and synaptic plasticity","description":"The cluster shows strong enrichment for brain-related processes: telencephalon development, visual perception, long-term potentiation, integrin-mediated signaling, and cell-matrix adhesion, all aligning with neural development and synaptic connectivity/plasticity. Other terms like mRNA processing and telomere maintenance appear peripheral to this core neural theme. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007160","count":8},{"id":"GO:0035994","count":8},{"id":"GO:0007229","count":7},{"id":"GO:0021537","count":7},{"id":"GO:0060291","count":7}]},{"hash":"520757658067852503","title":"Mitochondrial Lipid Metabolism and Dynamics","description":"The top terms cluster strongly around mitochondrial function and membrane biology: positive regulation of mitochondrial DNA replication, mitochondrial membrane potential, stress-induced mitochondrial fusion, and cardiolipin metabolic processes, alongside lipid localization. This points to a cohesive theme of mitochondrial lipid metabolism and dynamics driving cellular energy and signaling. Some immune/neuronal terms (IL-2 production, dopaminergic synaptic transmission) may reflect broader signaling contexts where mitochondria play a modulatory role, but the core pattern is mitochondria-centered. ","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0090297","count":7},{"id":"GO:0010876","count":7},{"id":"GO:1900210","count":7},{"id":"GO:0032623","count":7},{"id":"GO:0010918","count":7}]},{"hash":"264141704242471698","title":"Tetrapyrrole biosynthesis","description":"The cluster is enriched for GO terms related to the biosynthesis of tetrapyrroles, especially heme and cobalamin pathways (protoporphyrinogen IX biosynthesis, heme biosynthetic process, cobalamin biosynthetic process). While a few other metabolic terms appear, the dominant theme ties to tetrapyrrole formation, justifying this label.","confidence":"Medium","size":13,"edges":49,"triangles":91,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0048738","count":1}]},{"hash":"1857429463943682149","title":"Amino acid and cofactor biosynthesis with stress responses","description":"The top GO terms cluster around biosynthetic processes for amino acids (threonine, methionine), and cofactors/cofactors-related pathways (NAD+, CoA, pantothenate, tetrahydromethanopterin), plus lipid-related cholesterol biosynthesis. The presence of sporulation and xenobiotic/cadmium response terms suggests environmental stress responsiveness. Together, these indicate a metabolic module focused on biosynthesis with accompanying stress adaptation, rather than a single, tightly connected complex. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0046686","count":2},{"id":"GO:0009435","count":2},{"id":"GO:0009088","count":2}]},{"hash":"651446920059532783","title":"Endosomal-Vacuolar Trafficking","description":"The top GO terms cluster around endocytosis, Golgi/endosome transport, and multivesicular body sorting to the vacuole, indicating a shared role in endomembrane trafficking. Some terms are incidental noise (pregnancy, cardioblast fate), but the dominant theme is protein sorting and delivery to vacuoles via endosomes.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0007565","count":1},{"id":"GO:0032511","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0015032","count":1}]},{"hash":"250405679627432126","title":"Heart development and cardiac muscle signaling","description":"The top GO terms emphasize cardiac morphogenesis (outflow tract, left ventricle) and regulation of cardiac muscle electrophysiology (atrial action potential, Purkinje signaling) along with calcium handling in the sarcoplasmic reticulum, which together point to heart development and cardiac muscle function. Some terms like skin development and ossification appear less central and may reflect broader tissue associations in the cluster, but the dominant theme is cardiac formation and calcium-dependent signaling in heart muscle. ","confidence":"High","size":13,"edges":34,"triangles":41,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903244","count":9},{"id":"GO:0097050","count":7},{"id":"GO:0014808","count":7},{"id":"GO:0003151","count":7},{"id":"GO:0007275","count":7}]},{"hash":"717955062967008158","title":"Neural development and axon maturation","description":"These proteins are mainly associated with nervous system development, forebrain development, nerve maturation, and neuronal projection/axon targeting (e.g., sympathetic neuron projection extension and juxtaparanode axon localization), suggesting a coherent theme of neural development and axon maturation. A few terms (immune signaling or cardiac differentiation) are present but do not define the cluster; overall, the neural development signal is strong.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000727","count":1},{"id":"GO:0097490","count":1},{"id":"GO:0001805","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0061246","count":1}]},{"hash":"433995406546295467","title":"Unknown","description":"The GO terms span transcriptional regulation, amino acid metabolism, lignan biosynthesis/catabolism, and lipopolysaccharide biosynthesis, plus an obsolete redox term\u2014there is no clear, unifying function linking these proteins.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001081","count":1},{"id":"GO:0006541","count":1},{"id":"GO:1902131","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1902135","count":1}]},{"hash":"819722135691929081","title":"Sperm flagellum assembly and motility","description":"This cluster is enriched for terms related to cilia/axoneme structure and movement, particularly in sperm: axoneme assembly, flagellated sperm motility, and cilium movement. Also includes microtubule severing and tubulin polyglycylation, post-translational modifications important for stable axonemes. The presence of oogenesis and epithelial cilium movement broadens to germline ciliogenesis and ciliary functions in epithelia. Overall, the proteins likely participate in cilium/flagellum assembly and motility, especially in the sperm lineage.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0048477","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0018094","count":1}]},{"hash":"1225043716865226192","title":"Mitochondrial Transporters and Cofactor Uptake","description":"The cluster is dominated by GO terms describing transport of cofactors and metabolites across mitochondrial membranes (ADP, thiamine pyrophosphate, coenzyme A, pyrimidine nucleotides, thiosulfate, manganese ions) and mitochondrial localization/apoptosis, indicating a cohesive set of mitochondrial transport and related metabolic proteins; insulin response and pregnancy terms may reflect broader roles or annotation noise.","confidence":"High","size":13,"edges":17,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":4},{"id":"GO:0008637","count":3},{"id":"GO:0035349","count":3},{"id":"GO:0007565","count":3},{"id":"GO:0015709","count":3}]},{"hash":"848875564285327151","title":"Unknown","description":"The GO terms are highly diverse across membrane localization, autophagy, necroptosis, development, and sporulation, with no single unifying function. This heterogeneity suggests the cluster doesn\u2019t reflect a cohesive biological module, so a generic Unknown label is appropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072661","count":2},{"id":"GO:0010761","count":2},{"id":"GO:2000786","count":2},{"id":"GO:1990000","count":2},{"id":"GO:1901026","count":2}]},{"hash":"338308552037607929","title":"Calcium-Dependent Signaling and Stress Response","description":"The cluster is dominated by GO terms tied to calcium ion detection, regulation of calcineurin-NFAT signaling, and cardiac hypertrophy in response to stress, suggesting a core theme of calcium-mediated signaling linking immune and stress responses. While other terms (metabolic catabolic processes, development) appear, they are less central to the cluster\u2019s main signal transduction focus.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005513","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0060325","count":1},{"id":"GO:0000272","count":1}]},{"hash":"449407601058868173","title":"Rho GTPase\u2013Actin Cytoskeleton Regulation","description":"The cluster is centered on Rho signaling and actin cytoskeleton organization (regulation of Rho protein signal transduction, actin cytoskeleton organization, activation of GTPase activity), pointing to coordinated cytoskeletal remodeling driven by Rho GTPases. While other terms touch on broader signaling and remodeling contexts (synapse assembly, angiogenesis, insulin signaling), the dominant theme is cytoskeletal dynamics governed by Rho GTPases.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0030036","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0008286","count":3}]},{"hash":"1260415321975156313","title":"Meiosis Chromosome Condensation and Synaptonemal Complex Regulation","description":"This cluster is dominated by GO terms tied to meiotic chromatin dynamics, including synaptonemal complex assembly/disassembly, meiotic chromosome condensation and separation, and regulation of meiotic DSB formation, with related mitotic condensation terms suggesting a broader chromatin-organization theme. A couple of outliers (SNARE regulation, hydrogen peroxide\u2013related death) are present but don\u2019t override the primary meiotic/chromatin signal.","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0007130","count":1},{"id":"GO:0070550","count":1},{"id":"GO:0070194","count":1}]},{"hash":"671739761647869763","title":"Inflammation-driven vascular remodeling and ECM regulation","description":"Based on the GO terms, the cluster centers on inflammatory signaling (response to lipopolysaccharide, inflammatory response) and vascular/ECM dynamics (regulation of angiogenesis via endothelial proliferation, hyaluronan biosynthesis, glomerular basement membrane development, coagulation). The inclusion of mechanotransduction and a cocaine-related behavioral response reinforces a theme of stress-related vascular remodeling and ECM modulation. This combination supports a coherent label focusing on inflammation-associated vascular and extracellular matrix changes. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032496","count":3},{"id":"GO:1903588","count":3},{"id":"GO:0006954","count":3},{"id":"GO:1900127","count":3},{"id":"GO:0071260","count":3}]},{"hash":"111129049303692324","title":"Multisystem Developmental Signaling","description":"The top GO terms point to development and signaling across tissues\u2014nervous system and CNS development, B cell receptor signaling, angiogenesis regulation, integrin signaling, sarcomere organization, and left/right symmetry determination. This suggests a broad, pleiotropic developmental signaling module rather than a single, cohesive pathway. The absence of edges may reflect dispersed protein roles across systems or annotation noise. I label this as Multisystem Developmental Signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0007417","count":2},{"id":"GO:0045765","count":2},{"id":"GO:0045214","count":2}]},{"hash":"253557823239039039","title":"TLR4-driven inflammatory signaling and lipid metabolism","description":"These proteins collectively map to innate immune responses via TLR4/LPS and TNF pathways, including necroptosis, with concurrent associations to lipid storage and cholesterol homeostasis, suggesting an inflammation\u2013lipid metabolism module.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009615","count":3},{"id":"GO:0019915","count":3},{"id":"GO:0050885","count":3},{"id":"GO:0051345","count":3},{"id":"GO:0032760","count":3}]},{"hash":"544476978376505089","title":"Neurocardiac Ion Channel Clustering and Sarcomere Organization","description":"Top GO terms indicate clustering of voltage-gated potassium channels, heart and nervous system development, and sarcomere organization, pointing to a shared theme of ion-channel assembly and cytoskeletal/muscular development in neural and cardiac tissues. While some immune-related terms appear, the dominant signal centers on ion-channel organization and neuro-muscular development.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045163","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0045214","count":6},{"id":"GO:0032516","count":5}]},{"hash":"1471987698838466361","title":"Embryonic vascular ECM remodeling","description":"The top GO terms cluster around collagen fibril organization, endothelial proliferation, and lipoprotein transport/clearance, which together point to extracellular matrix remodeling during vascular development in embryogenesis/pregnancy. Other terms about somite development and immune clearance are present but the strongest signal aligns with developmental ECM-vascular processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016540","count":2},{"id":"GO:0007565","count":1},{"id":"GO:0043277","count":1},{"id":"GO:0006958","count":1},{"id":"GO:0070207","count":1}]},{"hash":"714914755679087415","title":"GABAergic synaptic vesicle cycling","description":"The top GO terms cluster around presynaptic vesicle trafficking and neurotransmission in GABAergic synapses (vesicle budding and recycling, endosome organization, GPCR internalization, and GABAergic transmission), suggesting a shared role in vesicle cycling and inhibitory signaling in neurons. Some terms are peripheral or obsolete, but the core signal points to synaptic vesicle dynamics in GABAergic neurons.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":2},{"id":"GO:1901998","count":2},{"id":"GO:0007032","count":2},{"id":"GO:0003374","count":2},{"id":"GO:1903423","count":2}]},{"hash":"895864563466619549","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046330","count":2},{"id":"GO:0001682","count":2},{"id":"GO:0039702","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1976992354510713280","title":"Cardiac conduction and mechanotransduction","description":"This cluster shows enrichment for terms tied to heart electrophysiology and mechanosensing, including SA node cell communication and regulation of SA node action potentials, as well as cellular responses to mechanical stimulus and muscle stretch, and maintenance of protein localization at the plasma membrane. While some terms (immune-related or apoptotic) are present, the strongest recurring theme is cardiac conduction and mechanotransduction, justifying a label focused on cardiac signaling and mechanical responsiveness.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002268","count":2},{"id":"GO:0086070","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0072660","count":2},{"id":"GO:0098907","count":2}]},{"hash":"863445978815811127","title":"Unknown","description":"The top GO terms mix inflammatory signaling (positive regulation of STAT phosphorylation, NF-kappaB activity, TNF and chemokine production) with development-related processes (axon guidance, neuron differentiation, salivary gland boundary specification, cardiac activity), showing no single cohesive function that ties all proteins together. This makes a definitive label uncertain.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042511","count":4},{"id":"GO:0002377","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0090197","count":3},{"id":"GO:0033564","count":3}]},{"hash":"449399715891000371","title":"Protein and RNA methyltransferases","description":"This cluster is dominated by GO terms for methylation: tRNA, rRNA, guanine-N7, and peptidyl methylation, indicating SAM-dependent methyltransferase activity on proteins and RNAs. The presence of related biosynthetic methylation steps (chlorophyll, cobalamin, antibiotic biosynthesis) supports a cohesive theme of methyltransferases involved in both RNA/protein modification and methylation-driven biosynthesis.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0018364","count":5},{"id":"GO:1901052","count":5},{"id":"GO:0018026","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0002098","count":5}]},{"hash":"1577135005368245679","title":"Neural development and neuroendocrine differentiation","description":"The top terms cluster around nervous system development, neuron differentiation and synapse maturation, plus neuroendocrine cell differentiation, suggesting a cohesive theme of neural and neuroendocrine development, with a few outliers from metabolism that may be incidental.","confidence":"Medium","size":12,"edges":13,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":2},{"id":"GO:0032981","count":2},{"id":"GO:0009089","count":2},{"id":"GO:0090128","count":1},{"id":"GO:0003062","count":1}]},{"hash":"1085142175348131732","title":"DNA replication and repair with developmental cues","description":"The cluster\u2019s top GO terms converge on DNA replication, repair, cell cycle, and DNA-templated transcription, indicating a core theme of genome maintenance. The inclusion of developmental processes (nervous system development, cranial skeleton morphogenesis, bipolar cell polarity, cardiac muscle differentiation) suggests these proteins also participate in developmental regulation or signaling, leading to a label that covers both genome integrity and developmental contexts.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0000706","count":10},{"id":"GO:0071479","count":10},{"id":"GO:0048701","count":10},{"id":"GO:0006351","count":10}]},{"hash":"2196602513659348150","title":"Embryonic organogenesis and tissue differentiation","description":"The GO terms point to broad developmental processes in utero and tissue-specific differentiation (heart/cardiac, muscle, eye, trachea, prostate, neural), with transcription regulation, suggesting a cluster of proteins involved in organizing embryonic organ formation across multiple tissues.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001701","count":4},{"id":"GO:0042551","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0014842","count":3},{"id":"GO:0060038","count":3}]},{"hash":"168395864587011519","title":"Stress-Responsive Metabolic Enzymes","description":"The top GO terms point to both stress responses (lipopolysaccharide response, nitrosative stress) and a variety of metabolic processes (fermentation, oxidation, detoxification, and biosynthesis). This suggests a cluster of proteins involved in adjusting metabolism under stress rather than a single specific pathway, spanning diverse contexts (plants to animals). Thus, a label that captures both stress responsiveness and metabolic versatility is appropriate.","confidence":"Medium","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0032496","count":4},{"id":"GO:0051409","count":4},{"id":"GO:0046294","count":4},{"id":"GO:1901159","count":4}]},{"hash":"2113123378204018811","title":"Nucleotide metabolism and RNA editing","description":"This cluster shows a clear enrichment in nucleotide-related processes: UMP salvage, cytidine/cytosine metabolism, deoxycytidine catabolism, and tRNA wobble adenosine-to-inosine editing, plus riboflavin biosynthesis which ties into broader nucleotide metabolism. The antibiotic response and apoptotic/cell proliferation terms are present but less central, so the core theme is nucleotide metabolism and RNA editing/modification.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0009231","count":3}]},{"hash":"123126688779671486","title":"Translation Regulation and mRNA Decay","description":"The dominant terms point to control of translational initiation and mRNA decay (including NMD), suggesting a cluster centered on RNA-level regulation of protein synthesis, despite some outlier or obsolete GO terms.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1905696","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0000184","count":2},{"id":"GO:2000507","count":2},{"id":"GO:0008315","count":2}]},{"hash":"1155727186487310385","title":"Neurodevelopment with axon targeting and immune differentiation","description":"The top GO terms cluster around nervous system development and axon-related processes (nervous system development, corpus callosum development, juxtaparanode protein localization to axon), with a smaller subset pointing to immune cell differentiation and regulation (neutrophil clearance, NK differentiation, T cell cytotoxicity). This suggests a module focused on neural development with some neuroimmune interactions, hence a neurodevelopmental label with an immune differentiation component.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0038161","count":8},{"id":"GO:1902948","count":8},{"id":"GO:0097350","count":8},{"id":"GO:0001915","count":8},{"id":"GO:0045663","count":8}]},{"hash":"600135475405557736","title":"Ribosome Biogenesis and Translation","description":"This cluster features GO terms for translation, rRNA maturation (SSU/5.8S/LSU), ribosome biogenesis, and various translation steps (initiation, preinitiation complex, reinitiation). The enrichment of ribosome assembly and protein synthesis processes suggests a cohesive role in building and operating ribosomes and translating mRNA, justifying this label.","confidence":"High","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0000462","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0048026","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1219151211698430720","title":"Unknown","description":"The GO terms are highly diverse (pronuclear migration, root meristem growth, telomerase assembly, glucocorticoid signaling, muscle and lung development, centrosomal localization, neuroblast polarity), with no clear shared function or tissue context linking the proteins, suggesting a non-cohesive or random cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035046","count":1},{"id":"GO:0010449","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0042921","count":1},{"id":"GO:0048642","count":1}]},{"hash":"1609077707756489265","title":"Unknown","description":"The GO terms span development (forebrain, neural tube closure, skeletal system), transcriptional regulation, cell cycle, and even stress/defense responses (cadmium, Gram-positive defense). The set lacks a single coherent theme tying the proteins together, making a concise, representative label difficult to justify.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":6},{"id":"GO:0030900","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0000278","count":5}]},{"hash":"801197761431623446","title":"DNA Damage Response and Telomere/Senescence Signaling","description":"The cluster\u2019s top GO terms point to cellular stress responses linked to DNA damage (gamma radiation response), cell fate decisions (replicative senescence, apoptosis regulation), and genome maintenance (telomere maintenance). The presence of a peptidyl-serine autophosphorylation term suggests kinase-driven signaling typical of DNA damage response pathways. Although some terms touch on immune or plant development, the dominant pattern is stress-induced genome maintenance and aging-related signaling.","confidence":"Medium","size":12,"edges":13,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0010449","count":2},{"id":"GO:2001240","count":2},{"id":"GO:0036289","count":2},{"id":"GO:1902895","count":2},{"id":"GO:0030889","count":2}]},{"hash":"126041815086476359","title":"Neuroimmune Behavioral Regulation","description":"The terms point to immune signaling (cytokine production; leukocyte immunity) alongside neural and behavioral processes (locomotion, fear and mating behaviors, ethanol response) plus metabolic and autonomic regulation (dopamine catabolism, glucose homeostasis, vasoconstriction). This suggests a cohesive theme of neuroimmune and neuroendocrine control of behavior and physiology, rather than a single isolated function.","confidence":"Medium","size":12,"edges":15,"triangles":6,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001816","count":3},{"id":"GO:0007626","count":3},{"id":"GO:0002443","count":3},{"id":"GO:0048149","count":3},{"id":"GO:0055114","count":3}]},{"hash":"2136400986067878510","title":"Transmembrane ion and metabolite transport","description":"This cluster is dominated by GO terms describing transport across membranes for various ions and small metabolites (ammonium, GABA, polyamines, carnitine, rubidium), along with related osmoregulatory responses (cell volume homeostasis, hypotonic salinity response). Although a couple of terms seem unrelated (germinal center formation, flower development), the shared theme is membrane transport of solutes, suggesting a cohesive set of transporter-like proteins. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006884","count":2},{"id":"GO:0070634","count":2},{"id":"GO:0098713","count":2},{"id":"GO:0035826","count":2},{"id":"GO:0015812","count":2}]},{"hash":"1471375973384469800","title":"Basement Membrane and Cell Adhesion Components","description":"Top GO terms consistently point to extracellular matrix interactions and tissue adhesion (cell-matrix adhesion; basement membrane development; junction assembly), with some signals tied to inner-ear structures (otolith tethering, sensory perception of sound) that rely on ECM organization. A few entries emphasize immune regulation and signaling (negative regulation of T cell cytotoxicity, neutrophil clearance, prolactin signaling), suggesting multifunctional proteins within this cluster. Overall, the common thread appears to be basement membrane/ECM-mediated adhesion across tissues.","confidence":"Medium","size":12,"edges":54,"triangles":121,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007160","count":3},{"id":"GO:0007605","count":2},{"id":"GO:0035889","count":2},{"id":"GO:0002853","count":2},{"id":"GO:0090528","count":2}]},{"hash":"1165243986657906589","title":"DNA Damage Response and Translesion Synthesis","description":"Based on GO terms such as UV-C cellular response (GO:0071494), DNA damage repair pathways including nucleotide-excision repair gap filling (GO:0006297) and DNA replication (GO:0006261), and both error-free (GO:0070987) and error-prone (GO:0042276) translesion synthesis, the cluster is best described as DNA damage response and TLS-mediated tolerance, with some metabolic terms appearing as background noise.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007613","count":2},{"id":"GO:0071494","count":1},{"id":"GO:0070987","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0006297","count":1}]},{"hash":"1863532463001394946","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034476","count":12},{"id":"GO:0006269","count":12},{"id":"GO:0043629","count":12},{"id":"GO:0008306","count":12},{"id":"GO:0000390","count":12}]},{"hash":"1810557653228828041","title":"Unknown","description":"The top GO terms cover diverse processes, including lignan biosynthesis/catabolism, lipopolysaccharide and other biosynthetic pathways, L-glutamine metabolism, and general transcription-related terms. There isn\u2019t a clear single function or pathway that ties these terms together across the proteins, so there isn\u2019t a single cohesive label that accurately represents the cluster.","confidence":"","size":12,"edges":11,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0001081","count":2},{"id":"GO:0006541","count":2},{"id":"GO:1902131","count":2},{"id":"GO:1902135","count":2}]},{"hash":"1265049676136604981","title":"Metabolic Stress Response and Signaling","description":"The cluster contains terms spanning temperature- and thermogenesis-related stress, calcium signaling, GPCR pathways, energy metabolism (ETC), and immune-related processes (apoptotic cell clearance, complement activation). This suggests a broad theme of cellular stress responses that integrate metabolism with signaling and immune clearance, justifying a label that reflects metabolic stress signaling without tying to a single specific function.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071502","count":3},{"id":"GO:0002024","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0045777","count":3},{"id":"GO:0010579","count":3}]},{"hash":"306292956756475393","title":"Calcium-regulated immune signaling","description":"This cluster shows multiple terms tied to immune signaling (T cell proliferation, T cell migration, monocyte chemotaxis, defense against virus, IL-6 production) and calcium-related processes (regulation of calcium-mediated signaling, calcium ion transport), suggesting a theme of immune signaling modulated by calcium dynamics, with palmitoylation as a possible regulatory layer. ","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007350","count":1},{"id":"GO:2000778","count":1},{"id":"GO:0050848","count":1},{"id":"GO:0042102","count":1},{"id":"GO:0071639","count":1}]},{"hash":"307202664171739461","title":"Angiogenesis and vascular development","description":"The cluster is dominated by GO terms tied to angiogenesis and blood vessel development, including positive regulation of angiogenesis, endothelial cell migration, and retina vasculature development. It also includes cell\u2013matrix adhesion and ERK signaling, consistent with vascular morphogenesis and remodeling; even cardiac-related differentiation and septation signaling align with cardiovascular development linked to vessel formation.","confidence":"High","size":12,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0032094","count":2},{"id":"GO:0007160","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0090331","count":2},{"id":"GO:0070374","count":2}]},{"hash":"1714147575288387890","title":"Neuronal migration and projection signaling","description":"The GO terms point to neuronal development and movement, including cerebellar granule cell precursor tangential migration and neuron projection extension, coupled with signaling pathways (RTK signaling, GTPase regulation) that control cytoskeletal dynamics and cell migration. While a few terms are less connected, the overall pattern supports proteins involved in neuronal migration and projection growth.