[{"hash":"126714320187529347","title":"Angiogenesis and vascular remodeling","description":"These terms cluster around blood vessel formation and remodeling: positive regulation of VEGF production, endothelial tip cell fate, pulmonary artery morphogenesis, smooth muscle cell proliferation, platelet aggregation, prostaglandin biosynthesis, and PI3K/AKT signaling. Together they point to angiogenesis and vascular remodeling as the central theme of this protein cluster.","confidence":"High","size":29,"edges":67,"triangles":108,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0051897","count":6},{"id":"GO:0048661","count":6},{"id":"GO:0043065","count":6},{"id":"GO:0001516","count":6}]},{"hash":"703485625536766939","title":"RNA processing and gene expression","description":"The top GO terms cluster around RNA metabolism and expression: transcription, mRNA processing (splicing and polyadenylation), mRNA export, and translation initiation/reinitiation. Although some terms touch on cell division and vesicle trafficking, the dominant signal is RNA processing leading to protein synthesis, suggesting a coherent theme of gene expression regulation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":11},{"id":"GO:0002188","count":11},{"id":"GO:0045292","count":10},{"id":"GO:0006378","count":9},{"id":"GO:0006351","count":8}]},{"hash":"894835509809779305","title":"Development-linked transcription and ribosome biogenesis","description":"Dominant GO terms point to core transcriptional machinery (RNAP I/II/III activities, RNA-templated transcription, elongation, termination) and ribosome biogenesis, with a hint of paraxial mesoderm development and paranode localization. The cluster appears to reflect a general gene-expression/biogenesis module with some developmental context.","confidence":"Medium","size":29,"edges":29,"triangles":1,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0048339","count":3},{"id":"GO:0006366","count":2},{"id":"GO:0001172","count":2},{"id":"GO:0006360","count":2},{"id":"GO:0006385","count":2}]},{"hash":"2251051975700372363","title":"Antiviral dsRNA sensing and interferon response","description":"This cluster is dominated by GO terms related to innate antiviral defense, including cellular responses to exogenous dsRNA, type I interferon signaling, and broader innate immune responses, suggesting a core antiviral defense role. Some members also relate to RNA processing and chromatin-related regulation, which may reflect supplementary functions or multifunctionality within the group.","confidence":"Medium","size":29,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0070389","count":7},{"id":"GO:0000492","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0071360","count":7}]},{"hash":"950188182281177664","title":"Neural pain signaling and dopaminergic plasticity","description":"These terms cluster around brain-mediated nociception and reward-related signaling. The prominent GO terms\u2014sensory perception of pain, response to morphine, and dopaminergic synaptic transmission\u2014point to neural pathways for pain processing and drug responses. The ERK1/2 cascade regulation further suggests activity-dependent signaling and plasticity tied to learning in these circuits. Additional terms like prostaglandin E stimulus, temperature response, and brain renin-angiotensin system indicate broader neuromodulatory and inflammatory signaling within brain networks. Together, they describe a coherent theme of neural pain modulation and dopaminergic signaling with plasticity.","confidence":"High","size":29,"edges":85,"triangles":27,"max_degree":13,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":19},{"id":"GO:0071502","count":17},{"id":"GO:0002024","count":17},{"id":"GO:0071380","count":15},{"id":"GO:0008542","count":15}]},{"hash":"805322338313831278","title":"Diverse Biosynthesis and Metabolism","description":"The top GO terms point to multiple, distinct biosynthetic and metabolic processes (poly-hydroxybutyrate, antibiotics, sphingolipids, retinol, tetrahydrobiopterin, phospholipids), suggesting a cluster of proteins involved in diverse biosynthetic pathways rather than a single coherent function. Obsolete or non-specific terms like lung development or blood vessel diameter may be annotation noise. With no clear single pathway tying all proteins together, this label captures the broader biosynthetic/metabolic theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0042619","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0030324","count":5},{"id":"GO:0097755","count":4}]},{"hash":"1403157927523753700","title":"Neuronal adhesion and synapse assembly","description":"The cluster shows strong enrichment for synapse assembly and regulation of synapse formation, plus dopaminergic and serotonergic neuron axon guidance terms. The presence of both heterophilic and homophilic cell\u2013cell adhesion terms supports a role in neuronal connectivity and synapse development, suggesting these proteins function together in neural circuit formation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051965","count":12},{"id":"GO:0007157","count":10},{"id":"GO:0007156","count":10},{"id":"GO:0007416","count":9},{"id":"GO:0043931","count":9}]},{"hash":"108841717511717572","title":"Hormone-responsive development and tissue homeostasis","description":"The cluster\u2019s top GO terms center on hormone-related processes (response to thyroid hormone; endocrine pancreas development) along with tissue development and homeostasis (skeletal muscle differentiation; tissue homeostasis). Mitochondrial transcription initiation and retinol metabolism add an energy/metabolic angle, suggesting a broad hormone-regulated development and metabolism program across tissues rather than a single pathway. The mixture of developmental and metabolic terms supports a cohesive but multi-tissue hormone-regulated theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097066","count":2},{"id":"GO:0001894","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0031018","count":2},{"id":"GO:0006391","count":2}]},{"hash":"1203585193154336052","title":"RNA stability and translation initiation","description":"The top GO terms show a clear focus on post-transcriptional RNA regulation and initiation of translation (mRNA stabilization, regulation of mRNA stability in response to stress, regulation of translational initiation, formation of the translation preinitiation complex). Some other terms (e.g., DNA replication, paranodal junction assembly) appear less central and may reflect multi-function annotations or noise, but the dominant theme is RNA stability and translation control, suggesting this cluster groups proteins involved in post-transcriptional gene expression rather than a single metabolic pathway.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0030913","count":2},{"id":"GO:0048255","count":1},{"id":"GO:0010610","count":1},{"id":"GO:0006446","count":1}]},{"hash":"800150627870664778","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster is defined by LSU-rRNA maturation, large subunit biogenesis, and snoRNA splicing, pointing to a core function in ribosome assembly and RNA processing; the peripheral signaling/regulatory terms do not outweigh this primary theme.","confidence":"High","size":29,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0034247","count":2},{"id":"GO:0098902","count":2},{"id":"GO:0008285","count":2}]},{"hash":"1467276322960087337","title":"Transcription Regulation and Nucleotide Salvage","description":"This cluster is anchored by terms for regulation of DNA-templated transcription and DNA-templated transcription, with phosphorylation highlighting signaling aspects. Nucleotide salvage terms (AMP/UMP salvage) point to a link between transcription control and nucleotide metabolism. Additional terms like cellular oxidant detoxification and viral process suggest broader cellular stress contexts, but the strongest signal centers on transcription regulation and nucleotide metabolism. ","confidence":"Medium","size":29,"edges":4,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0016310","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0044209","count":4},{"id":"GO:0016032","count":3}]},{"hash":"1399309210522980551","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms cluster around ubiquitination and the ERAD pathway, i.e., tagging proteins for degradation via the ubiquitin-proteasome system, including ubiquitin-dependent protein catabolic processes and ubiquitination itself. While there are additional terms spanning development and immune-related processes, these appear secondary to the dominant theme of proteostasis through ubiquitin-mediated degradation. Therefore, this cluster is best labeled as ubiquitin-dependent protein degradation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0042787","count":4},{"id":"GO:0060528","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0030900","count":3}]},{"hash":"1956997647140782968","title":"Craniofacial morphogenesis and neural development","description":"This cluster is dominated by embryonic development terms, especially craniofacial and neural patterning: roof of mouth development, face morphogenesis, embryonic skeletal system development, axis specification, and neuronal lineage commitment in forebrain. Together they indicate proteins involved in early developmental patterning and differentiation, particularly in craniofacial and neural contexts. A few terms (multicellular development, transcriptional regulation) reflect broader regulatory roles, and a lone SSU-rRNA maturation term appears incidental. Overall, the cluster seems to represent craniofacial morphogenesis with neural development.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0060021","count":2},{"id":"GO:0060325","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1877107695105361612","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":61,"triangles":80,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051897","count":7},{"id":"GO:0001890","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0090263","count":7},{"id":"GO:0060711","count":7}]},{"hash":"2013852929968421135","title":"Cytoskeleton Remodeling and Endomembrane Trafficking","description":"The cluster shows strong representation of actin cytoskeleton dynamics (regulation of actin cytoskeleton, lamellipodium assembly, cell migration) alongside vesicle trafficking processes (endosome to lysosome transport, endosome organization, lysosome organization), suggesting a coordinated program of cytoskeletal remodeling and endomembrane traffic that drives cell movement and intracellular transport.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0008333","count":2},{"id":"GO:0032956","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0007032","count":2}]},{"hash":"2094026991076313200","title":"Chromatin-based transcription regulation","description":"Based on the top GO terms, the cluster is dominated by processes related to transcription control and chromatin dynamics, including negative regulation of transcription by RNA polymerase II, transcription initiation-coupled chromatin remodeling, and establishment/localization of proteins to chromatin. The presence of RNA surveillance (non-stop decay) also aligns with nuclear quality control of transcripts. A few terms point to development or signaling, but the strongest signal is chromatin-mediated transcription regulation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006183","count":2},{"id":"GO:0071353","count":2},{"id":"GO:1904815","count":2},{"id":"GO:0070481","count":2}]},{"hash":"2238591541040613614","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008277","count":1},{"id":"GO:0072513","count":1},{"id":"GO:0035556","count":1},{"id":"GO:0042462","count":1},{"id":"GO:0007637","count":1}]},{"hash":"138563821632063286","title":"Developmental signaling and morphogenesis","description":"This cluster centers on morphogenesis and development (branching morphogenesis in labyrinthine layer, placental epithelial morphogenesis, nervous system development) and is linked to signaling processes (intracellular signal transduction, GTPase activity regulation, GPCR-related pathways). While some terms like amyloid fibril formation or ER calcium homeostasis are less directly related, the dominant theme is signaling governing developmental morphogenesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060670","count":4},{"id":"GO:0000742","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007205","count":3}]},{"hash":"111468047909056000","title":"Neural Development and Axon Guidance","description":"This cluster is dominated by GO terms tied to nervous system and sensory development, especially forebrain and cerebellum development, visual perception, and axon guidance for retinal ganglion and motor neurons. Although there are broader embryonic terms (multicellular organism development, heart/placenta development), the strongest signals point to neural development and axon pathfinding as the core theme.","confidence":"High","size":27,"edges":14,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":10},{"id":"GO:0031290","count":9},{"id":"GO:0008045","count":9},{"id":"GO:0007507","count":9},{"id":"GO:0007601","count":9}]},{"hash":"2155931958218021526","title":"Calcium signaling regulation in neural and muscle differentiation","description":"This cluster is dominated by terms about regulating calcium signaling and kinase activity (eg, postsynaptic calcium concentration, NFAT signaling, and negative regulation of protein kinase activity). While there are also terms tied to broader differentiation processes (dendrite morphogenesis, connective tissue replacement, lung differentiation), the common thread is modulation of calcium- and kinase-driven signaling pathways that influence neural and muscle cell differentiation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097274","count":12},{"id":"GO:0006469","count":10},{"id":"GO:0014883","count":9},{"id":"GO:0035562","count":9},{"id":"GO:0051533","count":9}]},{"hash":"1848849307643940119","title":"Post-transcriptional RNA processing and translation control","description":"The cluster is dominated by GO terms tied to post-transcriptional regulation: mRNA splicing (including negative regulation), mRNA stability and stabilization, and control of translation initiation (including formation of the preinitiation complex and IRES-dependent initiation). This suggests a coherent function focused on RNA processing and subsequent translation control rather than transcriptional regulation. Some terms are obsolete or development-related outliers, but the prevailing signal points to post-transcriptional gene expression regulation.","confidence":"High","size":27,"edges":134,"triangles":443,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":12},{"id":"GO:0010610","count":12},{"id":"GO:0045292","count":11},{"id":"GO:0048025","count":11},{"id":"GO:0048255","count":10}]},{"hash":"417226336908167178","title":"Cell Cycle and Neural Development Signaling","description":"These proteins are strongly linked to core cell cycle and DNA maintenance processes (mitotic cell cycle, DNA replication, DNA repair, DNA-templated transcription) while also showing clear signals of neural development and connectivity (hippocampus and nervous system development, axon extension, JNK cascade regulation). The presence of a T cell receptor signaling term adds some signaling breadth, but the dominant themes point to proliferation-linked neural development and associated signaling pathways. ","confidence":"Medium","size":27,"edges":9,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000278","count":25},{"id":"GO:0006260","count":25},{"id":"GO:0006281","count":24},{"id":"GO:0006351","count":24},{"id":"GO:0033138","count":23}]},{"hash":"2007369802163087984","title":"Nuclear transport and DNA replication","description":"Many top GO terms cluster around nucleus-centered processes: DNA replication and cell division (GO:0006260, GO:0051301) suggest genome duplication; multiple entries refer to nuclear import (NLS-bearing protein import into nucleus, ribosomal protein import into nucleus), mRNA export, and nuclear pore complex assembly, all core to nuclear transport. Chromatin-related process (silent mating-type cassette heterochromatin formation) further supports a chromatin/nuclear context. Together, these terms indicate a cluster of nuclear transport and replication machinery.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0030466","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0006607","count":6}]},{"hash":"902468958654457059","title":"Ribosome Biogenesis and Translation","description":"The cluster is enriched for translation-related terms: translation, ribosome biogenesis, initiation, termination, and ribosomal subunit assembly, plus mitochondrial translation and rRNA maturation, indicating proteins focused on protein synthesis machinery. Some secondary signals (response to antibiotic, glial cell proliferation) are present but less central to the core theme.","confidence":"High","size":27,"edges":346,"triangles":2806,"max_degree":26,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":24},{"id":"GO:0042254","count":6},{"id":"GO:0006415","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0006413","count":4}]},{"hash":"1477374339672643519","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0000289","count":3},{"id":"GO:0006261","count":3},{"id":"GO:0034415","count":3},{"id":"GO:0002107","count":3},{"id":"GO:0010606","count":3}]},{"hash":"611021926671475308","title":"Rac-Driven Actin Remodeling and Filopodium Assembly","description":"The top GO terms point to Rac signaling and actin-based structures, including filopodium and stress fiber assembly, and adhesion-related cell spreading, indicating a coherent theme of Rac-mediated cytoskeletal remodeling and morphological changes. Some neuronal-related terms (brain development, synaptic vesicle exocytosis) reflect broader actin roles in neural contexts, but the dominant signal is actin dynamics and cell shape changes driven by Rac. ","confidence":"High","size":27,"edges":12,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016601","count":7},{"id":"GO:0043552","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0051496","count":6},{"id":"GO:1900026","count":6}]},{"hash":"228090117312604036","title":"Embryonic organogenesis and morphogenesis","description":"These proteins show a cohesive theme of embryonic development and morphogenesis across multiple organs (eye, craniofacial skeleton, palate, tooth, inner ear, uterus, pancreas, heart). The top GO term for transcriptional regulation by RNA Pol II suggests regulatory roles during development, supporting a developmental-programming cluster rather than a single pathway.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":7},{"id":"GO:0003148","count":6},{"id":"GO:0048048","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0060021","count":6}]},{"hash":"1388714853958989033","title":"Mammary Epithelial Cell Cycle and Proliferation","description":"Top GO terms indicate DNA-templated transcription and multiple mitotic transitions (G1/S, G2/M), spindle dynamics, and overall cell division, with a strong signal for mammary gland epithelial cell proliferation. This pattern suggests a cohesive set of proteins coordinating transcriptional control with cell-cycle progression to promote epithelial proliferation, particularly in mammary tissue, with ancillary involvement of ER stress response and insulin signaling pathways.","confidence":"High","size":27,"edges":16,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0033598","count":12},{"id":"GO:0000082","count":12},{"id":"GO:0046626","count":12},{"id":"GO:0010696","count":12}]},{"hash":"1336382545334895137","title":"Actin Dynamics and Epithelial Cell Polarity","description":"The cluster is dominated by terms for actin polymerization and remodeling (actin filament polymerization and branching; Rho-regulated signaling) and for establishing and maintaining epithelial cell polarity, with related signaling via ephrin receptors and Wnt pathways and ruffle formation\u2014together pointing to a cohesive module of cytoskeletal dynamics linked to epithelial polarity.","confidence":"High","size":27,"edges":25,"triangles":10,"max_degree":12,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043552","count":4},{"id":"GO:0030838","count":4},{"id":"GO:0030041","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0090162","count":3}]},{"hash":"821062600446299343","title":"Ubiquitin-Dependent Proteolysis and ERAD","description":"This cluster is characterized by strong representation of ubiquitin-dependent protein catabolic processes, proteasomal degradation, autoubiquitination, and specific ubiquitin linkages (K48, K6), including SCF involvement and ERAD-related terms. The presence of peroxisomal protein import and DNA damage response terms likely reflects broader ubiquitin signaling roles in receptor recycling and genome maintenance. Overall, the dominant theme is tagging and degradation of proteins via the ubiquitin-proteasome system, with related pathways like ERAD and peroxisomal import contributing context. ","confidence":"High","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0031146","count":10},{"id":"GO:0051865","count":9},{"id":"GO:0042787","count":9},{"id":"GO:1902916","count":8},{"id":"GO:0030433","count":8}]},{"hash":"1681149834025064733","title":"Membrane transport and glycosylation","description":"The top GO terms cluster around transmembrane transport of amino acids and sugars (D-glucose transport, L-cystine transport, basic amino acid export, intracellular amino acid homeostasis) and dolichol-linked oligosaccharide biosynthesis, indicating glycosylation-related membrane processes. While a few terms are peripheral (grooming behavior, lens development, actin regulation), the dominant signal is membrane transport plus protein glycosylation.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":1},{"id":"GO:0034488","count":1},{"id":"GO:0080144","count":1},{"id":"GO:1904659","count":1},{"id":"GO:0015811","count":1}]},{"hash":"782580676995875093","title":"Unknown","description":"The terms span many unrelated processes (vasopressin secretion, actin cytoskeleton, NOD2 signaling, mRNA processing, plant SA signaling, membrane protein localization, cardiac SA node activity, prostate gland development, transcription regulation, and thermoception), with no single cohesive function linking the cluster notes.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030103","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0006397","count":4},{"id":"GO:2000031","count":4}]},{"hash":"1528159343810334960","title":"Neural synapse formation and actin remodeling with inflammation","description":"This cluster centers on terms tied to dendritic spine morphogenesis, actin cytoskeleton organization, and synapse assembly, indicating roles in neural synapse development and cytoskeletal changes. The presence of innate immune and inflammatory response terms suggests concurrent neuroimmune signaling that can accompany synaptic remodeling. Additional terms for ERK signaling and GTPase activity further support coordinated signaling that drives structural and functional synapse changes, with some breadth including phototransduction and temperature response that may reflect broader sensory signaling roles.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0060997","count":4},{"id":"GO:0006954","count":4},{"id":"GO:0030036","count":3},{"id":"GO:0008285","count":3}]},{"hash":"1456549307079656473","title":"Ribosome Biogenesis and rRNA Processing","description":"Most top GO terms point to rRNA maturation (LSU and 5.8S rRNA), ribosomal large subunit biogenesis, and preribosome assembly, indicating a coherent role in ribosome production. Additional terms about transcription regulation and splicing reflect broader RNA processing in the nucleus but do not override the ribosome-focused theme. Overall, the cluster appears to group proteins involved in ribosome maturation and RNA metabolism related to ribosome assembly.