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036083","count":1},{"id":"GO:0021935","count":1},{"id":"GO:0050918","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0043087","count":1}]},{"hash":"1706072893658908664","title":"RNA processing and translation regulation","description":"The cluster centers on RNA metabolism and protein synthesis control, with terms for cytoplasmic translation, mRNA processing, RNA splicing, and regulation of translation initiation in ER-stress conditions. Additional terms touch on nuclear export and broader signaling regulation, which complements the core theme but also introduces some dispersed signals. Overall, the dominant pattern is RNA processing and regulation of translation. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0046825","count":1},{"id":"GO:0071374","count":1}]},{"hash":"1974056186571526195","title":"Immune signaling and barrier integrity","description":"The cluster ties together immune-related signaling (B cell receptor signaling; IL-2 and IL-10 production) with factors governing epithelial/endothelial barrier function and cell junctions (establishment/maintenance of barrier, cell-cell junction maintenance, and cell polarity). This suggests a theme of signaling pathways that coordinate immune responses with barrier integrity, rather than a single, narrow function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0090557","count":3},{"id":"GO:2001181","count":2},{"id":"GO:0045217","count":2},{"id":"GO:0032005","count":2}]},{"hash":"158158829668409864","title":"Nervous, skeletal, muscle, and lens development","description":"These proteins are tied to broad developmental programs across several tissues: neural development (neuron projection development, nervous system development), skeletal/muscle differentiation (skeletal system development, positive regulation of myoblast differentiation), and lens differentiation (lens fiber cell differentiation). Regulatory processes like Rho signaling and vitamin D3 metabolism may modulate these differentiation pathways, and the juxtaparanode localization term hints at neuronal organization. Overall, the cluster centers on multi-tissue developmental roles rather than a single pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0031175","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0001501","count":5},{"id":"GO:0070306","count":4},{"id":"GO:0035023","count":4}]},{"hash":"1474184984833673951","title":"Insect imaginal disc morphogenesis and ecdysone signaling","description":"This set centers on imaginal disc development (eye-antennal and leg disc morphogenesis, ventral midline development) and hormonal control via ecdysone, including hormone-mediated apoptotic signaling and cellular responses to ecdysone, suggesting a theme of insect developmental remodeling driven by steroid signaling. Some terms also touch on locomotion and gravitaxis, but the core is disc morphogenesis and hormonal regulation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090180","count":2},{"id":"GO:0048092","count":2},{"id":"GO:0007478","count":2},{"id":"GO:0048060","count":2},{"id":"GO:0007455","count":2}]},{"hash":"1187158689193887798","title":"Developmental Morphogenesis Across Tissues","description":"The top GO terms point to embryonic and tissue-specific development across multiple organs (corpus callosum, notochord, nephric duct, female genitalia), plus proliferation and epidermal-related terms. This suggests a broad role in developmental morphogenesis rather than a single, cohesive pathway, so a general \u201cDevelopmental Morphogenesis Across Tissues\u201d label fits best.","confidence":"Medium","size":12,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007140","count":2},{"id":"GO:0043046","count":2},{"id":"GO:1905373","count":1},{"id":"GO:0010838","count":1},{"id":"GO:0031666","count":1}]},{"hash":"1882917390031581867","title":"Mitochondrial fission and apoptosis signaling","description":"Top GO terms show a strong emphasis on mitochondria-related processes (mitochondrial fission and apoptotic mitochondrial changes, plus activation-induced T cell death), implying a mitochondria-centered apoptosis theme. Additional terms point to broader signaling and trafficking connections (EGF response, endosomal transport, ARF/Rho regulation) and lipid metabolism, suggesting the cluster may couple mitochondrial apoptosis with membrane trafficking and signaling pathways. Overall, the dominant signal is mitochondrial dynamics and programmed cell death, with peripheral links to signaling networks.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000266","count":2},{"id":"GO:0008637","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0006687","count":1},{"id":"GO:0006924","count":1}]},{"hash":"1619333678057181672","title":"Proteoglycan Biosynthesis and Metabolism","description":"The top GO terms are dominated by glycosaminoglycan and proteoglycan biosynthesis and metabolism (heparan sulfate, dermatan sulfate, chondroitin sulfate) and related polysaccharide localization, pointing to proteins involved in extracellular matrix proteoglycan production and turnover. Some terms are obsolete, but the core theme remains proteoglycan biosynthesis/metabolism.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015014","count":1},{"id":"GO:0015768","count":1},{"id":"GO:0060676","count":1},{"id":"GO:0002063","count":1},{"id":"GO:0030208","count":1}]},{"hash":"1997910936692845773","title":"Developmental transcription regulators","description":"The top GO terms center on DNA-templated transcription and RNA polymerase II transcription, suggesting these proteins regulate gene expression. The accompanying developmental differentiation terms (amacrine cell differentiation, floor plate development, somitogenesis, lung vasculature development, mammary gland alveolus development, thymus T-cell proliferation, in utero embryonic development) indicate involvement in coordinating developmental programs across tissues. This points to a cohesive theme of transcriptional control during embryonic development.","confidence":"High","size":11,"edges":49,"triangles":115,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0035881","count":2},{"id":"GO:0061030","count":2},{"id":"GO:0033504","count":2}]},{"hash":"1819319936967540637","title":"ER-Golgi Vesicle Transport Regulation","description":"The dominant GO terms point to the secretory pathway and vesicle trafficking, especially ER-to-Golgi and Golgi-to-vesicle transport, plus downstream processes like melanosome assembly and ubiquitination that modulate trafficking and organelle formation. Terms related to adherens junction organization and development likely reflect the broader effects of vesicle trafficking on cell architecture and differentiation. Overall, the cluster seems best described as regulation of vesicle trafficking in the secretory pathway.","confidence":"Medium","size":11,"edges":23,"triangles":20,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0034260","count":10},{"id":"GO:0008283","count":10},{"id":"GO:0055108","count":9},{"id":"GO:0016567","count":9},{"id":"GO:0034332","count":9}]},{"hash":"671305717699034714","title":"Cell Cycle and Proteostasis with Stress Signaling","description":"The GO terms point to cell cycle regulation, protein ubiquitination and proteasome assembly (proteostasis), and various stress- or signal-response pathways (temperature sensing, capsazepine-related response, vitamin D signaling, and intracellular signaling). This suggests a theme where cell division is tied to protein turnover and environmental sensing.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0035994","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0070682","count":4},{"id":"GO:0050960","count":4}]},{"hash":"457302306439099338","title":"Unknown","description":"The top GO terms span metabolism, nuclear body organization, blood cell differentiation, immune regulation, platelet and vascular functions, and bacterial interactions with no clear common function tying them together; there are no edges or cohesive pathway signals, so a concise, representative label cannot be assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0030578","count":2},{"id":"GO:0045648","count":2},{"id":"GO:0002740","count":2}]},{"hash":"38750020740677685","title":"Embryonic Morphogenesis and Organ Development","description":"The top GO terms center on embryonic development and morphogenesis, including axial mesoderm and foregut morphogenesis, secondary heart field specification, and organ-related processes such as hair follicle development and ovarian function. This suggests the cluster reflects proteins involved in early tissue patterning and organogenesis, despite some peripheral terms.","confidence":"High","size":11,"edges":16,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048617","count":4},{"id":"GO:0048319","count":4},{"id":"GO:0051798","count":3},{"id":"GO:0033085","count":3},{"id":"GO:0090419","count":3}]},{"hash":"201646884611693242","title":"Muscle Metabolism and Immune Signaling","description":"The cluster features metabolic processes such as glycolysis and amino acid catabolism (L-alanine and L-leucine), along with signals related to muscle regeneration (satellite cell activation) and immune pathways (cellular response to interleukin-4 and NF-kappaB signaling). This mix suggests proteins involved in coordinating energy metabolism with muscle repair and immune signaling, rather than a single narrow function.","confidence":"Medium","size":11,"edges":27,"triangles":39,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0045654","count":2},{"id":"GO:0051597","count":2},{"id":"GO:0014718","count":2}]},{"hash":"2097438743228661801","title":"Cell Signaling Regulators","description":"The top GO terms cluster around regulation of signaling pathways (GTPase activity, TNF production, NF-kappaB signaling, phosphatidylinositol signaling) with some cardiac excitation-related terms, suggesting these proteins act broadly as regulators of signaling rather than a single pathway. Despite some diverse terms (sporulation, mitotic cycle), the common theme is modulation of cellular signaling processes. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0032760","count":2},{"id":"GO:0098910","count":2},{"id":"GO:0010881","count":2},{"id":"GO:0006919","count":2}]},{"hash":"1473191803719283357","title":"Neural development and myelination","description":"This cluster is dominated by terms related to nervous system formation and myelin organization, including nervous system and CNS development, post-embryonic retina morphogenesis, myelination, and Kv channel clustering at juxtaparanodes. A few terms touch on immune signaling, but the central theme centers on neuronal differentiation and myelin-related processes.","confidence":"High","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0097350","count":5},{"id":"GO:0045663","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0071206","count":5},{"id":"GO:0045163","count":5}]},{"hash":"1916911133558294302","title":"Neuronal development and ER-Golgi trafficking","description":"This cluster shows strong signals for vesicle trafficking between the ER and Golgi (COPII regulation and ER-to-Golgi transport) alongside neural development terms (nervous system development, brain development, neural tube patterning). The combination suggests proteins involved both in the secretory pathway and in neural development, justifying a label that captures both aspects.","confidence":"Medium","size":11,"edges":21,"triangles":9,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055108","count":4},{"id":"GO:1902953","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0010458","count":4},{"id":"GO:0000278","count":4}]},{"hash":"2111372736172031702","title":"Mitosis exit and DNA damage repair via ubiquitination","description":"The cluster centers on mitotic control (G2/M transition, exit from mitosis, chromosome segregation, mitotic DNA damage checkpoint signaling) and DNA repair pathways (HR and NER), with regulatory ubiquitin-related processes (SCF-dependent proteasomal degradation, K63-linked ubiquitination) and neddylation. This combination suggests a cohesive module linking mitotic progression to genome maintenance through ubiquitin-like modifications.","confidence":"High","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0010458","count":11},{"id":"GO:0000086","count":11},{"id":"GO:0016032","count":11},{"id":"GO:0007059","count":11},{"id":"GO:0070911","count":11}]},{"hash":"1182143056733341141","title":"Redox Stress, DNA Repair, and Growth Signaling","description":"The cluster centers on redox homeostasis, DNA damage repair (nucleotide-excision repair), and detoxification, indicating oxidative stress management. Additional terms tie in prostaglandin biosynthesis and growth-related signaling (EGF response, growth regulation, fibroblast proliferation), suggesting a link between stress responses and modulation of cell growth. The inclusion of starvation response further supports an overall stress-adaptation theme. Confidence: Medium","confidence":"","size":11,"edges":18,"triangles":21,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":9},{"id":"GO:0006289","count":8},{"id":"GO:0098869","count":8},{"id":"GO:0001516","count":7},{"id":"GO:0045471","count":7}]},{"hash":"1426637574940282191","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":50,"triangles":124,"max_degree":10,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006269","count":5},{"id":"GO:0000184","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0006265","count":5},{"id":"GO:0006268","count":5}]},{"hash":"943073012305753822","title":"Neural development and axon localization","description":"This cluster prominently features GO terms tied to nervous system development, including nervous system development, corpus callosum development, and establishment of protein localization to the juxtaparanode region of the axon, suggesting a theme of neuronal differentiation and axon organization. Collagen fibril organization implies ECM remodeling relevant to tissue morphogenesis, which can accompany neural development. Some immune-clearance terms (apoptotic/neutrophil clearance) may reflect remodeling processes that occur during development, though they are less specific to neurons. Overall, the strongest signal is neural development and axon targeting.","confidence":"Medium","size":11,"edges":20,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":6},{"id":"GO:0030199","count":6},{"id":"GO:0038161","count":5},{"id":"GO:1902948","count":5},{"id":"GO:0097350","count":5}]},{"hash":"1194815516806652325","title":"Developmental vascular-ECM remodeling","description":"The terms point to tissue development with active vascular formation (spinal cord/somite development; endothelial proliferation/migration) and extracellular matrix remodeling (collagen fibril organization). Lipoprotein transport/clearance and immune-related terms (complement activation, apoptotic clearance) appear as ancillary processes that can accompany developing tissues and vascular/ECS environments, supporting a theme of developmental angiogenesis coupled with ECM dynamics. Confidence: Medium","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":4},{"id":"GO:0043277","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0070207","count":3},{"id":"GO:0061053","count":3}]},{"hash":"1733793367803116780","title":"TNF-NF-\u03baB signaling via K63-linked ubiquitination","description":"This cluster is driven by GO terms for K63-linked ubiquitination, TNF-mediated signaling, and NF-\u03baB activation (I\u03baB phosphorylation, NF-\u03baB\u2013inducing kinase activity) and innate immune response, indicating a cohesive module of ubiquitin-dependent signaling leading to NF-\u03baB\u2013mediated transcription in immune signaling. Some terms (e.g., neural tube closure) are less central and may reflect broader or pleiotropic annotations, but the core theme centers on TNF/NF-\u03baB pathways.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":6},{"id":"GO:0033209","count":5},{"id":"GO:0051865","count":5},{"id":"GO:1903721","count":5},{"id":"GO:0090073","count":5}]},{"hash":"2077038653643098428","title":"Neuronal vesicle trafficking and endocytosis","description":"The cluster shows enrichment for endocytosis, synaptic vesicle budding/transport, and Golgi localization, with brain-specific terms such as Purkinje cell layer maturation and locomotory behavior, suggesting a cohesive role in neuronal vesicle trafficking and synaptic vesicle cycling.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0009615","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0051645","count":1},{"id":"GO:0048490","count":1}]},{"hash":"551098663393388537","title":"Unknown","description":"This cluster shows a mix of terms across development (heart, thymus), sensory perception (sound), immune signaling (interleukin-4, interleukin-7, lipopolysaccharide response), and cell motility/processes (lamellipodium assembly, cell migration) plus intracellular signaling (Ras). The absence of a single cohesive biological theme or pathway to tie these proteins together suggests no clear, representative label can be assigned beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0007605","count":3},{"id":"GO:0032633","count":3},{"id":"GO:0048538","count":3},{"id":"GO:0030032","count":3}]},{"hash":"472272134634230469","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0021942","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0032968","count":1}]},{"hash":"217109204367760341","title":"Embryonic cell-cycle and DNA replication regulation","description":"The cluster shows strong representation of DNA replication, nuclear cell cycle regulation (including the centrosome cycle), and embryonic development terms (cranial skeleton morphogenesis, embryonic organ development), along with essential nuclear processes like splicing and rRNA maturation. This pattern suggests a coherent theme of nuclear machinery controlling cell division and gene expression during embryogenesis, with housekeeping processes supporting rapid proliferation; the single neuronal GO term appears incidental rather than central. ","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0045944","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0007098","count":5},{"id":"GO:0000466","count":5}]},{"hash":"1269719618305103909","title":"Cytokinesis and Cell Division Machinery","description":"The cluster's GO terms mainly describe cell division processes (cytokinesis, septum assembly, spindle organization), with terms like FtsZ-dependent cytokinesis and mitotic spindle assembly, indicating a shared function in division machinery across organisms. Translation is present but appears ancillary. Therefore a label focused on division and cytokinesis best captures the cluster's essence.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0051258","count":1},{"id":"GO:0090529","count":1},{"id":"GO:1902408","count":1},{"id":"GO:0043093","count":1}]},{"hash":"1982936600846933665","title":"Embryonic Development and Vascular Remodeling","description":"The terms cluster around developmental processes (somite development, collagen fibril organization) and vascular growth (endothelial cell proliferation) with supporting immune and lipid clearance roles (complement activation, apoptotic cell clearance, lipoprotein transport/clearance), suggesting a theme of embryonic development coupled with vascular remodeling and associated immune/lipid handling rather than a single, tightly defined function.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":10},{"id":"GO:0043277","count":10},{"id":"GO:0006958","count":10},{"id":"GO:0070207","count":10},{"id":"GO:0061053","count":10}]},{"hash":"28332843153393607","title":"NF-kappaB-Driven Immune Signaling and Ubiquitination","description":"The terms cohere around ubiquitin-mediated regulation (polyubiquitination and ERAD) and immune signaling pathways, notably TNF and both canonical and non-canonical NF-kappaB activation, along with T cell proliferation, innate immunity, TLR signaling regulation, and host defense against viral release.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0000209","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0033209","count":5},{"id":"GO:0043123","count":5},{"id":"GO:0042098","count":5}]},{"hash":"1930281297878898387","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018032","count":5},{"id":"GO:1902187","count":5},{"id":"GO:0007014","count":5},{"id":"GO:0035278","count":5},{"id":"GO:0001519","count":5}]},{"hash":"441032584721056032","title":"K63-Linked Ubiquitination in Innate Immunity","description":"This cluster is dominated by GO terms for K63-linked ubiquitination, autoubiquitination, and innate immune signaling (including NF-\u03baB and TNF pathways), plus related antiviral and LPS-regulated responses and actin ubiquitination. The common theme is ubiquitin-dependent signaling that modulates innate immunity and inflammatory responses, rather than proteasomal degradation alone.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0070534","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0051092","count":6},{"id":"GO:0045087","count":6},{"id":"GO:1903265","count":6}]},{"hash":"1339276264186052173","title":"Developmental Signaling Pathways","description":"The cluster is enriched for GO terms spanning nervous system and germ-cell development, ossification, and immune cell movement, with several key signaling routes like Smoothened (Hedgehog), Roundabout (ROBO), and ERK/MAPK cascades, plus regulatory processes (GTPase activity and oxidative phosphorylation) and protein trafficking. This pattern points to coordinated signaling networks that control development, differentiation, and cellular migration rather than a single, narrow function. ","confidence":"Medium","size":11,"edges":27,"triangles":16,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0034260","count":3},{"id":"GO:0007224","count":3},{"id":"GO:0007286","count":3},{"id":"GO:0002551","count":3}]},{"hash":"1403936334143506313","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0006438","count":2},{"id":"GO:0030206","count":2},{"id":"GO:0015012","count":2}]},{"hash":"279321197115878671","title":"Neuronal signaling and development","description":"The most representative terms point to neural communication and development: nervous system development, excitatory postsynaptic potential, cellular response to dopamine, and calcium-dependent exocytosis, with supporting hints from Wnt signaling in development. While immune-related terms (mast cell degranulation, T cell receptor signaling) and general transcription/mitosis terms appear, they are less central to the cluster\u2019s core theme. Therefore, a neuron-focused label best captures the common functional thread, with moderate confidence due to some term outliers.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0090263","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0007399","count":4},{"id":"GO:0043304","count":4}]},{"hash":"372154802126330811","title":"NF-kB-mediated neuroimmune signaling","description":"The cluster features GO terms centered on I-kappaB phosphorylation (NF-kB activation) and innate immune responses (LPS, dsRNA detection, interferon-beta production, defense against Gram-positive bacteria), together with neural-associated terms (corpus callosum development, positive regulation of synapse assembly, pain-related behavioral response). This combination suggests proteins participating in cross-talk between neural signaling and immune pathways, with NF-kB signaling as a core motif.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007252","count":7},{"id":"GO:0022038","count":6},{"id":"GO:0045359","count":6},{"id":"GO:0071222","count":6},{"id":"GO:1903351","count":6}]},{"hash":"1774795738980626226","title":"Actin Cytoskeleton Remodeling and Rho/GTPase Signaling","description":"The terms point to a common theme of actin cytoskeleton dynamics and its regulation by signaling pathways: Rho GTPase activity, actin filament depolymerization/bundle assembly, PI3K/AKT signaling, and GPCR-mediated signaling, with a contextual note of heart development. This suggests a cluster focused on actin remodeling driven by Rho/GTPase and related pathways.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0071364","count":2},{"id":"GO:0045792","count":2},{"id":"GO:0030836","count":2},{"id":"GO:0007266","count":2}]},{"hash":"211652992683312236","title":"Unknown","description":"The terms include signaling activities (GTPase activation, protein autophosphorylation, phosphorelay) but also nuclear/DNA-related processes (DNA integration, telomerase assembly, sister chromatid segregation) and unrelated responses (phototransduction, cocaine response). The lack of a single, coherent functional theme across the cluster suggests no clear shared function. ","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0033160","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0000819","count":1}]},{"hash":"104810261083070003","title":"Bone and muscle development signaling","description":"This cluster centers on musculoskeletal development and signaling, with terms for bone morphogenesis, multicellular organism development, and myoblast differentiation, supported by receptor tyrosine kinase signaling and vitamin D3 metabolism. Ubiquitination and Rho signaling appear related to regulation of differentiation/morphogenesis, while a couple of terms (TLR4 signaling, luteolysis apoptosis) seem less central noise. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0007169","count":2},{"id":"GO:0060349","count":2},{"id":"GO:0016567","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1141056604982439650","title":"Golgi-MVB trafficking during mitosis","description":"This cluster centers on Golgi organization and multivesicular body (MVB) assembly/sorting, indicating vesicle trafficking pathways. It also includes cell division and mitotic exit terms, plus microtubule dynamics, suggesting coordination between membrane trafficking and mitotic processes. A few terms related to immune signaling (NLRP3 inflammasome and interferon response) are present but secondary to the trafficking/mitosis theme.","confidence":"Medium","size":11,"edges":14,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007030","count":3},{"id":"GO:0036258","count":2},{"id":"GO:0071985","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1902902","count":2}]},{"hash":"1304076237916362376","title":"Developmental signaling and morphogenesis","description":"Top terms cluster around developmental processes and signaling, notably BMP pathway regulation and forebrain/multicellular development, as well as cell morphogenesis. While some terms touch on immune signaling, the strongest pattern is developmental signaling and tissue morphogenesis, with BMP-related regulation as a core thread.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0031663","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0030513","count":3}]},{"hash":"539185456372996318","title":"Diverse solute transmembrane transporters","description":"The top GO terms are dominated by various transmembrane transport activities for different substrates (vitamin, phosphate, galactose, nitrite/nitrate, potassium, xenobiotic, sialic acid, etc.), pointing to a common function as broad-range membrane transporters. An outlier term for Toll-like receptor 9 signaling appears unrelated but does not negate the overall transporter pattern. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0015757","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0015707","count":1}]},{"hash":"2284379583872325904","title":"Unknown","description":"The top terms are highly diverse, spanning DNA replication, protein refolding, plant development (meristem identity), photosystem balance, multiple signaling pathways (Wnt, TGF-beta, MAPK), and germ-line masculinization. There's no single coherent function tying these proteins together, so a precise label isn't possible; Unknown is the appropriate placeholder.","confidence":"","size":10,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0048745","count":2},{"id":"GO:0010074","count":2},{"id":"GO:0016055","count":2}]},{"hash":"1222079348087341833","title":"Ubiquitin-Proteasome System Regulation","description":"These proteins are enriched for ubiquitin-dependent proteolysis, K63-linked ubiquitination, sumoylation, ERAD, and proteasome-related processes, with connections to NF-kappaB signaling. The common thread is regulation of protein turnover and post-translational modifications via the ubiquitin-proteasome system, i.e., proteostasis control.","confidence":"High","size":10,"edges":37,"triangles":70,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0043123","count":2}]},{"hash":"1712432584603582144","title":"Developmental signaling and organogenesis","description":"The top GO terms point to development across multiple organs (placenta, liver, digits, ureteric bud branching, interneuron guidance) and to signaling and transcriptional regulation (cGMP signaling, DNA-templated transcription). This indicates a cluster of proteins involved in broad developmental processes rather than a single tissue-specific function. The presence of an olfactory term may reflect shared developmental regulation in sensory tissues or pleiotropy. Overall, the theme is developmental coordination across organs, rather than a narrow pathway.","confidence":"Medium","size":10,"edges":15,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0007608","count":2},{"id":"GO:0010754","count":2}]},{"hash":"978940006190065653","title":"Protein ubiquitination and proteasome function","description":"The cluster shows enrichment for ubiquitination and proteasome regulatory particle assembly, pointing to a core theme of protein tagging and degradation. While other terms touch on signaling, temperature and vitamin D responses, and cell migration, the strongest common thread is involvement in protein turnover machinery.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060743","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0050960","count":3},{"id":"GO:0035556","count":3}]},{"hash":"2035260665661754259","title":"Unknown","description":"The GO terms are diverse and span lipopolysaccharide biosynthesis, amino acid biosynthesis/catabolism, lipid metabolism and signaling (phospholipid dephosphorylation, epoxygenase P450 pathway), and even hormonal signaling (response to testosterone, intracellular calcium homeostasis), with several obsolete terms. There isn\u2019t a single clear, cohesive function tying these proteins together, so a specific, high-confidence label isn\u2019t supported. ","confidence":"","size":10,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":4},{"id":"GO:0019518","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0046839","count":3}]},{"hash":"1549055983500032763","title":"Photoreceptor Signaling and Retina Development","description":"This cluster is dominated by GO terms tied to retina development in camera-type eyes, blue light signaling, and photoreceptor-associated signaling pathways (including guanylyl cyclase and cAMP signaling) as well as intracellular signal transduction, suggesting a cohesive theme around photoreceptor/retina function rather than disparate cellular processes. Some less specific terms (e.g., Golgi-to-ER transport) appear, but the retina/phototransduction-related terms provide the primary signal for naming. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008284","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0007168","count":2}]},{"hash":"125953997708221902","title":"Developmental Signaling and Immune Regulation","description":"The top GO terms point to multiple signaling pathways involved in development (Roundabout/ROBO, Smoothened/Hedgehog, nervous system and kidney development, myoblast differentiation) as well as immune-related signaling (T cell receptor signaling, regulation of T cell cytotoxicity, neutrophil clearance) and prolactin signaling. This suggests a cluster of proteins functioning in signaling networks that coordinate developmental processes with immune responses, hence the label.","confidence":"Medium","size":10,"edges":31,"triangles":43,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0001822","count":5},{"id":"GO:0035385","count":5},{"id":"GO:0007224","count":5}]},{"hash":"801229894282631976","title":"ER Stress and Proteostasis","description":"The terms cluster around ER stress and proteostasis: unfolded protein response, ER-stress\u2013driven translation initiation, regulation of protein export, and ER-associated degradation. Additional signals involve kinase activity and ATP-dependent regulation, fitting a proteostasis/ER stress signaling module.","confidence":"Medium","size":10,"edges":19,"triangles":16,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006986","count":4},{"id":"GO:0036494","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0046825","count":3}]},{"hash":"364829854593268438","title":"Unknown","description":"The top GO terms span very different biological contexts (bacterial mycothiol biosynthesis, plant melatonin and leaf formation, chromatin and histone acetylation, and polyamine metabolism), with no clear, single shared function across the cluster. While there is a minor thread around acetylation, it is not cohesive enough to define a specific biological theme for all proteins.","confidence":"","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":5},{"id":"GO:0071962","count":5},{"id":"GO:0006348","count":5},{"id":"GO:0060358","count":5},{"id":"GO:0043967","count":5}]},{"hash":"2181178935247211713","title":"Membrane Targeting and ER Stress Response","description":"The cluster shows strong enrichment for SRP- and cotranslational protein targeting to membranes, plus terms related to unfolded protein response and ER stress quality control, suggesting a shared role in protein maturation at membranes. Some terms (e.g., DNA replication, karyogamy) are less directly connected, so the core theme centers on membrane targeting and ER-associated protein quality control.","confidence":"Medium","size":10,"edges":10,"triangles":3,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031204","count":7},{"id":"GO:0006880","count":7},{"id":"GO:0000742","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0006616","count":7}]},{"hash":"2083861943579422902","title":"Protein and histone acetylation","description":"The cluster contains several acetylation-related GO terms (peptidyl-lysine N6-acetylation, N-terminal peptidyl-glutamic acid acetylation, putrescine acetylation, spermine catabolic/acetylation-related processes) and chromatin-associated terms (subtelomeric heterochromatin formation, centromeric cohesion, histone H4 acetylation). This points to a common theme of acetylation-driven regulation of protein function and chromatin structure, with a few peripheral annotations (mycothiol biosynthesis, leaf formation) likely reflecting organism-specific contexts. Overall, the acetylation-centric signal best defines the cluster.","confidence":"Medium","size":10,"edges":25,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":7},{"id":"GO:0010125","count":6},{"id":"GO:0071962","count":6},{"id":"GO:0006348","count":6},{"id":"GO:0060358","count":6}]},{"hash":"2004351662983673667","title":"Immune and neural development regulation","description":"The terms point to broad regulatory roles across both immune processes (interleukin-3 production, neutrophil clearance, dendritic cell differentiation, hypersensitivity) and nervous system development (nervous system development, axon-area protein localization), with additional terms related to Rho signaling and myoblast differentiation, plus vitamin D3 metabolism. This suggests a cluster of proteins involved in coordinating signaling and differentiation in immune and neural contexts, rather than a single, cohesive pathway. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045401","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0097151","count":1},{"id":"GO:0097350","count":1},{"id":"GO:0001805","count":1}]},{"hash":"1829254103451773562","title":"Post-transcriptional mRNA processing and translation initiation regulation","description":"This cluster centers on post-transcriptional control: frequent terms for mRNA splicing (spliceosome, splice site recognition), polyadenylation, mRNA modification, and regulation of translational initiation, plus assembly of the eIF4F complex and stress-linked mRNA stability. Together these indicate proteins coordinated in RNA processing and controlling translation, i.e., post-transcriptional gene expression regulation.","confidence":"High","size":10,"edges":18,"triangles":11,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0006376","count":3},{"id":"GO:0097010","count":3},{"id":"GO:0010610","count":3}]},{"hash":"1156997241758369529","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":18,"triangles":13,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":8},{"id":"GO:0031047","count":8},{"id":"GO:0006260","count":7},{"id":"GO:0071051","count":6},{"id":"GO:0034476","count":6}]},{"hash":"687025151812519731","title":"RNA processing and gene expression regulation","description":"These proteins show enrichment in multiple RNA-centric processes, including mRNA splicing regulation via the spliceosome, ncRNA-mediated gene silencing, transcription initiation by RNA polymerase II, maturation of rRNA, mRNA splice site recognition, eIF4F complex assembly for translation initiation, and regulation of mRNA stability and modification. Together they reflect a cohesive theme of RNA metabolism and layered control of gene expression from transcription through RNA processing to translation, justifying this label.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0045944","count":4},{"id":"GO:0000466","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1539776160808335195","title":"Plant plasmodesmata and virus interaction","description":"The terms point to plant-specific cell wall remodeling and plasmodesmata organization (cell wall modification, cellulose biosynthesis regulation, plasmodesma organization) and developmental processes (sepal formation). The presence of viral-related terms (host-mediated activation of viral genome replication, viral uncoating, viral release) suggests interactions between plant hosts and viral infection, often involving plasmodesmatal transport. Overall, the cluster seems to reflect plant cell wall/plasmodesmata dynamics with virus\u2013host interaction components.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009831","count":1},{"id":"GO:2001009","count":1},{"id":"GO:0009663","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0010849","count":1}]},{"hash":"1713700765884893015","title":"Neuronal signaling and dendrite development in sensory systems","description":"Based on GO terms like receptor clustering, opioid receptor signaling, receptor guanylyl cyclase signaling, Rho protein signal transduction, dendrite development, and auditory receptor cell stereocilium organization, along with behavior terms such as grooming and vocalization, this cluster appears to center on neural signaling and the morphogenesis of sensory neurons (notably auditory). The set suggests a cohesive theme of receptor organization driving dendritic/sensory function and related behaviors.","confidence":"High","size":10,"edges":9,"triangles":1,"max_degree":5,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0043113","count":9},{"id":"GO:2000821","count":9},{"id":"GO:0035023","count":8},{"id":"GO:2000670","count":8},{"id":"GO:0007168","count":8}]},{"hash":"1589615876855500797","title":"Chromatin and Transcription Regulation","description":"Although a few terms touch on immune or biofilm processes, the dominant signals are transcription-related (RNA polymerase II elongation, Pol I termination, preinitiation complex assembly) and chromatin-associated (heterochromatin formation, pericentric heterochromatin, nucleosome density). This suggests the cluster comprises proteins involved in controlling transcription via chromatin state.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060303","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0002467","count":2},{"id":"GO:0006363","count":1}]},{"hash":"1892561391574404454","title":"Quinone biosynthesis and fatty acid oxidation","description":"The top GO terms cluster around phylloquinone and menaquinone biosynthesis (quinones) and fatty acid beta-oxidation, with supporting glycolysis and TCA-cycle terms. This points to a metabolic module linking quinone production to fatty acid catabolism and energy metabolism\u2014antibiotic biosynthesis appears ancillary.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0010124","count":7},{"id":"GO:0006635","count":7},{"id":"GO:0042372","count":7},{"id":"GO:0009234","count":7}]},{"hash":"2292145375596464273","title":"Unknown","description":"Top GO terms are not provided for this cluster, so no coherent functional theme can be inferred from the terms; with only network metrics (36 edges, 64 triangles, max degree 9) and protein IDs, a meaningful label cannot be assigned.","confidence":"","size":10,"edges":36,"triangles":64,"max_degree":9,"top_function":null,"top_go_terms":[]},{"hash":"48077391662391005","title":"Mitochondrial Transporters and Nucleotide Import","description":"This cluster is dominated by GO terms describing transport across mitochondrial membranes (ADP/ATP, thiamine pyrophosphate, CoA, thiosulfate, manganese ions, pyrimidine nucleotides) and mitochondrial localization/related processes, indicating a shared role in mitochondrial transport and nucleotide import. A single outlier term (female pregnancy) appears unrelated to the main theme.","confidence":"High","size":10,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":2},{"id":"GO:0035349","count":2},{"id":"GO:0007565","count":2},{"id":"GO:0015709","count":2},{"id":"GO:0006828","count":2}]},{"hash":"811116387884224239","title":"Neural Development and Signaling Cluster","description":"This cluster centers on nervous system development and signaling, with prominent terms such as nervous system development, Roundabout signaling, Smoothened signaling, and regulation of long-term neuronal synaptic plasticity, suggesting a core theme of neural development and synaptic communication. Other terms like T cell receptor signaling, adherens junction organization, and ubiquitination are present but appear auxiliary, indicating some cross-talk with broader signaling or regulatory processes rather than a single non-neural function.","confidence":"Medium","size":10,"edges":15,"triangles":16,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0050852","count":6},{"id":"GO:0035385","count":6},{"id":"GO:0007049","count":5},{"id":"GO:0007224","count":5}]},{"hash":"147808450844973676","title":"Membrane remodeling and endocytosis during cell migration","description":"This cluster centers on actin dynamics (actin filament organization, filopodium assembly) and membrane remodeling processes (membrane invagination, caveola assembly, caveolin-mediated endocytosis), with regulatory terms for endocytosis and protein localization. The convergence on actin-driven membrane changes and caveolae-related pathways suggests a theme tied to membrane remodeling during cell migration and leading-edge dynamics, including glial process extension. Therefore, the label is representative and specific to the cluster\u2019s core functions.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021816","count":4},{"id":"GO:0097320","count":4},{"id":"GO:0010324","count":4},{"id":"GO:0007015","count":4},{"id":"GO:0046847","count":4}]},{"hash":"1339434870519544323","title":"Lipid-derived Hormone Metabolism","description":"This cluster centers on lipid and steroid-related biosynthesis and metabolism, including prostaglandins, progesterone, retinoic acid, and epoxygenase P450 pathways, suggesting a common theme of lipid signaling and hormone production. Some terms (e.g., brassinosteroid biosynthesis, ozone response) extend into related lipid or stress-related pathways, but the dominant signal is lipid- and hormone-related metabolism.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034653","count":5},{"id":"GO:0001516","count":5},{"id":"GO:0002933","count":5},{"id":"GO:0060137","count":5},{"id":"GO:0042448","count":5}]},{"hash":"624394655620737464","title":"Diverse membrane substrate transport","description":"The top GO terms are all related to transport across membranes for a variety of substrates (lipoproteins, cobalt ions, branched-chain amino acids, vitamins, ceramide, doxorubicin, etc.), with one outlier (cell-matrix adhesion). This pattern points to a general membrane transport function acting on diverse substrates rather than a single substrate type, justifying a broad \u201cmembrane transport of diverse substrates\u201d label.","confidence":"Medium","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042953","count":2},{"id":"GO:0007160","count":2},{"id":"GO:1900753","count":1},{"id":"GO:0015689","count":1},{"id":"GO:0015803","count":1}]},{"hash":"2037061881059301627","title":"Ubiquitin-Dependent Protein Regulation","description":"Top terms are dominated by ubiquitination-related processes (ubiquitin-dependent protein catabolic process; protein ubiquitination; negative regulation of protein ubiquitination), suggesting a core function in ubiquitin-mediated protein modification and turnover. Secondary terms touch on neural development, mRNA processing, and signaling, but the central theme remains ubiquitin-driven regulation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0031397","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0032212","count":3}]},{"hash":"1677415445927451947","title":"Unknown","description":"No GO terms provided in Top Terms, so there is no detectable functional theme to group these proteins. With no shared annotations, the safest label is Unknown.","confidence":"","size":10,"edges":15,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"1671481551538014226","title":"Bacterial carbohydrate biosynthesis and LPS production","description":"Top GO terms cluster around biosynthesis of cell-surface polysaccharides (O antigen, lipopolysaccharide) and various sugar metabolic pathways (galactose, glucose-1-phosphate, GDP-mannose, glycogen, inosine/guanosine catabolism). This points to a cohesive role in bacterial carbohydrate production and utilization, especially envelope polysaccharide synthesis, with a few unrelated terms present. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009243","count":1},{"id":"GO:0019388","count":1},{"id":"GO:0046115","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0009590","count":1}]},{"hash":"793211915936923925","title":"Lipid transport and vascular development","description":"This cluster\u2019s top GO terms cluster around lipoprotein transport and clearance (lipid handling in plasma) and vascular/ECM processes such as endothelial cell proliferation and collagen fibril organization, suggesting a theme of lipid metabolism integrated with vascular development and extracellular matrix remodeling. The presence of terms linked to pregnancy and somite development further supports a developmental vascular context (e.g., placental or embryonic vasculature). Overall, the most coherent label is lipid transport linked to vascular development/remodeling.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042953","count":4},{"id":"GO:0006883","count":4},{"id":"GO:0007565","count":3},{"id":"GO:0043277","count":3},{"id":"GO:0006958","count":3}]},{"hash":"1265269235588161563","title":"Ubiquitination-Driven Immune Signaling","description":"The top GO terms are dominated by ubiquitination-related processes (protein ubiquitination, K63-linked ubiquitination, autoubiquitination) with accompanying immune-system associations (suppression of viral release by host, regulation of LPS signaling) and RNA processing (miRNA metabolism). This combination suggests the cluster centers on ubiquitin-mediated regulation of immune and antiviral signaling, with vitamin D response and GTPase regulation as related signals. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033280","count":6},{"id":"GO:0016567","count":5},{"id":"GO:1902261","count":3},{"id":"GO:1902187","count":3},{"id":"GO:0043547","count":3}]},{"hash":"1867994265848378180","title":"Unknown","description":"The terms span metabolism (TCA cycle), RNA processing (snoRNP assembly), developmental and hormonal processes (prostate gland development, male sex differentiation, steroid hormone receptor complex assembly), signaling (GPCR pathway regulation), and immune responses (interferon response, innate immunity, antiviral defense). The absence of a common, cohesive function and the lack of connecting edges suggest there isn\u2019t a single clear theme tying these proteins together, so the cluster is best labeled Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0000492","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0008277","count":2},{"id":"GO:0071357","count":2}]},{"hash":"765094470181489344","title":"Auditory signaling and cytoskeletal dynamics","description":"The GO terms cluster around sensory perception of sound, stereocilium organization, and neuronal/cytoskeletal remodeling (Rho signaling, dendrite development, centrosome localization), suggesting a cohesive theme of auditory system signaling coupled with cytoskeletal/dendritic organization. ","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0007605","count":6},{"id":"GO:2000670","count":5},{"id":"GO:0007168","count":5},{"id":"GO:2000474","count":5}]},{"hash":"306684624477410649","title":"Developmental adhesion and neural development","description":"The cluster is enriched for integrin-mediated signaling and cell-matrix adhesion, along with developmental processes across tissues (skin, forebrain/telencephalon, multicellular development) and neural plasticity (long-term potentiation). This points to a cohesive theme of developmental signaling and tissue organization with a notable emphasis on neural development.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:0007160","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0021537","count":2},{"id":"GO:0060291","count":2}]},{"hash":"31859610063754868","title":"Mitogenic Kinase Signaling Regulation","description":"This cluster is dominated by GO terms tied to activating and regulating kinase activity (GTPase activity, serine/threonine kinase activity, and protein autophosphorylation) and processes related to cell cycle progression and proliferation, indicating a core theme of kinase-driven signaling that promotes cell division. Additional terms for mRNA transport and various signaling responses (hypoxia, LPS, neurotransmitter release) suggest broader roles in cellular communication and stress responses, but the central pattern is kinase-mediated regulation of proliferation.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0071902","count":3},{"id":"GO:0051028","count":3}]},{"hash":"2294777178915840946","title":"Developmental Signaling and Cytoskeletal Dynamics","description":"The terms point to development across tissues (skin, spinal cord, seminiferous tubule) and organ identity maintenance, paired with cytoskeletal movement and signaling pathways (GPCR, TORC1, VEGF). This suggests proteins involved in coordinating development with cytoskeletal dynamics and signaling, with a minor link to immune defense in skin. The spread of terms makes a highly specific single function unlikely, so a broad developmental signaling/cytoskeletal theme fits best. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0048496","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0000132","count":3},{"id":"GO:0072520","count":3}]},{"hash":"708695229469013955","title":"Cell cycle control and protein ubiquitination","description":"The top GO terms are dominated by cell cycle-related processes (cell cycle; transcription regulation in G1/S) and protein turnover mechanisms (protein ubiquitination; proteasome regulatory particle assembly; centrosome localization), suggesting the cluster centers on regulating cell division via ubiquitin-proteasome pathways. Some sensory terms (thermoception, capsazepine, vitamin D response) appear peripheral and do not define the core theme. Thus, the cluster is best described as proteins coordinating cell cycle progression through protein degradation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051660","count":2},{"id":"GO:0060292","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0070682","count":2}]},{"hash":"364051921311919806","title":"Unknown","description":"The Top Terms span immune signaling (germinal center formation, B cell receptor signaling), nervous system and muscle development, a mitotic/process localization term (spindle midzone), general protein catabolic and ubiquitin-dependent pathways, plus unusual terms like wybutosine biosynthetic and glucosinolate catabolism. The mix across development, immune, cell cycle, metabolism, and even plant-specific processes suggests there is no single coherent biological function tying these proteins together, despite the ReCIPE re-additions. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":4},{"id":"GO:0007399","count":4},{"id":"GO:2000312","count":4},{"id":"GO:0035853","count":4},{"id":"GO:0070294","count":4}]},{"hash":"526488503926768533","title":"Unknown","description":"The GO terms are highly diverse (immune signaling; germinal center formation; GTPase regulation; nervous system and flower development; spindle localization; kainate receptor activity; renal ion transport; wybutosine biosynthesis) with no clear shared pathway or function, and there are no edges indicating a cohesive cluster; thus a concise, representative label cannot be reliably assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0034260","count":2},{"id":"GO:0002467","count":2},{"id":"GO:0007399","count":2}]},{"hash":"1220848942475437675","title":"Unknown","description":"The terms span diverse processes (protein oligomerization, gluconeogenesis regulation, vacuolar protein catabolism, DNA damage response, cytokine production, GTPase regulation, synaptic plasticity, and developmental patterning) with no clear shared pathway or context, and there are no edges linking the proteins. This lack of a cohesive theme makes it inappropriate to assign a specific functional label. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0045721","count":1},{"id":"GO:0007039","count":1},{"id":"GO:2000002","count":1},{"id":"GO:0010569","count":1}]},{"hash":"892934017198795578","title":"Nervous System Development and Axon Differentiation","description":"The cluster is dominated by GO terms centered on nervous system development, axon extension and regeneration, mechanoreceptor differentiation, and nerve impulse transmission, with supporting signaling from fibroblast growth factor receptor pathways. These collectively point to neural development and axon-related functions as the core theme, despite one outlier term related to vacuolar transport. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0090080","count":6},{"id":"GO:0035584","count":6},{"id":"GO:0048691","count":6},{"id":"GO:0007275","count":6}]},{"hash":"909353058757874247","title":"ER Targeting and Unfolded Protein Response","description":"This cluster is dominated by GO terms linked to targeting proteins to membranes (SRP-dependent cotranslational targeting and post-translational targeting to membranes) and to protein quality control under stress (cellular response to unfolded protein, ER stress-related apoptotic signaling). The presence of terms regulating inclusion body assembly and negative regulation of heat response further supports a proteostasis/ER-stress theme. Some terms like DNA replication and karyogamy are peripheral, but the strongest theme centers on ER-associated protein targeting and stress responses.","confidence":"Medium","size":9,"edges":30,"triangles":48,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031204","count":7},{"id":"GO:0006880","count":7},{"id":"GO:0000742","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0006616","count":7}]},{"hash":"91709536832986038","title":"Plant defense and detoxification metabolism","description":"The terms point to oxidative stress response and detoxification (cellular oxidant detoxification; response to toxic substance; oxidation-reduction process) along with defense-related metabolism (stilbene catabolic process; antibiotic biosynthetic process) and related plant development/metabolic activities (secondary shoot formation). This combination suggests a cohesive theme of plant defense and detoxification rather than a single, narrow function. Some terms are broader metabolic processes, but the predominance of detoxification/defense signals supports this label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007160","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0009636","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0046272","count":3}]},{"hash":"1231988828919764735","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007568","count":5},{"id":"GO:0007369","count":4},{"id":"GO:0016575","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0043588","count":4}]},{"hash":"1008524205478176581","title":"Unknown","description":"The top GO terms span neural development (nervous system and corpus callosum development, axon protein localization) and immune differentiation/regulation (neutrophil clearance, NK cell differentiation, T cell cytotoxicity), plus other developmental processes. There isn\u2019t a single cohesive function tying these terms together, so a concise, representative label cannot be determined.","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0038161","count":9},{"id":"GO:1902948","count":9},{"id":"GO:0097350","count":9},{"id":"GO:0001915","count":9},{"id":"GO:0045663","count":9}]},{"hash":"464529710849832807","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0071051","count":1},{"id":"GO:0034476","count":1}]},{"hash":"1611625554535562350","title":"Neural signaling and development with bone remodeling","description":"Top terms indicate a core theme of neural signaling and development (nervous system development, GABAergic synaptic transmission, dopamine uptake regulation, ERK/MAPK cascade) with supportive skeletal remodeling processes (ossification, bone resorption). While keratinization and neuromuscular balance broaden tissue context, the predominant pattern is neural signaling associated with developmental processes and some bone dynamics, justifying the chosen label.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0043931","count":3},{"id":"GO:0031424","count":3},{"id":"GO:0051932","count":3},{"id":"GO:0050885","count":3}]},{"hash":"1838054324840998820","title":"Neural Development and Axonogenesis","description":"The top terms cluster around nervous system development and axon-focused processes (positive regulation of axonogenesis, nervous system development, corpus callosum development, juxtaparanode protein localization), indicating a cohesive theme of CNS neuron differentiation and axon maturation. Immune-related terms appear in the list but are less central to the dominant neural-axon signal in this cluster, suggesting the core function is neural development rather than immune processes.","confidence":"High","size":9,"edges":14,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0050772","count":3},{"id":"GO:0038161","count":2},{"id":"GO:1902948","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0001915","count":2}]},{"hash":"1923992813859120308","title":"Unknown","description":"The top GO terms span photosynthesis, DNA replication, chromatin dynamics, ER stress\u2013related translation, cilium assembly, histone modification, ubiquitination, cell cycle transitions, and organ identity maintenance. These diverse functions do not point to a single cohesive biological theme for the cluster, indicating no clear shared function beyond broad intracellular activities. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0006271","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0036494","count":2},{"id":"GO:1905515","count":2}]},{"hash":"2210392888941492976","title":"Spliceosome Assembly and Splicing Regulation","description":"The top GO terms are centered on mRNA splicing via the spliceosome, including spliceosomal complex and snRNP assembly, splice site recognition, and regulation of splicing, with additional notes on mRNA stability under stress and RNA-mediated silencing. This points to a coherent cluster of proteins involved in spliceosome assembly and regulation of RNA splicing.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":6},{"id":"GO:0048026","count":4},{"id":"GO:0010610","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000245","count":2}]},{"hash":"380778957923295919","title":"Regulators of Signaling Pathways","description":"These proteins are annotated with GO terms pointing to modulation of multiple signaling cascades\u2014Rho signaling, VEGF signaling, insulin receptor signaling, T cell receptor signaling, and STAT phosphorylation\u2014along with related processes like membrane depolarization and ectodomain proteolysis. The shared theme is broad regulatory influence over signaling rather than a single pathway, suggesting a cluster of signaling regulators across immune, neural, and metabolic contexts.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0051045","count":2},{"id":"GO:1900746","count":2},{"id":"GO:0008286","count":2}]},{"hash":"2280279217715162650","title":"Virus-host Interaction and Immune Response","description":"The cluster centers on viral infection processes (viral life cycle, uncoating, release) and host responses (leukocyte migration), suggesting proteins work in virus-host interactions and immune signaling. Some terms appear noisy or obsolete (sepal formation, certain regulatory terms), but the core theme points to virus entry/replication and host defense. Thus, a label reflecting virus-host interaction with immune components is appropriate.","confidence":"Medium","size":9,"edges":9,"triangles":0,"max_degree":5,"top_function":"protein folding","top_go_terms":[{"id":"GO:0048453","count":3},{"id":"GO:0010849","count":3},{"id":"GO:0044829","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0071492","count":3}]},{"hash":"565622551542489470","title":"Innate immune signaling and cytoskeletal regulation","description":"The top GO terms point to innate immune response and multiple signaling cascades (GTPase regulation, JNK cascade, tyrosine phosphorylation, TGF-beta response) alongside cytoskeletal processes (barbed-end actin filament capping) and outcomes like apoptosis and barrier establishment. Together these suggest a functional cluster of proteins that couple immune signaling with cytoskeletal remodeling to influence endothelial/epithelial barrier function and stress responses. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0090557","count":3},{"id":"GO:0050731","count":3},{"id":"GO:0006915","count":3}]},{"hash":"1752505334050123124","title":"Unknown","description":"The GO terms are highly diverse (fungal sterol regulation, nitrogen assimilation, oxidative stress/aging, pH response, and even vertebrate vascular terms), with no single coherent function linking the proteins. This cluster lacks a clear shared biology, so a specific label cannot be confidently assigned.","confidence":"","size":9,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0048773","count":2},{"id":"GO:0071291","count":2},{"id":"GO:0019430","count":2}]},{"hash":"1649740394555849032","title":"Actin Cytoskeleton Remodeling and Endocytosis","description":"The prominent GO terms point to actin filament organization, Arp2/3-mediated nucleation, and endocytosis, plus Rho signaling and membrane localization, indicating proteins involved in cytoskeleton-driven membrane trafficking. Other terms (cell division, ribosome biogenesis, apoptosis) suggest broader cellular roles, but the core theme remains actin dynamics and vesicle trafficking.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050731","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0007015","count":2},{"id":"GO:0048488","count":2},{"id":"GO:0000747","count":2}]},{"hash":"10241524203645126","title":"Translation initiation and cell cycle regulation","description":"Proteins in this cluster are linked to controlling gene expression at both transcriptional and translational levels, with specific emphasis on translation initiation complex assembly and regulation of the cell cycle and cell division. While immune signaling and hormone response terms appear, the dominant signal centers on coordinating protein synthesis with cell proliferation and transcriptional control.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":1},{"id":"GO:0007527","count":1},{"id":"GO:0035660","count":1},{"id":"GO:0045948","count":1},{"id":"GO:0007049","count":1}]},{"hash":"1895469500653236395","title":"Vascular remodeling and angiogenesis","description":"The top terms cluster around blood vessel formation and remodeling: angiogenesis, regulation of vasoconstriction, smooth muscle proliferation, collagen fibril organization, prostaglandin biosynthesis, and ERK signaling. These together point to vascular development and signaling pathways involved in extracellular matrix remodeling and vascular tone, with supporting inflammatory context (LPS and ion responses). Confidence: Medium","confidence":"","size":9,"edges":12,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":3},{"id":"GO:0045907","count":2},{"id":"GO:0051968","count":2},{"id":"GO:0048661","count":2},{"id":"GO:0030199","count":2}]},{"hash":"1398038950996988760","title":"Epithelial morphogenesis and cell adhesion","description":"This cluster centers on epithelial development and movement: terms about palatal shelf morphogenesis, epithelial apoptotic processes, epithelial cell migration, and calcium-independent cell-matrix adhesion, plus anoikis regulation and sprouting angiogenesis. Sphingolipid biosynthesis suggests membrane remodeling supporting these processes. Some terms (e.g., antibiotic biosynthetic process) may reflect annotation noise, but the core signal points to epithelial morphogenesis and adhesion/migration.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:1990134","count":5},{"id":"GO:0014909","count":5},{"id":"GO:0007161","count":5},{"id":"GO:0051968","count":5}]},{"hash":"617224214166709622","title":"Isoprenoid and cholesterol biosynthesis enzymes","description":"This cluster is dominated by GO terms tied to isoprenoid biosynthesis, including cholesterol biosynthetic process, the mevalonate pathway, and the broader isoprenoid biosynthetic process, as well as the methylerythritol phosphate pathway term. The recurring signal across top terms points to enzymes involved in the production of isoprenoid compounds and cholesterol precursors, with a few obsolete glycosaminoglycan biosynthesis terms likely contributing noise. Overall, the set most coherently maps to a group of proteins functioning in isoprenoid/cholesterol biosynthesis.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0019287","count":2},{"id":"GO:0008299","count":2},{"id":"GO:0030206","count":2},{"id":"GO:0015015","count":2}]},{"hash":"15422923228487130","title":"Mitochondrial transporters and metabolism","description":"The cluster shows a clear enrichment for mitochondrial-focused processes: transmembrane transport of ADP, CoA, thiamine pyrophosphate, pyrimidine nucleotides, thiosulfate, and manganese, along with mitochondrial membrane localization and apoptotic mitochondrial changes. These collectively point to a cohesive theme of mitochondrial transport and metabolic maintenance, possibly including enzymes or transporters involved in mitochondrial nucleotide and cofactor handling. ","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":8},{"id":"GO:0008637","count":7},{"id":"GO:0035349","count":7},{"id":"GO:0007565","count":7},{"id":"GO:0015709","count":7}]},{"hash":"1010163249461871645","title":"K63-linked ubiquitination and NF-kappaB signaling","description":"The top GO terms cluster strongly around specific ubiquitination processes (K63-linked and K6-linked ubiquitination, autoubiquitination, ubiquitin-dependent degradation) and regulation of NF-kappaB signaling, TNF signaling, and histone turnover. This points to a coherent theme of ubiquitin-mediated regulation of immune signaling and chromatin dynamics, possibly influencing host defense (e.g., suppression of viral release) and inflammatory pathways.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0070534","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0043123","count":8},{"id":"GO:1903265","count":8}]},{"hash":"1165239422836926109","title":"Golgi Transport and Organization","description":"Top GO terms indicate a core role in Golgi trafficking and organization, with ER-to-Golgi and endosome-to-Golgi transport and regulation of Golgi structure dominating; other terms appear peripheral to this main theme.","confidence":"Medium","size":9,"edges":9,"triangles":1,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0034498","count":3},{"id":"GO:1903358","count":3},{"id":"GO:0042832","count":3},{"id":"GO:0002181","count":3}]},{"hash":"13563322722481649","title":"Transcriptional and chromatin regulation","description":"The top GO terms cluster around regulation of transcription by RNA polymerase II and chromatin-modifying processes (histone methylation, histone deacetylase activity, heterochromatin formation), suggesting a shared function in controlling gene expression through chromatin state. Some terms touch on immune signaling or plant development, but the core theme is transcriptional control via chromatin regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:1904388","count":4},{"id":"GO:2000410","count":4},{"id":"GO:0090308","count":4},{"id":"GO:0048655","count":4}]},{"hash":"627222645633529699","title":"Neural and cardiac development signaling and adhesion","description":"The top GO terms cluster around neural development (nervous system development, Schwann cell development) and heart development, with concurrent signaling and adhesion processes (Wnt signaling, ERK cascade, integrin-mediated signaling, cell-matrix adhesion). This suggests a coherent theme of developmental signaling and cell interactions in neural and cardiac contexts. An outlier term like sperm capacitation appears to be noise relative to the main theme. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0060045","count":4},{"id":"GO:0014044","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0007160","count":4}]},{"hash":"10523073791579796","title":"Immune signaling and cytokine production","description":"This cluster centers on immune cell activation, cytokine production, and receptor-mediated signaling, with terms like IL-3 and IL-4 production, NK cell differentiation, mast cell cytokine production, and angiogenesis regulation highlighting innate/adaptive immune processes. A single term about corpus callosum development appears peripheral, but the dominant theme is immune cell communication and cytokine signaling.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0038063","count":9},{"id":"GO:0045401","count":9},{"id":"GO:0097350","count":9},{"id":"GO:0032633","count":9},{"id":"GO:0022038","count":9}]},{"hash":"199433729691515930","title":"TNF-NF-\u03baB signaling and ubiquitination","description":"Predominant GO terms point to TNF-mediated signaling and NF-\u03baB activation, including IKK activation and NF-\u03baB induction. Ubiquitination terms (autoubiquitination, K63-linked ubiquitination) reflect signal transduction roles in this pathway, with some annotations to osteoclast differentiation and Th1 immune responses, consistent with inflammatory signaling in immune cells.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":8},{"id":"GO:0051865","count":8},{"id":"GO:1903721","count":8},{"id":"GO:0090073","count":8},{"id":"GO:1903265","count":8}]},{"hash":"1344898777147113266","title":"Unknown","description":"The terms span diverse processes across plants and animals (DNA repair, pollen and embryo development, various developmental processes like corpus callosum and notochord formation, keratinocyte proliferation, lipid biosynthesis, and immune signaling), with no single unifying function. This heterogeneity makes it inappropriate to assign a specific functional label; thus Unknown is the best fit.","confidence":"","size":9,"edges":9,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006302","count":1},{"id":"GO:0009555","count":1},{"id":"GO:0009553","count":1},{"id":"GO:0007131","count":1},{"id":"GO:1905373","count":1}]},{"hash":"1957523693012279147","title":"Neural development and signaling","description":"The top terms point to neural development (axonogenesis, corpus callosum development) and neuronal signaling (dopamine receptor signaling, GPCR signaling), with additional annotation for neuroimmune pathways (TLR signaling) and regulation of signaling via ubiquitination, suggesting a cohesive theme of brain development and neuronal communication with regulated signaling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0016567","count":1},{"id":"GO:1902499","count":1},{"id":"GO:0034142","count":1}]},{"hash":"1945022698796521346","title":"Innate Immune and Inflammatory Signaling","description":"The cluster is dominated by innate immune and inflammatory terms (innate immune response, inflammatory response, lipopolysaccharide-mediated signaling, peptidoglycan recognition protein signaling, TNF production, immunoglobulin production), pointing to a common role in immune recognition and cytokine signaling. A few developmental terms (axon guidance, pyramidal neuron differentiation, salivary gland boundary specification) may reflect multifunctional proteins or annotation breadth, but the strongest signal centers on innate immunity and inflammation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032760","count":2},{"id":"GO:0033564","count":2},{"id":"GO:0061057","count":2},{"id":"GO:0021859","count":2},{"id":"GO:0007432","count":2}]},{"hash":"1169593736732793987","title":"Retroviral Entry, Integration, and Latency","description":"The terms point to a retroviral lifecycle: entry into the host cell, penetration into the nucleus, RNA-templated DNA synthesis, DNA replication and recombination, and establishment of integrated proviral latency, with DNA integration as a key feature. The prominence of proviral latency and integration terms strongly supports a retrovirus interpretation, though some terms about host apoptosis and symbiont-related processes may reflect broader host\u2013virus interactions rather than core replication steps. Overall, this cluster is best described as retroviral entry and proviral integration with latency.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006147","count":2},{"id":"GO:0075713","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006310","count":1}]},{"hash":"1849103006582354468","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0006356","count":1},{"id":"GO:0000494","count":1}]},{"hash":"1452645447145583375","title":"Neuronal maturation and mitochondrial fission","description":"This cluster centers on neuronal development and signaling, highlighted by neuron maturation and GABAergic synaptic transmission, while also showing mitochondrial dynamics (mitochondrial and membrane fission) and apoptosis-related processes (apoptotic process, apoptotic mitochondrial changes). The co-occurrence of stress-related terms (response to cold, lipopolysaccharide) with neural-specific terms suggests a theme of neural maturation influenced by mitochondrial dynamics and stress-induced apoptosis.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0051932","count":3},{"id":"GO:0000266","count":3}]},{"hash":"2108457982982686052","title":"Lipid and Steroid Biosynthesis","description":"The top GO terms cluster around biosynthetic processes for lipids and steroid-related metabolites (sphingolipid biosynthesis, mycolic acid biosynthesis, retinoic acid, estrogen biosynthesis, androgen-related processes) with additional biosynthesis terms like poly-hydroxybutyrate and tetrahydrobiopterin. While there is some noise (e.g., response to methotrexate, antibiotic biosynthesis), the dominant theme is the production of lipids and hormone-related molecules. Confidence: Medium.","confidence":"","size":8,"edges":18,"triangles":22,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042619","count":7},{"id":"GO:0030148","count":5},{"id":"GO:0006703","count":5},{"id":"GO:0031427","count":5}]},{"hash":"1130739382353884930","title":"Gene Expression and Proteostasis","description":"The top GO terms cluster around DNA-templated transcription, ribosome biogenesis, histone acetylation, and ubiquitin-mediated processes, pointing to core gene expression regulation and protein quality control. The inclusion of ERAD-related terms supports proteostasis, while some items (skin development, exploration behavior, inflammatory cytokine production) appear as outliers or broader annotations that may not define the cluster. Overall, the dominant theme is transcriptional machinery coupled with protein turnover. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0043984","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1150916401316579311","title":"Ubiquitin-like modifications and autophagy","description":"This cluster is dominated by post-translational modification terms: protein ubiquitination, sumoylation, and neddylation, pointing to ubiquitin-like signaling pathways. It also includes macroautophagy, suggesting a link between these modifications and autophagic processes. Although a few terms touch on unrelated areas, the core theme is ubiquitin-like protein modification coupled with autophagy.","confidence":"High","size":8,"edges":25,"triangles":40,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":5},{"id":"GO:0016236","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0021764","count":3},{"id":"GO:0016567","count":3}]},{"hash":"747071476767304572","title":"ECM remodeling and integrin adhesion","description":"Most terms cluster around extracellular matrix dynamics and cell adhesion: regulation of collagen catabolic process, negative regulation of extracellular matrix disassembly, and regulation of cell-cell adhesion mediated by integrin. Other terms (rRNA methylation, formaldehyde catabolic process, hypoxia, insulin secretion, psychomotor behavior) appear as outliers, suggesting a mixed or broad set of roles rather than a single cohesive function. Because there is no interaction evidence (edges) and several unrelated terms dilute a clear theme, this label is tentative and best reflects the dominant ECM/adhesion signals.","confidence":"Low","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":2},{"id":"GO:1902362","count":1},{"id":"GO:0033632","count":1},{"id":"GO:0046294","count":1},{"id":"GO:0010710","count":1}]},{"hash":"271776830257928363","title":"Ubiquitin-Dependent Proteolysis in Cell Cycle","description":"This cluster is dominated by GO terms for ubiquitination pathways (ERAD, SCF, K11- and K63-linked), proteasomal degradation, and autoubiquitination, plus mitotic cell cycle and related processes, indicating proteins involved in targeted protein turnover during cell division (with some ties to chromatin and DNA repair).","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0070979","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0070534","count":4}]},{"hash":"644396110073581621","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030851","count":1},{"id":"GO:0033077","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0046638","count":1},{"id":"GO:0071425","count":1}]},{"hash":"134462345661646876","title":"Translation initiation and ribosome assembly","description":"Most of the terms indicate components of the protein synthesis machinery: translation, translational initiation, and cytosolic ribosome assembly. These points suggest roles in ribosome biogenesis and initiation of translation. A few terms (energy homeostasis, gonad development) appear ancillary, but the core signal is clearly translation-related.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":1},{"id":"GO:0006412","count":1},{"id":"GO:1905696","count":1},{"id":"GO:0042256","count":1},{"id":"GO:0001541","count":1}]},{"hash":"632319454681082103","title":"Diverse Membrane Transporters","description":"This cluster is dominated by GO terms related to moving a wide range of molecules across membranes (lipoproteins, vitamins, amino acids, metals/ions, drugs like doxorubicin, ceramide, bacteriocins, etc.), suggesting a core function as transport proteins or transport-associated factors. The presence of immune-related terms likely reflects contextual roles or co-associated processes, but the strongest signal is transmembrane transport across diverse substrates.","confidence":"High","size":8,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042953","count":4},{"id":"GO:0043277","count":3},{"id":"GO:0045087","count":3},{"id":"GO:1900753","count":2},{"id":"GO:0015689","count":2}]},{"hash":"1152832278326918298","title":"RNA splicing and translation initiation regulation","description":"The terms cluster around RNA processing (splicing, spliceosome activity, mRNA modification) and control of translation initiation, mRNA stability, and spliceosome-related processes, suggesting a functional group focused on RNA maturation and translational regulation. A couple of terms touch on vacuolar acidification, but the dominant theme is RNA processing and translation control.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":1},{"id":"GO:0070072","count":1},{"id":"GO:0006376","count":1},{"id":"GO:0097010","count":1},{"id":"GO:0010610","count":1}]},{"hash":"2064203805749666449","title":"RNA Splicing Machinery and Post-Transcriptional Regulation","description":"This cluster is enriched for mRNA splicing via the spliceosome, spliceosomal snRNP assembly, and post-transcriptional gene silencing, along with some rRNA maturation and ubiquitination terms. The dominant theme points to RNA processing and post-transcriptional control, with a few outliers.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0000387","count":1},{"id":"GO:0000481","count":1}]},{"hash":"144089951346961774","title":"Proteoglycan biosynthesis and skeletal development","description":"The dominant GO terms point to proteoglycan biosynthesis (chondroitin sulfate and heparan sulfate) and related glycosylation, with concurrent terms in ossification, skeletal joint development, mesoderm and gastrulation, and FGFR signaling. This pattern suggests a cluster focused on extracellular matrix proteoglycan production and its role in skeletal/embryonic development.","confidence":"High","size":8,"edges":11,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":3},{"id":"GO:0019276","count":3},{"id":"GO:0050650","count":3},{"id":"GO:0001503","count":2},{"id":"GO:0072498","count":2}]},{"hash":"1462251911078338666","title":"Calcineurin\u2013NFAT signaling and synaptic calcium regulation","description":"This cluster is enriched for terms tied to calcineurin-NFAT signaling regulation and neuronal synaptic functions, including regulation of presynaptic calcium concentration and synaptic plasticity. The presence of positive regulation of GTPase activity and lipid remodeling terms suggests broader signaling and membrane-context processes, while other terms reflect stress-response signaling in cardiac and epithelial contexts. Overall, the common thread appears to be calcium-dependent signaling involving the calcineurin-NFAT axis that influences neural synaptic function, with some related signaling and remodeling aspects.","confidence":"Medium","size":8,"edges":22,"triangles":28,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042554","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0051531","count":7},{"id":"GO:0014898","count":7},{"id":"GO:0048168","count":7}]},{"hash":"249735953777796677","title":"Unknown","description":"The GO terms are a mix of carbohydrate metabolism (galactose metabolic process, inositol/ sorbitol pathways) and transcriptional/regulatory controls (negative regulation of transcription by RNA polymerase II, negative regulation of kinase activity), with several obsolete terms. There is no single coherent function tying all proteins together, and the lack of edges supports a heterogeneous collection rather than a shared pathway.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006012","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0019310","count":2},{"id":"GO:0019877","count":2}]},{"hash":"432330014112167119","title":"Unknown","description":"The GO terms span transcription, nervous system development, multiple metabolic/catabolic processes (glycoside, glucosylceramide, bile acids) and a few post-translational modifications, with no clear shared function linking the proteins.","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0021954","count":1},{"id":"GO:0016139","count":1},{"id":"GO:0008206","count":1},{"id":"GO:0006680","count":1}]},{"hash":"508764551234458635","title":"Chondroitin sulfate proteoglycan biosynthesis and cartilage development","description":"The top GO terms are dominated by chondroitin sulfate biosynthesis and cartilage-related processes (chondroitin sulfate proteoglycan biosynthetic process, cartilage development, chondrocyte development). This suggests the cluster is centered on cartilage extracellular matrix components and sulfation of proteoglycans. Some terms appear ancillary or cross-species, but the core theme remains cartilage ECM formation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030206","count":3},{"id":"GO:0006486","count":3},{"id":"GO:0050650","count":3},{"id":"GO:0060876","count":2},{"id":"GO:0002063","count":2}]},{"hash":"1228772911407710307","title":"Mitochondrial Translation and tRNA Charging","description":"The dominant GO terms are mitochondrial tRNA aminoacylation (lysine, aspartate, asparagine) and translation, indicating proteins that participate in mitochondrial protein synthesis and tRNA charging. While a few unrelated terms appear, the core pattern supports a mitochondrial translation-focused cluster.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070154","count":1},{"id":"GO:0071915","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0070146","count":1},{"id":"GO:0070145","count":1}]},{"hash":"1473994783736105056","title":"MVB-Mediated Endosomal Sorting and Lysosomal Degradation","description":"Prominent GO terms describe multivesicular body formation and sorting, trafficking to the vacuole/lysosome, and ubiquitin-dependent protein catabolism, as well as MVB-lysosome fusion and ER targeting, which together define endosomal sorting and lysosomal degradation pathways. The presence of autophagy-related regulation and host antiviral suppression further supports cross-talk between MVB sorting, autophagy, and degradation pathways. A few cell cycle terms are likely background noise rather than the main function. Therefore, the cluster is best labeled as MVB-mediated endosomal sorting and lysosomal degradation.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":7},{"id":"GO:0071985","count":6},{"id":"GO:1902902","count":6},{"id":"GO:0010458","count":6},{"id":"GO:0051301","count":6}]},{"hash":"593194082386635549","title":"Centrosome and Cilium\u2013Related Cell Cycle Regulation","description":"This cluster\u2019s top GO terms point to centrosome-associated processes (pericentriolar material localization), non-motile cilium assembly, and mitotic progression (metaphase/anaphase), suggesting a core theme of centrosome/cilium functions coordinating cell division. Other terms hint at ubiquitin-mediated proteostasis and ER stress responses, which can intersect with centrosome biology. While some terms are obsolete or less directly related, the strongest common thread appears to be regulation of the cell cycle via centrosome and cilium pathways, hence the label.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903070","count":2},{"id":"GO:0036494","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0016576","count":1},{"id":"GO:0070979","count":1}]},{"hash":"520630867895285729","title":"Neurotrophin signaling and neural differentiation","description":"This cluster is enriched for neural development signals: multiple terms point to neurotrophin TRK receptor signaling, nervous system and forebrain development, and retinal bipolar cell polarity along with retinoic acid response, suggesting a cohesive role in neural differentiation and retinal development. Some terms like angiogenesis or cardiac differentiation appear as broader developmental associations, but the dominant theme is neural development.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0048011","count":7},{"id":"GO:0045766","count":7},{"id":"GO:0014902","count":7},{"id":"GO:0071300","count":7},{"id":"GO:2000727","count":6}]},{"hash":"1261786009462164741","title":"Cardiovascular development","description":"The top GO terms center on heart and vessel formation (right atrium morphogenesis, venous endothelial differentiation, Notch signaling in heart-field proliferation) and general cell cycle activity, pointing to a cohesive theme of heart and vascular development. Some terms appear as broader developmental processes or tissue-specific patterns, but the dominant signal is cardiovascular development.