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0042273","count":2}]},{"hash":"10817660772985620","title":"RNA splicing and translation regulation","description":"This cluster is enriched for GO terms centered on RNA processing\u2014splicing, mRNA stability, and spliceosome regulation\u2014as well as initiation of translation and translation preinitiation, including IRES-dependent initiation. The convergence on spliceosome- and translation-related processes suggests a cohesive role in post-transcriptional control.","confidence":"High","size":26,"edges":253,"triangles":1260,"max_degree":24,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":19},{"id":"GO:0048026","count":19},{"id":"GO:0010610","count":16},{"id":"GO:1901407","count":15},{"id":"GO:0048255","count":14}]},{"hash":"712722008986100863","title":"Glycosylation-Driven Development and Cell Surfaces","description":"The cluster centers on glycosylation and glycoprotein metabolism (Lewis a epitope biosynthesis, poly-N-acetyllactosamine biosynthesis, O-linked glycosylation via hydroxyproline, arabinogalactan protein metabolism, and AGP-related processes) combined with developmental processes affecting cell surfaces and adhesion (root hair development, follicle epithelium polarity, seed coat mucilage biosynthesis, and related developmental terms). This suggests a theme of extracellular matrix/glycoprotein modifications guiding development and cell\u2013cell interactions across species.","confidence":"High","size":26,"edges":12,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":4},{"id":"GO:0007299","count":3},{"id":"GO:0048354","count":3},{"id":"GO:0042248","count":3},{"id":"GO:0010493","count":3}]},{"hash":"345652577356061071","title":"Germline Development and Ciliogenesis","description":"The cluster centers on germ cell formation (spermatogenesis and oogenesis) and ciliogenesis/centrosome biology (intraciliary transport, motile cilium assembly, and microtubule anchoring at the centrosome), with additional cytoskeletal organization signals. While transcription regulation and apoptosis terms are present, the strongest shared theme is germline development coupled with ciliary/centrosomal processes.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0035735","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0051017","count":6},{"id":"GO:0006351","count":6}]},{"hash":"1594042271788832896","title":"Wnt-driven cardiac development signaling","description":"The top GO terms cluster around heart development and canonical Wnt signaling, with supporting signals from integrin and Kit pathways and transcriptional regulation, suggesting a cohesive module coordinating cardiac development through Wnt-related signaling networks. Some noise terms exist, but the core theme remains developmental signaling for the heart.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008542","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0043552","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0010863","count":5}]},{"hash":"1471598013123500679","title":"Developmental signaling and cell-cycle regulation","description":"This cluster centers on development and growth control, with multicellular and neuron projection development terms, cell proliferation, and cell-cycle and stress signaling (G1 checkpoint, G0\u2192G1 transitions), plus GPCR\u2013PLC signaling and nutrient/glucose responses, all tied to proteasomal protein turnover. The adaxial/abaxial pattern formation term hints at broader developmental patterning, but the overarching theme is developmental signaling linked to growth regulation.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0031175","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0072432","count":3}]},{"hash":"1145278174734437192","title":"Neuronal axon guidance and migration","description":"This cluster is strongly enriched for terms related to neuron development and axon pathfinding, including motor neuron migration, commissural and sensory neuron axon guidance (and anterior/posterior guidance), as well as Wnt/calcium and planar cell polarity pathways implicated in axon guidance. Multicellular development and peptide hormone processing appear as broader context, but the neuronal guidance/migration terms clearly dominate, suggesting a cohesive neuronal development function.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905485","count":2},{"id":"GO:0007223","count":2},{"id":"GO:0071679","count":2},{"id":"GO:1905488","count":2},{"id":"GO:1904938","count":2}]},{"hash":"1546148747270034844","title":"ER Stress and Redox Protein Quality Control","description":"These proteins cluster around ER-associated handling of proteins and redox regulation: GO terms point to ER stress response, protein repair, and deglutathionylation, as well as cellular redox homeostasis and oxidative stress response. GPI anchor biosynthesis also occurs in the ER and ties into protein maturation, supporting a theme of ER-related quality control under redox stress. The presence of some non-ER/transcription terms suggests some heterogeneity, but the dominant signal is ER-associated redox/protein quality control.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0033158","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006662","count":2}]},{"hash":"1251088991176604859","title":"Multicellular organism development","description":"This cluster shows enrichment for broad developmental processes across multiple tissues (gonad, retina, brain, prostate, bone) and includes the overarching term multicellular organism development, indicating a general role in organismal development rather than a single tissue pathway. The presence of transcriptional regulation also aligns with developmental gene control. ","confidence":"High","size":25,"edges":18,"triangles":3,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008584","count":7},{"id":"GO:0060041","count":6},{"id":"GO:0007338","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0000122","count":6}]},{"hash":"1040841074897625206","title":"RNA Processing and Ribosome Biogenesis","description":"The cluster\u2019s top GO terms are dominated by RNA-centric processes: translation, maturation of rRNA (both SSU and LSU), ribosomal large subunit biogenesis, and spliceosome-related mRNA splicing regulation. These converge on RNA metabolism and ribosome assembly as the main theme, with a few additional terms (e.g., transcription termination, ncRNA-mediated silencing) that are less central to the core signal. Confidence that this label represents the cluster\u2019s function is Medium.","confidence":"","size":25,"edges":34,"triangles":8,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0000463","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0042273","count":5}]},{"hash":"1184200825515026297","title":"Retroviral entry, replication, and latency","description":"This cluster is dominated by GO terms tied to retroviral activity: viral penetration into the host nucleus, symbiont/virus entry into host cells, viral genome replication, establishment of integrated proviral latency, DNA integration, and RNA-templated DNA biosynthesis. These collectively point to a cohesive retroviral lifecycle theme (entry, reverse transcription, integration, and latent provirus), with general DNA replication/recombination terms complementing the signal. ","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006310","count":5},{"id":"GO:0006278","count":4},{"id":"GO:0039651","count":3},{"id":"GO:0075732","count":3}]},{"hash":"1681438345442601800","title":"Unknown","description":"The GO terms span diverse functions (immune signaling via NFAT, ubiquitin-TGF\u03b2/SMAD turnover, actin cytoskeleton regulation, multiple developmental processes, and metabolism) with no single unifying theme; the sparse connections further suggest no coherent cluster function.","confidence":"","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070886","count":7},{"id":"GO:0030579","count":7},{"id":"GO:0030835","count":6},{"id":"GO:0021521","count":6},{"id":"GO:0046013","count":6}]},{"hash":"1369425590557341722","title":"Protein Synthesis and Central Metabolism","description":"The cluster is dominated by translation and core metabolic pathways (glycolysis, TCA cycle, 2-oxoglutarate, ribosome biogenesis), indicating a cohesive theme around protein production and energy metabolism, with some peripheral signals and transport terms.","confidence":"Medium","size":25,"edges":27,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0006099","count":4},{"id":"GO:0033512","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0006096","count":3}]},{"hash":"1968605638327466735","title":"Secretory Pathway Trafficking and Actin Assembly","description":"The dominant GO terms describe vesicle transport in the secretory pathway (ER-to-Golgi and Golgi-to-plasma membrane) and actin filament assembly, pointing to coordination of trafficking with cytoskeletal dynamics. Other terms about protein transport and heterooligomerization fit into protein processing and complex assembly in this pathway, with a few legacy mitochondrial or oogenesis terms being less central. Overall this cluster reflects secretory pathway trafficking together with actin organization.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0090324","count":2},{"id":"GO:0043001","count":2},{"id":"GO:0045859","count":2}]},{"hash":"168176136479872873","title":"Developmental signaling and cytoskeletal regulation","description":"This cluster centers on signals that regulate development (placenta, spermatid, multicellular organism development) and cytoskeletal dynamics (regulation of Rho signaling, sarcomere organization, calcium-mediated signaling). The presence of signaling (Rho, calcium, IL-2) alongside structural organization suggests proteins that coordinate growth, differentiation, and the cytoskeleton. While terms span various tissues (placenta, spermatids, pigmentation, neurons), the unifying theme is developmental signaling coupled with cytoskeletal regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0001893","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0048070","count":2},{"id":"GO:0045214","count":2}]},{"hash":"569451410526056133","title":"Neuronal Signaling and Synaptic Plasticity","description":"The cluster centers on neuronal signaling and synaptic function: GTPase/Rho regulation, calcium-responsive signaling, phosphatidylinositol pathways, brain development, and\u2014critically\u2014synaptic vesicle exocytosis, neurotransmitter release, and long-term potentiation, suggesting roles in synapse formation and plasticity. Some terms (e.g., mating projection growth) are less connected but do not dominate the set.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0043087","count":5},{"id":"GO:0071277","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0048015","count":4}]},{"hash":"1960804721521594197","title":"Keratinocyte development and epithelial wound healing","description":"The cluster shows strong enrichment for skin-related terms: keratinocyte development, epithelial morphogenesis, and wound healing, indicating a keratinocyte/epithelial repair program. Supporting terms on Golgi trafficking and Rho signaling suggest cytoskeletal rearrangements and intracellular transport necessary for keratinocyte migration and proliferation during epidermal repair, with cell division and apoptosis reflecting turnover in healing tissue. High","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0003382","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0044319","count":2}]},{"hash":"104223001303082759","title":"Developmental signaling and differentiation","description":"This cluster centers on developmental processes across multiple tissues, including forebrain development, neural tube closure, keratinocyte differentiation, and skeletal muscle development, with involvement in key signaling pathways (Wnt, Hippo) and transcriptional regulation, plus apoptosis. The overall theme is regulation of development and tissue differentiation rather than a single tissue or pathway.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006915","count":16},{"id":"GO:0090263","count":16},{"id":"GO:0035329","count":16},{"id":"GO:0006351","count":16},{"id":"GO:0060044","count":16}]},{"hash":"239950699537668516","title":"Developmental transcriptional regulation and stress responses","description":"Top GO terms show DNA-templated transcription and vertebrate development (neural tube closure, forebrain development), plus stress responses (ER stress\u2013induced apoptosis, metal response, immune defense). This points to a common theme of developmental transcriptional regulation integrated with stress signaling, though some terms (yeast invasive growth) reduce coherence, hence a medium confidence.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0001403","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0050830","count":6},{"id":"GO:0006349","count":6}]},{"hash":"862292206126440458","title":"Ribosome biogenesis and translation machinery","description":"Top terms indicate strong enrichment for translation and ribosome biogenesis, pointing to a cluster centered on ribosome production and protein synthesis. Additional signals for ER stress response and nuclear transport regulation suggest supporting roles in protein processing and trafficking, but ribosome-related functions are the primary theme.","confidence":"High","size":25,"edges":25,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0033158","count":1}]},{"hash":"866603060957715604","title":"ER-Golgi trafficking and Golgi organization","description":"This cluster is dominated by GO terms related to ER-to-Golgi vesicle transport, COPI coating, Golgi ribbon formation, and ER lumen protein retention, pointing to a cohesive theme of intracellular trafficking and maintenance of the Golgi apparatus. Some developmental terms appear, likely reflecting pleiotropic roles or broader annotations, but the strongest signal is vesicular transport between ER and Golgi and Golgi organization.","confidence":"Medium","size":25,"edges":27,"triangles":2,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0048042","count":1},{"id":"GO:0007311","count":1},{"id":"GO:0001893","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0048205","count":1}]},{"hash":"54744565103953101","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster is dominated by GO terms for ribosome biogenesis, rRNA maturation (5.8S), export of the large ribosomal subunit, and formation of the translation preinitiation complex, pointing to a shared role in assembling ribosomes and initiating translation. There are additional transcription-related terms, but the strongest signal centers on ribosome production and initiation of protein synthesis.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0000466","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2091335731373124481","title":"Vertebrate Development and Signaling","description":"The cluster is dominated by vertebrate developmental processes (gonad development, neural tube closure, retina development, general multicellular development) and signaling pathways (RTK signaling, NFAT regulation, transcription). While there are a few immune and cardiovascular terms, the common theme appears to be developmental biology linked to signaling, rather than a single specific function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":3},{"id":"GO:0007169","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0060041","count":2}]},{"hash":"217172936919069863","title":"Ribosome biogenesis and rRNA maturation","description":"The top terms are strongly about ribosomal RNA maturation (5.8S, SSU, LSU) and ribosomal subunit biogenesis, indicating a coherent cluster of proteins involved in ribosome assembly and RNA processing within the nucleus. A minor signal for spliceosome-related mRNA processing is present, but the dominant theme is ribosome biogenesis.","confidence":"High","size":24,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000466","count":8},{"id":"GO:0000462","count":8},{"id":"GO:0000463","count":8},{"id":"GO:0000398","count":8},{"id":"GO:0042273","count":8}]},{"hash":"829849037238817325","title":"Phospholipid Biosynthesis and Membrane Lipid Metabolism","description":"Based on the GO terms, the cluster shows strong signals for various phospholipid biosynthetic processes (PI, PS, PG, PE) and related lipid metabolism (platelet activating factor biosynthesis, response to phosphatidylethanolamine), with additional linkages to mitochondrial membrane processes (calcium import into the mitochondrion). While translation is also listed, the lipid-related terms predominate, suggesting the core function is lipid biosynthesis and membrane lipid regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0010512","count":1},{"id":"GO:0006659","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0006655","count":1}]},{"hash":"148684994169007909","title":"Bone formation and mineralization","description":"This cluster centers on skeletal development and mineralization, with cementum mineralization and endochondral ossification and a vitamin D response, pointing to osteogenesis. Vesicle docking and SNARE regulation terms suggest secretory processes that could relate to matrix deposition and related cellular activity in bone-forming contexts.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0071529","count":2}]},{"hash":"700936422582817827","title":"ER quality control and autophagy with transcription regulation","description":"This cluster centers on ER-to-Golgi trafficking, ER-associated degradation, autophagy (including nuclear autophagy), and protein modification (sumoylation), with added transcription-related GO terms. The dominant theme is cellular protein turnover and quality control linking to gene expression, justifying an ER quality-control/autophagy label with transcription regulation as a secondary tie.","confidence":"Medium","size":24,"edges":92,"triangles":175,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0007488","count":3},{"id":"GO:0006357","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2153288730318912739","title":"Developmental Signaling and Transcription","description":"These proteins appear to function in transcriptional regulation linked to broad developmental programs, including heart development and axonogenesis, as well as growth signaling via the insulin pathway and cell-cycle-related processes. The presence of DNA-templated transcription, DNA replication, and regulation of phosphorylation supports a theme of transcriptional control coupled to developmental signaling; the ABA term is likely an annotation artifact. Confidence: Medium","confidence":"","size":24,"edges":10,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0000278","count":6},{"id":"GO:0007507","count":6},{"id":"GO:2001275","count":6},{"id":"GO:0008286","count":6}]},{"hash":"2155446719273998693","title":"Wnt Signaling and Developmental Cell Cycle","description":"The cluster is enriched for terms related to the canonical Wnt signaling pathway, centrosome cycle, DNA replication, and embryonic morphogenesis, all pointing to coordinated signaling and cell-cycle events that drive development. While some terms like sperm capacitation or ion transport are less connected, the dominant signals converge on Wnt-regulated development and cell-cycle progression. ","confidence":"Medium","size":24,"edges":29,"triangles":13,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":12},{"id":"GO:0007098","count":11},{"id":"GO:0010571","count":11},{"id":"GO:0048701","count":11},{"id":"GO:0006260","count":11}]},{"hash":"2234383439101696753","title":"Dopaminergic Signaling and Behavioral Response","description":"The top GO terms converge on neural signaling and behavioral outputs, especially dopaminergic synaptic transmission, ERK pathway regulation, and responses to drugs like cocaine, along with related cognitive processes such as visual learning. While some terms touch on sensory stimuli (temperature, pain) or peripheral systems, the central theme appears to be dopamine-mediated neural communication and stimulus-driven behavior.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":16},{"id":"GO:0071502","count":14},{"id":"GO:0002024","count":14},{"id":"GO:0071380","count":12},{"id":"GO:0008542","count":12}]},{"hash":"1768863785242552511","title":"Neuronal vesicle trafficking and cytoskeleton dynamics","description":"The cluster shows coordinated themes of endocytosis, ER-Golgi vesicle transport, tubulin/microtubule assembly, actin cytoskeleton remodeling, and cell polarity, along with neuronal-specific processes like neurotransmitter receptor transport and ROBO signaling, suggesting a focus on vesicle trafficking combined with cytoskeletal remodeling in neurons. A single hepatocyte apoptotic term is present but does not override the dominant neuronal vesicle/cytoskeleton pattern.","confidence":"High","size":24,"edges":132,"triangles":209,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031532","count":7},{"id":"GO:0071963","count":6},{"id":"GO:0006897","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0007021","count":5}]},{"hash":"7240406751007423","title":"DNA replication, repair, and recombination with proviral integration","description":"This cluster is dominated by GO terms related to DNA replication, recombination, telomere maintenance via recombination, and various DNA repair pathways, including translesion synthesis. The presence of DNA integration and proviral latency links suggests genome integration processes in addition to repair, implying a cohesive theme of genome maintenance and damage tolerance in this group.","confidence":"High","size":24,"edges":101,"triangles":196,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006310","count":5},{"id":"GO:0000722","count":4},{"id":"GO:0036297","count":4},{"id":"GO:0015074","count":4}]},{"hash":"465238796167802034","title":"Amino Acid Metabolism and Redox Biosynthesis","description":"The cluster is enriched for amino acid metabolic activities (L-alanine catabolic, L-serine biosynthetic, kynurenine catabolic) and redox-related processes, with other biosynthetic and regulatory terms that support a broader metabolic/developmental theme. The strongest, most coherent signal is amino acid metabolism linked to redox chemistry.","confidence":"Medium","size":24,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042853","count":6},{"id":"GO:0006564","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0017000","count":4}]},{"hash":"1210576087350416877","title":"Translational Initiation and mRNA Stability Regulation","description":"This cluster centers on terms governing translation initiation, preinitiation complex formation, and reinitiation (including IRES-dependent viral translation), along with mRNA stability and stress-responsive regulation. The common thread is control of protein synthesis at the initiation stage and the management of mRNA fate, suggesting these proteins work together in translational regulation and RNA metabolism (with one blastocyst formation term likely incidental). ","confidence":"High","size":24,"edges":7,"triangles":2,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006446","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0075522","count":5},{"id":"GO:0075525","count":5},{"id":"GO:0002188","count":5}]},{"hash":"2276576721177646938","title":"Splicing and mRNA stability regulation","description":"This cluster is dominated by post-transcriptional gene expression control, notably mRNA splicing via the spliceosome (positive/negative regulation), mRNA stability, and regulation of translational initiation, with supportive roles from regulatory ncRNA-mediated silencing and mRNA stabilization. The blastocyst formation term suggests developmental contexts where these RNA processing controls are crucial.","confidence":"High","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":13},{"id":"GO:0045292","count":12},{"id":"GO:1901407","count":11},{"id":"GO:0031047","count":11},{"id":"GO:0006378","count":11}]},{"hash":"819065073267573348","title":"Neural development & morphogen signaling","description":"The proteins are enriched for neural development terms (nervous system development, neurogenesis, CNS development) and signaling pathways linked to morphogenesis (Roundabout signaling, Smoothened signaling). Additional terms for angiogenesis and apoptosis fit developmental processes, supporting a cohesive theme of neural/tissue development driven by morphogenic signaling, despite one outlier term (T cell receptor signaling). ","confidence":"High","size":24,"edges":242,"triangles":1399,"max_degree":23,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035385","count":9},{"id":"GO:0007399","count":9},{"id":"GO:0050852","count":9},{"id":"GO:0022008","count":8},{"id":"GO:0001525","count":8}]},{"hash":"2159600901925752940","title":"Organ Development Signaling Pathways","description":"The cluster\u2019s top GO terms center on organ development (skeletal system, heart, kidney) and include several signaling pathways (Notch, Kit, Fc-epsilon receptor) as well as dexamethasone response, suggesting proteins involved in vertebrate organogenesis and developmental signaling, despite low connectivity among members.