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0003213","count":3},{"id":"GO:0060843","count":3},{"id":"GO:0003270","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1972882258952041539","title":"Zinc Ion Transport and Homeostasis","description":"These proteins cluster around zinc handling: multiple GO terms point to zinc ion import across the plasma membrane, intracellular zinc ion homeostasis, and detoxification of zinc ions, plus related metal transport (cadmium). The presence of zinc-related terms and metal ion transport suggests a shared function in zinc uptake and homeostasis, with occasional unrelated annotations such as limb development or nitrate assimilation likely reflecting broad or indirect associations.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006831","count":2},{"id":"GO:1903615","count":2},{"id":"GO:0034224","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0006882","count":2}]},{"hash":"1791123592647397058","title":"Developmental transcriptional regulation in nervous system","description":"Based on GO terms, the proteins cluster around neural development and transcriptional regulation. Multiple entries point to nervous system development, forebrain development, and bipolar cell polarity, alongside DNA-templated transcription and transcription factor activity, indicating a role in transcriptional control during neural differentiation. Some terms related to immune signaling and other tissue development are present but appear peripheral to the central neural-development/transcription theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2000727","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0061246","count":5},{"id":"GO:0032633","count":5},{"id":"GO:0043433","count":5}]},{"hash":"1611504403754195853","title":"TNF-NF-\u03baB Signaling via K63 Ubiquitination","description":"The proteins in this cluster co-occur with TNF-mediated signaling and multiple steps of NF-\u03baB activation, including K63-linked ubiquitination and autoubiquitination, as well as I\u03baB phosphorylation and NF-\u03baB induction. This pattern points to a coherent signaling module governing innate immune responses to inflammatory cues. A histone catabolic term appears less central to the core theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033209","count":5},{"id":"GO:0070534","count":5},{"id":"GO:0051865","count":5},{"id":"GO:1903721","count":5},{"id":"GO:0090073","count":5}]},{"hash":"830621160843765502","title":"Unknown","description":"The top GO terms are scattered across neuronal development (neuron projection development, synaptic plasticity) and glial/apoptotic processes, plus chromatin organization, DNA repair, and unrelated signaling terms. There isn\u2019t a single cohesive function tying these proteins together, so a specific, representative label can\u2019t be confidently assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002534","count":1},{"id":"GO:0051441","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0031915","count":1},{"id":"GO:2000011","count":1}]},{"hash":"2288258927045859864","title":"ER Stress and Secretory Trafficking","description":"This cluster shows strong enrichment for endoplasmic reticulum\u2013related processes: unfolded protein response, protein localization to the ER, and COPII vesicle budding, along with ER calcium homeostasis. These together point to ER proteostasis and the early secretory pathway, with the Smoothened signaling term being less central to the overall theme.","confidence":"Medium","size":8,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":2},{"id":"GO:0044828","count":1},{"id":"GO:0030968","count":1},{"id":"GO:0070972","count":1},{"id":"GO:0006874","count":1}]},{"hash":"1476867658909013145","title":"Developmental morphogenesis and tissue differentiation","description":"This cluster shows a thematic grouping around developmental processes across multiple tissues, including organ morphogenesis (coronary vein, metanephric kidney, palatal shelf), keratinocyte differentiation, neuron axon fasciculation and synapse assembly, and regulation of signaling pathways (Smoothened, FGF production). The common thread is developmental morphogenesis and differentiation signals rather than a single, narrow function.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0071372","count":8},{"id":"GO:0045880","count":8},{"id":"GO:0051965","count":7},{"id":"GO:0030216","count":7},{"id":"GO:0097155","count":7}]},{"hash":"1297506402319464627","title":"Muscle contraction and ion transport","description":"The Top Terms cluster around excitation-contraction coupling: regulation of skeletal muscle and heart contraction, multiple ion transport processes (sodium, calcium, potassium, manganese) across membranes, and mitochondrial calcium homeostasis. A related term on long-term synaptic potentiation hints at calcium signaling roles in excitability. Together, these terms point to a theme of muscle function tied to membrane ion flux and calcium-dependent signaling.","confidence":"Medium","size":8,"edges":15,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0014819","count":1},{"id":"GO:0007154","count":1},{"id":"GO:0051560","count":1},{"id":"GO:0097369","count":1},{"id":"GO:1990034","count":1}]},{"hash":"725004355468618526","title":"Organelle Protein Import and Membrane Targeting","description":"The top GO terms emphasize import into mitochondria (matrix and inner membrane) and into chloroplast stroma, along with membrane insertion, indicating a shared theme of transporting and targeting proteins to organelles and membranes. Other terms (brush border assembly, equilibrioception) appear less connected and may reflect mixed annotations, but the strongest signal is organelle protein import.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904970","count":2},{"id":"GO:0050957","count":2},{"id":"GO:0045037","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0030150","count":1}]},{"hash":"1982387382398775563","title":"Growth and cell cycle regulation","description":"This cluster centers on proliferation and growth signaling (endothelial proliferation, TORC1 signaling), coordination of DNA replication and mitotic/nuclear events (regulation of DNA replication, mitotic nuclear membrane reassembly, female meiotic division), and growth-related transcription (RNA polymerase III). These terms together suggest a cohesive module for growth, division, and associated transcriptional control.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001938","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0045945","count":2},{"id":"GO:0021510","count":2}]},{"hash":"1313379623146452065","title":"Rho GTPase\u2013driven cytoskeletal remodeling","description":"The top GO terms center on small GTPase-mediated signaling and actin dynamics, including filopodium assembly and regulation, cell spreading, and negative regulation of cell size. Endosomal transport and neural/immune signaling plausibly relate to cytoskeleton-dependent trafficking and membrane signaling. Together, they point to a cohort of proteins coordinating actin cytoskeleton remodeling via Rho-family GTPases. High","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0045792","count":4},{"id":"GO:1900026","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0046847","count":4},{"id":"GO:0051932","count":4}]},{"hash":"534246971238439354","title":"Ubiquitination and Proteasome Assembly","description":"The strongest, recurring terms are protein ubiquitination and proteasome regulatory particle assembly, suggesting a core role in proteostasis. While other terms relate to signaling and environmental responses, they do not clearly define a single cohesive function for the cluster. Thus, the label emphasizes proteostasis with a medium confidence.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0050960","count":2},{"id":"GO:0035556","count":2},{"id":"GO:1901594","count":2}]},{"hash":"1009331118104589168","title":"Ribosome biogenesis and RNA processing","description":"The cluster is dominated by RNA maturation and ribosome-related processes: rRNA modification, guanine-N7 methylation, 7-methylguanosine capping, and ITS1 rRNA processing, indicating involvement in ribosome biogenesis and RNA processing. There are also terms for transcription and DNA replication, suggesting broader nuclear gene expression machinery, while development-related terms and the cocaine-response term are likely incidental annotations. Overall, the common theme is RNA processing and ribosome assembly.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0030900","count":2}]},{"hash":"1100356927170775280","title":"Ubiquitin signaling in TNF and antiviral defense","description":"This cluster centers on ubiquitination processes (protein, histone, actin, autoubiquitination) and immune/antiviral functions (TNF-mediated signaling, suppression of viral release, negative regulation of intracellular viral transport) with roles in regulating apoptosis. The shared theme is ubiquitin-mediated modulation of signaling, chromatin dynamics, and antiviral responses.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033209","count":4},{"id":"GO:1902187","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0042981","count":4}]},{"hash":"1831761040547190580","title":"Chromatin-based transcriptional regulation","description":"The top terms are centered on regulation of gene expression via chromatin modifications and transcription control (negative regulation of transcription by RNA polymerase II; histone H3-K4 methylation and H3-K27 acetylation). Although some GO terms are obsolete and a few metabolism-related terms appear as outliers, the core signal across the cluster points to chromatin-mediated transcriptional regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010216","count":2},{"id":"GO:2001040","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0044648","count":2},{"id":"GO:1901674","count":2}]},{"hash":"1638669970951168219","title":"DNA Damage Response and Repair","description":"The top GO terms cluster around DNA replication, repair, and G2 DNA damage checkpoint signaling, with related responses to ionizing radiation and meiotic DSB processing, suggesting a core function in genome integrity maintenance; a few development or signaling terms may reflect broader annotations.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032792","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0007095","count":2},{"id":"GO:0006260","count":2}]},{"hash":"626774335315130274","title":"Platelet Activation and Coagulation","description":"This cluster centers on platelet activation and coagulation, with accompanying vascular stability and angiogenesis regulation (Tie signaling, negative regulation of angiogenesis and vascular permeability), plus immune-related modulation. The convergence of platelet, coagulation, and vascular terms suggests a thrombo-inflammatory vascular function theme, making Platelet Activation and Coagulation a concise, representative label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002740","count":4},{"id":"GO:0030168","count":4},{"id":"GO:0001867","count":4},{"id":"GO:0043116","count":4},{"id":"GO:0007160","count":4}]},{"hash":"135840237342633392","title":"Platelet Activation, Coagulation, and Angiogenesis","description":"The cluster centers on platelet activation, coagulation (blood coagulation, common pathway), and angiogenesis-related signaling (Tie pathway, negative regulation of angiogenesis, vascular permeability), with supporting roles for immune/modulatory functions (complement activation, negative regulation of cytokine production) and cell-matrix adhesion. This combination suggests a cohesive module linking hemostasis, vascular remodeling, and immune regulation.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002740","count":7},{"id":"GO:0030168","count":7},{"id":"GO:0001867","count":7},{"id":"GO:0043116","count":7},{"id":"GO:0007160","count":7}]},{"hash":"1503657974991229783","title":"Mitotic Cell Cycle and DNA Damage Response","description":"This cluster combines strong signals for mitosis (mitotic cycle, G2/M transition), DNA damage repair (homologous recombination, G1 checkpoint signaling), chromatin organization, and protein regulation via ubiquitination and neddylation (SCF-dependent, K11/K63-linked). Together, these terms point to coordinated control of cell division, chromatin dynamics, and protein turnover in development.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001701","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0000086","count":7},{"id":"GO:0070979","count":7},{"id":"GO:0031146","count":7}]},{"hash":"632325812987586049","title":"Neural Development and Axon Targeting","description":"Based on strong signals for nervous system development (central nervous system development and nervous system development), corpus callosum development, and a term about protein localization to the juxtaparanode region of an axon, the cluster appears to group proteins involved in neural development and axon organization. Some non-neural terms (angiogenesis, prolactin signaling, immune-related terms) are present but do not dominate the theme; the core function is neural development and axon targeting.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007417","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0038161","count":1},{"id":"GO:1902948","count":1},{"id":"GO:0097350","count":1}]},{"hash":"2226339634502462456","title":"TLR-driven innate immune signaling with ubiquitination","description":"This cluster is most clearly linked by GO terms around Toll-like receptor signaling (MyD88-dependent and TLR10), regulation of dendritic cell cytokine production, and protein ubiquitination, plus the NFAT-related calcineurin signaling context. While there are also terms related to Wnt signaling, CAMKK-AMPK signaling, and cell-cycle regulation, the dominant theme points to innate immune activation in dendritic cells and associated ubiquitination processes.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":2},{"id":"GO:1904887","count":1},{"id":"GO:0002755","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0016567","count":1}]},{"hash":"916343108956343677","title":"Vertebrate neural development and transcription","description":"This cluster is strongly enriched for neural development and transcription-related terms: forebrain development and neural tube closure point to brain morphogenesis, while multicellular organism development and skeletal system development suggest broader embryonic patterning; DNA-templated transcription and mitotic cell cycle indicate essential gene regulation and proliferation that support development. A few terms such as defense response to Gram-positive bacterium and cadmium ion response may reflect general stress responses present in the proteins but do not define the core theme. Overall, the dominant signal is vertebrate neural development and its transcriptional control.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0030900","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0001403","count":3}]},{"hash":"1588407773710411600","title":"mRNA splicing and translation regulation","description":"The GO terms are dominated by mRNA processing and spliceosome-mediated splicing, with additional signals for regulation of translation initiation and mRNA stability in response to stress, suggesting a coherent module tying mRNA maturation to translational control.","confidence":"Medium","size":7,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006376","count":2},{"id":"GO:0097010","count":2},{"id":"GO:0010610","count":2}]},{"hash":"1710459718435794884","title":"Neural development and synaptic signaling","description":"The top terms point to neural development (Schwann cell development, visual perception) and synaptic function (excitatory postsynaptic potential, long-term potentiation), with additional hints of broader developmental processes and cell-cycle regulation. This suggests a cluster tied to developmental processes with a focus on neural signaling rather than a single molecular function, though the presence of diverse terms introduces some heterogeneity.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007520","count":3},{"id":"GO:0014044","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1020888942596659076","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045717","count":1},{"id":"GO:0006552","count":1},{"id":"GO:0044205","count":1}]},{"hash":"2129482202754586015","title":"Mitotic cell cycle and ubiquitin-mediated proteolysis","description":"The top GO terms show a clear emphasis on cell division processes (mitotic cell cycle, mitotic spindle assembly) and ubiquitin-dependent protein degradation (polyubiquitination, SCF-dependent proteasomal pathways). Translation-related terms are present but appear secondary; the dominant theme ties mitosis to controlled proteolysis, suggesting coordination of cell cycle progression with protein turnover.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":4},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0031146","count":3}]},{"hash":"11692139076332539","title":"Inflammatory signaling and programmed cell death","description":"This cluster is enriched for GO terms tied to innate immune responses and cell fate decisions, such as response to lipopolysaccharide, necroptotic signaling, activation-induced cell death of T cells, TNF production, and JNK cascade. While a few terms pertain to development or plant immunity, the prevalent theme centers on inflammatory signaling pathways and apoptosis/necroptosis, suggesting the proteins function together in stress-induced immune signaling and cell death decisions.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:2000666","count":2},{"id":"GO:0051798","count":2},{"id":"GO:0097527","count":2},{"id":"GO:0006924","count":2}]},{"hash":"205103299716549705","title":"Developmental transcription and differentiation","description":"The cluster's terms are centered on developmental processes (nervous system, forebrain, cardiac muscle differentiation, bipolar cell polarity) and on DNA-templated transcription, suggesting these proteins are broadly involved in developmental regulation rather than a single, specific pathway. Some immune-related terms appear but are less cohesive with the primary developmental/transcription theme, and there are few edges among members, indicating a general association with transcriptional control during development.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000727","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0061246","count":1},{"id":"GO:0032633","count":1},{"id":"GO:0043433","count":1}]},{"hash":"1831834825604447037","title":"Endosomal MVB Trafficking and Degradation","description":"This cluster is dominated by terms for multivesicular body (MVB) assembly, MVB-lysosome fusion, and vacuolar protein sorting via ubiquitin-dependent pathways, plus endosome transport toward the lysosome/vacuole. These indicate endosomal trafficking and degradation as the core theme, with a few peripheral cell cycle terms that are less central to the cluster\u2019s main function.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009190","count":1},{"id":"GO:0043328","count":1},{"id":"GO:1902187","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0061763","count":1}]},{"hash":"1407656990695433645","title":"Neural development and synaptic regulation","description":"These proteins cluster around neural development and synaptic maturation: neuroblast proliferation, tangential migration toward the olfactory bulb, dendritic spine morphogenesis, and regulation of synaptic vesicle exocytosis, with supporting signals from Wnt signaling and small GTPase pathways; mitochondrial distribution and CAMKK-AMPK regulation further reflect neuronal energy needs and signaling. An outlier term about osteoclast development is present but does not change the overall neural theme.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904887","count":3},{"id":"GO:0022028","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0036035","count":3},{"id":"GO:1905289","count":3}]},{"hash":"1736820533287567057","title":"Neuronal actin remodeling and spine development","description":"The terms cluster around neuronal actin dynamics and synaptic structure: regulation of actin assembly and capping, Rac signaling, dendritic spine development, and synaptic plasticity, with supporting cues from neuron development signals. Other terms like defense response to fungus appear less central. Overall, the data point to actin remodeling in neurons guiding spine formation and plasticity.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007406","count":2},{"id":"GO:0044379","count":1},{"id":"GO:0032232","count":1},{"id":"GO:0031915","count":1},{"id":"GO:0050832","count":1}]},{"hash":"1179548196618908692","title":"Vesicle trafficking and vacuolar ion homeostasis","description":"The cluster centers on processes related to the vacuole (protein targeting to vacuole, vacuolar acidification, vacuole organization) and vesicle movement along actin filaments, plus proton/ion transport and energy-linked transport across membranes. This suggests a coherent module of intracellular trafficking to the vacuole with regulation of ion homeostasis and membrane potential, aided by actin-based vesicle transport. The obsolete mitochondrion-targeting term is a historical artifact and does not outweigh the vacuolar/trafficking theme.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0007035","count":1}]},{"hash":"2195549030312547325","title":"Unknown","description":"The terms cover energy metabolism, ER-stress\u2013driven translation, ciliogenesis, histone dephosphorylation, ubiquitination, mitotic progression, and developmental identity, with no single dominant function linking the proteins. This makes a cohesive label difficult; thus Unknown with None confidence.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2000984","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0036494","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0016576","count":1}]},{"hash":"873667456656144802","title":"Unknown","description":"The top GO terms are highly diverse (proviral latency, brain development, DNA repair, interferon production, salinity response, etc.) and there are no edges linking the proteins, so there is no coherent function or pathway that ties them together. Hence a meaningful label cannot be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":2},{"id":"GO:0048660","count":1},{"id":"GO:0071475","count":1},{"id":"GO:1904430","count":1},{"id":"GO:0097680","count":1}]},{"hash":"1278270018195754023","title":"Neural development and synapse assembly","description":"Most frequent GO terms center on development and neural connectivity: multicellular organism development, forebrain development, positive regulation of synapse assembly, receptor clustering, and cell-matrix adhesion point toward processes of synaptogenesis and neural tissue organization. Although there are some terms related to skeletal/brown fat lineages and pain perception, the convergent theme is brain development and synaptic organization, suggesting these proteins cluster around neural development and synaptic functions.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0051965","count":5},{"id":"GO:0001501","count":5},{"id":"GO:0030900","count":4},{"id":"GO:0090336","count":4}]},{"hash":"656757834991756302","title":"Lipid and steroid metabolism via P450 enzymes","description":"The cluster\u2019s top GO terms converge on lipid- and hormone-related metabolism, including prostaglandin biosynthesis, progesterone and triglyceride metabolism, retinoic acid catabolism, lipid hydroxylation, and epoxygenase (P450) pathways. These together suggest a theme of lipid-derived hormone and oxylipin processing mediated by cytochrome P450 enzymes, despite a few outlier terms that resemble noise. ","confidence":"Medium","size":7,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034653","count":5},{"id":"GO:0001516","count":5},{"id":"GO:0002933","count":5},{"id":"GO:0060137","count":5},{"id":"GO:0042448","count":5}]},{"hash":"788732778781447843","title":"Neural Development and Transcription","description":"The top GO terms center on nervous system development, forebrain development, and cell polarity related to neural cells, plus DNA-templated transcription and transcriptional regulation, with some signals pointing to broader developmental differentiation including cardiac muscle differentiation. While there are immune cytokine production terms, they seem secondary to the primary neural development/transcription theme, making this label representative of the cluster\u2019s core function.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2000727","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0061246","count":7},{"id":"GO:0032633","count":7},{"id":"GO:0043433","count":7}]},{"hash":"2171927896679250495","title":"Neural development and synaptic plasticity","description":"The top GO terms cluster around forebrain development and synaptic remodeling functions, including dendritic spine morphogenesis, regulation of excitatory postsynaptic potentials, and synapse structural plasticity, which together point to neural development and plasticity processes. Cytoskeletal regulation (actin organization, Rho signaling) supports these synaptic changes. A few terms are peripheral (endothelial barrier, dendritic cell apoptosis), but the dominant theme is neural development and synaptic remodeling.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0090557","count":3},{"id":"GO:0071625","count":3},{"id":"GO:0035176","count":3},{"id":"GO:0051835","count":3}]},{"hash":"1196801656447581761","title":"Calcium-dependent signaling and neural development","description":"The cluster centers on calcium-mediated signaling, with terms for regulation of calcineurin-NFAT signaling and presynaptic calcium concentration, plus neural crest and neural development-related processes. While additional terms touch on EMT and cardiac hypertrophy, the strongest shared theme is calcium-dependent signaling impacting neural development and synaptic function.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001837","count":2},{"id":"GO:0042554","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0051531","count":1},{"id":"GO:0014032","count":1}]},{"hash":"2281967641409606755","title":"Developmental Transcriptional Regulation","description":"This cluster is enriched for DNA-templated transcription and mRNA processing, with additional links to forebrain development, cell migration, Wnt signaling modulation, and adipogenic differentiation, suggesting a group of proteins that coordinate gene expression during development and lineage specification, with metabolic differentiation supporting the broader theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030900","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0045819","count":2},{"id":"GO:0006397","count":2}]},{"hash":"546594551568177437","title":"Bacterial cell wall synthesis and division","description":"This cluster centers on peptidoglycan biosynthesis and turnover, plus cell wall organization and cell division/cell cycle terms, pointing to a cohesive theme of bacterial cell wall biogenesis and division. Some outlier terms related to multicellular development and angiogenesis appear, likely due to annotation noise, but do not define the core function of the cluster.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009252","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0009254","count":3},{"id":"GO:0071555","count":3}]},{"hash":"650186975590633018","title":"Chromatin Modification and Transcription Regulation","description":"The top GO terms cluster around nuclear processes: histone modification (H3-K9 methylation), chromatin organization, and DNA-templated transcription, along with DNA damage repair and cell cycle activities. While a few terms (cytokine production, synaptic plasticity, pattern formation) are peripheral, the dominant signal points to chromatin regulation and transcription control. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051567","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0002534","count":2}]},{"hash":"225672874963752258","title":"Rho/Rac-driven actin remodeling and protrusions","description":"The top GO terms are dominated by Rho/Rac signaling and actin-based protrusion assembly (lamellipodium, filopodium, microspike), indicating proteins involved in cytoskeletal remodeling and formation of cell protrusions. While a couple terms touch on development or growth hormone pathways, the core signal is clear: actin dynamics governed by Rho family GTPases. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0043552","count":2},{"id":"GO:1904424","count":2},{"id":"GO:0046847","count":2}]},{"hash":"1405123058300128749","title":"Unknown","description":"The GO terms in this cluster are scattered across apoptosis, immune signaling, endosomal transport, neuronal plasticity, and stress responses, with no single dominant function or pathway tying the proteins together, so a cohesive label cannot be confidently assigned.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":1},{"id":"GO:0010794","count":1},{"id":"GO:0006924","count":1},{"id":"GO:0032425","count":1},{"id":"GO:0048168","count":1}]},{"hash":"2284475118668732131","title":"Developmental apoptosis and growth control","description":"This cluster is dominated by GO terms tied to programmed cell death and mitochondrial quality control (neuron apoptotic process, apoptotic process, type 2 mitophagy) and growth-regulating signaling (hippo signaling), with additional developmental context (cell cycle, paraxial mesoderm development, vasculogenesis). While translation-related terms and a neural sensory term appear, the strongest theme centers on how development, growth, and cell fate are coordinated through apoptosis and growth-control pathways.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043525","count":2},{"id":"GO:0061734","count":2},{"id":"GO:0035329","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0007605","count":2}]},{"hash":"213829996067458887","title":"Embryonic organogenesis","description":"The GO terms cluster around development and morphogenesis across multiple organs (retina, digits, ureteric bud, heart, prostate) and early patterning processes (primitive streak, endoderm fate). This suggests a common theme of embryonic organogenesis and tissue morphogenesis rather than a single tissue-specific function.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":3},{"id":"GO:0060133","count":2},{"id":"GO:0042733","count":2},{"id":"GO:0072095","count":2},{"id":"GO:0097376","count":2}]},{"hash":"1257655556481548854","title":"Neural development and chromatin-regulated transcription","description":"The GO terms are dominated by neural development and transcription control: neuron maturation, positive regulation of neuron projection development, in utero embryonic development, and transcription by RNA polymerase II, along with chromatin-binding regulation. Although a couple of terms hint at broader immune responses (lipopolysaccharide), the strongest signal ties neural development to transcriptional and chromatin-level regulation, suggesting a module of neural-development genes governed by chromatin state.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0032496","count":2}]},{"hash":"1167006180566857102","title":"Unknown","description":"The top GO terms span translation, insulin signaling, immune regulation, and various developmental processes with no obvious common function, and the cluster has no edges or cohesive connectivity, suggesting no single cohesive theme. Therefore this cluster is best labeled Unknown. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0008286","count":2},{"id":"GO:0002924","count":2},{"id":"GO:0051798","count":1},{"id":"GO:0033085","count":1}]},{"hash":"811743104090852103","title":"Ubiquitin-dependent TNF/NF-\u03baB signaling","description":"This cluster centers on ubiquitination-related processes (K63-linked ubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic processes) and TNF-mediated signaling, with links to NF-\u03baB activation and innate immune response, suggesting a cohesive role in ubiquitin-regulated inflammatory signaling leading to NF-\u03baB activity.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033209","count":4},{"id":"GO:0070534","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0042787","count":4}]},{"hash":"369025968589828002","title":"Epigenetic transcriptional repression","description":"The top GO terms are dominated by epigenetic control of gene expression, including CpG island methylation\u2013mediated silencing and negative regulation of transcription by RNA polymerase II, pointing to transcriptional repression as the core theme. Peripheral terms touch on protein turnover, kinetochore localization, and some immune/developmental processes, but the strongest signal centers on epigenetic silencing of transcription.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044027","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0042176","count":2},{"id":"GO:0034501","count":2}]},{"hash":"2138734460324258987","title":"DNA Damage Response & Chromatin Regulation","description":"This cluster centers on double-strand break repair (HR), mitotic DNA damage signaling, chromatin organization, and ubiquitin/neddylation pathways, indicating a coordinated DNA damage response with chromatin remodeling. The presence of neddylation, K63-linked ubiquitination, and autoubiquitination, alongside DDR and meiotic DSB formation terms, suggests a shared function in DDR regulation through ubiquitin-related modification of chromatin and repair proteins.","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0045116","count":6},{"id":"GO:0070534","count":6},{"id":"GO:0000724","count":6},{"id":"GO:0031571","count":6},{"id":"GO:0031497","count":6}]},{"hash":"259521817714748599","title":"mRNA Splicing and Translation Initiation Regulation","description":"These proteins cluster around post-transcriptional control: mRNA splicing and modification (spliceosome regulation, splice site recognition, mRNA modification) together with regulation and initiation of translation (eIF4F complex assembly, translational initiation control), plus stress-responsive mRNA stability and even IRES-dependent viral translation initiation. This points to a coordinated module of mRNA processing linked to initiation of translation, especially under stress. ","confidence":"High","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":3},{"id":"GO:0097010","count":3},{"id":"GO:0010610","count":3},{"id":"GO:1905663","count":3},{"id":"GO:0048026","count":3}]},{"hash":"24399327522889953","title":"DNA damage response and chromatin regulation via ubiquitination","description":"Top GO terms emphasize protein ubiquitination/neddylation (neddylation, K63-linked ubiquitination, autoubiquitination) and DNA damage response processes (double-strand break repair by homologous recombination, meiotic DSB formation, mitotic G1 checkpoint) along with chromatin organization. This combination suggests a module of proteins that regulate genome integrity and chromatin state through ubiquitin-like modifiers. Some annotations like ABA response or BMP signaling may be incidental to broader signaling roles but do not define the core function of this cluster.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0045116","count":6},{"id":"GO:0070534","count":6},{"id":"GO:0000724","count":6},{"id":"GO:0031571","count":6},{"id":"GO:0031497","count":6}]},{"hash":"159510056628551893","title":"RNA Splicing and Processing","description":"The proteins are enriched for RNA metabolism: multiple spliceosome-related terms (mRNA splicing via spliceosome, spliceosomal snRNP assembly), mRNA decay/processing (deadenylation-dependent decapping, P-body assembly), and RNA maturation (tRNA processing), with nuclear import, indicating a cohesive RNA processing/RNP biogenesis cluster.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0051170","count":4},{"id":"GO:1990141","count":4},{"id":"GO:0009414","count":4},{"id":"GO:0000387","count":4}]},{"hash":"1031782403485771411","title":"Cross-tissue Stress-Response Signaling","description":"This cluster centers on signaling pathways activated by cellular stress and growth cues across different tissues. Terms point to cardiac hypertrophy regulation, NFAT/calcium signaling, glucocorticoid signaling, unfolded protein response, DNA repair, and immune modulation, suggesting a general theme of stress adaptation and growth signaling rather than a single tissue-specific function.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001034","count":6},{"id":"GO:0051531","count":6},{"id":"GO:0014898","count":6},{"id":"GO:0001915","count":6},{"id":"GO:0060487","count":6}]},{"hash":"270352492052298081","title":"Histone exchange and chromatin remodeling","description":"The prominent terms reflect histone exchange, nucleosome mobilization, and heterochromatin formation/maintenance, along with RNA polymerase transcription regulation; together these indicate a chromatin remodeling/transcription control module. A couple of terms (developmental morphogenesis, biofilm adhesion) appear as outliers, likely annotation noise.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043486","count":5},{"id":"GO:0042766","count":5},{"id":"GO:0006363","count":3},{"id":"GO:0070870","count":3},{"id":"GO:1900189","count":3}]},{"hash":"1655485831403891149","title":"Embryonic organ development and morphogenesis","description":"The GO terms point to embryonic development and organ morphogenesis across multiple tissues (kidney, heart, nervous system, digits, pituitary, bone). This supports naming the cluster as Embryonic organ development and morphogenesis.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0045672","count":1},{"id":"GO:0060133","count":1},{"id":"GO:0042733","count":1},{"id":"GO:0072095","count":1}]},{"hash":"1350512665230465731","title":"Microtubule-Driven Transport and Mitosis","description":"The GO terms cluster around microtubule-based functions: spindle assembly, chromosome alignment, axonemal microtubule dynamics, various forms of microtubule-dependent transport (plus- and minus-end directed), and nuclear/chloroplast movement along microtubules. Together these indicate a cohesive theme of microtubule dynamics and transport, including mitotic processes and organelle/vesicle movement.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0060404","count":4},{"id":"GO:0032886","count":4},{"id":"GO:0098971","count":4}]},{"hash":"40092792682997472","title":"Ribosome biogenesis and RNA processing","description":"The cluster's top GO terms center on translation, rRNA maturation, and RNA splicing, pointing to functions in ribosome assembly and RNA processing rather than generic metabolism. Presence of translation/fidelity and SSU rRNA maturation suggests a cohesive ribosome-related module.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006450","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0034337","count":1}]},{"hash":"594324275574458530","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":3},{"id":"GO:0045019","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0050713","count":2},{"id":"GO:0033209","count":2}]},{"hash":"1565665653276682281","title":"ER Stress and Proteostasis","description":"The cluster shows GO terms centered on the unfolded protein response, ER stress signaling, translation initiation under ER stress, ER-associated degradation, and protein export regulation, all pointing to maintenance of protein quality in the endoplasmic reticulum. Some terms touch on broader developmental processes, but the core signal is ER stress\u2013related proteostasis. ","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001707","count":2},{"id":"GO:0036494","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0046825","count":1},{"id":"GO:0071374","count":1}]},{"hash":"913740382192161455","title":"Actin dynamics and cell migration","description":"These proteins are linked by actin cytoskeleton remodeling and cell movement. The top GO terms emphasize actin filament organization and polymerization, Rho/GTPase signaling regulation, membrane invagination, and processes associated with cellular motility (e.g., extension of leading processes in neural migration). While a few terms touch on immune signaling, the shared theme centers on actin-driven cytoskeletal dynamics that facilitate movement and membrane remodeling.","confidence":"High","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903286","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0021816","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0034136","count":2}]},{"hash":"806108880583405542","title":"Unknown","description":"The top GO terms span ribosome biogenesis and translation, chloroplast targeting, and a mix of cell division, conjugation, and metabolic stress responses with no clear unifying function. With no edges and only six proteins, there isn't a coherent theme to name a specific cluster beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042274","count":4},{"id":"GO:0090529","count":4},{"id":"GO:0006007","count":4},{"id":"GO:1903833","count":4},{"id":"GO:0045036","count":4}]},{"hash":"410464890936721317","title":"Innate Immune Signaling and Neutrophil Response","description":"The top GO terms indicate a clear focus on innate immunity, including innate immune response, detection of lipoteichoic acid, and regulation of TLR/MyD88 signaling, as well as neutrophil clearance and inflammatory hypersensitivity. These collectively point to proteins involved in bacterial sensing and neutrophil-mediated responses, with some additional terms reflecting broader immune regulation. Overall, the cluster seems best described by innate immune signaling and neutrophil-related activity.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:1905404","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0070392","count":2},{"id":"GO:0034125","count":2}]},{"hash":"656122534905559882","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006207","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0006189","count":3}]},{"hash":"1144277533431768647","title":"Unknown","description":"The GO terms show a mixed bag of functions: multiple small-molecule metabolic processes (glycolate, mandelate, purine, lactate oxidation), general redox activity, plus immune signaling (IL-4 response, lymphocyte proliferation) and retina development. There is no clear, single unifying function across these terms, so a specific, representative label cannot be confidently assigned.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046296","count":3},{"id":"GO:0009854","count":3},{"id":"GO:0006144","count":3},{"id":"GO:0018924","count":3},{"id":"GO:0019516","count":3}]},{"hash":"2158098555509161295","title":"DNA replication, repair, and transcription","description":"The top GO terms cluster around DNA replication (GO:0006260), mitotic cell cycle (GO:0000278), DNA repair (GO:0006281), and DNA-templated transcription (GO:0006351), pointing to nuclear DNA metabolism and transcriptional control during cell division. Development-related terms (neural and cardiac differentiation) appear as secondary associations, suggesting broader regulatory roles in some proteins, but the core theme is maintenance of genome integrity and transcriptional regulation.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0006281","count":5},{"id":"GO:2000727","count":4},{"id":"GO:0007399","count":4}]},{"hash":"2204614399381400541","title":"Neural development and axon fasciculation","description":"The top GO terms cluster around nervous system development, forebrain development, nervous system formation, and specific processes like fasciculation of sensory neuron axons and cell polarity in neural cells, supported by cell-matrix adhesion. While a few terms relate to immune signaling (IL-4 production and muramyl dipeptide response) or broader development, the dominant theme is neural development and axon organization, suggesting this cluster represents proteins involved in neural differentiation, connectivity, and maintenance. ","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0030900","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0007160","count":5},{"id":"GO:0032495","count":5},{"id":"GO:0071372","count":5}]},{"hash":"1313952009468549881","title":"Ciliogenesis and Cell Cycle Regulation","description":"This cluster centers on non-motile cilium assembly and cell-cycle\u2013related regulation (mitotic transition) with ubiquitin-mediated control, suggesting a module linking ciliogenesis to cell cycle progression and protein modification. Some terms (dsRNA response, sex differentiation, steroid receptor complex assembly) are more divergent, so the overall theme is moderate in strength.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1905515","count":3},{"id":"GO:0016576","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0045842","count":3},{"id":"GO:0031400","count":3}]},{"hash":"638523879165866138","title":"Mitochondrial Complex Assembly and Protein Import","description":"The dominant GO terms are mitochondrial respiratory chain complex I and IV assembly and import into the mitochondrial matrix, with related ROS production, indicating a cluster focused on mitochondrial biogenesis and assembly of respiratory machinery; a few unrelated terms may reflect broader signaling or annotation noise.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042135","count":2},{"id":"GO:0033617","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0032981","count":1},{"id":"GO:0090351","count":1}]},{"hash":"19154543783343453","title":"Ubiquitination and Proteasome in Innate Signaling","description":"Top GO terms cluster around protein ubiquitination, proteasome regulatory particle assembly, and innate immune response, with vitamin D\u2013related immune regulation and broader intracellular signaling also represented; this points to a theme of ubiquitin-proteasome\u2013linked regulation within immune signaling pathways, rather than a single, narrow process.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0033280","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0070682","count":2},{"id":"GO:0050960","count":2}]},{"hash":"2215980887862482147","title":"Cytoskeletal signaling and adhesion","description":"Based on the GO terms, the proteins cluster around cytoskeletal remodeling, cell\u2013cell adhesion, and mechanotransduction, highlighted by Rac signaling, adherens junction organization, axon extension regulation, and responses to mechanical stimuli, with supporting roles in vesicle trafficking and ubiquitination that can modulate these processes. This suggests a cohesive theme of controlling cell shape, movement, and junctional integrity in response to mechanical cues.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0045773","count":1},{"id":"GO:0016601","count":1}]},{"hash":"278200813861194875","title":"Seed lipid and phenylpropanoid metabolism","description":"The proteins show a convergence on lipid-related processes (long-chain fatty acid metabolic process, long-chain fatty acid import into cell) and seed biology (seed coat development, seed germination regulation), with supporting signals for phenylpropanoid metabolism. While a couple of terms point to microbial biosynthesis, the dominant theme aligns with plant seed lipid and secondary metabolite pathways, justifying this label as representative of the cluster.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001676","count":1},{"id":"GO:0043041","count":1},{"id":"GO:0019290","count":1},{"id":"GO:1902987","count":1},{"id":"GO:0009234","count":1}]},{"hash":"910722128571151771","title":"Developmental ECM Remodeling","description":"I named this cluster Developmental ECM Remodeling because the top GO terms converge on extracellular matrix breakdown and restructuring (collagen catabolic process, basement membrane disassembly, proteolysis) along with morphogenesis processes (lung tube branching, bone resorption, intramembranous ossification), suggesting a shared role in developmental tissue remodeling rather than a single-signal pathway.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060441","count":1},{"id":"GO:0035593","count":1},{"id":"GO:0045453","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034769","count":1}]},{"hash":"683526729119697345","title":"Unknown","description":"The top GO terms span development (spinal cord development, epithelial cell differentiation), cell division (mitotic M phase), signaling/modulation (peptidyl-tyrosine dephosphorylation), and redox-related/sulfur biology (tRNA seleno-modification, urmylation, molybdopterin cofactor biosynthesis, redox homeostasis). This mixture of processes across organisms and contexts makes it hard to identify a single coherent functional theme for the cluster, so there is no clear, representative label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000087","count":2},{"id":"GO:0018192","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0032447","count":2},{"id":"GO:0006777","count":2}]},{"hash":"728968553048237550","title":"TNF\u2013NF-\u03baB signaling and ubiquitination","description":"The top GO terms point to TNF-mediated signaling and NF-\u03baB activation, including TNF signaling, I\u03baB phosphorylation, and NF-\u03baB\u2013inducing kinase activity. The presence of protein ubiquitination and autoubiquitination suggests regulation of these pathways by ubiquitin, which is a key mechanism in TNF/NF-\u03baB signaling and in controlling apoptosis; the histone ubiquitination hint aligns with broader ubiquitin-related regulation. Overall, the cluster appears to represent a TNF/NF-\u03baB signaling module modulated by ubiquitination and linked to apoptotic regulation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":4},{"id":"GO:0051865","count":4},{"id":"GO:1903721","count":4},{"id":"GO:0090073","count":4},{"id":"GO:0007250","count":4}]},{"hash":"2212802890523465988","title":"Unknown","description":"The top GO terms are highly diverse, spanning ribosome-associated ubiquitin-dependent degradation and rescue of stalled ribosomes, mRNA deadenylation, apoptosis signaling, DNA damage response, viral genome activation, and MHC II biosynthesis regulation. This lack of a common, cohesive functional theme makes it difficult to assign a specific, representative label to the cluster, so the safest choice is Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018937","count":1},{"id":"GO:1990116","count":1},{"id":"GO:0072344","count":1},{"id":"GO:1902167","count":1},{"id":"GO:0000289","count":1}]},{"hash":"1053255156710198487","title":"Membrane Transporters and Exocytosis","description":"These proteins are linked by GO terms that span transmembrane transport of a wide range of substrates (vitamins, potassium, xenobiotics, carbohydrates, amino acids, molybdate) and a vesicle docking step in exocytosis. The common theme is membrane-associated transport and vesicle trafficking, justifying a label focused on transmembrane transporters with vesicle docking involvement.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":6},{"id":"GO:0071805","count":6},{"id":"GO:0006855","count":6},{"id":"GO:0042908","count":6},{"id":"GO:1900753","count":4}]},{"hash":"2194158838768418689","title":"Membrane protein targeting and ER stress response","description":"The top GO terms cluster around SRP-dependent cotranslational and post-translational targeting of proteins to membranes, indicating a role in directing nascent proteins to the ER/membranes. Additional terms about unfolded protein response and ER stress regulation support involvement in protein quality control within the secretory pathway. A few other terms (DNA replication, karyogamy, iron-sulfur cluster assembly) are less connected, suggesting possible multifunctional annotations, but the main pattern points to membrane targeting and ER-associated protein handling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006616","count":1}]},{"hash":"23304940564393807","title":"Notch-Regulated Developmental Patterning","description":"The top terms center on positive regulation of Notch signaling, with several tissue development and patterning terms (imaginal disc-derived leg segmentation, compartment pattern specification, intestinal epithelial development, hypochord development). This suggests a theme of Notch-associated control of development and tissue patterning across different contexts, despite some unrelated entries. ","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1902367","count":3},{"id":"GO:0045747","count":3},{"id":"GO:0060576","count":3},{"id":"GO:0032092","count":3},{"id":"GO:0036011","count":3}]},{"hash":"520785334405126088","title":"Unknown","description":"The top GO terms include fungal lipid metabolism (ergosterol biosynthesis regulation, unsaturated fatty acid biosynthesis, MIPC metabolism) along with several unrelated processes (NO biosynthesis, myelin maintenance, sebaceous gland differentiation, nitrate assimilation, mitochondrial inheritance, ER exit site localization), showing no single cohesive function for the cluster.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0006636","count":2}]},{"hash":"541060562099651875","title":"Ubiquitination-Proteasome Signaling","description":"This cluster's top GO terms center on protein ubiquitination and proteasome regulatory particle assembly, pointing to a proteostasis core. The accompanying terms for intracellular signal transduction and selective environmental responses (thermoception, capsazepine, vitamin D) suggest these proteins may participate in signaling pathways that couple protein turnover with cellular responses, potentially linking immune-related processes such as cell migration and follicular dendritic cell differentiation. Overall, the dominant theme is ubiquitin-mediated protein regulation with supportive signaling roles.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0050960","count":2},{"id":"GO:0035556","count":2},{"id":"GO:1901594","count":2}]},{"hash":"829674215836819926","title":"Actin Cytoskeleton Remodeling in Neurons and Muscle","description":"The dominant GO terms describe actin filament polymerization and organization, cortical patches, and postsynaptic actin cytoskeleton organization, with additional muscle adaptation terms, suggesting a shared theme of actin-driven remodeling in neural and muscular contexts. Several chromatin-related terms are labeled obsolete and likely represent noise rather than core function.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":5},{"id":"GO:0043981","count":5},{"id":"GO:0043503","count":5},{"id":"GO:0051666","count":5},{"id":"GO:0098974","count":5}]},{"hash":"822338611219947760","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0019079","count":4},{"id":"GO:0034476","count":3},{"id":"GO:0006269","count":3},{"id":"GO:0006363","count":3}]},{"hash":"448506454649814632","title":"Unknown","description":"The top GO terms cover eye and ear development, bile duct formation, immune signaling, and various DNA repair processes, with no single dominant function tying the proteins together. With only one edge and no triangles, there\u2019s limited evidence for a cohesive cluster function, so a definite label is not supported.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061303","count":2},{"id":"GO:0050718","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045063","count":1},{"id":"GO:0035622","count":1}]},{"hash":"1663040068427601067","title":"Unknown","description":"GO terms span cytoskeletal transport (anterograde dense core vesicle transport, microtubule-based movement, cilium movement) and DNA-related processes (DNA replication, transposition/integration, ribosomal subunit assembly); there is no single unifying function connecting all proteins, so a cohesive label cannot be confidently assigned.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0031412","count":1},{"id":"GO:1990048","count":1},{"id":"GO:0007018","count":1},{"id":"GO:0003341","count":1},{"id":"GO:0000027","count":1}]},{"hash":"1755374422486777829","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071051","count":2},{"id":"GO:0034476","count":2},{"id":"GO:0010501","count":2},{"id":"GO:0006269","count":2},{"id":"GO:0035315","count":2}]},{"hash":"760816539252105225","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0071051","count":2},{"id":"GO:0034476","count":2},{"id":"GO:0010501","count":2}]},{"hash":"1084677161981985421","title":"DNA Damage Response and Chromatin Modification","description":"The cluster is strongly enriched for post-translational modification through neddylation and ubiquitination, together with chromatin organization and DNA damage repair signals (homologous recombination, meiotic DSB formation, and G1 DNA damage checkpoint), suggesting a cohesive module linking DNA damage sensing/repair to chromatin dynamics. Some signaling terms (ABA response, BMP pathway) are less central but do not negate the core theme.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0045116","count":5},{"id":"GO:0070534","count":5},{"id":"GO:0000724","count":5},{"id":"GO:0031571","count":5},{"id":"GO:0031497","count":5}]},{"hash":"1276548968842777389","title":"Unknown","description":"Due to missing GO terms in the Top Terms (no shared biological process or molecular function terms provided), there is no clear common function to label this cluster. Without GO signals, I cannot assign a meaningful, specific label beyond Unknown.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"737188818970824505","title":"Lung development and ECM remodeling","description":"The terms show clear focus on lung branching morphogenesis (GO:0060448), basement membrane disassembly (GO:0034769), collagen catabolic process (GO:0030574), and surfactant homeostasis (GO:0043129). Together they point to a coordinated program of lung development and extracellular matrix remodeling, with surfactant maintenance as a functional readout of lung physiology. There are also immune-related terms (macrophage apoptotic process, T cell mediated cytotoxicity) that may reflect immune activity in lung tissue or incidental annotations, but the core signal is lung development and ECM/remodeling.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":2},{"id":"GO:0030574","count":1},{"id":"GO:0050790","count":1},{"id":"GO:0060448","count":1},{"id":"GO:0007614","count":1}]},{"hash":"2146796809068573697","title":"Neural development and axon organization","description":"The cluster\u2019s strongest signals are nervous system development, corpus callosum development, and axon-region protein localization, which together point to CNS development and neuron polarization/organization. Other terms (immune cell differentiation, prolactin signaling, megakaryocyte development) are less connected and likely reflect background associations. Therefore Neural development and axon organization is the best overarching label.","confidence":"Medium","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0038161","count":2},{"id":"GO:0035855","count":2},{"id":"GO:1902948","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0001915","count":2}]},{"hash":"91648283185371840","title":"ER-targeting and secretory protein transport","description":"The GO terms are dominated by SRP-dependent cotranslational targeting to membranes and various aspects of ER/membrane targeting and Sec-mediated transport, indicating a cohesive role in directing proteins to and through the secretory pathway; developmental terms appear secondary noise.