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":2},{"id":"GO:0045747","count":2},{"id":"GO:0071549","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0038109","count":2}]},{"hash":"1339131767444592349","title":"Cardiac morphogenesis and endothelial differentiation","description":"The top GO terms point to heart development and vascular differentiation (cardiac right atrium morphogenesis, venous endothelial cell differentiation) with supporting signals in Notch pathway regulation of heart-field cardioblasts and cytoskeletal organization (actin filament bundle assembly). While there are some general processes like hypoxia response and mRNA transport, the core theme centers on heart formation and vascular lineage specification, justifying a name focused on cardiac morphogenesis and endothelial differentiation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071456","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0003213","count":4},{"id":"GO:0060843","count":4}]},{"hash":"416996291513376364","title":"Embryonic morphogenesis and organ development","description":"The cluster is dominated by embryonic morphogenesis terms across multiple organs (eye, inner ear, muscle, lung) and neural development (neural crest, habenula). This suggests a cohesive developmental program governing organogenesis and neural crest-derived tissues, with transcription by RNA polymerase II reflecting active gene regulation during development.","confidence":"High","size":23,"edges":229,"triangles":1335,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0048048","count":13},{"id":"GO:0060441","count":12},{"id":"GO:0043010","count":12},{"id":"GO:0021986","count":11}]},{"hash":"657155228655658040","title":"MAPK/ERK signaling regulation in neural development","description":"The cluster centers on regulation of the ERK/MAPK cascade (negative regulation of ERK1/ERK2 and related signaling) and T cell receptor signaling, but it also includes neural development terms like Bergmann glial cell differentiation and cerebellar cortex formation, plus insulin signaling. This collection suggests a coherent theme: modulation of MAPK/ERK signaling pathways in neural development and glial differentiation, with connections to broader signaling networks. ","confidence":"High","size":23,"edges":250,"triangles":1711,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0050860","count":16},{"id":"GO:0000200","count":16},{"id":"GO:0070373","count":16},{"id":"GO:2001275","count":13},{"id":"GO:0048679","count":13}]},{"hash":"589355267786671621","title":"Cell Growth and Fate Signaling Network","description":"This cluster centers on core nuclear processes (DNA-templated transcription, DNA replication) while also enriching for signaling pathways (Wnt, Hippo) that govern growth, survival, and differentiation, plus related processes like apoptosis, chemotaxis, and cytokine response, suggesting a coordinated network regulating cell fate and proliferation.","confidence":"Medium","size":23,"edges":130,"triangles":284,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0006260","count":13},{"id":"GO:0046827","count":11},{"id":"GO:0006935","count":11},{"id":"GO:0006915","count":11}]},{"hash":"2000329699880527374","title":"Embryonic Neural and Sensory System Development","description":"This cluster is driven by GO terms tied to development, especially neural and sensory system formation\u2014axon guidance for motor and retinal neurons, cerebellum and inner ear development, and visual perception. While there are broader embryonic organogenesis terms (placenta, heart, skeletal muscle), the prevalent pattern centers on neural patterning and sensory organogenesis during embryonic development.","confidence":"High","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0008045","count":6},{"id":"GO:0001890","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0007519","count":5},{"id":"GO:0021549","count":5}]},{"hash":"1147638629170573643","title":"Neurocardiac development and apoptosis signaling","description":"The cluster shows strong signals for neurodevelopment (hippocampus development) and heart development, paired with multiple apoptosis-related terms (neuron apoptotic process, extrinsic apoptotic signaling, and regulation of apoptosis). Additional terms on gene expression regulation, lipid homeostasis, and xenobiotic response suggest broader regulatory and stress-response roles that commonly accompany developmental processes. Overall, a coherent theme of developmental signaling with apoptosis regulation best fits these proteins.","confidence":"Medium","size":23,"edges":69,"triangles":35,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010628","count":4},{"id":"GO:0055091","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0042493","count":3},{"id":"GO:0021766","count":3}]},{"hash":"665582535748517599","title":"Neuronal vesicle trafficking and calcium signaling","description":"The GO terms cluster around Rab GTPase regulation, Rab-mediated signal transduction, intracellular protein transport, cellular calcium responses, and synapse assembly, all pointing to vesicle trafficking and calcium-dependent signaling in neurons. Brain development supports a neural context, while PI signaling and apoptotic regulation fit broader signaling roles in neurons. Some terms (e.g., ABA signaling) may be annotation noise rather than brain-specific functions, but the dominant theme is neuronal vesicle trafficking and calcium signaling.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":3},{"id":"GO:0032483","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0036324","count":2}]},{"hash":"1014246047542136294","title":"Vesicle trafficking and exocytosis regulation","description":"Top terms cluster around vesicle-related processes (acrosome reaction, synaptic vesicle priming, intracellular protein transport) and regulation of signaling pathways (Rho, Ras), suggesting a shared role in controlling vesicle fusion and trafficking, with added cytoskeletal signaling coordination. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007340","count":3},{"id":"GO:0060313","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0043314","count":3},{"id":"GO:0046580","count":3}]},{"hash":"1221076903989301919","title":"Chromatin silencing and epigenetic regulation","description":"This cluster is enriched for chromatin localization, heterochromatin formation, histone modification (methylation and phosphorylation), and transcriptional regulation (including dosage compensation and rRNA transcription control), indicating a coherent chromatin-based epigenetic regulatory module.","confidence":"High","size":23,"edges":212,"triangles":1059,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1904815","count":15},{"id":"GO:0070481","count":15},{"id":"GO:0071169","count":15},{"id":"GO:0033128","count":15},{"id":"GO:0045618","count":15}]},{"hash":"1784611109848527993","title":"Rho GTPase\u2013driven angiogenic migration signaling","description":"The cluster is dominated by GO terms for small GTPase signaling, Rho regulation, lamellipodium assembly, VEGF response, and regulation of cell migration in sprouting angiogenesis, pointing to a module that coordinates actin cytoskeleton remodeling and directed migration in angiogenic vessels. Insulin/IGF receptor signaling and interleukin-7 response appear as broader signaling connections but do not define the core function. Overall, the proteins seem to function together in signaling that drives angiogenic cell movement and cytoskeletal dynamics.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0098761","count":2},{"id":"GO:0045907","count":2},{"id":"GO:0090051","count":2},{"id":"GO:0030032","count":2}]},{"hash":"1080632671291210354","title":"Developmental growth and translation","description":"The cluster\u2019s top GO terms combine protein synthesis (translation) with several development- and growth-related processes (somite development, compound eye morphogenesis, multicellular organism growth, collagen catabolic process). This suggests a loose grouping around general growth/development programs that also involve translation, rather than a single precise molecular function. Some terms are labeled obsolete, indicating annotation noise. Overall it points to a broad \u201cdevelopment plus translation\u201d theme, not a specific pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0061053","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0035736","count":1},{"id":"GO:0035264","count":1}]},{"hash":"907912653206574592","title":"RNA Processing and Transcription Machinery","description":"The dominance of transcription, splicing, and RNA processing terms (DNA-templated transcription, spliceosome-mediated mRNA processing, ribosomal subunit export, nucleosome disassembly) points to a coordinated gene-expression machinery cluster; a few developmental and cilium-related terms appear as less representative outliers. Therefore, this label reflects the main theme with moderate confidence.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":2},{"id":"GO:0006616","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0006351","count":2}]},{"hash":"618191641672571834","title":"Embryonic development and organogenesis","description":"The proteins cluster around broad developmental processes across multiple tissues: cartilage/skeletal morphogenesis, placenta and pancreatic cell development, left-right patterning, and EMT-related heart development. The GO terms point to embryogenesis, tissue differentiation, and organ formation, with Wnt signaling involvement, suggesting a label that captures general developmental orchestration rather than a single tissue. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060536","count":4},{"id":"GO:0060806","count":4},{"id":"GO:0035270","count":4},{"id":"GO:0060972","count":4},{"id":"GO:0060707","count":4}]},{"hash":"1101097706740191128","title":"Metal and Oxidative Stress Response","description":"Top GO terms point to cellular responses to hydrogen peroxide and to various metal ions (manganese, zinc, lead), with an additional mechanical stress term (fluid shear). While a few unrelated terms are present, the dominant pattern is responsiveness to environmental/chemical stressors, especially oxidative and metal-associated. This makes \"Metal and Oxidative Stress Response\" a concise, representative label for the cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0010042","count":2},{"id":"GO:0071498","count":2},{"id":"GO:0010043","count":2}]},{"hash":"1976931281321104139","title":"ER-Golgi Transport and Reticulophagy","description":"Top GO terms emphasize ER-to-Golgi vesicle transport, reticulophagy, ER stress\u2013related apoptotic signaling, and protein complex localization, with some transcription-related terms. This suggests a cohesive cluster focused on ER homeostasis, quality control, and ER-associated autophagy, rather than general signaling alone. High","confidence":"","size":22,"edges":168,"triangles":764,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":13},{"id":"GO:0050852","count":9},{"id":"GO:0090263","count":9},{"id":"GO:0032258","count":8},{"id":"GO:0006915","count":8}]},{"hash":"2194106308001673133","title":"Developmental Gene Regulation and Differentiation","description":"Based on the top GO terms, the proteins appear linked to developmental processes (forebrain development, neural tube closure, prostate gland differentiation, fertilization) and to gene expression control (DNA-templated transcription, mRNA transport) with supporting signaling regulation (positive regulation of GTPase activity, protein autophosphorylation) and protein interactions (homooligomerization). This suggests a cluster of factors involved in orchestrating development through transcriptional and post-translational regulation rather than a single specific pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0060528","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0007338","count":4},{"id":"GO:0071456","count":4}]},{"hash":"643858828398844614","title":"Translation Initiation and mRNA Export","description":"The cluster is dominated by translation-related GO terms (translation, formation of translation preinitiation complex, regulation of translational initiation, IRES-dependent viral translation initiation, and viral termination-reinitiation) and mRNA export from the nucleus, pointing to a cohesive group of proteins involved in protein synthesis and RNA processing. A few cell-cycle terms appear but the strongest signal centers on translation initiation and mRNA export, suggesting these proteins work together to coordinate gene expression at the level of translation.","confidence":"Medium","size":22,"edges":30,"triangles":16,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006406","count":5},{"id":"GO:0006412","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0051260","count":4}]},{"hash":"284901838595277982","title":"Neural development and organ morphogenesis signaling","description":"The GO terms are dominated by neural development (synaptic plasticity, axonogenesis, axon fasciculation) and organogenesis (nephric duct morphogenesis, urogenital system development, salivary gland boundary specification) with associated signaling pathways (BMP, prolactin), and pericyte differentiation. The combination suggests a cluster of proteins involved in developmental signaling coordinating neural patterning and organ morphogenesis.","confidence":"Medium","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0048170","count":20},{"id":"GO:2000525","count":20},{"id":"GO:0072178","count":20},{"id":"GO:0007432","count":20},{"id":"GO:1904238","count":20}]},{"hash":"680532004075775566","title":"Mitotic Chromosome Cohesion and Spindle Machinery","description":"The dominant GO terms cluster around mitosis: sister chromatid cohesion and biorientation, spindle orientation checkpoint signaling, and septin-mediated cytokinetic organization, indicating proteins involved in chromosome segregation and spindle control. A few terms are more general, but the overall signature is mitotic machinery.","confidence":"High","size":22,"edges":21,"triangles":0,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":4},{"id":"GO:0031578","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0031134","count":2},{"id":"GO:0006470","count":2}]},{"hash":"2049974636806347862","title":"Proteoglycan Biosynthesis and ECM Maintenance","description":"The cluster is dominated by proteoglycan biosynthesis pathways (heparan sulfate, chondroitin sulfate, heparin) and UDP-D-xylose metabolism, pointing to glycosaminoglycan production and extracellular matrix components. Additional terms like lens transparency maintenance and kidney morphogenesis reflect ECM integrity in tissues, while leukocyte tethering/rolling involves proteoglycan-rich endothelial surfaces.","confidence":"High","size":22,"edges":12,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":6},{"id":"GO:0015012","count":5},{"id":"GO:0050650","count":5},{"id":"GO:0030210","count":4},{"id":"GO:0042403","count":3}]},{"hash":"323642303758194934","title":"GTPase signaling and neural development","description":"This cluster is enriched for positive regulation of GTPase activity and small GTPase-mediated signaling, including forebrain development, suggesting a module centered on GTPase-driven signaling in neural development. Additional terms such as DNA-templated transcription, ribosomal RNA maturation, IGF receptor signaling, TNF production, and multicellular development indicate broader roles in growth, gene expression, and immune responsiveness, but the main theme appears to be GTPase signaling in neural development.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0032760","count":3}]},{"hash":"1708272538189221528","title":"Endosomal trafficking and MVB formation","description":"The top GO terms are dominated by endosome-to-lysosome transport, early-to-late endosome maturation, and intralumenal vesicle formation, which together point to vesicle trafficking within the endosomal/MVB pathway. A couple of terms appear incidental (olfactory bulb development, symbiont entry), but the core signal supports endosomal trafficking and multivesicular body formation. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0021772","count":2},{"id":"GO:0046718","count":2}]},{"hash":"519527005427142288","title":"Axon guidance and synaptic remodeling","description":"This cluster is enriched for neural development and synaptic function terms, notably axon guidance, regulation of dendritic spine morphogenesis, and regulation of synaptic vesicle exocytosis (Roundabout signaling). While a few non-neural terms appear, the prominent theme is neuron connectivity and synaptic remodeling. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007411","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0002551","count":2},{"id":"GO:0061001","count":2},{"id":"GO:0031384","count":2}]},{"hash":"834621996104835467","title":"Endomembrane trafficking and vesicle transport","description":"The cluster is enriched for GO terms describing transport between the endoplasmic reticulum and Golgi, retrograde Golgi-ER transport, endocytosis, multivesicular body assembly, and protein targeting to the vacuole. These reflect core processes of the endomembrane system and vesicle trafficking. A few mitosis-related terms appear, which may indicate shared cellular machinery, but the primary signal is vesicle trafficking and organelle targeting.","confidence":"High","size":22,"edges":25,"triangles":9,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006890","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1548473174167498319","title":"Cytoskeletal dynamics and cell division","description":"These proteins are enriched for actin cytoskeleton remodeling (microspike assembly, Rho signaling), cell migration and wound healing, and cell division processes (mitotic spindle assembly, centrosome localization). While a few terms touch on transcription or viral/symbiont interactions, the dominant theme centers on cytoskeletal regulation driving movement and mitosis.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042060","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035025","count":2},{"id":"GO:0030035","count":2},{"id":"GO:0090307","count":2}]},{"hash":"2147900853460726271","title":"Neural and craniofacial development","description":"The top GO terms point to development of neural and craniofacial structures (brain/midbrain, inner ear, palate, retinal ganglion cell axon guidance, trigeminal ganglion), plus broader behavioral outcomes and a transcriptional regulatory role. This suggests a coherent theme of neural and sensory organ development with associated regulatory processes, rather than a single isolated function. ","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0048839","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0007626","count":6}]},{"hash":"1755598675309000211","title":"Neuronal Synaptic Plasticity and Signaling","description":"This cluster is dominated by terms tied to neuronal communication and plasticity, including excitatory postsynaptic potential, long-term synaptic potentiation, and visual learning, plus a signalable response to cocaine. While there are peripheral terms related to metabolism and angiogenesis, the core theme centers on synaptic signaling and plasticity in neural contexts.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060079","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0045766","count":3},{"id":"GO:0010800","count":3}]},{"hash":"913227419682621002","title":"Skeletal muscle development and cytoskeletal remodeling","description":"The cluster is enriched for GO terms related to skeletal muscle fiber development and cytoskeletal processes (filopodium assembly, Rho signaling, actomyosin contractile ring), plus NMJ-related regulation, which together point to muscle differentiation and cytoskeletal remodeling. Some terms (DNA repair, unfolded protein response) are less connected, but the dominant signals support the muscle/cytoskeleton theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0006303","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0035023","count":2}]},{"hash":"344527724488812010","title":"Neural development and synaptic organization","description":"The top GO terms are dominated by neural-related processes: brain development, inner ear development, glutamatergic synaptic transmission, positive regulation of synapse assembly, and locomotory behavior, suggesting a cluster of proteins involved in neural development and synaptic function. Additional terms on cell adhesion and apical localization support broader tissue organization contexts but reinforce the emphasis on neural connectivity and development.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903142","count":9},{"id":"GO:0035249","count":8},{"id":"GO:0048839","count":8},{"id":"GO:0007420","count":8},{"id":"GO:0007626","count":8}]},{"hash":"295157950626339560","title":"Cell Cycle and Translation Initiation","description":"The cluster shows enrichment for core cell cycle processes (cell cycle, regulation of cell cycle, cell division, mitotic spindle assembly, spindle organization) alongside translation initiation components (formation of cytoplasmic translation initiation complex, eIF2 complex assembly, positive regulation of translational initiation). This suggests a module where cell cycle progression, particularly mitosis, is coordinated with the initiation of translation, potentially via kinase signaling that activates initiation machinery during cell division. ","confidence":"Medium","size":22,"edges":21,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":1},{"id":"GO:0007050","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0001732","count":1},{"id":"GO:1905143","count":1}]},{"hash":"1535868152415297712","title":"Cell differentiation, migration, and apoptosis in tissues","description":"These terms cluster around development and cell fate across tissues: epithelial polarity establishment, cerebellar granule cell differentiation, spinal cord development, and cell migration point to morphogenetic processes, while hepatocyte and myeloid apoptotic processes and calcium signaling indicate regulated cell survival/death during tissue remodeling. The diverse tissue contexts suggest a broad theme of tissue development and differentiation with apoptosis, rather than a single, cohesive pathway. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":4},{"id":"GO:0021707","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0097284","count":3}]},{"hash":"1859853691359686326","title":"RNA processing and transcription regulation","description":"These terms cluster around mRNA processing, miRNA processing, and transcription control (DNA-templated transcription, negative regulation of transcription by RNA polymerase II), indicating proteins involved in RNA maturation and regulation of transcription. While other terms such as embryo sac development, sensory perception of sound, and multi-ciliated epithelial cell differentiation appear, they are less central and may reflect broader or cross-species annotations; the strongest common thread is RNA processing and transcription regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0009553","count":2},{"id":"GO:0007605","count":2}]},{"hash":"622742700126287678","title":"Mitotic cell cycle and chromosome segregation","description":"The top GO terms are centered on mitotic processes, including mitotic cell cycle, cell division, mitotic sister chromatid segregation, and APC/C- or ubiquitin-mediated protein turnover (K11-linked ubiquitination). Additional terms on replication processing during mitosis and actin cytoskeleton changes during mitosis support a coherent mitotic/ cell division theme, with some differentiation terms appearing secondary. Overall, the cluster reflects mitosis-driven regulation and proteolysis.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0030042","count":3},{"id":"GO:0070979","count":3},{"id":"GO:1903461","count":3}]},{"hash":"343443448745408575","title":"Regulated translation initiation and mRNA stability","description":"The cluster is dominated by GO terms centered on translation initiation and reinitiation (IRES-dependent initiation, formation of the preinitiation complex, translation reinitiation) and on mRNA stability/regulation in response to stress, indicating a cohesive module of translational control and RNA fate. A couple of outlier terms (blastocyst formation, regulation of alternative mRNA splicing) are present but not defining the cluster.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":4},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0002188","count":3}]},{"hash":"685742911114964386","title":"Epithelial Polarity and Cytoskeletal Regulation","description":"Top GO terms converge on epithelial polarization and cytoskeletal regulation: tight junction and apical/basal polarity establishment, Rho-mediated cytoskeletal remodeling, centrosome localization, and podosome assembly, with developmental terms like lens fiber differentiation and endoderm development suggesting tissue organization roles.","confidence":"High","size":21,"edges":25,"triangles":14,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0070830","count":4},{"id":"GO:0051660","count":4},{"id":"GO:0051301","count":3}]},{"hash":"2005118087320221466","title":"mRNA processing and translation control","description":"These GO terms indicate post-transcriptional control of gene expression, spanning splicing (spliceosome activity and splice-site recognition), mRNA export, stability, and initiation/reinitiation of translation, including ncRNA-mediated silencing. The shared theme is coordinated regulation of mRNA maturation and ribosome recruitment, often under stress. Therefore the label mRNA processing and translation control captures the main function of the cluster.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0001731","count":8},{"id":"GO:0006376","count":8},{"id":"GO:0002188","count":8}]},{"hash":"2087434822714169032","title":"Membrane transport and GTPase signaling in development","description":"The cluster centers on ion transmembrane transport (potassium, sodium, phosphate) and membrane potential regulation, coupled with small GTPase-mediated signaling and its positive regulation. Developmental and tissue-context terms like heart development, epithelial polarity establishment, and cell division suggest these signaling and transport processes are linked to tissue morphogenesis and differentiation, with an additional neural context indicated by long-term synaptic potentiation. This combination supports a cohesive label around membrane dynamics and GTPase signaling in developmental settings.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1686162591056814478","title":"Endocytic trafficking and developmental regulation","description":"This cluster's top GO terms cluster around brain and multicellular organism development, as well as vesicle trafficking steps such as endosome to lysosome transport and protein transport. The presence of negative regulation of EGFR signaling and regulation of ubiquitin-dependent endocytosis suggests control of signaling via endocytosis, which ties into developmental growth processes and exosome assembly. Taken together, these proteins likely function in coordinating development through vesicular trafficking and signaling modulation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0008333","count":1},{"id":"GO:0042059","count":1},{"id":"GO:0045571","count":1}]},{"hash":"1390198698685998673","title":"Mitotic Cell Cycle and Vesicle Trafficking","description":"The cluster centers on cell proliferation and growth, with strong mitosis-related terms (mitotic cell cycle, mitotic spindle assembly, cell division) and growth-related terms (spermatid development, multicellular organism growth). It is complemented by ribosome biogenesis and secretory pathway activity (COPII budding, Golgi-to-ER transport), suggesting a cohesive theme of proliferative cells coordinating growth with secretory trafficking.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0007286","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0090114","count":4},{"id":"GO:0090307","count":4}]},{"hash":"1944596563163910735","title":"Stress-Responsive Lipid Metabolism","description":"The cluster is enriched for stress response and lipid-related processes, including triglyceride catabolism and poly-hydroxybutyrate biosynthesis, plus lipid signaling (phospholipid dephosphorylation) and signals related to host-symbiont dormancy and endocannabinoid pathways, suggesting proteins that mediate metabolic adaptation under stress and host interaction.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":5},{"id":"GO:0085014","count":5},{"id":"GO:0006950","count":5},{"id":"GO:0046272","count":5},{"id":"GO:0046839","count":5}]},{"hash":"746742276275272963","title":"Developmental transcription and immune differentiation","description":"The cluster centers on transcriptional regulation (RNA polymerase II) and includes differentiation-related terms such as macrophage and plasma cell differentiation, plus developmental processes like segmental identity specification and placenta development, suggesting a broad theme of transcription-driven development and immune cell differentiation, with some vascular remodeling signals. This points to a cohesive but multi-context developmental-immunological role rather than a single pathway.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0035470","count":7},{"id":"GO:2000016","count":6},{"id":"GO:0007381","count":6},{"id":"GO:0035356","count":6}]},{"hash":"1344936012034614705","title":"RNA processing and translation initiation","description":"The top GO terms cluster around cytoplasmic translation, regulation of translational initiation, and mRNA processing/splicing, including preinitiation complex formation, indicating a group focused on post-transcriptional control of gene expression. A developmental term and a dephosphorylation term appear but are less representative. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1509978854521895742","title":"Developmental Cytoskeletal Remodeling","description":"The terms point to cytoskeletal dynamics driven by Rho signaling and actin/microtubule remodeling, coupled with developmentally oriented processes (neural, lens, skeletal), including vesicle transport, suggesting a cohesive theme of cytoskeletal changes guiding development.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0030042","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0001501","count":2}]},{"hash":"2189355331101354840","title":"Neuronal migration and axon guidance","description":"The top GO terms are concentrated on neuron migration and retinal ganglion cell axon guidance, indicating a cluster enriched for neuronal development and axon pathfinding. The presence of embryonic cranial skeleton morphogenesis hints at broader developmental programs during early embryogenesis. Overall, the core signal centers on neuronal development with some ancillary embryonic development terms; the lack of strong connectivity edges suggests these proteins may span related but not tightly connected processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001764","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0048701","count":2},{"id":"GO:1905696","count":2},{"id":"GO:1905618","count":2}]},{"hash":"727490789339268963","title":"Auditory system development and mechanosensation","description":"The cluster is dominated by GO terms for inner ear receptor cell development and detection of mechanical stimuli involved in hearing, indicating a cohesive role in auditory system development and mechanosensory function. Additional terms on left-right patterning and heart looping point to broader developmental patterning, but the clearest shared function is ear mechanosensory maturation and hearing. ","confidence":"High","size":21,"edges":28,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0002053","count":2},{"id":"GO:0060972","count":2},{"id":"GO:0060013","count":2},{"id":"GO:0010719","count":2},{"id":"GO:0050910","count":2}]},{"hash":"803956643107040803","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":31,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000389","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0048024","count":1},{"id":"GO:0010087","count":1}]},{"hash":"2167255270958140022","title":"Cytoskeleton Assembly & Proteostasis","description":"This cluster centers on cytoskeletal organization (actin and microtubule/tubulin assembly) with related processes in proteostasis (folding and quality control) and chaperone activity, suggesting coordinated cytoskeleton dynamics with protein homeostasis.","confidence":"Medium","size":21,"edges":24,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":1},{"id":"GO:0034314","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0000147","count":1},{"id":"GO:0032968","count":1}]},{"hash":"1697782808203152404","title":"Actin-driven Protrusions and Immune Cell Chemotaxis","description":"This cluster is dominated by GO terms for actin-based protrusions (lamellipodium, filopodium, microspike assembly) and chemotaxis in immune cells (neutrophils, dendritic cells), pointing to a shared function in cytoskeletal remodeling and directed cell migration. A single outlier term on iron-sulfur cluster assembly does not alter this overall theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0030593","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0002408","count":2}]},{"hash":"312438142853397656","title":"Cross-tissue Development and Differentiation","description":"The top GO terms cluster around developmental processes across various tissues (skeletal muscle development, megakaryocyte/platelet formation, somitogenesis) and related cytoskeletal and signaling activities, suggesting a broad theme of tissue differentiation rather than a single pathway. Some terms (like pollen development and ethylene response) are plant-specific but still reflect developmental regulation, supporting a high-level connection to developmental processes rather than a specific function. Confidence is Medium.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":3},{"id":"GO:0009555","count":2},{"id":"GO:0090043","count":2},{"id":"GO:0035855","count":2},{"id":"GO:0001756","count":2}]},{"hash":"1101912564961423402","title":"Unknown","description":"The top GO terms are a mix of neuronal signaling (excitatory postsynaptic potential, responses to ethanol and cocaine) and various developmental and cellular processes (optic nerve morphogenesis, placental development, ER-Golgi transport, mRNA processing, sphingolipid biosynthesis). There is no coherent, single function tying all proteins, so a meaningful label cannot be assigned.","confidence":"","size":20,"edges":54,"triangles":55,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0071361","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0021631","count":2},{"id":"GO:0001893","count":2}]},{"hash":"1313171145745535815","title":"Mitochondrial Respiratory Chain and Protein Import","description":"The cluster is dominated by GO terms tied to mitochondrial energy production and handling: proton motive force-driven ATP synthesis, NADH to ubiquinone electron transport, mitochondrial respiratory chain complex I assembly, and protein import into the mitochondrial matrix. These together point to a coherent theme of mitochondrial function and energy metabolism, with translation being a broader supportive signal and neural development terms likely reflecting tissue-specific expression. Overall, the data support a mitochondria-centered interpretation of the cluster.","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":4},{"id":"GO:0021762","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0099132","count":2},{"id":"GO:0030150","count":2}]},{"hash":"265501559412387205","title":"Unknown","description":"The terms are highly diverse, spanning transcription regulation (RNA Pol II/III), GTPase activation, and development processes (cerebral cortex, photomorphogenesis), with several obsolete terms. There is no clear, cohesive functional theme tying the 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:0090630","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0043457","count":1},{"id":"GO:0045898","count":1},{"id":"GO:1900446","count":1}]},{"hash":"2113950673506397772","title":"Immune Cell Migration and Actin Remodeling","description":"The top GO terms show strong enrichment for neutrophil chemotaxis, lamellipodium assembly, Rho-mediated signaling, and mast cell degranulation, all of which involve actin cytoskeleton rearrangements enabling directed movement and immune responses. While a couple terms (neuron projection development, symbiont entry) are less directly related, the dominant signal points to actin-driven migration and immune cell activation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0043303","count":2},{"id":"GO:0031175","count":2},{"id":"GO:0046718","count":2}]},{"hash":"2036132972792016682","title":"ER-Golgi trafficking and protein quality control","description":"Top GO terms point to intracellular transport and ER-to-Golgi trafficking as the core function, with ERAD and autophagy highlighting protein quality control within the endomembrane system. The combination suggests a cluster centered on handling and turnover of proteins in the secretory pathway, with auxiliary signals from broader cellular processes. Confidence: Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006915","count":2}]},{"hash":"903109843191473951","title":"Neuronal axon guidance and vesicle trafficking","description":"The Top Terms cluster around neuronal development and intracellular trafficking: dorsal/ventral axon guidance, regulation of motor neuron axon guidance, and regulation of synaptic vesicle endocytosis, along with intralumenal vesicle formation and Golgi retention. These collectively suggest a theme of growth cone navigation and vesicle transport in neurons. Some outliers (gravitropism, ubiquinone biosynthesis, transcription) may reflect broader cellular processes or annotation noise, but the dominant signal points to neural trafficking and guidance.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009958","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006744","count":1}]},{"hash":"1468617983645094228","title":"Neural development and synaptic assembly","description":"This cluster is dominated by terms related to nervous system development and synaptic function: brain development, nervous system development, synapse assembly, and glutamatergic transmission, suggesting roles in neural differentiation and synaptic connectivity, with supporting terms reflecting general cellular morphogenesis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":3},{"id":"GO:0060444","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0007416","count":3},{"id":"GO:0007399","count":3}]},{"hash":"2098074297003784477","title":"Developmental and Neural Signaling","description":"The cluster\u2019s terms center on signaling pathways (Rho, Smoothened/Hedgehog, PI signaling) that regulate development and neural function (brain development, inhibitory postsynaptic potential), with additional signals related to angiogenesis and adaptive immunity. This suggests a core theme of signaling in developmental and neural contexts, even though some terms reflect broader or peripheral roles (e.g., immune response, symbiont entry). ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0007224","count":3},{"id":"GO:0002250","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0046718","count":2}]},{"hash":"1167209311137808367","title":"Growth Factor Signaling and Angiogenesis","description":"The terms point to a set of receptor- and growth-factor\u2013mediated signaling pathways (integrin, ephrin, PDGFR, insulin receptor, tyrosine autophosphorylation) and an angiogenesis context, suggesting a cohesive theme around signaling that drives endothelial behavior and vascular development, with related processes like nitric oxide response and caveolin-mediated endocytosis supporting this network.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071732","count":2},{"id":"GO:0038083","count":2},{"id":"GO:0007229","count":2},{"id":"GO:0048538","count":2},{"id":"GO:0001525","count":2}]},{"hash":"563255651519105049","title":"Cerebellar development and neural signaling","description":"This cluster is dominated by terms related to cerebellar development and neural function: Bergmann glial cell differentiation, cerebellar cortex formation, axon regeneration regulation, and insulin receptor signaling, all pointing to neural development and signaling in the cerebellum. Additional terms on transcription and general cellular regulation (proteasome activity, nuclear export) are broad but commonly linked to developing neural cells. While an immune signaling term (T cell receptor signaling) appears, the neural development theme is the strongest signal overall, making this a coherent label. ","confidence":"Medium","size":20,"edges":101,"triangles":210,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001275","count":13},{"id":"GO:0048679","count":13},{"id":"GO:0008285","count":13},{"id":"GO:0050852","count":13},{"id":"GO:0008286","count":13}]},{"hash":"927160224061851024","title":"Neural development and synapse formation","description":"This cluster is dominated by GO terms related to neural development and synapse organization, such as neuron migration, axonal fasciculation, and positive regulation of synapse assembly, with supporting terms for cell adhesion and multicellular development. While there are some unrelated terms (angiogenesis, immune regulation, symbiont entry), the prevailing pattern points to neural development and synaptic assembly as the core function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001764","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0007413","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0001525","count":2}]},{"hash":"1923883611245750719","title":"Transcription and ribosome biogenesis","description":"This cluster is dominated by GO terms related to chromatin remodeling and nucleosome assembly, transcription initiation, and ribosome biogenesis/translation initiation, suggesting a shared role in gene expression machinery. A couple of terms (cornea development, IL-1\u03b2 production) are less central and may reflect pleiotropy or context-specific roles.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050718","count":2},{"id":"GO:0061303","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0000462","count":1}]},{"hash":"979459611930848518","title":"Unknown","description":"The Top Terms cover a broad spectrum: heart development, corticospinal neuron axon guidance, salivary gland boundary specification, mast cell degranulation, regulation of developmental pigmentation, neuron migration, defense response to bacterium, lymphoid progenitor cell differentiation, positive regulation of collateral sprouting, and general axon guidance. This mix spans cardiovascular, neural development, epithelial patterning, immune responses, and pigmentation, with no single cohesive function or tissue type tying them together. The lack of shared function and the absence of edge-based connectivity further support the lack of a tight module. Therefore, I label this cluster Unknown with None confidence. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0021966","count":2},{"id":"GO:0007432","count":2},{"id":"GO:0043303","count":2},{"id":"GO:0048070","count":2}]},{"hash":"2264093549073822035","title":"Glycan biosynthesis and glycoprotein ECM components","description":"This cluster is dominated by GO terms for glycosylation and glycan biosynthesis (poly-N-acetyllactosamine biosynthetic process, arabinogalactan protein metabolism, Lewis a epitope biosynthesis, O-linked glycosylation via hydroxyproline, mucilage biosynthesis). The presence of terms related to follicle epithelium adhesion and polarity maintenance suggests roles in cell surface glycoproteins and extracellular matrix interactions that guide tissue organization; other terms touching development in seeds, roots, and insect tissues reflect broad roles for glycans in morphogenesis. Taken together, the proteins are best characterized as a glycan/glycoprotein biosynthesis and ECM-related cluster involved in cell adhesion and polarity. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030311","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0001744","count":2},{"id":"GO:0075015","count":2},{"id":"GO:0042248","count":2}]},{"hash":"1176451228843324978","title":"Yeast pseudohyphal/invasive growth under glucose limitation","description":"Top GO terms include pseudohyphal growth and invasive growth in response to glucose limitation, suggesting a morphological switch in yeast under nutrient stress. Additional terms point to cell cycle, translation, and secretory pathway remodeling, indicating a coordinated growth and secretion program during stress. Together, these terms support labeling the cluster as a yeast nutrient-stress growth program focused on filamentous/invasive growth and associated secretory processes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0007124","count":1},{"id":"GO:0061060","count":1},{"id":"GO:2000010","count":1}]},{"hash":"1351152634482360948","title":"Nucleocytoplasmic RNA export and protein transport","description":"The top GO terms cluster around nuclear import/export (RNA import into nucleus, pre-miRNA export, tRNA re-export, regulation of protein export from nucleus) and intracellular transport, with additional hints of RNA processing. This pattern points to proteins involved in nucleocytoplasmic trafficking and RNA handling rather than a single cytosolic pathway, supporting a label focused on nuclear transport and RNA processing.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042176","count":2},{"id":"GO:0006929","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0042493","count":1},{"id":"GO:0009944","count":1}]},{"hash":"663566344849506539","title":"Skin development and actin cytoskeleton signaling","description":"This cluster prominently features GO terms tied to skin development and multicellular development, alongside strong signals for signaling kinase activity (positive regulation of GTPase, serine/threonine and tyrosine phosphorylation) and actin cytoskeleton remodeling (Arp2/3-mediated nucleation). The overlap of developmental processes with cytoskeletal remodeling and cell-cycle related terms suggests a module involved in epidermal differentiation and dynamic cell movement. While hypoxia response and mRNA transport are present, the clearest cohesive theme is regulated signaling driving skin development and actin remodeling.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0031954","count":8},{"id":"GO:0071902","count":8},{"id":"GO:0071456","count":7},{"id":"GO:0051028","count":7}]},{"hash":"1412583922548390326","title":"Glycan biosynthesis and glycoprotein modification in development","description":"The top GO terms cluster around glycosylation processes (poly-N-acetyllactosamine biosynthesis, arabinogalactan protein metabolism, hydroxyproline O-linked glycosylation) and cell-surface/polarity roles (follicle epithelium polarity maintenance, follicle cell adhesion, root hair cell development), with several development-related terms across insect and plant contexts. This suggests a unifying theme: glycan synthesis and glycoprotein modification shaping cell surfaces and tissue development. Some broader terms (neuronal action potential, relaxation of cardiac muscle) appear as general contexts rather than core drivers. ","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055119","count":3},{"id":"GO:0019228","count":2},{"id":"GO:0030311","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0001744","count":2}]},{"hash":"1745501208764240139","title":"Embryonic neural development and morphogenesis","description":"The top GO terms cluster around embryonic development and tissue morphogenesis, especially neural development (forebrain morphogenesis, motor neuron axon fasciculation) and other morphogenetic processes (placenta, cranial skeleton, smooth muscle). The inclusion of negative regulation of Rac/Rho signaling points to cytoskeletal control during morphogenesis, while transcription by RNA Pol II reflects broad developmental gene regulation.","confidence":"Medium","size":19,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0045617","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0048853","count":2}]},{"hash":"331792712647528637","title":"Potassium transport and skeletal muscle function","description":"The top terms point to potassium ion transport across the plasma membrane and muscle-related processes (relaxation, fast-twitch contraction) and T-tubule organization, suggesting a module that links potassium homeostasis to skeletal muscle excitation-contraction coupling. A few terms (e.g., otolith mineralization) are less directly related.","confidence":"High","size":19,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0090076","count":1},{"id":"GO:0031448","count":1}]},{"hash":"1506555655760683964","title":"Neural Development and Innate Immunity","description":"The top GO terms show a strong signal for neural development (axonogenesis, corpus callosum development, retina development, regulation of synapse assembly), suggesting a core theme around neural formation and connectivity. A secondary, but notable, set of terms pertains to innate immunity (innate immune response, defense against Gram-positive bacteria), implying immune signaling aspects that can accompany neural development or glial involvement. Some terms are more peripheral (viral mRNA export, fungal cell wall regulation), likely reflecting broader cellular processes or annotations in this cluster. Overall, the cluster seems to center on neural development with associated innate immune functions.