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:2000727","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0043952","count":1},{"id":"GO:0031204","count":1}]},{"hash":"1810445616347724536","title":"Multi-Substrate Membrane Transporters","description":"The cluster is dominated by transmembrane transport GO terms across diverse substrates (phosphate, galactose, nitrite, nitrate, potassium, vitamin, hydroxyphenylacetate), indicating a cohesive set of membrane transport proteins; DNA replication terms appear incidental and do not define the group.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0035435","count":2}]},{"hash":"2033332435397611893","title":"Nuclear transport and spindle dynamics","description":"This cluster centers on Ran-dependent nuclear transport and spindle/centrosome regulation: terms include snRNP import into the nucleus, regulation of protein export from the nucleus, Ran signal transduction, and astral microtubule organization, plus centrosome duplication control. These together suggest a core theme of coordinating nuclear-cargo transport with mitotic spindle/centrosome dynamics, with other terms being less central outliers. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006608","count":2},{"id":"GO:0046825","count":2},{"id":"GO:0031291","count":2},{"id":"GO:0030953","count":2}]},{"hash":"860585808612881128","title":"Axon growth and Schwann cell development","description":"The cluster contains GO terms centered on axon extension, fasciculation of sensory neuron axons, and Schwann cell development, with supporting terms on cell adhesion and receptor clustering that facilitate neurite outgrowth and guidance. While a few terms are broader developmental processes, the dominant theme is neuronal growth and peripheral glial maturation.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034446","count":4},{"id":"GO:0043113","count":4},{"id":"GO:0097155","count":4},{"id":"GO:0045773","count":3},{"id":"GO:0090251","count":3}]},{"hash":"1165567778546122522","title":"Embryonic vascular development and ECM remodeling","description":"The cluster's terms emphasize endothelial proliferation/migration and collagen fibril organization (vascular development and ECM), along with somite development and pregnancy signals of embryogenesis; lipoprotein transport/clearance hints at lipid handling during development, while apoptotic clearance and complement activation reflect immune remodeling. Together these point to an embryonic development program focused on blood vessel formation and extracellular matrix remodeling, with metabolic context.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":5},{"id":"GO:0043277","count":5},{"id":"GO:0006958","count":5},{"id":"GO:0070207","count":5},{"id":"GO:0061053","count":5}]},{"hash":"483328884253583682","title":"ASPH-Mediated Notch Beta-Hydroxylation","description":"GO terms point to peptidyl-aspartic acid and asparagine hydroxylation, typical of aspartyl/asparaginyl beta-hydroxylases that modify Notch EGF repeats. The inclusion of Notch signaling regulation and vasculogenesis opportunities further supports a Notch-related hydroxylase cluster. This suggests an ASPH-like activity group centered on Notch beta-hydroxylation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042264","count":2},{"id":"GO:0045668","count":2},{"id":"GO:0061428","count":2},{"id":"GO:0042265","count":2},{"id":"GO:0036138","count":2}]},{"hash":"1421206030881808217","title":"Mitotic Division and ER-Golgi Trafficking","description":"The cluster centers on mitosis-related processes (mitotic cell cycle, cell division, mitotic spindle assembly, cell population proliferation) and vesicle trafficking between the ER and Golgi (COPII-coated vesicle budding, retrograde vesicle transport, Golgi to ER), suggesting a role in coordinating cell division with intracellular transport. A single term about viral mRNA export is present but does not define the group\u2019s main function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0090114","count":2},{"id":"GO:0090307","count":2}]},{"hash":"2106587443941375452","title":"GABAergic Synapse and Cytoskeletal Remodeling","description":"The top GO terms cluster around GABAergic synaptic transmission together with filopodium/actin remodeling, Rho/small GTPase signaling, and cell spreading, suggesting a functional group of proteins coordinating neurotransmission with cytoskeletal dynamics and adhesion. Mitochondrial fission and apoptotic changes may reflect broader cellular regulation but do not override the core theme of synaptic signaling linked to actin remodeling.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0051932","count":4},{"id":"GO:0051489","count":4},{"id":"GO:0045792","count":4},{"id":"GO:1900026","count":4},{"id":"GO:0007264","count":4}]},{"hash":"189565382603827520","title":"Ubiquitin-like Modifications (SUMO/NEDD8/UFM1)","description":"This cluster is characterized by enrichment for protein post-translational modifications with ubiquitin-like modifiers, notably SUMOylation, NEDDylation, and UFMylation. These pathways regulate protein stability, localization, and activity, suggesting a cohesive theme around ubiquitin-like modification processes. Some other terms (amygdala development, defense against fungi, transcription regulation) may reflect broader roles of the included proteins or annotation noise, but the dominant pattern supports a modification-focused cluster.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0021764","count":3},{"id":"GO:0018192","count":3},{"id":"GO:0050832","count":3},{"id":"GO:0044805","count":3}]},{"hash":"375513447114882415","title":"Pol II Transcription Initiation and Nucleolar Organization","description":"Top GO terms center on RNA polymerase II transcription initiation and related nuclear processes (nucleolus organization, snRNA transcription, open complex formation, transcription regulation); a few viral-related terms appear as outliers, but the dominant theme is Pol II transcription regulation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007000","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0042795","count":1},{"id":"GO:0001113","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1792552451057562517","title":"Histone methylation and chromatin regulation","description":"The top terms cluster around histone modifications (H4K20me, H3K27me, H3K9me, H3K4me) and chromatin-related processes (nucleosome disassembly, heterochromatin formation), indicating these proteins are involved in chromatin modification and regulation of gene expression. The inclusion of DNA damage\u2013related apoptotic signaling and Notch pathway regulation further supports a chromatin-centric regulatory role. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034773","count":1},{"id":"GO:1900477","count":1},{"id":"GO:0098532","count":1},{"id":"GO:0036124","count":1},{"id":"GO:1902231","count":1}]},{"hash":"913742935505898028","title":"Unknown","description":"These GO terms cover contrasting biological contexts: vertebrate immune processes (germinal center formation, B cell receptor signaling) and plant-specific signaling and development (brassinosteroid signaling, flower development, circadian rhythm), plus a general mitochondrial assembly term. With no single unifying function or pathway and no edges connecting proteins, there is no coherent theme to name this cluster. Therefore the cluster is Unknown with no confident assignment.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":2},{"id":"GO:0009911","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0009742","count":2},{"id":"GO:0042752","count":2}]},{"hash":"461966831063580068","title":"Unknown","description":"The GO terms span diverse plant developmental processes (endosperm and embryo development, seed dormancy, pattern formation) and separate areas like vesicle transport and signaling, with no clear shared function or pathway linking the proteins; the lack of edges further suggests there is no cohesive cluster to name.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032515","count":1},{"id":"GO:0009960","count":1},{"id":"GO:0009793","count":1},{"id":"GO:0035526","count":1},{"id":"GO:0002534","count":1}]},{"hash":"1398443473104838696","title":"Actin Dynamics and Rho-Dependent Motility","description":"The cluster centers on actin cytoskeleton remodeling and regulation of Rho/GTPase signaling, with terms for actin filament organization and polymerization and processes linked to cell motility and neural migration. While some immune-related terms appear, the dominant theme is actin-driven motility and Rho-mediated cytoskeletal control.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903286","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0021816","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0034136","count":1}]},{"hash":"1502958276427046699","title":"Ubiquitin-Dependent Immune Signaling","description":"This cluster is dominated by ubiquitination-related GO terms (protein ubiquitination, K63-linked ubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process) and immune/signaling terms (adaptive immune response, TNF-mediated signaling, JNK/ERK regulation), suggesting proteins that connect protein turnover with immune signaling pathways.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0002250","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3}]},{"hash":"432761626144885266","title":"Immune signaling and osteoclast differentiation","description":"This cluster\u2019s GO terms focus on inflammatory signaling (TNF pathway, NF-kB regulation, LPS signaling), immune cell differentiation (dendritic cells, Th1 response), and positive regulation of osteoclast differentiation, suggesting a theme where immune signaling interfaces with bone remodeling. A concise label capturing immune activation linked to osteoclastogenesis fits the shared functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045672","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0032088","count":1},{"id":"GO:0070534","count":1},{"id":"GO:0042088","count":1}]},{"hash":"929514853478043341","title":"Meiosis and Gametogenesis","description":"The five proteins show strong representation of meiosis-related GO terms: DNA recombination, meiotic double-strand break formation, homologous chromosome pairing at meiosis, oogenesis, and spermatogenesis, suggesting a shared role in meiotic and gamete development processes; other terms about membrane targeting and ubiquitin-dependent trafficking appear secondary.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":1},{"id":"GO:0042138","count":1},{"id":"GO:0048477","count":1},{"id":"GO:0007129","count":1},{"id":"GO:0007283","count":1}]},{"hash":"2008420451128170300","title":"Auxin-Driven Plant Morphogenesis","description":"The GO terms cluster around plant development and growth regulation: inflorescence morphogenesis, lateral root formation, auxin polar transport, and photomorphogenesis, all pointing to auxin signaling and light-responsive growth shaping morphology. The ubiquitin-dependent protein catabolic process may reflect protein turnover linked to developmental transitions, while one term about perineurial glial growth appears as an outlier but does not dominate the theme. Overall, these terms suggest auxin-mediated morphogenesis and light-directed growth in plants.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048281","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0010311","count":1},{"id":"GO:0042066","count":1},{"id":"GO:0009926","count":1}]},{"hash":"2093506824478871031","title":"Plant nitrate and peptide transport in plants","description":"The cluster\u2019s top GO terms cluster around nitrate assimilation and transmembrane transport, plus dipeptide/oligopeptide transport, suggesting transporters that mediate nitrogen and peptide uptake in plants. Hormone signaling terms (auxin, gibberellin) and herbicide response are present but appear secondary to the transport theme, so the main representation is nitrate/peptide transport in plants.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0035672","count":4},{"id":"GO:0010336","count":4},{"id":"GO:0010167","count":4},{"id":"GO:0042938","count":4}]},{"hash":"1103132159784636740","title":"Ubiquitination in immune regulation","description":"This cluster is dominated by GO terms about ubiquitination (general, K63-linked, autoubiquitination, histone ubiquitination) and includes immune-related processes (lipopolysaccharide signaling, suppression of antiviral responses, vitamin D response). The common thread is ubiquitination-mediated regulation of immune and antiviral signaling, suggesting a cohesive functional theme despite some obsolete terms.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:1902261","count":5},{"id":"GO:0016567","count":5},{"id":"GO:1902187","count":5},{"id":"GO:0070534","count":5},{"id":"GO:0031664","count":5}]},{"hash":"78271019981898534","title":"Far-red light signaling and circadian regulation","description":"The top GO terms cluster around light-responsive signaling (far-red light signaling pathway, red/far-red phototransduction) and circadian rhythm regulation, plus transcriptional regulation activity, suggesting a small set of proteins involved in light-driven transcriptional control. The presence of a few unrelated metabolic terms and the lack of edges imply some annotation noise, but the core theme points to light-circadian function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010018","count":1},{"id":"GO:0042753","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0009585","count":1},{"id":"GO:0042355","count":1}]},{"hash":"260504986522892930","title":"Sterol and lipid biosynthesis","description":"Many GO terms point to sterol and lipid metabolism, including cholesterol biosynthesis via lathosterol, ergosterol biosynthesis, fatty acid biosynthesis, ether lipid metabolism, and sphingolipid precursor metabolism. A few terms (B cell chemotaxis, CNS myelin maintenance) are peripheral, but the dominant signature is lipid/sterol biosynthesis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035754","count":2},{"id":"GO:0006696","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0080065","count":2},{"id":"GO:0046485","count":2}]},{"hash":"415289537105893285","title":"RDNA-associated heterochromatin formation","description":"GO terms point to heterochromatin formation and transcriptional repression at nucleolar rDNA repeats, pericentric and subtelomeric regions, suggesting a chromatin-silencing module around rDNA and centromeric/telomeric chromatin; while some obsolete terms and an unrelated metabolic term appear, the dominant signal is chromatin organization.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034503","count":4},{"id":"GO:0030702","count":4},{"id":"GO:0071922","count":4},{"id":"GO:0000117","count":4},{"id":"GO:0016479","count":4}]},{"hash":"1289442544428315142","title":"Muscle and vascular development regulators","description":"The proteins cluster around DNA-templated transcription and regulatory control influencing differentiation in muscle and cardiovascular lineages. Key terms include negative regulation of myotube and skeletal muscle fiber development, cardiac right ventricle morphogenesis, dorsal aorta morphogenesis, and regulation of vasculogenesis, with BMP signaling and Notch pathway involvement. This points to a cohesive group of transcriptional regulators coordinating muscle and heart/vasculature development rather than a single isolated process.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0010832","count":2},{"id":"GO:0045668","count":2},{"id":"GO:0003215","count":2},{"id":"GO:0071773","count":2}]},{"hash":"1348459796868486798","title":"Ubiquitin-Dependent TNF/NF-\u03baB Signaling","description":"The GO terms cluster around ubiquitination (K48- and K63-linked), general protein ubiquitination, regulation of apoptotic processes, TNF-mediated signaling, and NF-\u03baB pathway modulation (including non-canonical NF-\u03baB). This points to a core function in ubiquitin-mediated control of inflammation and cell death, with connections to necroptosis regulation and viral-host interactions. Peripheral terms (histone catabolic process, obsolete dosage compensation) do not override the central theme. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":2},{"id":"GO:0060546","count":2},{"id":"GO:1900095","count":2},{"id":"GO:1902187","count":2},{"id":"GO:0016567","count":2}]},{"hash":"116783823087344462","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0034476","count":1}]},{"hash":"21200871256005441","title":"Unknown","description":"The top terms span neural development (olfactory bulb development; sympathetic neuron projection extension), immune regulation (antigen presentation via MHC II; neutrophil clearance; IL-3 production), and vascular/hematopoietic development (megakaryocyte development; vascular smooth muscle differentiation), with no single dominant shared function tying all proteins together. This appears to be a heterogeneous cluster with no clear cohesive theme.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021772","count":3},{"id":"GO:0045401","count":2},{"id":"GO:1905404","count":2},{"id":"GO:0097490","count":2},{"id":"GO:1905065","count":2}]},{"hash":"617632064805427859","title":"Nuclear RNA Processing and Chromatin Regulation","description":"This cluster centers on nuclear RNA processing and chromatin-related activities, with terms for import into the nucleus, spliceosomal snRNP assembly, tRNA processing, and nuclear mRNA decapping/deadenylation, plus pericentric heterochromatin formation. Some plant stress-response terms (abscisic acid, water deprivation) may reflect transcriptional regulation that involves nuclear RNA processing; a few terms like P-body assembly hint at broader RNA metabolism beyond the nucleus. Overall, the common theme is RNA processing intertwined with chromatin dynamics in the nucleus.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":4},{"id":"GO:1990141","count":4},{"id":"GO:0009414","count":4},{"id":"GO:0000387","count":4},{"id":"GO:0070317","count":4}]},{"hash":"872249262833252778","title":"Neuronal signaling and calcium regulation","description":"The terms cluster around neural function: neural crest development, sensory perception, regulation of presynaptic calcium, and regulation of synaptic plasticity, all pointing to neuronal signaling and calcium-dependent pathways (including NFAT signaling). A single term on cardiac hypertrophy hints at shared calcium/NFAT signaling in cardiac tissue, but the core pattern remains neural signaling and calcium regulation, with supporting lipid remodeling context. Overall, the cluster supports a neuronal signaling theme, though some terms are broader.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042554","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0051531","count":1},{"id":"GO:0014032","count":1},{"id":"GO:0014898","count":1}]},{"hash":"186966264904638410","title":"Multisystem Stress Response Signaling","description":"The top GO terms point to a common theme of stress-responsive signaling across diverse tissues (calcium/NFAT signaling, glucocorticoid signaling, unfolded protein response, and hypertrophic responses to stress), with additional ties to development in lung and Schwann cells. This suggests the cluster centers on multisystem stress-response pathways that modulate differentiation and immune regulation rather than a single tissue-specific function.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2001034","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0001915","count":2},{"id":"GO:0060487","count":2}]},{"hash":"1340054329199137413","title":"Nervous System Development","description":"The cluster is dominated by nervous system\u2013related GO terms, including nervous system development, corpus callosum development, and establishment of protein localization to the juxtaparanode region of axons, pointing to neural development and axon organization as the core function. Some immune-related terms are present but appear less cohesive with the main neural theme, so the neural development label remains the best fit. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0038161","count":4},{"id":"GO:1902948","count":4},{"id":"GO:0097350","count":4},{"id":"GO:0001915","count":4},{"id":"GO:0045663","count":4}]},{"hash":"1849732966206062802","title":"Mitochondrial protein import and chaperone assembly","description":"The cluster includes a direct GO hit for protein import into the mitochondrial intermembrane space and for chaperone-mediated protein complex assembly, plus protein stabilization, pointing to a mitochondrial protein handling and folding/assembly role. The ischemia and ATP response terms further support a stress- and energy-related context in which mitochondrial proteostasis is key.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002931","count":1},{"id":"GO:0045041","count":1},{"id":"GO:1901998","count":1},{"id":"GO:0033198","count":1},{"id":"GO:0051131","count":1}]},{"hash":"1093332751011113018","title":"Translation and ribosome biogenesis","description":"This cluster is dominated by GO terms for translation and ribosome assembly, including translation, translational initiation, frameshifting, ribosomal small subunit biogenesis, and hypusine biosynthesis linked to translation. Other terms about elongation and termination regulation reinforce a translation-centric theme; a couple defense-related terms appear as peripheral associations but do not define the core function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0006452","count":1},{"id":"GO:0034050","count":1},{"id":"GO:0008612","count":1}]},{"hash":"1810237869313049161","title":"Aminoacyl-tRNA Synthesis and Translation","description":"This cluster is strongly enriched for tRNA aminoacylation terms (lysyl-tRNA and mitochondrial lysyl-tRNA, plus phenylalanyl-tRNA) and the general translation term, indicating a group of proteins involved in tRNA charging for protein synthesis, including mitochondrial variants. The folate-related terms are present but far less dominant, suggesting they are incidental rather than defining features.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015942","count":1},{"id":"GO:0046657","count":1},{"id":"GO:0009396","count":1},{"id":"GO:0035999","count":1},{"id":"GO:0070154","count":1}]},{"hash":"1339083461816899141","title":"Co-translational Membrane Targeting and ER Stress Response","description":"The top GO terms are dominated by SRP-dependent cotranslational targeting to the membrane and responses to unfolded protein/ER stress, suggesting a theme of membrane targeting of nascent peptides and ER quality control. While additional terms (iron-sulfur cluster assembly, DNA replication) appear, they are less central to the main pattern, possibly reflecting pleiotropy or annotation noise. Confidence in this thematic labeling is Medium.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":2},{"id":"GO:0006880","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006616","count":2}]},{"hash":"1311193259711414253","title":"Microtubule dynamics and intracellular transport","description":"These proteins cluster around microtubule-based processes: spindle assembly and chromosome alignment during mitosis, plus/minus- and plus-end directed microtubule movements, nuclear migration along microtubules, and vesicle/receptor transport along microtubules in axons and dendrites. The top GO terms consistently point to microtubule organization and transport functions, indicating a cohesive theme of microtubule dynamics in cellular transport and division.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0060404","count":2},{"id":"GO:0032886","count":2},{"id":"GO:0098971","count":2}]},{"hash":"221197296883406798","title":"Diverse Transmembrane Transporters","description":"The top GO terms point to multiple transmembrane transport activities across a variety of substrates (vitamins, xenobiotics, metals, amino acids, lipids), indicating the proteins function as membrane transporters with broad substrate specificity rather than a single ligand or pathway.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0006855","count":2},{"id":"GO:1900753","count":1},{"id":"GO:0015689","count":1},{"id":"GO:0015803","count":1}]},{"hash":"2088364257211355105","title":"Neuronal migration signaling and cytoskeletal regulation","description":"GO terms point to neuronal development and movement: neuron projection extension, cerebellar granule cell precursor tangential migration, RTK signaling, and regulation of GTPase activity. Together they indicate processes controlling neuronal migration and cytoskeletal dynamics.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036083","count":1},{"id":"GO:0021935","count":1},{"id":"GO:0050918","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0043087","count":1}]},{"hash":"929957952697872880","title":"Actin Cytoskeleton Remodeling and Inflammatory Signaling","description":"Top GO terms are dominated by actin-related processes (ARP2/3-mediated actin nucleation; sarcomere organization) and cytoskeleton-driven functions like phagocytosis and platelet aggregation, with concurrent immune signaling (cytokine production) and small GTPase regulation. Although a few terms (skin development, obsolete histone acetylation) appear, the shared theme is cytoskeletal dynamics linked to inflammatory responses, suggesting proteins in this cluster coordinate actin remodeling with immune cell activities.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0043981","count":3},{"id":"GO:0043982","count":3},{"id":"GO:0034314","count":3}]},{"hash":"680923829680311491","title":"Innate Immunity and Endothelial Remodeling","description":"The terms show strong representation of innate immune processes: complement activation (classical pathway), innate immune response, and apoptotic cell clearance. The presence of endothelial/matrix-related terms (endothelial cell proliferation and migration, collagen fibril organization, plasma lipoprotein clearance) suggests the cluster also encompasses vascular-ECM remodeling and lipoprotein handling. Together, these proteins likely participate in innate immune clearance in a vascular context, linking immune activity to endothelial and ECM dynamics.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0043277","count":2},{"id":"GO:0070207","count":2},{"id":"GO:0061053","count":2}]},{"hash":"1358987938772725946","title":"Unknown","description":"The GO terms span metabolism, immune responses, neural signaling, vesicle trafficking, neuromuscular control, bone development, and host-symbiont interactions with no common theme. With just four proteins and no edges, there is no cohesive function tying them together, so a specific label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044381","count":1},{"id":"GO:0035455","count":1},{"id":"GO:0009607","count":1},{"id":"GO:0097091","count":1},{"id":"GO:0099638","count":1}]},{"hash":"1919933166644731246","title":"Unknown","description":"The GO terms across this cluster are highly diverse, spanning ubiquitination (K63-linked), various immune signaling processes, and developmental topics, with no single cohesive function tying the proteins together. This makes a clear, representative label infeasible.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":2},{"id":"GO:0038161","count":2},{"id":"GO:0070534","count":2},{"id":"GO:1902948","count":2},{"id":"GO:0097350","count":2}]},{"hash":"1897649159524112318","title":"ER stress and ER-Golgi trafficking","description":"The GO terms point strongly to an ER stress response and vesicle transport between the ER and Golgi, including positive regulation of ER-to-Golgi transport and general Golgi-related trafficking. Protein ubiquitination supports a role in quality control and turnover within the secretory pathway. While some terms touch on unrelated processes (nerve development, melanosome assembly), the core cluster centers on ER stress signaling and ER\u2013Golgi trafficking, making this a coherent label.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903206","count":2},{"id":"GO:0034976","count":2},{"id":"GO:0055108","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0034332","count":1}]},{"hash":"557544560881663196","title":"Unknown","description":"The top GO terms cover a broad and disparate set of processes (ion transport, GTPase/Rho signaling, neuronal migration, TLR signaling, sulfur oxidation, membrane invagination, mitochondrial apoptotic signaling), with no clear common function linking the proteins. This suggests no cohesive, interpretable theme for the cluster.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903286","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0021816","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0034136","count":1}]},{"hash":"255258481577265437","title":"Neurodevelopment and cytokine signaling","description":"The top GO terms cluster around neural development (forebrain development, nervous system development, bipolar cell polarity) and cytokine signaling (interleukin-4 production, interleukin-18-mediated signaling), with additional annotations related to cardiac differentiation, and other broad regulatory processes. This suggests the proteins may be involved in developmental signaling with notable immune/cytokine involvement, though some terms are peripheral to a single cohesive function. ","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2000727","count":4},{"id":"GO:0031031","count":4},{"id":"GO:0006924","count":4},{"id":"GO:0032425","count":4},{"id":"GO:0007399","count":4}]},{"hash":"539214900971732750","title":"Actin Cytoskeleton Assembly and Regulation","description":"The top GO terms cluster around actin filament polymerization, stress fiber and contractile ring assembly, and regulation of actin dynamics by GTPases, indicating a cytoskeletal remodeling module involved in shape changes, cytokinesis, and related processes.