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":2},{"id":"GO:0022038","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0070317","count":2}]},{"hash":"32274475607855924","title":"Neural and vascular development","description":"Terms point to vertebrate embryonic development, especially neural tube patterning (floor plate development, somitogenesis) and neural differentiation (amacrine cells), plus vascular development and wound healing, and modulation of excitatory signaling (AMPA receptor activity, excitatory postsynaptic potential). Taken together, these terms suggest a cluster centered on development and maturation of neural and vascular tissues, with associated synaptic regulation.","confidence":"Medium","size":19,"edges":168,"triangles":920,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":11},{"id":"GO:0001756","count":7},{"id":"GO:0060426","count":7},{"id":"GO:0033504","count":7},{"id":"GO:0035881","count":7}]},{"hash":"303207649653141705","title":"Cardiac muscle contraction and sarcomere organization","description":"These proteins are enriched for muscle contraction and sarcomere organization, plus heart development and channel clustering, pointing to a cardiac muscle structure/function module. Cytoskeletal remodeling and membrane trafficking terms (Rho signaling, Golgi to plasma membrane transport) support the idea of coordinated muscle fiber organization and signaling necessary for cardiac tissue. Overall, the cluster coherently represents cardiac muscle architecture and function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0043001","count":2},{"id":"GO:0006936","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0045163","count":2}]},{"hash":"2020670088837723702","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"The terms co-occur around actin cytoskeleton organization (lamellipodium/podosome assembly), cell migration, and polarity establishment, with positive regulation of GTPase activity guiding actin dynamics. This points to a shared function in actin-driven remodeling and movement rather than a single pathway, justifying a label focused on actin-mediated migration and polarity.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0098761","count":2}]},{"hash":"2144104344164126854","title":"Embryonic neural and organ development","description":"Top terms indicate neural development and axon guidance (retinal ganglion and motor neuron axon guidance; forebrain/retina/cerebellum development) alongside development of non-neural organs (heart, placenta, skeletal muscle). This points to a shared theme of embryonic development across multiple tissues, with neural patterning as a central aspect. ","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031290","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0030900","count":7},{"id":"GO:0060041","count":7},{"id":"GO:0007519","count":6}]},{"hash":"702936137764810140","title":"mRNA splicing and translation initiation","description":"This cluster shows strong representation of mRNA processing and splicing terms (spliceosome-mediated splicing, alternative splicing regulation) alongside translation-related terms (translation initiation, preinitiation complex formation, translation reinitiation, ribosome biogenesis, IRES-dependent initiation). Together these suggest a functional group of proteins involved in mRNA maturation and the control of translation initiation.","confidence":"High","size":19,"edges":48,"triangles":77,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":3},{"id":"GO:0075522","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0042254","count":3}]},{"hash":"777052671737163062","title":"Developmental transcription and cell cycle control","description":"The cluster centers on transcriptional regulation (DNA-templated transcription) and cell cycle progression (mitotic cell cycle), with strong links to multicellular development and DNA metabolism (DNA repair, DNA replication). Additional signals in phosphorylation, calcium signaling, and plant-associated pathways suggest integrated transcriptional and signaling programs governing development, with context-dependent responses. ","confidence":"High","size":19,"edges":14,"triangles":16,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0007275","count":8},{"id":"GO:0006281","count":6},{"id":"GO:0006260","count":6}]},{"hash":"1198400018347309369","title":"Unknown","description":"The top GO terms are from very disparate processes (developmental morphogenesis, transcription, immune signaling, metabolism, and cell adhesion) with no clear, cohesive biological theme connecting most proteins. With no edges and mixed functional signals, there isn\u2019t a reliable, unified function to assign.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036302","count":2},{"id":"GO:0048705","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000920","count":2},{"id":"GO:0070131","count":1}]},{"hash":"708240218218582909","title":"Cell cycle and DNA replication","description":"The cluster is dominated by GO terms tied to DNA-templated transcription, DNA replication, mitotic checkpoint signaling, spindle assembly, centrosome duplication, and meiotic cell cycle, all of which point to cell cycle control and DNA metabolism. A few terms (sodium transport, cholesterol biosynthesis, visual learning, polarity establishment) are less directly related, likely reflecting broader multifunctionality or annotation noise, but the core signal centers on cell cycle/DNA replication processes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0072428","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0090307","count":2}]},{"hash":"969466002266091575","title":"Unknown","description":"The GO terms cover several unrelated processes (lipid signaling, autophagy, cell division, immune regulation, development, transcription). There are no edges or a dominant function connecting the 19 proteins, and the terms span multiple biological contexts, making it unclear to assign a specific, cohesive label. Therefore this cluster is best described as Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":2},{"id":"GO:1902902","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0043314","count":1},{"id":"GO:0090038","count":1}]},{"hash":"1379777813468862935","title":"Translation Initiation and Reinitiation","description":"The top GO terms cluster around translation initiation and reinitiation, including preinitiation complex formation and IRES-dependent/viral translation, suggesting a cohesive theme of control of protein synthesis; some development and metabolism terms are present but secondary.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060528","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0075522","count":3}]},{"hash":"66488922496642892","title":"DNA replication and cell cycle regulation","description":"The strongest signal is DNA replication (GO:0006260) with 18 proteins, suggesting the cluster mostly comprises components of the replication machinery. Supporting evidence includes cell-cycle/centrosome-related regulation (e.g., negative regulation of protein localization to centrosome) and DNA damage response (response to camptothecin). Additional terms related to mRNA processing and signaling (prostaglandin E stimulus, GPCR desensitization) appear to be ancillary but can intersect with proliferation and gene expression. Overall, the cluster centers on DNA replication with linked cell-cycle and signaling contexts.","confidence":"Medium","size":18,"edges":79,"triangles":96,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":18},{"id":"GO:0007519","count":16},{"id":"GO:0090153","count":16},{"id":"GO:0006397","count":16},{"id":"GO:0071380","count":16}]},{"hash":"1496958575232262327","title":"Unknown","description":"The terms cover many unrelated processes (calcium transport, miRNA metabolism, cell polarity, heart rhythm, kinase and chromatin regulation, neural and muscle development, xenobiotic response, and insulin secretion). No single cohesive function emerges for this cluster, so Unknown is the best label.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070588","count":3},{"id":"GO:0010586","count":3},{"id":"GO:0090162","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0006469","count":2}]},{"hash":"1700237798907584547","title":"Diverse Metabolite Biosynthesis","description":"The GO terms span menaquinone, serine, acetyl-CoA, various fatty-acid and lipid-related processes, bile acid metabolism, and lipoteichoic acid biosynthesis, indicating proteins involved in multiple, diverse biosynthetic pathways rather than a single function. This suggests a cluster centered on the production and modification of diverse metabolites and lipid cofactors.","confidence":"Medium","size":18,"edges":123,"triangles":439,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":5},{"id":"GO:0006564","count":4},{"id":"GO:0019427","count":4},{"id":"GO:0010030","count":4},{"id":"GO:0009698","count":4}]},{"hash":"1286946770778399133","title":"Ribosome Biogenesis and Cell Growth","description":"The cluster\u2019s top terms prominently point to ribosome maturation and rRNA processing (5.8S and LSU), along with transcription, mitotic cell cycle, and cell proliferation, plus SCF-dependent proteasomal degradation. Taken together, these suggest a theme of ribosome assembly and generalized cell growth/proliferation, with a couple of development-related terms that may reflect broader roles or annotation noise.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000466","count":4},{"id":"GO:0007018","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0021510","count":4}]},{"hash":"229894735968516974","title":"DNA repair and mitosis regulation via ubiquitin","description":"The cluster centers on global genome nucleotide-excision repair, G2/M transition and chromosome segregation, mitotic exit, and chiasma assembly, all linked with ubiquitin-dependent proteolysis (SCF, ERAD, autoubiquitination, K11-linked). This suggests a cohesive module where DNA repair and mitotic progression are coordinated through ubiquitin-mediated degradation. A viral process term is present but does not dominate; overall theme is genome maintenance coupled to cell-cycle control by ubiquitin-proteasome pathways.","confidence":"High","size":18,"edges":137,"triangles":605,"max_degree":17,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070911","count":12},{"id":"GO:0000086","count":12},{"id":"GO:0031146","count":12},{"id":"GO:0030433","count":11},{"id":"GO:0051865","count":11}]},{"hash":"845553011577519638","title":"Calcium-regulated keratinocyte differentiation","description":"The strongest signals are keratinocyte differentiation and calcium signaling (calcium ion transport and calcium-dependent adhesion), pointing to calcium-controlled epidermal development. Other terms like multicellular development, hypoxia response, and bone ossification are broader or less specific to this cluster, so the core theme is epidermal differentiation driven by calcium dynamics.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0001666","count":3},{"id":"GO:0051592","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0043931","count":3}]},{"hash":"1737932836919878937","title":"Neuronal axonogenesis and synaptic plasticity","description":"This cluster is dominated by neuronal development signals, especially positive regulation of long-term neuronal synaptic plasticity, positive regulation of axonogenesis, and fasciculation of sensory neuron axons, pointing to roles in axon growth, guidance, and synaptic modulation. Additional terms related to BMP signaling and general development fit within a broad neural-development context but do not override the strong neuronal connectivity theme. The dense interactions suggest a cohesive neuronal signaling module.","confidence":"High","size":18,"edges":151,"triangles":784,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0048170","count":14},{"id":"GO:2000525","count":14},{"id":"GO:0072178","count":14},{"id":"GO:0007432","count":14},{"id":"GO:1904238","count":14}]},{"hash":"1551841515865394919","title":"Ribosome biogenesis and cell cycle","description":"Most terms point to ribosome biogenesis and translation (ribosome biogenesis, cytoplasmic translation, ribosomal large subunit export from nucleus, tRNA modification) and to cell cycle/cell division processes (cell cycle, cell division). The cluster likely includes factors coordinating ribosome production with cell growth and division, with some ancillary links to stress-related growth regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0090529","count":1}]},{"hash":"378191933875994558","title":"Choline Metabolism and Phospholipid Biosynthesis","description":"The top GO terms converge on the CDP-choline pathway, choline and ethanolamine metabolism, and phosphatidylethanolamine biosynthesis, indicating a cohesive focus on phospholipid formation and related metabolic processes. A few outliers (response to antibiotic, chemical exposure) are present but do not dominate the set. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904681","count":1},{"id":"GO:0006657","count":1},{"id":"GO:0019284","count":1},{"id":"GO:0019695","count":1},{"id":"GO:0009088","count":1}]},{"hash":"366272415456371590","title":"Neurodevelopment: axon guidance and synapse assembly","description":"The top GO terms cluster around nervous system development, axon guidance, ROBO signaling, Hedgehog (smoothened) signaling, regulation of synapse assembly, and neurogenesis, with peripheral nervous system development and embryonic morphogenesis also represented. This pattern indicates proteins involved in neural development and establishing neural connections, so the label captures the core theme of axon guidance and synapse formation in neurodevelopment.","confidence":"High","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0007411","count":1},{"id":"GO:0007224","count":1},{"id":"GO:0051963","count":1},{"id":"GO:0035385","count":1}]},{"hash":"1945983095681669352","title":"Ciliary assembly and intracellular transport","description":"The top GO terms point to intracellular trafficking pathways (ER-Golgi transport) and structural assembly related to cilia and centrosomes (motile cilium assembly, intraciliary transport, microtubule anchoring at centrosome), with supporting terms on actin bundles and nuclear pore assembly. This suggests a cohesive theme of building and organizing ciliary/centrosomal structures and the vesicular transport that supports them, with some developmental morphogenesis terms as broader context. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0048477","count":3},{"id":"GO:0044458","count":3},{"id":"GO:0035735","count":3},{"id":"GO:0008407","count":3}]},{"hash":"1051717754866481352","title":"Paranode and Juxtaparanode Protein Localization","description":"The cluster is enriched for GO terms related to localization of proteins to axonal paranode and juxtaparanode regions and to paranodal junction assembly, suggesting a common function in organizing axonal domain specialization; while other terms (lens fiber differentiation, hair follicle morphogenesis, cartilage morphogenesis, thyroid hormone response) appear, they are less central to the core theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":2},{"id":"GO:0071205","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0048339","count":2},{"id":"GO:0050860","count":2}]},{"hash":"1244062649128178201","title":"Diverse Substrate Transmembrane Transporters","description":"Top terms indicate transmembrane transport of xenobiotics, vitamins, ions, and simple sugars, pointing to a cluster of diverse membrane transporters rather than a single substrate. The combination of xenobiotic, vitamin, sugar, and ion transport terms supports naming as broad-spectrum transporter proteins.","confidence":"High","size":18,"edges":47,"triangles":44,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":16},{"id":"GO:0035461","count":16},{"id":"GO:0071805","count":14},{"id":"GO:0042908","count":13},{"id":"GO:0042891","count":9}]},{"hash":"824501575495864069","title":"Immune signaling regulation and myeloid growth","description":"The top terms point to down-regulation of inflammatory signaling and neutrophil behavior, along with myeloid progenitor proliferation and growth regulation, plus EGFR-related response and detoxification processes. This suggests a cluster centered on controlling innate immune activity and cell growth under stress.","confidence":"Medium","size":18,"edges":70,"triangles":150,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":10},{"id":"GO:0098869","count":9},{"id":"GO:0042178","count":8},{"id":"GO:0002182","count":8},{"id":"GO:0010804","count":8}]},{"hash":"1415904291526832214","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":22,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:2001032","count":1},{"id":"GO:0071318","count":1},{"id":"GO:0030036","count":1},{"id":"GO:0098976","count":1}]},{"hash":"1759539075919281906","title":"Developmental Epigenetic Regulation","description":"The proteins cluster around chromatin modification and transcriptional control in developmental contexts, with GO terms for histone ubiquitination, regulation of transcription by RNA Pol II, ubiquitin-dependent proteolysis, and developmental processes like nervous system development and placental morphogenesis, suggesting a theme of epigenetic regulation during development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0036353","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0070562","count":2}]},{"hash":"1031145200534068892","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0071031","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0019068","count":1}]},{"hash":"120699490987757025","title":"Nervous System and Visual Development","description":"The top GO terms are dominated by nervous system development, sensory perception of pain, visual perception, and visual learning, indicating a cluster focused on neural/sensory development and function. Additional terms lie in broader developmental processes (multicellular organism development, heart development, angiogenesis), suggesting a general developmental program with strong neural/visual emphasis. Inflammatory-related terms (lipopolysaccharide response, prostaglandin stimulus) appear as secondary signals rather than core themes. Confidence: Medium","confidence":"","size":17,"edges":7,"triangles":2,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":10},{"id":"GO:0007275","count":9},{"id":"GO:0071222","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0007399","count":7}]},{"hash":"1792286410918253726","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006265","count":17},{"id":"GO:0043629","count":17},{"id":"GO:0000466","count":17},{"id":"GO:0071031","count":17},{"id":"GO:0006363","count":17}]},{"hash":"1509143754010713983","title":"Neural development and synaptic adhesion","description":"The strongest signals come from GO terms related to nervous system development, neuron cell-cell adhesion, and synapse assembly, pointing to proteins involved in neural wiring and synaptic contacts. While there are additional terms spanning broader developmental processes (bone ossification, nephron development, tissue morphogenesis), the core theme is neural development and cell adhesion, justifying this label.","confidence":"Medium","size":17,"edges":15,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":8},{"id":"GO:0007156","count":6},{"id":"GO:0007157","count":6},{"id":"GO:0007399","count":5},{"id":"GO:0072006","count":5}]},{"hash":"40625365871707601","title":"Rab-Mediated Neuronal Signaling and Spine Development","description":"The top GO terms point to Rab and small GTPase\u2013mediated signaling, along with nervous system development and dendritic spine development, suggesting a cluster focused on vesicle trafficking and synaptic maturation in neurons. Some terms like bone resorption and ribosomal export appear less directly related and may reflect broader cellular processes, but the dominant theme is Rab-driven signaling in neuronal development.","confidence":"High","size":17,"edges":59,"triangles":99,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032482","count":8},{"id":"GO:0050771","count":8},{"id":"GO:0045453","count":7},{"id":"GO:0034629","count":7},{"id":"GO:0007264","count":7}]},{"hash":"435523215905540998","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":10},{"id":"GO:0060041","count":10},{"id":"GO:0000466","count":9},{"id":"GO:0000462","count":9},{"id":"GO:0008584","count":9}]},{"hash":"288293006266331382","title":"RNA Processing and Spliceosome Assembly","description":"The top terms cluster around RNA metabolism and processing: transcription termination by RNA polymerase II, rRNA maturation, mRNA splicing via the spliceosome and its assembly, tRNA processing, histone mRNA metabolism, and mRNA decay pathways. This makes RNA processing and maturation the coherent theme of the cluster, with some plant-growth regulatory terms (ABA response, hair cycle) likely reflecting broader cellular regulation in plants rather than changing the core function. High","confidence":"","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006369","count":9},{"id":"GO:0030490","count":8},{"id":"GO:0045292","count":8},{"id":"GO:0008334","count":7},{"id":"GO:0000245","count":7}]},{"hash":"582629181807642226","title":"Dopaminergic signaling and sensory behavior","description":"This cluster shows strong enrichment for neural and sensory terms: dopaminergic synaptic transmission, visual perception/learning, pain perception, and behavioral response to cocaine, along with ERK signaling regulation. While there are broad development terms present, the dominant pattern centers on neural signaling and sensory/behavioral processes, especially dopamine-related reward pathways.","confidence":"High","size":17,"edges":116,"triangles":420,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019233","count":10},{"id":"GO:0007275","count":7},{"id":"GO:0071380","count":7},{"id":"GO:0008542","count":7},{"id":"GO:0070374","count":7}]},{"hash":"1636095712445041894","title":"Cardiac muscle development and contraction regulation","description":"The terms cluster around heart-specific processes: ventricular morphogenesis, cardiac myofibril assembly, regulation of heart contraction, and electrical coupling in cardiac conduction, indicating a cohesive cardiac muscle function module despite a couple of outliers.","confidence":"High","size":17,"edges":25,"triangles":19,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0014883","count":10},{"id":"GO:0032465","count":10},{"id":"GO:1901844","count":10},{"id":"GO:0072286","count":10},{"id":"GO:0099509","count":10}]},{"hash":"1245011591002815633","title":"Viral life cycle and host interaction","description":"The cluster shows strong enrichment for virus-related processes: viral life cycle, virion assembly, viral release, proviral latency, and fusion of viral membranes with host cells, indicating stages of virus replication and host interaction. A few terms like leukocyte migration or protein secretion may reflect host responses, but the dominant theme is viral replication and host-virus interplay.","confidence":"High","size":17,"edges":93,"triangles":234,"max_degree":15,"top_function":"protein folding","top_go_terms":[{"id":"GO:0050900","count":3},{"id":"GO:0050714","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0019064","count":3}]},{"hash":"2031254181936769963","title":"Cardiac Stress Response and Calcium Signaling","description":"The top GO terms cluster around heart function and calcium signaling (positive regulation of cardiac muscle hypertrophy in response to stress; regulation of SA node cell action potential; positive regulation of calcium ion transport; calcium-dependent cell-matrix adhesion), with supportive links to hormonal stress responses (vasopressin secretion; cortisol biosynthetic process) and related apoptotic signaling under stress. While development and ossification terms appear, the strongest theme is cardiac stress signaling intertwined with calcium regulation and endocrine influence.","confidence":"Medium","size":17,"edges":44,"triangles":46,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1903244","count":13},{"id":"GO:0007275","count":13},{"id":"GO:0043931","count":13},{"id":"GO:0030103","count":12},{"id":"GO:0051928","count":12}]},{"hash":"2132785504082152246","title":"Neural development and dendritic spine morphogenesis","description":"The top GO terms cluster around nervous system development (nervous system development, hippocampus development), and synaptic/actin remodeling processes (regulation of dendritic spine morphogenesis, positive regulation of lamellipodium assembly), plus axon guidance signals (Roundabout signaling). This suggests a group of proteins coordinating neural development and synaptic structure, with associated trafficking and cytoskeletal dynamics.","confidence":"High","size":17,"edges":88,"triangles":191,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":3},{"id":"GO:2000785","count":3},{"id":"GO:0035385","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0007399","count":3}]},{"hash":"1044086469675005901","title":"Stress-response signaling and transcriptional regulation","description":"Top terms point to stress- and development-related signaling: cellular responses to toxins (cadmium), TGF-beta signaling, immune defense, and growth-related processes, with supporting transcription regulation and cell-cycle activity (DNA-templated transcription, mitotic cell cycle, multicellular growth). The common thread is integration of environmental cues with transcriptional and growth signaling in a multicellular context, rather than a single, cohesive pathway. Therefore, the label captures a broad Stress-response signaling and transcriptional regulation theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0001403","count":3},{"id":"GO:0050731","count":3}]},{"hash":"562317206402192800","title":"Cardiac development and cytoskeletal signaling","description":"This cluster is dominated by heart development and structural remodeling terms (heart development, sarcomere organization) alongside cytoskeletal dynamics (lamellipodium assembly, Rho signaling and its regulation) and cell adhesion, suggesting a core theme of cardiac development with cytoskeletal remodeling. Some neuronal terms appear but are peripheral to the main signal. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006887","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0007406","count":2},{"id":"GO:0045214","count":2}]},{"hash":"1946011095110093464","title":"Cross-tissue Development and Neural Differentiation","description":"The proteins show GO terms across various developmental processes in multiple tissues (forebrain, lens, skeletal, megakaryocytes) and neuron-related features (neuron projection development, synapse organization), plus endosome-lysosome transport and Rho signaling regulation. This suggests a broad developmental program with neural differentiation aspects rather than a single specific pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0048070","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0001501","count":2}]},{"hash":"1006293821302653304","title":"Golgi trafficking and SNARE-mediated vesicle fusion","description":"The cluster is dominated by GO terms for ER-Golgi and intra-Golgi vesicle transport, SNARE complex assembly, and vesicle fusion with the Golgi, plus exocytic insertion of neurotransmitter receptors to the postsynaptic membrane and links to synaptic potentiation. This points to a cohesive module of Golgi- and SNARE-directed vesicle trafficking that delivers receptors to the plasma membrane at synapses, driving synaptic plasticity.","confidence":"High","size":17,"edges":26,"triangles":5,"max_degree":12,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":9},{"id":"GO:0090161","count":8},{"id":"GO:0035493","count":7},{"id":"GO:0098967","count":7},{"id":"GO:0006891","count":7}]},{"hash":"466237908922302312","title":"Neuronal synaptic vesicle trafficking and spine development","description":"The cluster is dominated by GO terms related to synaptic vesicle exocytosis and priming, microtubule-based movement for transport, and dendritic spine/spinal cord development, all centering on neuronal synaptic function and development. Catecholamine secretion aligns with neurotransmitter release in neurons, though some terms reflect broader developmental roles; overall, the neuronal synaptic theme is clear, justifying this label.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007018","count":3},{"id":"GO:0010765","count":3},{"id":"GO:0016079","count":3},{"id":"GO:0061000","count":3},{"id":"GO:0021510","count":3}]},{"hash":"1911707965513217174","title":"Synapse formation and exocytosis","description":"The top GO terms cluster around synaptic interfaces and membrane trafficking: immunological synapse formation, protein localization to synapse, exocytosis, and zonula adherens assembly, pointing to cell junctions and synaptic signaling. Additional terms like cardiac muscle development and Rho signaling suggest cytoskeletal and adhesion contexts that can influence junctions and trafficking. Overall, this cluster is best described by a role in synapse assembly and exocytotic membrane trafficking.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055013","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006887","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0035176","count":2}]},{"hash":"2024892070761776951","title":"cAMP-Dependent Signaling and Axonogenesis","description":"This cluster centers on GO terms tied to cAMP signaling and protein phosphorylation, with supporting terms for axonogenesis and neuronal morphogenesis (dendrite/axon development) and regulation of these processes. While there are a few outliers and obsolete terms, the dominant themes suggest a group of proteins involved in cAMP-responsive signaling and phosphorylation events that influence neurite/axon formation, making a neuronal signaling/axogenesis label appropriate.","confidence":"Medium","size":17,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0043950","count":2},{"id":"GO:0050774","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0043065","count":2}]},{"hash":"2078045028682155523","title":"Meiosis: cohesion and recombination","description":"The cluster is dominated by GO terms related to meiotic processes, including synaptonemal complex assembly, centromeric chromatid cohesion, telomere attachment to the nuclear envelope, spindle attachment during meiosis I, male meiosis I, fertilization, and replication-born DSB repair via sister chromatid exchange. These together suggest proteins involved in meiotic chromosome pairing, cohesion, and recombination, with some ties to fertilization.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0003187","count":1},{"id":"GO:0007130","count":1},{"id":"GO:0051754","count":1},{"id":"GO:0070197","count":1},{"id":"GO:0072520","count":1}]},{"hash":"1766630681860913568","title":"Ubiquitin-Proteasome Regulation","description":"The GO terms are dominated by ubiquitination and ubiquitin-dependent proteasomal degradation (protein polyubiquitination, SCF-dependent proteasomal pathways, autoubiquitination, ERAD-related), indicating a core focus on tagging and degrading proteins. Additional terms related to regulation of transcription, cell cycle, necroptosis, apoptosis, and TLR signaling reflect downstream regulatory roles tied to ubiquitin-mediated turnover. Therefore, a concise label capturing ubiquitin-dependent protein degradation and its regulatory outcomes is appropriate.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0000209","count":10},{"id":"GO:0042787","count":8},{"id":"GO:0000122","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0060544","count":5}]},{"hash":"1843613034399261807","title":"Unknown","description":"The terms span ubiquitin-dependent degradation, muscle and kidney development, plant metabolism, immune cell processes, neural signaling, and viral latency, with no connecting function and no edges, so there is no cohesive theme to label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0051260","count":4},{"id":"GO:0019762","count":4},{"id":"GO:0007519","count":4},{"id":"GO:0072156","count":4}]},{"hash":"1258235803098698188","title":"Unknown","description":"These terms span several unrelated domains: intracellular signaling, adipocyte differentiation, cardiac action potential regulation, vasopressin secretion, actin cytoskeleton assembly, neural differentiation, innate immune signaling, and mRNA processing. The lack of a single cohesive biological theme across the top terms suggests no clear functional cluster name.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":4},{"id":"GO:0045444","count":4},{"id":"GO:1900827","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0030103","count":3}]},{"hash":"1875133916864683480","title":"Pathogen entry and genome manipulation","description":"The GO terms converge on host-pathogen interactions, including viral penetration into the host nucleus, symbiont entry into host cells, and symbiont-mediated host apoptosis, alongside DNA-centric processes like replication, transcription, and integration. These together suggest a theme of entry into host cells coupled with genome-related manipulation, with a signaling component via Rho/GTPase pathways that can support entry. A few terms (e.g., axonogenesis) appear less connected and may reflect background signals.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007266","count":2},{"id":"GO:0050771","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1290156400300511399","title":"Mitotic chromosome segregation and spindle assembly","description":"The cluster includes terms directly tied to mitosis, such as mitotic sister chromatid segregation, cohesion, and spindle assembly, as well as Okazaki fragment processing in mitotic DNA replication, suggesting a core focus on cell division machinery. Other terms like splicing, actin depolymerization, and COPII vesicle budding appear as less central or ancillary processes, but do not outweigh the prominent mitotic signals.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0031081","count":2}]},{"hash":"2155257829155245652","title":"ECM Remodeling and Branching Morphogenesis","description":"The cluster is dominated by terms about extracellular matrix remodeling and tissue morphogenesis, including basement membrane disassembly, collagen catabolic process, bone resorption, intramembranous ossification, and branching morphogenesis in the lung. While there are additional terms related to peptide catabolism and thyroid hormone response, the strongest signals point to ECM remodeling driving organogenesis and branching structures. This supports a cohesive theme of remodeling linked to morphogenesis rather than disparate processes.","confidence":"Medium","size":16,"edges":38,"triangles":40,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":4},{"id":"GO:0034769","count":4},{"id":"GO:0001957","count":4},{"id":"GO:0010813","count":4},{"id":"GO:0045453","count":4}]},{"hash":"1226162988051762703","title":"Neural development and synaptic signaling","description":"The cluster is dominated by GO terms tied to neuronal growth and synaptic function, such as axonogenesis, long-term synaptic potentiation, and excitatory postsynaptic potential, with supporting hints from Schwann cell development. While there are outliers (plant ABA signaling, cell cycle terms) that introduce noise, the strongest common theme across terms is neuronal development and synaptic activity, suggesting these proteins collectively contribute to neural development and synaptic signaling processes.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":13},{"id":"GO:0007409","count":13},{"id":"GO:0009738","count":13},{"id":"GO:0043065","count":13},{"id":"GO:0060291","count":13}]},{"hash":"475664474441190541","title":"Sex hormone biosynthesis and gonad development","description":"The cluster shows strong representation of androgen and testosterone biosynthetic processes, as well as female gonad development, indicating a prominent endocrine/reproductive theme. While there are additional terms (retinoid metabolism, cell adhesion, neural development, and immune signaling) that are present, they are less central to the overall pattern, so the label focuses on the dominant reproductive/hormonal functions.","confidence":"Medium","size":16,"edges":65,"triangles":155,"max_degree":12,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046013","count":6},{"id":"GO:0007160","count":6},{"id":"GO:0042572","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0008209","count":6}]},{"hash":"1327411112664393568","title":"Glycoprotein ERAD and N-glycan trimming","description":"The terms cluster around mannose trimming in ERAD and glycoprotein processing, including ER-to-cytosol retrograde transport and Golgi-associated N-glycan trimming, indicating a focus on glycoprotein quality control and degradation pathways.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904382","count":1},{"id":"GO:1904154","count":1},{"id":"GO:0036511","count":1},{"id":"GO:0006486","count":1},{"id":"GO:1904381","count":1}]},{"hash":"713255086242075061","title":"Mitotic Cytoskeleton and Cell Polarity","description":"This cluster features proteins linked to actin filament organization, contractile ring and sarcomere-related assembly, and spindle formation during mitosis, along with cell adhesion and polarity regulation. Together, these terms point to cytoskeletal remodeling driving cell division and maintenance of cell shape.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0070493","count":3},{"id":"GO:0007155","count":3},{"id":"GO:0035023","count":3},{"id":"GO:1903478","count":3},{"id":"GO:0071963","count":3}]},{"hash":"1807793542987596467","title":"Developmental morphogenesis and cytoskeletal dynamics","description":"The terms cluster around actin-driven processes such as lamellipodium and ruffle assembly, dendrite extension, Rac signaling, and integrin-mediated adhesion, all pointing to cytoskeletal remodeling during development and morphogenesis. Additional terms note various developmental programs (eye morphogenesis, chaeta formation, multicellular development), supporting a unifying theme of growth and shape changes, despite some outliers like cognition.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":2},{"id":"GO:0097484","count":1},{"id":"GO:0016601","count":1},{"id":"GO:1900029","count":1},{"id":"GO:0030032","count":1}]},{"hash":"1154041260113251166","title":"Growth-control signaling and differentiation (Wnt/Hippo)","description":"The cluster\u2019s top GO terms cluster around cell proliferation and fate decisions: mitotic cell cycle, Wnt signaling, Hippo signaling, keratinocyte differentiation, apoptotic processes, and regulation of protein export and GTPase activity. This suggests a cohesive theme of growth control and differentiation governed by major signaling networks, with some terms pointing to broader tissue development roles (e.g., visual perception). Overall, the data point to a functionally connected set involved in growth regulation and cell fate decisions.","confidence":"Medium","size":16,"edges":117,"triangles":519,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0007601","count":9},{"id":"GO:0046827","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0035329","count":8}]},{"hash":"706414852853383482","title":"Nuclear transcription and chromatin dynamics","description":"This cluster\u2019s terms are dominated by nuclear processes: DNA-templated transcription, transcription preinitiation complex assembly, nucleosome assembly, heterochromatin formation, and DNA replication, suggesting roles in gene expression regulation and chromatin remodeling. A few terms relate to neuronal plasticity or development, but they appear as outliers rather than the core signal. Overall, the cohesive theme is nuclear transcription and chromatin regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060292","count":2},{"id":"GO:0060670","count":2},{"id":"GO:0034396","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0030574","count":1}]},{"hash":"2091768788084543083","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are strongly centered on ubiquitination and protein turnover (ubiquitin-dependent protein catabolic process, autoubiquitination, and K48-linked ubiquitination), pointing to a cluster of proteins involved in tagging substrates for proteasomal degradation and related ubiquitin signaling.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0051865","count":5},{"id":"GO:1903762","count":4},{"id":"GO:0009048","count":4},{"id":"GO:1901253","count":4}]},{"hash":"2300199785206737982","title":"Transcriptional Regulation and RNA Metabolism","description":"This cluster's top GO terms center on DNA-templated transcription and regulation by RNA polymerase II, with concurrent signals of RNA turnover (histone mRNA and rRNA catabolic processes). Though other processes (mitotic spindle orientation, ER-Golgi transport) appear, the dominant theme is control of gene expression and RNA turnover, implying a function in transcriptional regulation coupled with RNA metabolism.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000132","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1591412044112743411","title":"Ciliary and flagellar assembly and motility","description":"This cluster is dominated by GO terms related to cilium and flagellum function\u2014axoneme assembly, cilium movement, sperm flagellum motility, and microtubule-based processes like microtubule severing and tubulin post-translational modifications (polyglutamylation, polyglycylation). Together these indicate a cohesive theme of ciliogenesis and flagellar/microtubule-driven motility, particularly in sperm. A few terms like DNA replication appear unrelated noise, but the surrounding emphasis on ciliary/axonemal processes supports this naming.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0003351","count":1},{"id":"GO:0018095","count":1},{"id":"GO:0030516","count":1}]},{"hash":"1791131861004279914","title":"RNA processing and ribosome biogenesis","description":"The terms converge on RNA maturation and assembly of ribonucleoprotein complexes, including 90S preribosome assembly, pre-catalytic spliceosome assembly, rRNA processing/modification, and RNP localization. A lone DNA damage signaling term and a few obsolete annotations likely reflect incidental annotations rather than a single pathway. Overall, the cluster represents RNA processing and ribosome/spliceosome biogenesis activities.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072423","count":1},{"id":"GO:0034463","count":1},{"id":"GO:0000354","count":1},{"id":"GO:0042868","count":1},{"id":"GO:1903220","count":1}]},{"hash":"1781038744776012991","title":"Neuronal actin dynamics and synapse assembly","description":"Dominant terms point to actin cytoskeleton regulation (Arp2/3-mediated nucleation, lamellipodium dynamics, and actin cortical patch localization) and synaptic processes (synapse assembly and neurotransmitter secretion), suggesting proteins involved in neuronal actin remodeling that supports synapse formation and transmission. Some members also relate to ribosomal RNA maturation and DNA repair, indicating additional housekeeping roles or annotation overlap, but the core signal remains neuronal actin dynamics linked to synaptic function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034316","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0007416","count":2},{"id":"GO:0007269","count":2}]},{"hash":"162910654594948891","title":"Embryonic organ morphogenesis and patterning","description":"The terms show diverse morphogenesis across cartilage, placenta, endocrine organs, heart, pancreas, and cochlea, plus left-right patterning and transcriptional regulation during development, indicating a cluster of proteins involved in broad embryonic development rather than a single tissue. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060536","count":3},{"id":"GO:0060806","count":3},{"id":"GO:0035270","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0060707","count":3}]},{"hash":"2189965833410618606","title":"Fungal meiosis and cytokinesis with actin dynamics","description":"The top GO terms center on cell division and spindle-associated processes (vacuole inheritance, mitotic cytokinesis, meiotic chromosome movement), cytoskeletal organization (actin filament bundle assembly), sporulation (ascospore wall assembly), and calcium-responsive signaling, suggesting a cluster of proteins involved in fungal meiosis/cytokinesis and related cytoskeletal remodeling. ","confidence":"Medium","size":15,"edges":59,"triangles":157,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000011","count":8},{"id":"GO:0032508","count":7},{"id":"GO:0000281","count":7},{"id":"GO:0030476","count":6},{"id":"GO:0090131","count":6}]},{"hash":"148061215312070914","title":"Mitotic spindle assembly and microtubule dynamics","description":"The top GO terms cluster around cytoplasmic microtubule organization, spindle midzone assembly, nucleation, and cytokinesis, all central to mitotic spindle function and cell division. Additional terms on microtubule polymerization and division-site positioning reinforce this theme; a few terms about neuron migration and IL-4 response may reflect broader cytoskeletal signaling, but the core signal is microtubule organization during mitosis.","confidence":"High","size":15,"edges":103,"triangles":430,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0031122","count":15},{"id":"GO:0051256","count":15},{"id":"GO:0007049","count":15},{"id":"GO:0071353","count":15},{"id":"GO:0007020","count":15}]},{"hash":"1995115971104206769","title":"Neuronal development and Golgi dynamics","description":"The terms include cerebral cortex development and neuron migration, plus membrane depolarization and action potential\u2013related processes, pointing to neuronal development and activity. The presence of Golgi reassembly and establishment of Golgi localization suggests Golgi apparatus dynamics are involved in these neural processes. A few terms about epidermal keratinocyte proliferation and apoptosis appear, but the dominant theme is neural development and Golgi function.","confidence":"Medium","size":15,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001836","count":4},{"id":"GO:0010482","count":4},{"id":"GO:0071901","count":4},{"id":"GO:0090168","count":4},{"id":"GO:0086010","count":4}]},{"hash":"950271707417748974","title":"Mitotic spindle assembly and microtubule dynamics","description":"The top GO terms heavily emphasize mitotic spindle biology and microtubule function (mitotic spindle assembly, lateral attachment of spindle microtubules to kinetochores, minus-end directed microtubule sliding), indicating a cohesive theme around cell division machinery. Some terms touch on development and transcription, but they can reflect broader proliferation contexts; overall the cluster centers on spindle dynamics and chromosome segregation.","confidence":"High","size":15,"edges":10,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0060528","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1617754276551991388","title":"Cyclic nucleotide GPCR signaling (cAMP/cGMP)","description":"Dominant GO terms point to cAMP and cGMP biosynthesis and signaling via GPCRs and receptor guanylyl cyclases, including forskolin response and adenosine/adrenergic receptor pathways; the hypoxia detection term supports a connected cyclic-nucleotide signaling context.","confidence":"High","size":15,"edges":69,"triangles":144,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006171","count":6},{"id":"GO:0035556","count":6},{"id":"GO:0006182","count":6},{"id":"GO:0070483","count":6},{"id":"GO:0007168","count":6}]},{"hash":"286115862877152705","title":"Amino acid transport across plasma membrane","description":"The top GO terms point to transmembrane import of amino acids (arginine, lysine, ornithine, and D-serine) across the plasma membrane, and an arginine-related metabolic link to nitric oxide production. Despite some obsolete terms, the dominant theme is amino acid transport across membranes, suggesting this cluster comprises amino acid transporters or related proteins.