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":1},{"id":"GO:2000300","count":1},{"id":"GO:1900028","count":1},{"id":"GO:1903477","count":1},{"id":"GO:0030041","count":1}]},{"hash":"2193098253657815596","title":"COPII-mediated ER-Golgi transport","description":"The dominant GO terms point to COPII-coated vesicle budding and ER-to-Golgi transport, indicating a vesicle trafficking-focused cluster. Related terms such as protein ubiquitination and adherens junction organization can connect to trafficking and protein turnover, supporting a theme around vesicle-mediated processing and cellular organization rather than a single enzymatic activity.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0055108","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0034332","count":1},{"id":"GO:0032949","count":1}]},{"hash":"1642341983101404465","title":"Complement Activation and Regulation","description":"The GO terms show a clear focus on the complement system: activation via classical, lectin, and alternative pathways, plus negative regulation of classical pathway activation. While other terms touch on development, transposition, and other processes, the strongest signal centers on immune complement activity, justifying a label around complement activation and its regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":1},{"id":"GO:0016598","count":1},{"id":"GO:0006957","count":1},{"id":"GO:0001701","count":1},{"id":"GO:0007338","count":1}]},{"hash":"2216344997744255580","title":"Unknown","description":"No GO terms or evident shared function among the four proteins (no edges, no top terms), so there is no clear theme to label this cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2250810561978392184","title":"Epithelial development and wound healing","description":"Based on the top GO terms, the cluster centers on epithelial biology: epithelial cell polarity, epithelial morphogenesis, keratinocyte development, and wound healing processes. Other terms (ubiquitination, various apoptotic processes, mechanotransduction) appear less central, suggesting a primary epithelial-development/wound-healing theme with some related regulatory signals.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0003334","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0044319","count":2},{"id":"GO:2000171","count":2}]},{"hash":"21952289913073400","title":"Cell Polarity and Vesicle Trafficking","description":"The cluster is dominated by terms about maintaining cell polarity and organizing adherens junctions, plus several vesicle trafficking processes between the ER and Golgi and to Golgi-derived transport. Protein ubiquitination likely regulates these trafficking and junctional activities. Although some terms refer to broader contexts (nervous system development, melanosome assembly), the recurring themes point to coordinated control of cell polarity and vesicle transport. This suggests a cohesive role in epithelial architecture and intracellular trafficking.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043124","count":2},{"id":"GO:0030011","count":2},{"id":"GO:0055108","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0034332","count":1}]},{"hash":"927843135710011073","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015937","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0030206","count":1},{"id":"GO:0015012","count":1},{"id":"GO:0050427","count":1}]},{"hash":"508835467199450221","title":"Lipid metabolism and retinol metabolism","description":"Dominated by GO terms for lipid metabolism, retinol/vitamin A metabolism, and adipose tissue regulation (with supporting lipid transport). A few unrelated terms (DNA repair, lead ion response) may reflect annotation noise, but the core theme is lipid and retinol metabolism.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071284","count":1},{"id":"GO:0006653","count":1},{"id":"GO:1904177","count":1},{"id":"GO:0070292","count":1},{"id":"GO:0006776","count":1}]},{"hash":"21861400704635413","title":"Ribosome Biogenesis and Translation","description":"The cluster is enriched for GO terms related to ribosome assembly and function, including ribosomal small subunit biogenesis, cytoplasmic translation, and ribosomal large subunit export from the nucleus, as well as tRNA modification. These converge on a core theme of ribosome production and protein synthesis. Additional terms about cell cycle and division may reflect growth coordination with translation machinery, supporting a cohesive role in ribosome biogenesis and translation.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0090529","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0007049","count":2}]},{"hash":"437003968787490882","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001308","count":1},{"id":"GO:0000288","count":1},{"id":"GO:1902039","count":1},{"id":"GO:0016441","count":1},{"id":"GO:0000056","count":1}]},{"hash":"218517158027674220","title":"Unknown","description":"The GO terms listed are very diverse (DNA integration, p53-mediated apoptosis, ribosome rescue/degradation, toxin/nitroglycerin metabolism, protein tetramerization, mitochondrial fusion, cardiac membrane potential regulation), with no clear common function or shared pathway, and there are no interactions among proteins in this cluster. Therefore there isn\u2019t a coherent label that accurately represents the cluster\u2019s function.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:1902167","count":1},{"id":"GO:0072344","count":1},{"id":"GO:0046256","count":1},{"id":"GO:1990116","count":1}]},{"hash":"1888277288488151915","title":"Ubiquitin-Dependent Immune Regulation","description":"This cluster centers on protein ubiquitination and related pathways (ERAD, polyubiquitination) and includes immune and survival signals (adaptive immune response, NF-kappaB regulation, negative regulation of apoptosis), suggesting a cohesive role in ubiquitin-mediated immune signaling and cell survival, with some developmental context reflected by growth and brain development terms.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0002250","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0030433","count":3}]},{"hash":"113338781812896815","title":"Skin Development and Wound Healing","description":"The top GO terms center on skin biology and repair, including establishment of the skin barrier, keratinocyte differentiation regulation, and wound healing, with additional developmental terms suggesting broader organismal development. Overall, the strongest theme is skin formation and tissue repair, pointing to a developmental/repair role for these proteins.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001836","count":1},{"id":"GO:0042219","count":1},{"id":"GO:0006750","count":1},{"id":"GO:0061436","count":1},{"id":"GO:0003208","count":1}]},{"hash":"1126542423960161743","title":"Unknown","description":"The GO terms span several unrelated processes (development, transcription regulation, apoptosis, signaling, miRNA metabolism, viral-host interaction) with no clear shared function or pathway, and there are no edges linking the proteins, so a cohesive cluster function cannot be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":1},{"id":"GO:1902187","count":1},{"id":"GO:0003334","count":1},{"id":"GO:0001822","count":1},{"id":"GO:0016479","count":1}]},{"hash":"1310682058690507542","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0006954","count":2},{"id":"GO:0036269","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0019441","count":1}]},{"hash":"757074520495491098","title":"Neural signaling and behavior modulation","description":"The terms point to neural signaling and behavioral regulation, including prepulse inhibition, locomotory behavior, ethanol response, and receptor guanylyl cyclase signaling with cross-talk to adenylate cyclase pathways; a non-neural term appears as noise, but the overall theme is brain signaling and behavior. ","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060134","count":3},{"id":"GO:0010226","count":3},{"id":"GO:0009253","count":3},{"id":"GO:0031631","count":3},{"id":"GO:0007626","count":3}]},{"hash":"1619018066779258705","title":"Developmental Chromatin Regulation","description":"This cluster centers on chromatin state changes (histone deacetylation, H3K9 methylation regulation) and developmental processes (gastrulation, in utero embryonic development, neuron maturation), suggesting a theme of chromatin regulation during development. Some terms are obsolete or broad, but the core pattern supports this label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0032496","count":1}]},{"hash":"1663623762412615661","title":"P450-Mediated Lipid Metabolism and Detoxification","description":"GO terms point to lipid catabolic processes and epoxygenase P450 pathway activity, with a broader signal of detoxification responses; together these suggest a coherent theme around lipid metabolism coupled to P450-based detoxification, though some terms may reflect noise or plant-specific processes.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0046272","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0010223","count":1}]},{"hash":"299440132417518509","title":"Organogenesis and vascular development","description":"Organogenesis and vascular development. The terms cluster around tissue and organ formation across systems\u2014hair follicle development, ovulation, heart field specification, lymphatic vessel development, and vascular wound healing\u2014along with cell migration, pointing to broad developmental and morphogenetic processes rather than a single pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051798","count":1},{"id":"GO:0033085","count":1},{"id":"GO:0090419","count":1},{"id":"GO:0001542","count":1},{"id":"GO:0035470","count":1}]},{"hash":"1957179425529032822","title":"Neural development and synaptic signaling","description":"The proteins in this cluster are linked to nervous system development, axon guidance, and synaptic regulation, with GO terms spanning nervous system development, axon midline point recognition, regulation of synapse structure/activity, and ionotropic glutamate receptor signaling, suggesting a shared role in neural development and synaptic function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048669","count":1},{"id":"GO:0016199","count":1},{"id":"GO:1990000","count":1},{"id":"GO:0060670","count":1},{"id":"GO:0050803","count":1}]},{"hash":"475691615427200365","title":"Neuroimmune Regulation of Behavior","description":"The GO terms cover immune signaling (cytokine production, leukocyte-mediated immunity) alongside behavioral and neural processes (locomotory and mating behavior, fear response, dopamine metabolism, ethanol response, glucose homeostasis), suggesting these proteins link immune signaling to behavioral regulation. This label captures the integrated theme of neuroimmune influence on behavior.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001816","count":3},{"id":"GO:0007626","count":3},{"id":"GO:0002443","count":3},{"id":"GO:0048149","count":3},{"id":"GO:0055114","count":3}]},{"hash":"2155574049103216597","title":"Mitochondrial import and chaperone stress response","description":"The terms emphasize mitochondrial intermembrane space protein import, chaperone-mediated assembly/stabilization, and stress-related responses (ischemia, ATP, cocaine). This suggests a cohesive theme around mitochondrial protein handling coupled with general protein quality control under stress, despite some broader terms like cell cycle.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002931","count":3},{"id":"GO:0045041","count":3},{"id":"GO:1901998","count":3},{"id":"GO:0033198","count":3},{"id":"GO:0051131","count":3}]},{"hash":"480003622098874182","title":"Developmental differentiation and morphogenesis","description":"The top GO terms point to diverse developmental and morphogenetic processes across tissues (pancreas, midbrain, spinal cord, cerebellum) and related cellular activities (ciliary motility, chromatin remodeling, and left-right asymmetry), suggesting the proteins participate in general development/differentiation and morphogenesis rather than a single, specific pathway. Confidence in this linkage is moderate given the broad spread of terms.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090104","count":1},{"id":"GO:0030901","count":1},{"id":"GO:0035774","count":1},{"id":"GO:0006337","count":1},{"id":"GO:0021516","count":1}]},{"hash":"1648622349964785822","title":"Germline development and meiosis","description":"The most distinctive terms point to germline biology: female germ-line stem cell population maintenance, in utero embryonic development, and meiosis I, indicating a cluster centered on germline development and meiotic progression. Additional terms on translation initiation and RNA handling may reflect broader gene-expression regulation during development but do not override the germline/meiosis signal. Thus, Germline development and meiosis is an appropriate, concise label.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000715","count":2},{"id":"GO:0036099","count":1},{"id":"GO:0001701","count":1},{"id":"GO:0000338","count":1},{"id":"GO:0000973","count":1}]},{"hash":"1160830673791344320","title":"Unknown","description":"The terms in this cluster are highly diverse and include metabolic processes (carbohydrate metabolism, magnesium homeostasis/transport), signaling (activation of protein kinase activity), stress/response (cellular response to glucose starvation, interleukin-4), development (retina development), and several obsolete GO terms. With only a single edge and no clear shared pathway, there isn\u2019t a cohesive, identifiable function linking these proteins. Therefore, a reliable single-label theme cannot be assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0071353","count":1}]},{"hash":"1049331481775312965","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0034476","count":2},{"id":"GO:0006269","count":2},{"id":"GO:0006363","count":2}]},{"hash":"1594616618322467934","title":"RNA processing and translation regulation","description":"Proteins in this cluster show GO terms centered on RNA metabolism and control of translation, including mRNA splicing and spliceosome activity, polyadenylation and mRNA modification, regulation of mRNA stability in response to stress, and initiation of translation via EIF4F complex assembly. Together these terms point to a cohesive theme of post-transcriptional RNA processing and regulation of protein synthesis, with a few obsolete terms not affecting the overall picture.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0006376","count":1},{"id":"GO:0097010","count":1},{"id":"GO:0010610","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1796974931938756898","title":"Unknown","description":"The proteins share a highly diverse set of GO terms (immune response to lipopolysaccharide and interleukin-12 production, circadian rhythm, hormone secretion, platelet activation, bone remodeling, eosinophil regulation, photoreceptor maintenance, and GTPase signaling) with no clear unifying biological theme, so a cohesive, specific functional label cannot be determined.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":1},{"id":"GO:0022410","count":1},{"id":"GO:0046879","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0030168","count":1}]},{"hash":"1480037418391178478","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009615","count":1},{"id":"GO:0000494","count":1},{"id":"GO:0045071","count":1},{"id":"GO:0035280","count":1},{"id":"GO:0016075","count":1}]},{"hash":"172914579959474035","title":"Rho/Rac GTPase signaling and lamellipodium-driven migration","description":"Top terms indicate regulation of Rho/Rac GTPase signaling, lamellipodium assembly, and cell migration, suggesting a module centered on cytoskeletal dynamics and motility. Some immune-related terms appear but the shared theme is GTPase-driven actin remodeling and movement.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0032633","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0001865","count":3}]},{"hash":"84924266664505340","title":"Vacuolar Ion Transport and Acidification","description":"The top GO terms are centered on vacuole-related processes (protein targeting to vacuole, vacuole organization, vacuolar acidification) and proton/ion transport (proton transmembrane transport, proton motive force-driven ATP synthesis, sodium ion transport, copper ion homeostasis). This points to a coherent theme of vacuolar membrane function and maintenance of the proton gradient and ion homeostasis, consistent with V-ATPase\u2013driven acidification and associated transport. Some terms are less related (nitrogen catabolite repression, galacturonate biosynthesis), but they do not override the dominant vacuolar/ion transport signal. High","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0007035","count":1}]},{"hash":"2025692605067763789","title":"Unknown","description":"The Top Terms are highly diverse and only loosely point to mitochondria or metabolism (e.g., mitochondrial translation, TCA cycle) while others refer to unrelated processes like intestinal absorption and development. There isn\u2019t a clear, single functional theme uniting these proteins, so a specific label isn\u2019t justifiable.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0019298","count":1},{"id":"GO:0009098","count":1}]},{"hash":"1144683332897602105","title":"Mitochondrial Translation & Fatty Acid Oxidation","description":"The top GO terms strongly point to mitochondrial processes, with mitochondrial translation and fatty acid catabolic processes suggesting a link to mitochondrial protein synthesis and energy metabolism. The transamidation of glutaminyl-tRNAGln further supports a translation-related role in mitochondria. The ER organization and nylon catabolic process terms are less coherent with this theme and may reflect broader annotations or artifacts, but do not override the mitochondrial-centric signals. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019876","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0009062","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0032543","count":1}]},{"hash":"1377766285864127562","title":"ERAD and ubiquitin-proteasome regulation","description":"This cluster centers on protein quality control and turnover, with deubiquitination, proteasomal regulation, and ER-associated degradation (ERAD) cues, plus tail-anchored protein insertion into the ER membrane\u2014together pointing to proteostasis in the ER and related membrane trafficking. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0071816","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0033132","count":3},{"id":"GO:1904378","count":3}]},{"hash":"1159366705475824603","title":"ERAD and Proteostasis Regulation","description":"The GO terms cluster around endoplasmic reticulum quality control and protein turnover: deubiquitination, proteasomal regulation, ER-associated degradation (ERAD), and insertion of tail-anchored proteins into the ER membrane, plus translation-related steps. Together these suggest a shared role in maintaining protein homeostasis via ER-associated processing and degradation pathways, despite some tangential terms appearing in the list. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0071816","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0033132","count":3},{"id":"GO:1904378","count":3}]},{"hash":"266305131164715307","title":"Unknown","description":"The GO terms are scattered across immune signaling, neuronal function, chromatin/DNA repair, and even plant patterning, with no single cohesive theme tying the proteins together. The low and mixed representation prevents a clear, specific label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0002534","count":1},{"id":"GO:0051441","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0031915","count":1}]},{"hash":"69458461729001603","title":"Rac-driven dendritic spine morphogenesis and lamellipodium remodeling","description":"Top GO terms center on Rac signal transduction and actin-driven membrane protrusions (lamellipodium and ruffle assembly) and dendritic spine development/morphogenesis, with hippocampus development indicating a neuronal context and Golgi-to-plasma membrane transport suggesting membrane supply for remodeling. Together these terms suggest Rac-mediated cytoskeletal remodeling supporting spine formation and lamellipodial dynamics in neurons, hence the chosen label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":2},{"id":"GO:0010592","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0016601","count":2},{"id":"GO:0060999","count":2}]},{"hash":"1378058575865052637","title":"Transcription Machinery and Transcription-Coupled Repair","description":"These terms cluster around RNA polymerase\u2013driven transcription (Pol I/II/III), including initiation/preinitiation complex assembly, elongation, and termination, as well as nucleolar rRNA transcription, with a prominent link to transcription-coupled nucleotide-excision repair, suggesting a cohesive transcription-centered module with genome maintenance connections.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006283","count":2},{"id":"GO:0001172","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0006362","count":1},{"id":"GO:0042797","count":1}]},{"hash":"2114323339475801395","title":"Neural Development and Transcriptional Regulation","description":"The dominant terms center on nervous system development (forebrain development, neuronal polarity) and DNA-templated transcription, suggesting these proteins cooperate in neuronal differentiation and regulation of gene expression. Some immune signaling terms may reflect broader regulatory roles or cross-talk but do not outweigh the neural development signal.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000727","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0061246","count":2},{"id":"GO:0032633","count":2},{"id":"GO:0043433","count":2}]},{"hash":"1475297091792721966","title":"Unknown","description":"The GO terms are extremely diverse with no apparent shared function among the proteins (tyrosine dephosphorylation, host-symbiont modification, arsenic response, liver development, photoperiodism, organ regeneration, and mRNA decay). There are no edges or triangles, and only 3 proteins, making it unlikely to infer a coherent biological theme or label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":1},{"id":"GO:0052046","count":1},{"id":"GO:0046685","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0048571","count":1}]},{"hash":"1864354370451425931","title":"Rho-regulated actin remodeling and endocytosis","description":"The top GO terms cluster around actin filament organization and cytoskeletal reorganization, regulated by Rho and GTPases, with endocytosis and related engulfment processes. This points to a cohesive theme of actin dynamics driving membrane internalization, despite a few stray or obsolete terms that don\u2019t fit as well with the core function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":2},{"id":"GO:1903286","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0031666","count":1}]},{"hash":"1116490360288972585","title":"TNF/NF-\u03baB Signaling and Ubiquitination","description":"Rationale: The terms cluster around TNF-mediated signaling, NF-\u03baB activation (including non-canonical), and regulation of apoptosis/necroptosis, with a strong emphasis on ubiquitination (including K63-linked ubiquitination). Additional terms reflect antiviral host responses and broader immune regulation (LPS signaling, T-helper cell differentiation), suggesting a cohesive function in inflammatory signaling modulated by ubiquitin. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":2},{"id":"GO:0060546","count":2},{"id":"GO:1902187","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0036205","count":2}]},{"hash":"1192010518812320460","title":"Axon Guidance and Neural Crest Migration","description":"The cluster is dominated by nervous system development terms (nervous system development, neural crest cell migration) and specific axon-related localization/projection terms (paranode/juxtaparanode localization, sympathetic neuron projection extension), plus Rho-mediated cytoskeletal regulation relevant to neurite outgrowth. While a few immune-related terms appear, the neuronal development/axon targeting signals best explain the group. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:2001181","count":2},{"id":"GO:0045217","count":2},{"id":"GO:0097490","count":2},{"id":"GO:0007399","count":2}]},{"hash":"933157221117957024","title":"Glycan Metabolism","description":"The cluster is named Glycan Metabolism because two of the top GO terms point to carbohydrate processing (glycoside catabolic process and fucose metabolic process), suggesting a shared glycan-degradation function; the third term likely reflects incidental host interaction.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016139","count":1},{"id":"GO:2000535","count":1},{"id":"GO:0006004","count":1}]},{"hash":"1342088233393255972","title":"Lipid biosynthesis and sphingolipid metabolism","description":"The top GO terms cluster around lipid pathways\u2014ergosterol biosynthetic regulation, unsaturated fatty acid biosynthesis, and sphingolipid metabolism (MIPC)\u2014suggesting a shared function in membrane lipid/sterol production, with other terms (nitrogen metabolism, mitochondrial inheritance) likely representing noise or broader cellular context.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006636","count":3}]},{"hash":"1033730907539888383","title":"Unknown","description":"The two translation-related GO terms (formation of translation preinitiation complex and translation reinitiation) alongside multiple diverse membrane transport terms (arsenite, citrate, sodium, malate, phosphate transport, etc.) do not reveal a single coherent function or pathway for this small cluster of proteins. Without a unifying theme, a specific functional label cannot be reliably assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0098656","count":1},{"id":"GO:0015700","count":1},{"id":"GO:0055085","count":1}]},{"hash":"1980147074359493458","title":"Ubiquitination in immune signaling","description":"The top GO terms center on ubiquitination (K63-linked ubiquitination, autoubiquitination, actin ubiquitination) and immune-related processes (lipopolysaccharide signaling, suppression of viral release, MHC class I biosynthesis), suggesting these proteins participate in ubiquitin-mediated regulation of immune pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902261","count":2},{"id":"GO:1902187","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0031664","count":2},{"id":"GO:0010586","count":2}]},{"hash":"1096289272015333695","title":"Unknown","description":"Top terms are too heterogeneous (immune encapsulation, brain segmentation, plant development, broad carbohydrate metabolism, glycosylation/glycoside catabolic processes, and NO regulation), with several obsolete terms. There is no clear, shared function linking these proteins, so a cohesive label cannot be assigned with confidence.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035010","count":1},{"id":"GO:0035284","count":1},{"id":"GO:0006049","count":1},{"id":"GO:0006486","count":1},{"id":"GO:0005975","count":1}]},{"hash":"1172294990842548472","title":"Apoptosis and Innate Immunity","description":"Based on the GO terms, the cluster is centered on programmed cell death (apoptosis, pyroptotic inflammatory response) and innate immune activation, with ubiquitination as a regulatory motif. Although one term references mitotic spindle assembly, the strongest signals are apoptosis and innate immune signaling, suggesting these proteins may function in inflammatory cell death pathways and immune responses.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":1},{"id":"GO:0070269","count":1},{"id":"GO:0090307","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0045087","count":1}]},{"hash":"680010546613398466","title":"Unknown","description":"The top GO terms span immune, neural, plant development, metabolism, and more with no clear shared function or pathway; there are zero edges or triangles to suggest a cohesive interaction. Because the terms are so diverse, there isn\u2019t a single interpretable function to label the cluster beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":1},{"id":"GO:0007399","count":1},{"id":"GO:2000312","count":1},{"id":"GO:0035853","count":1},{"id":"GO:0009911","count":1}]},{"hash":"272707906318583024","title":"Unknown","description":"The GO terms are highly diverse, spanning glucose and amino acid transport, protein transport, glycosylation, lens development, grooming behavior, and T cell cytokine production, with no single cohesive function linking the proteins. There are no interactions (edges) to suggest a shared pathway, so a meaningful, specific label cannot be inferred. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":1},{"id":"GO:0007625","count":1},{"id":"GO:0002088","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0015811","count":1}]},{"hash":"1139175126924095729","title":"Transmembrane Transporters","description":"The GO terms are all about transporting various substrates across membranes (vitamins, ions, sugars, xenobiotics, neurotransmitter loading), pointing to membrane transporter proteins as the core function of this cluster. The inclusion of a neurotransmitter loading term also supports a transporter role in neurons. Confidence: High","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0015757","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0015707","count":3}]}]