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035826","count":1},{"id":"GO:0006884","count":1},{"id":"GO:0006527","count":1},{"id":"GO:0097639","count":1},{"id":"GO:0098713","count":1}]},{"hash":"1660086047905239593","title":"Neurodevelopmental and Immune Signaling Pathways","description":"These terms cluster around developmental signaling pathways, notably Roundabout (Robo) signaling and Smoothened (Hedgehog) signaling, with strong representation of nervous system and brain development. Immune signaling is also present (T cell receptor signaling and mast cell chemotaxis), alongside synaptic vesicle exocytosis related to neuronal communication. Taken together, the proteins appear to participate in diverse developmental signaling across neural and immune contexts, justifying a label focused on developmental signaling with neuro-immune context.","confidence":"High","size":15,"edges":79,"triangles":220,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035385","count":6},{"id":"GO:0007224","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0050852","count":6},{"id":"GO:0001822","count":6}]},{"hash":"1408090280748471209","title":"Neural development and axon guidance","description":"This cluster\u2019s terms converge on nervous system development and neuronal connectivity: axon guidance, peripheral and broader nervous system development, and specific signaling pathways (Roundabout/ROBO, SHH/Smoothened, Wnt) that regulate neural patterning and synapse assembly. The combination of these neuronal development terms suggests the proteins function together in neural wiring rather than general cell proliferation or epithelial processes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050680","count":1},{"id":"GO:0010633","count":1},{"id":"GO:0090090","count":1},{"id":"GO:0007411","count":1},{"id":"GO:0007224","count":1}]},{"hash":"2003219297980354596","title":"NAD biosynthesis and central carbon metabolism","description":"This cluster is dominated by terms tied to core carbon metabolism (TCA cycle, glyoxylate cycle, alanine catabolism) and NAD biosynthesis via tryptophan/kynurenine pathways (kynurenine catabolic process and quinolinate biosynthetic process). The presence of [2Fe-2S] cluster assembly and response to vitamin B6 suggests a broader metabolic enzyme-cofactor context, while oxalic acid secretion fits with metabolite turnover in central pathways. The Notch signaling term appears more like an annotation outlier than a core shared function. Overall, the cluster seems to group proteins involved in energy metabolism and NAD-related biosynthesis rather than a single signaling pathway.","confidence":"Medium","size":15,"edges":84,"triangles":237,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0097053","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0007219","count":5},{"id":"GO:0019878","count":4}]},{"hash":"435737539158370741","title":"Early embryonic neural and craniofacial development","description":"This cluster is enriched for embryonic and neural/craniofacial processes, including brain and inner ear development, axis specification, primitive streak formation, and orofacial/craniofacial formation, indicating a cohesive set of proteins involved in early embryogenesis and neural crest\u2013related morphogenesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007626","count":5},{"id":"GO:0060021","count":5},{"id":"GO:0048839","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0007338","count":4}]},{"hash":"1431459572911255835","title":"Neural synapse organization and sensory behavior","description":"This cluster is enriched for synaptic and spine-related processes (protein localization to synapse, dendritic spine morphogenesis, receptor clustering, and Rho signaling), pointing to neural connectivity and plasticity. The presence of sensory perception terms (sound and light) and behaviors (vocalization, grooming regulation) suggests involvement in neural circuits governing sensory processing and behavior. A single proliferation term is peripheral to the main theme but does not override it.","confidence":"High","size":15,"edges":31,"triangles":18,"max_degree":11,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0008285","count":12},{"id":"GO:0060997","count":12},{"id":"GO:0035418","count":11},{"id":"GO:0007266","count":11},{"id":"GO:0043113","count":11}]},{"hash":"173448520956209417","title":"TNF-NF-kappaB signaling and apoptosis","description":"The cluster centers on TNF-mediated signaling and NF-kappaB regulatory activity, paired with an intrinsic apoptotic pathway triggered by DNA damage, and a cellular response to lipopolysaccharide\u2014together pointing to an inflammatory/stress-response program that can lead to apoptosis. Some terms related to transcription and transport appear incidental to this theme.","confidence":"Medium","size":15,"edges":19,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042347","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1}]},{"hash":"1395115279737112384","title":"Embryonic and organ morphogenesis","description":"Top GO terms indicate development and morphogenesis across multiple tissues (gonads, brain, inner ear, myotome, placenta, eye, prostate structures, habenula, outflow tract), with no single dominant pathway. This suggests a broad role in embryonic tissue morphogenesis rather than a specific process, hence the label Embryonic and organ morphogenesis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008585","count":3},{"id":"GO:0061055","count":3},{"id":"GO:0048839","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0060527","count":3}]},{"hash":"791094277487687321","title":"Ubiquitin-dependent protein turnover and cell cycle regulation","description":"These proteins cluster around processes tied to tagging proteins for degradation (polyubiquitination, ubiquitin-dependent ERAD, ubiquitin-mediated catabolic process) and controlling the cell cycle (cell division, G0 to G1 transition, G1 checkpoint signaling). The presence of transcription-related GO terms may reflect regulatory roles of ubiquitin pathways on gene expression. While a couple of terms (GPCR signaling, plant pattern formation) are less central, the dominant theme is ubiquitin-mediated proteolysis linked to cell cycle control.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000209","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0051301","count":3}]},{"hash":"1156301911031814478","title":"Cytoskeletal Dynamics and Mechanotransduction","description":"The top GO terms cluster around actin cytoskeleton processes (actin filament bundle assembly), spindle assembly, and cellular responses to mechanical stimuli, pointing to cytoskeletal remodeling and mechanosensitive signaling as the central theme. Additional terms touching on growth, membrane trafficking, and tissue-specific contexts (neural and cardiac) fit within broad cytoskeletal and signaling roles across cell types, supporting a cohesive label focused on cytoskeletal dynamics and mechanotransduction rather than a single tissue-specific function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0048549","count":3}]},{"hash":"1193035546614429536","title":"Unknown","description":"The top terms span multiple disparate processes (NF-kappaB regulation, cardiac depolarization, vasopressin secretion, actin assembly, neuronal differentiation, mRNA processing, and even plant salicylic acid signaling), and there are no network connections among the proteins. This lacks a coherent, single theme, so a meaningful cluster label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007253","count":4},{"id":"GO:0032088","count":4},{"id":"GO:1900827","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0030103","count":3}]},{"hash":"1906281758616574217","title":"Cilium Assembly and Centrosome Localization","description":"The cluster\u2019s top GO terms point to ciliary biology: regulation of cilium assembly, intraciliary transport, and centrosome localization, with related cues about left/right symmetry. These collectively define functions tied to cilium structure and function, often linked to sensory systems (e.g., hearing). A few other terms (mitophagy, apoptosis-related release) appear peripheral, but the strongest signal is ciliogenesis and centrosomal organization, justifying this label as representative of the cluster.","confidence":"High","size":14,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1902017","count":2},{"id":"GO:0016079","count":2},{"id":"GO:0035735","count":1},{"id":"GO:0007368","count":1},{"id":"GO:0090267","count":1}]},{"hash":"655036582282516","title":"ER Stress Response and Protein Targeting","description":"The cluster is dominated by GO terms linked to unfolded protein response and ER-associated processes, notably cellular response to unfolded protein and SRP-dependent cotranslational protein targeting to membranes. These points strongly indicate a core theme around protein folding/processing and ER function. There are a few outlier terms (DNA replication, fungal mating, iron-sulfur assembly) that are less central to this theme, but they do not outweigh the main signal. Overall, \"ER Stress Response and Protein Targeting\" best captures the main functional coherence of the cluster.","confidence":"Medium","size":14,"edges":87,"triangles":322,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":9},{"id":"GO:1903382","count":9},{"id":"GO:0006880","count":9},{"id":"GO:0000902","count":9},{"id":"GO:0016226","count":9}]},{"hash":"184553834095467129","title":"Skeletal muscle development and GPCR signaling regulation","description":"The cluster prominently features skeletal muscle tissue development, with concurrent signals related to GPCR signaling desensitization, prostaglandin response, and broader signaling pathways, plus supporting processes like mRNA processing and regulation of protein localization. This suggests a cohesive role in muscle development coupled with GPCR- and lipid-mediated signaling and post-transcriptional control.","confidence":"Medium","size":14,"edges":88,"triangles":329,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007519","count":13},{"id":"GO:0090153","count":13},{"id":"GO:0006397","count":13},{"id":"GO:0071380","count":13},{"id":"GO:0002029","count":13}]},{"hash":"390254119313722161","title":"Ribosome Biogenesis and Proteostasis","description":"The cluster is dominated by terms for translation, ribosome biogenesis, and mRNA export, with supporting signals for proteostasis (aggresome assembly, ubiquitin-dependent ERAD) and protein oligomerization, suggesting a cohesive group of proteins involved in ribosome production and protein quality control; a few outlier terms about viral replication and transformation appear incidental.","confidence":"High","size":14,"edges":37,"triangles":39,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0070842","count":4},{"id":"GO:0042254","count":4}]},{"hash":"2235667052257810753","title":"Embryonic Development and Organogenesis","description":"Based on the GO terms, the cluster centers on developmental processes across multiple tissues and organ systems, including cartilage morphogenesis, placenta development, left-right patterning, EMT in heart/endocardial cushion formation, and development of pancreatic and prostate tissues, with actin filament assembly supporting morphogenesis. This points to a general theme of embryonic development and tissue patterning rather than a single, specific pathway.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060536","count":3},{"id":"GO:0060806","count":3},{"id":"GO:0035270","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0060707","count":3}]},{"hash":"1549606647325484802","title":"Ubiquitin-Dependent Degradation and ER Quality Control","description":"The cluster is dominated by GO terms for ubiquitination, ubiquitin-dependent protein catabolic processes, and ER-associated degradation (ERAD), plus autophagy, indicating a consistent theme of protein turnover and ER quality control. Additional terms related to ER-Golgi transport and immune signaling reflect broader stress responses but do not overshadow the central degradation/autophagy focus.","confidence":"High","size":14,"edges":4,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0006914","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0002250","count":4},{"id":"GO:0042787","count":4}]},{"hash":"1615190999787362666","title":"Glycolysis and TCA cycle with Fe-S assembly","description":"Most represented GO terms center on core carbon metabolism: glycolytic process, tricarboxylic acid cycle, and oxaloacetate metabolism, which points to energy production. Iron-sulfur cluster assembly further suggests involvement in maturation of Fe-S enzymes that drive these pathways. Some terms are obsolete or broad (e.g., DNA-templated transcription), but they do not override the main theme. Overall, the cluster reflects central metabolic processes with Fe-S protein assembly.","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0019878","count":4},{"id":"GO:0006096","count":3},{"id":"GO:1902987","count":3}]},{"hash":"287459832390439178","title":"Regulated signaling, adhesion, and mitochondrial dynamics","description":"This cluster shows a mix of GO terms spanning signaling pathways (PKC signaling, TLR3 signaling, SREBP signaling), cell-cell adhesion and extracellular matrix remodeling, muscle contraction regulation, and mitochondrial processes (inner mitochondrial membrane organization, mitochondrial DNA replication). The common thread appears to be broader regulation of cellular signaling together with structural/mitochondrial dynamics, rather than a single specific function, so a high-level label focusing on signaling, adhesion, and mitochondrial dynamics is appropriate.","confidence":"Medium","size":14,"edges":28,"triangles":25,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0031448","count":3},{"id":"GO:1903905","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2000049","count":2},{"id":"GO:0034141","count":2}]},{"hash":"1173853655688932236","title":"Skeletal Muscle Development and GPCR Signaling Regulation","description":"Anchored by skeletal muscle development and GPCR signaling modulation, this cluster also shows links to sphingolipid biosynthesis, mRNA processing, and stress responses, suggesting a coordinated muscle-related signaling and gene-expression program rather than a single pathway.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007519","count":13},{"id":"GO:0090153","count":13},{"id":"GO:0006397","count":13},{"id":"GO:0071380","count":13},{"id":"GO:0002029","count":13}]},{"hash":"823649589279150505","title":"Redox Balance and EMT/Polarity Signaling","description":"The top GO terms center on redox control (negative regulation of ROS, NADPH regeneration, redox homeostasis) and on epithelial polarity and EMT regulation, suggesting a shared theme of managing cellular redox state while governing epithelial cell behavior. Some ubiquitin-related terms imply proteostasis connections under redox stress, while a ancillary metabolic term is less central. Overall, the cluster seems to reflect redox balance linked to epithelial polarity and EMT dynamics.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000378","count":2},{"id":"GO:0006740","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1903094","count":2},{"id":"GO:2000157","count":2}]},{"hash":"1996264043770856022","title":"Developmental Regulation and Cell Cycle Control","description":"The cluster is enriched for development-related terms (multicellular organism development, skin development, pattern formation) along with cell division and G1 checkpoint signaling, suggesting a coordinated developmental program that couples growth with cell cycle control. Additional terms for GPCR-PLC signaling and protein homooligomerization point to signaling and assembly processes that support development. Overall, the proteins likely participate in development with regulation of cell proliferation, rather than a narrow single function.","confidence":"Medium","size":14,"edges":21,"triangles":10,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0000920","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2286902239587508594","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":64,"triangles":132,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006508","count":3},{"id":"GO:0046944","count":2},{"id":"GO:0000722","count":2},{"id":"GO:0072670","count":2}]},{"hash":"1422011111506726882","title":"Nutrient signaling and cell cycle with actin remodeling","description":"These terms point to nutrient- and glucose-responsive signaling, cell cycle transitions (G0 to G1) and DNA damage signaling, along with transcription/chromatin activity (histone acetylation) and actin cytoskeleton dynamics (actin depolymerization, Arp2/3 regulation). Although there are some broader or less direct terms (like pattern formation and GPCR signaling), the strongest common theme is nutrient-driven control of the cell cycle coupled with actin remodeling. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007584","count":3},{"id":"GO:0043966","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0072432","count":2},{"id":"GO:0007200","count":2}]},{"hash":"1202235071281875255","title":"Neuronal spine development and Golgi trafficking","description":"The cluster centers on dendritic spine morphogenesis and neuronal development, supported by Rac signaling and actin remodeling (lamellipodium/ruffle), alongside vesicle trafficking between ER, Golgi, and plasma membrane (including retrograde endosome-to-Golgi transport). Hippocampus development and regulation of spine growth fit this theme, suggesting a module coordinating cytoskeleton dynamics with membrane trafficking to shape synaptic structures.","confidence":"High","size":14,"edges":7,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045792","count":7},{"id":"GO:0043001","count":7},{"id":"GO:0097178","count":7},{"id":"GO:0021766","count":7},{"id":"GO:0061001","count":7}]},{"hash":"709366545167154971","title":"Unknown","description":"The top GO terms are highly diverse (apoptotic process, autophagy, spindle assembly, sensory perception of sound, myotube differentiation, plus some lineage- and signaling-related terms), with several obsolete terms also present. This spread suggests no single coherent biological function or pathway dominates the cluster, and may reflect mixed or noisy annotations. Therefore, there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0014902","count":2}]},{"hash":"1423610148518019281","title":"Multi-lineage transcriptional regulation","description":"Top GO terms point to transcriptional control (DNA-templated transcription; negative regulation of transcription by RNA polymerase II) and chromatin-related processes (rDNA heterochromatin formation; nucleosome density), paired with multiple lineage differentiation cues (skeletal muscle cell differentiation; endocrine pancreas development; negative regulation of osteoblast differentiation) and a muscle-adaptation signal (response to denervation). This suggests a cluster of proteins that broadly regulate transcription and chromatin state to influence differentiation across tissues, with a notable emphasis on muscle-related regulation. ","confidence":"Medium","size":14,"edges":58,"triangles":126,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0060766","count":8},{"id":"GO:0045668","count":8},{"id":"GO:0031018","count":6},{"id":"GO:0035914","count":6}]},{"hash":"1594234570447950474","title":"GPCR signaling and actin remodeling during development","description":"The top GO terms center on acetylcholine GPCR signaling and desensitization, activation of GTPases, and assembly of lamellipodia and filopodia, indicating cytoskeletal remodeling and cell migration. Additional terms link to adhesion-dependent spreading, suggesting coordinated movement and attachment. Developmental signals like midbrain morphogenesis and fat cell differentiation imply broader roles for GPCR signaling in tissue patterning and differentiation. Taken together, the cluster seems to reflect GPCR-driven signaling that governs cytoskeletal dynamics and cell behavior during development.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":3},{"id":"GO:0007213","count":3},{"id":"GO:0043314","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0030032","count":2}]},{"hash":"934077930631097616","title":"DNA Damage Response under Xenobiotic Stress","description":"The cluster centers on DNA repair processes (BER and DSB repair regulation) and damage from depurination, complemented by responses to xenobiotic and ethanol exposure and an inflammatory signal, suggesting a broader DNA damage/stress response to chemical insults rather than a single specific pathway.","confidence":"Medium","size":14,"edges":77,"triangles":223,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0071555","count":3},{"id":"GO:1901291","count":2}]},{"hash":"1862807325020704899","title":"RNA Translation and mRNA Decay","description":"The top GO terms cluster around translation and RNA turnover (translational termination, mitochondrial translation, ribosomal large subunit assembly, and deadenylation-dependent/independent mRNA decay), indicating a core theme of RNA metabolism and protein synthesis. Some outliers like DNA repair and lipid catabolism appear, but the strongest signal supports translation machinery and mRNA decay as the cluster's focus.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006415","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0031086","count":1},{"id":"GO:0000288","count":1}]},{"hash":"982285775972895465","title":"Transmembrane Transporters for Diverse Substrates","description":"This cluster is dominated by GO terms for transmembrane transport across membranes of a wide range of substrates (xenobiotics, vitamins, sugars, phosphate, and ions) and includes a vesicle-related process (neurotransmitter loading into synaptic vesicles). This suggests a cohesive theme of membrane transport proteins handling diverse cargo, including vesicular transport components. ","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":10},{"id":"GO:0035461","count":10},{"id":"GO:1900754","count":9},{"id":"GO:0035435","count":9},{"id":"GO:0015757","count":9}]},{"hash":"1170715107535794252","title":"GTPase-driven cytoskeletal remodeling","description":"The top GO terms point to positive regulation of GTPase activity together with actin-related processes (actin filament bundle assembly, ruffle assembly) and junctional regulation, suggesting a unifying theme of cytoskeletal dynamics controlled by small GTPases. Additional terms touching development and immune signaling may reflect how actin remodeling influences morphogenesis and immune responses. Overall, the cluster appears centered on GTPase-mediated cytoskeletal remodeling.","confidence":"Medium","size":14,"edges":15,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0034136","count":1},{"id":"GO:1905664","count":1},{"id":"GO:2000821","count":1}]},{"hash":"317131643216958953","title":"Proteostasis and Protein Quality Control","description":"These proteins cluster around proteostasis mechanisms: misfolded protein transport, ER-associated degradation (ERAD), ubiquitin-proteasome\u2013mediated quality control, and chaperone/refolding pathways, including nuclear quality control. While a few terms touch on development or RNA processing, the dominant themes point to maintaining protein homeostasis across compartments.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0030433","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0032781","count":1}]},{"hash":"1040246976918683302","title":"Protein and polyamine acetylation","description":"Most frequent GO terms center on acetylation of various substrates (spermidine, putrescine, peptidyl-lysine, and N-terminal acetylation/propionylation), indicating a core theme of acetylation-driven regulation. Additional terms cover related biosynthetic and metabolic processes, which may reflect broader metabolic or chromatin-associated roles. Overall, the cluster is best described by acetylation-related processes of proteins and amines.","confidence":"High","size":14,"edges":42,"triangles":50,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":8},{"id":"GO:0060358","count":8},{"id":"GO:0071962","count":8},{"id":"GO:0045150","count":8},{"id":"GO:0018003","count":8}]},{"hash":"542477625414584270","title":"Membrane raft signaling and caveolae dynamics","description":"The set of top GO terms centers on membrane organization and signaling: plasma membrane raft distribution, caveola assembly, and plasma membrane tubulation describe membrane domains and their remodeling, while peptidyl-tyrosine phosphorylation and autophosphorylation point to membrane-anchored signaling cascades. The lysosome localization term suggests trafficking aspects, and a few terms reference developmental processes, which may be incidental background noise. Overall, the cluster appears to capture proteins involved in membrane microdomain organization coupled to tyrosine-based signaling.","confidence":"Medium","size":14,"edges":18,"triangles":3,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0061462","count":7},{"id":"GO:2000821","count":7},{"id":"GO:1904179","count":7},{"id":"GO:0050731","count":7},{"id":"GO:0060017","count":7}]},{"hash":"2063563205032665445","title":"Unknown","description":"The GO terms span a mix of nuclear processes (DNA replication, CENP-A chromatin assembly, mRNA export, cell division) and cytoplasmic trafficking/structure (protein homooligomerization, ER-to-Golgi transport, microtubule severing, ERAD-related activity) with no clear unifying function and no network edges, making a consistent, specific label unlikely.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0006260","count":3}]},{"hash":"842022889712507740","title":"Mitochondrial Transport and Cofactor Metabolism","description":"Top GO terms include mitochondrial membrane fission, iron import into the mitochondrion, and transmembrane transport of cofactors such as thiamine pyrophosphate and pyridoxal phosphate, plus glycine import across membranes. This points to a mitochondrial-centered theme of transport and metabolism for cofactors and metals. The remaining terms (DNA-templated transcription, keratinocyte migration, liver regeneration, female pregnancy) are more disparate and not clearly mitochondrial, indicating overall heterogeneity with a mitochondrial core. Confidence is Medium.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051546","count":2},{"id":"GO:0031921","count":2},{"id":"GO:0090149","count":2},{"id":"GO:0030974","count":2}]},{"hash":"2058919257769924641","title":"Cell cycle and chromatin remodeling with cytoskeletal dynamics","description":"Dominant GO terms cluster around regulation of the cell cycle and transcription initiation-coupled chromatin remodeling, suggesting a core role in cell-division control. Additional signals relate to chromatin state maintenance and protein turnover (proteasome localization), as well as cytoskeletal and cell\u2013cell junction organization (adherens junction assembly; microtubule dynamics), which are essential for mitosis and tissue architecture. A few vesicle/transport terms appear, but the overarching theme ties cell cycle progression to chromatin state and cytoskeletal/cell-adhesion processes.","confidence":"Medium","size":13,"edges":76,"triangles":264,"max_degree":12,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007050","count":9},{"id":"GO:0015991","count":9},{"id":"GO:0048096","count":8},{"id":"GO:0071255","count":8},{"id":"GO:1904793","count":8}]},{"hash":"637174593268098842","title":"ER Protein Folding and Unfolded Protein Response","description":"The top GO terms cluster around endoplasmic reticulum\u2013mediated protein folding, the unfolded protein response, and ER stress, with supporting redox homeostasis and detoxification terms, indicating a module focused on ER quality control and oxidative stress management.","confidence":"High","size":13,"edges":35,"triangles":33,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":9},{"id":"GO:0034975","count":9},{"id":"GO:0006986","count":6},{"id":"GO:0033158","count":5},{"id":"GO:0055114","count":5}]},{"hash":"1429035306974742205","title":"Immune signaling and ubiquitin-regulated protein turnover","description":"The cluster centers on immune-related signaling (T cell receptor, Fc-epsilon receptor pathways) and antigen processing/presentation via MHC I, alongside ubiquitin-related processes (deubiquitination and proteasomal or ubiquitin-regulated degradation). Together, these terms point to a coherent theme where immune signaling components interface with ubiquitin-proteasome\u2013mediated protein turnover and antigen processing, with some links to Wnt and cell-cycle regulation potentially reflecting broader regulatory cross-talk. ","confidence":"Medium","size":13,"edges":21,"triangles":11,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0010499","count":3},{"id":"GO:0006521","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0090090","count":3}]},{"hash":"1796150339366779176","title":"Broad Developmental Processes","description":"The top GO terms point to development across multiple organ systems (male gonad, forebrain, placenta, heart) and general multicellular development, with a couple of broader transcription/translation terms. The lack of specific pathway coherence (no edges) suggests these proteins are related to development in a broad, non-specific sense rather than a single shared function. Therefore, a broad label is most appropriate.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008584","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1594233585098878012","title":"Neuronal signaling and ER trafficking","description":"The GO terms show a dual theme: neuronal/CNS functions (response to morphine and amphetamine, regulation of pain perception, prepulse inhibition, visual learning) alongside secretory pathway and protein handling in the ER (ER-to-Golgi transport, SRP-dependent targeting, misfolded protein response). This suggests a cluster of proteins involved in CNS signal modulation together with secretory pathway processing and quality control, rather than a single isolated function. The outlier term related to cell wall catabolic processes is likely noise or cross-species annotation. Confidence reflects a plausible, cohesive theme linking neural signaling with ER trafficking.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0051967","count":2},{"id":"GO:0001975","count":2},{"id":"GO:0051930","count":2}]},{"hash":"314200486993191578","title":"Retinoid Metabolism and Regulation","description":"The top GO terms are dominated by retinol and retinal metabolic processes, with a notable signal about negative regulation of retinoic acid biosynthesis, indicating a core retinoid metabolism theme. Additional terms link lipid signaling and hormone metabolism (prostaglandin response, androgen metabolism) and pregnancy-related processes, suggesting broader regulatory context around retinoid signaling in development and reproduction. Overall, the cluster centers on retinoid metabolism with regulatory and signaling connections.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":12},{"id":"GO:0042574","count":12},{"id":"GO:2000353","count":11},{"id":"GO:0031098","count":11},{"id":"GO:0055114","count":11}]},{"hash":"263970641361828353","title":"mRNA processing and translation regulation","description":"This cluster centers on post-transcriptional control: mRNA stability and stress-regulated regulation, translation initiation and preinitiation complex formation, IRES-driven initiation, spliceosomal mRNA splicing, and RNA modification, indicating a cohesive role in coordinating mRNA fate and translation.","confidence":"High","size":13,"edges":30,"triangles":30,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0006446","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0001825","count":4}]},{"hash":"393315861010640843","title":"Neural development and neuron migration","description":"The cluster centers on neural development, highlighted by cortical neuron migration (radially oriented migration) and regulation of canonical Wnt signaling in neural contexts, with additional signals for neuronal survival and synaptic activity. While some terms touch on broader morphogenesis and intracellular transport, the dominant theme is neural development and migration.","confidence":"High","size":13,"edges":14,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0007097","count":3},{"id":"GO:0021799","count":3},{"id":"GO:0043524","count":3},{"id":"GO:0060079","count":3}]},{"hash":"2177396066412167304","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around ribosome assembly (cytosolic and preribosome), ribosome biogenesis, and translation, with supporting terms for rRNA and tRNA maturation and even regulation of mitochondrial translation. This points to a cohesive set of proteins involved in ribosome construction and protein synthesis, with antibiotic response likely reflecting antibiotics targeting ribosomes. Overall, the cluster represents ribosome biogenesis and translation machinery.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070475","count":1},{"id":"GO:1902626","count":1}]},{"hash":"2090475684696043860","title":"Unknown","description":"The top GO terms span energy metabolism (aerobic respiration, insulin catabolic process), membrane transport (proton transmembrane transport), catabolic/hormone turnover (bradykinin catabolic, hormone catabolic), protein turnover (ubiquitin recycling, protein heterooligomerization), lifespan regulation, and host-symbiont interaction. This mixture does not reveal a single coherent function or pathway that ties all members together, so a precise, representative label is not evident.","confidence":"","size":13,"edges":13,"triangles":0,"max_degree":8,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:1902600","count":4},{"id":"GO:0033326","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0010815","count":3},{"id":"GO:0008340","count":3}]},{"hash":"1031386932011661992","title":"Glandular development and immune signaling","description":"The terms strongly point to development of glandular tissues (uterus, parathyroid, mammary gland branching) and secretory/trafficking processes (Golgi to plasma membrane transport, calcium handling) with additional immune signaling components (TLR2, interferon pathways, nitric oxide response). This suggests a theme of gland development in tandem with signaling and secretory regulation, rather than a single narrow function.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0034136","count":2},{"id":"GO:1905664","count":2},{"id":"GO:0002333","count":2},{"id":"GO:0060065","count":2}]},{"hash":"1859219521121517352","title":"Dopaminergic and Glycinergic Neurotransmission","description":"The top GO terms collectively emphasize neurotransmitter handling and signaling, especially uptake and metabolism of dopamine and serotonin, and glycine-related synaptic transmission, including glycine secretion. While a few terms touch on development and glial growth, the dominant pattern points to monoamine and amino acid neurotransmission and uptake processes, with a supportive glial context. This makes the label a concise and representative summary of the cluster\u2019s function.","confidence":"High","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042420","count":1},{"id":"GO:0021984","count":1},{"id":"GO:1903346","count":1},{"id":"GO:0015734","count":1},{"id":"GO:0051583","count":1}]},{"hash":"541577608029852731","title":"Mitochondrial translation machinery","description":"The top GO terms point to mitochondrial protein synthesis, with several tRNA aminoacylation activities (lysyl-, aspartyl-, asparaginyl-) and translation (GO:0006412) indicating a cluster centered on mitochondrial translation and tRNA charging. Some terms like neurotransmitter secretion or cadherin-mediated adhesion are peripheral and likely incidental, but the dominant signal is mitochondrial translation. ","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007269","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0072581","count":2},{"id":"GO:0070154","count":2},{"id":"GO:0071915","count":2}]},{"hash":"2222571160534853161","title":"Neuroimmune GPCR Signaling and Behavior","description":"The top GO terms mix immune/inflammatory processes (inflammatory response, immunological synapse, dendritic cell homeostasis) with GPCR signaling and neural/behavioral outputs (adenylyl cyclase-inhibiting GPCR pathway, fear and feeding regulation, enteric/gut-related changes). This suggests a cluster centered on neuroimmune communication and GPCR-driven regulation of gut-brain signaling and behavior.","confidence":"Medium","size":13,"edges":19,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006954","count":2},{"id":"GO:0007197","count":1},{"id":"GO:2000522","count":1},{"id":"GO:0060160","count":1},{"id":"GO:0035815","count":1}]},{"hash":"429560531576655367","title":"Immune Activation and Antigen Presentation Signaling","description":"The proteins group around immune system processes: thymic T cell selection, B cell proliferation, T-helper 1 lineage commitment, and regulation of MHC class II biosynthesis, along with modulation of TLR2 signaling and calcium signaling\u2014hallmarks of immune activation and antigen presentation regulation. Small GTPase\u2013mediated signaling underpins these pathways, tying the set together through intracellular signaling cascades. A couple of terms (axonogenesis, cellular response to mechanical stimulus) are less directly connected but may reflect shared signaling and cytoskeletal dynamics in immune cells. Overall, this cluster appears to represent immune activation and antigen presentation regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045060","count":2},{"id":"GO:0002322","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0007264","count":2}]},{"hash":"865920964637147395","title":"RNA methylation and capping cluster","description":"Based on the Top Terms, the strongest signal is for RNA modification and processing: tRNA wobble uridine modification, RNA guanine-N7 methylation, tRNA methylation, and 7-methylguanosine mRNA capping. A secondary pattern includes related protein post-translational modifications (N-terminal trimethylation, peptidyl-arginine hydroxylation) and stress-related responses, but the core theme points to RNA modification mechanisms. Some lipid biosynthesis terms appear as outliers, which reduces a single cohesive functional story, but the RNA modification signal dominates.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010189","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0030488","count":2}]},{"hash":"1968299777232855286","title":"GPCR-Rho Signaling and Thermoregulation","description":"The top GO terms converge on GPCR signaling and Rho-mediated pathways (e.g., positive regulation of Rho signaling and GPCR-related pathways), with additional cues for temperature response and pain perception, vascular permeability, and immune-endothelial interactions. This suggests a module centered on signaling regulation that spans thermoregulatory and sensory processes, with broader physiological regulation. The lack of network edges hints at a set of multifunctional regulators rather than a tightly connected complex, but the common theme is signaling control across systems.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035025","count":3},{"id":"GO:0071502","count":3},{"id":"GO:0042391","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0043114","count":3}]},{"hash":"2035486737323706270","title":"Proteostasis and ER stress response","description":"The cluster centers on protein quality control and stress responses, with frequent GO terms for unfolded protein response, ER stress signaling, proteostasis (inclusion body regulation, SRP-targeting to ER), and oxidative-stress\u2013related apoptosis regulation. Some fungal-specific terms appear as noise, but the dominant theme is proteostasis under stress.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":12},{"id":"GO:1903382","count":12},{"id":"GO:0006880","count":12},{"id":"GO:0016226","count":12},{"id":"GO:0070880","count":12}]},{"hash":"1398114686664710285","title":"ECM remodeling and bone turnover","description":"This cluster is anchored by collagen catabolic process, basement membrane disassembly, and bone resorption, pointing to extracellular matrix remodeling and bone turnover as the central theme. Other terms, such as lung branching morphogenesis and thyroid hormone response, suggest broader tissue remodeling or signaling roles, while transmembrane transport terms may be ancillary. Overall, the core function appears to be matrix remodeling with related signaling contexts.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0030574","count":1},{"id":"GO:0045453","count":1}]},{"hash":"1154793684598860209","title":"Cell Adhesion and Spreading","description":"I labeled this as Cell Adhesion and Spreading because the top GO terms strongly point to cell-matrix adhesion processes, with hemidesmosome assembly and substrate adhesion-dependent cell spreading dominating the cluster. Other terms indicate regulatory layers (protein deubiquitination, ERAD-related processes, transcription regulation) that likely reflect downstream signaling and cellular quality-control networks interfacing with adhesion dynamics, but the adhesion theme is the clearest common thread.","confidence":"Medium","size":12,"edges":31,"triangles":51,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0031581","count":3},{"id":"GO:0035001","count":3},{"id":"GO:0034446","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0021888","count":2}]},{"hash":"2089759830396749779","title":"Neural development and ciliogenesis","description":"This cluster centers on neuronal development and ciliogenesis, evidenced by terms for neurogenesis, synaptic target recognition, and morphogenesis, together with cilium assembly and intraflagellar transport, and cytoskeletal organization (actin and microtubule/centrosome). While broader developmental processes like oogenesis and chaeta morphogenesis appear, the dominant theme ties neural formation to ciliary and cytoskeletal functions.","confidence":"High","size":12,"edges":49,"triangles":98,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0022008","count":9},{"id":"GO:0006915","count":9},{"id":"GO:0048477","count":5},{"id":"GO:0044458","count":5},{"id":"GO:0035735","count":5}]},{"hash":"1369605448813239425","title":"Unknown","description":"The GO terms span diverse cellular processes including DNA replication, mRNA export, vesicle transport, protein oligomerization, energy metabolism, stress responses, and even viral replication, with no clear single function tying them together. Therefore a specific, representative label is not apparent.","confidence":"","size":12,"edges":21,"triangles":8,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0048219","count":2},{"id":"GO:0072389","count":2}]},{"hash":"2209434299844221369","title":"mRNA processing and translation regulation","description":"The cluster is dominated by post-transcriptional RNA processes: mRNA stability and modification, spliceosome-mediated mRNA splicing, and regulation of translational initiation including preinitiation complex formation and IRES-dependent translation. This pattern suggests a cohesive group of proteins that coordinate RNA maturation with the control of protein synthesis, even though a few terms (like blastocyst formation) are incidental. Therefore, a concise label reflecting both RNA processing and translation control is appropriate.","confidence":"High","size":12,"edges":59,"triangles":166,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":10},{"id":"GO:0045292","count":10},{"id":"GO:0048255","count":9},{"id":"GO:0006446","count":9},{"id":"GO:1901407","count":9}]},{"hash":"461701933077215607","title":"Neural signaling and sensory perception","description":"This cluster is dominated by GO terms tied to nervous system function: sensory perception of pain, visual perception and learning, dopaminergic synaptic transmission, behavioral response to cocaine, and ERK signaling, all pointing to neural processing and reward-related pathways. While a couple terms (heart development, macrophage chemotaxis) appear, they are peripheral to the main neural/sensory theme, which justifies a label centered on neural signaling and sensory perception.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":9},{"id":"GO:0071380","count":8},{"id":"GO:0008542","count":8},{"id":"GO:0010759","count":8},{"id":"GO:0001963","count":8}]},{"hash":"709561458604665236","title":"Epithelial Morphogenesis and Cell Polarity","description":"This cluster emphasizes epithelial tissue organization: adherens junction assembly, establishment/maintenance of cell polarity, and morphogenesis of epithelium, plus protein localization to the cell surface, suggesting a cohesive role in epithelial architecture. Some signaling terms (Ras regulation) and other morphogenesis contexts appear but do not override the core epithelial theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046580","count":2},{"id":"GO:0034394","count":1},{"id":"GO:0034333","count":1},{"id":"GO:0007568","count":1},{"id":"GO:2001241","count":1}]},{"hash":"1061753090786442029","title":"RNA Pol II Transcriptional Regulation","description":"This cluster is dominated by transcription by RNA polymerase II (GO:0006366) with 9 proteins, and includes multiple GO terms about regulating Pol II\u2013driven transcription under different conditions (nutrient signaling, ER stress, and related regulatory contexts). The other terms point to development, immune signaling, and circadian regulation, which are often controlled at the transcriptional level by Pol II. Overall, the common theme is transcriptional control by RNA Pol II across diverse biological contexts, rather than a single downstream pathway.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":9},{"id":"GO:0035470","count":6},{"id":"GO:0071353","count":6},{"id":"GO:1990440","count":5},{"id":"GO:0001892","count":5}]},{"hash":"794570513973731292","title":"Mitochondrial Cofactor Transport and Metabolism","description":"This cluster is enriched for transport of cofactors and metabolites into mitochondria (pyridoxal phosphate, thiamine pyrophosphate, iron import, glycine, phosphate), plus mitochondrial membrane fission, pointing to mitochondrial metabolism and dynamics. Some terms also reflect growth and survival signaling (IGF response, liver regeneration, pregnancy) and anti-necroptotic regulation, suggesting a link to cellular growth/survival programs tied to mitochondrial function.","confidence":"Medium","size":12,"edges":20,"triangles":6,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0031921","count":9},{"id":"GO:0090149","count":9},{"id":"GO:0030974","count":9},{"id":"GO:0007565","count":9},{"id":"GO:0048250","count":9}]},{"hash":"1718716288170850224","title":"Lymphocyte development and immune signaling","description":"This cluster centers on lymphocyte maturation and immune regulation, with terms for T cell differentiation (TH1 commitment, beta selection) and B cell differentiation (transitional B cell differentiation, IgE isotype switching), plus regulatory controls on TLR signaling, cytokine production, integrin-mediated adhesion, and cell cycle. Although a single term like uterus development appears, the prevailing pattern ties to immune development and signaling.","confidence":"High","size":12,"edges":19,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0002296","count":9},{"id":"GO:0071638","count":9},{"id":"GO:0034136","count":9},{"id":"GO:1905664","count":9},{"id":"GO:0048295","count":9}]},{"hash":"542415184466312991","title":"Vesicle trafficking and secretory pathway regulation","description":"The cluster is enriched for endosome-to-lysosome transport, multivesicular body assembly, regulation of the secretory pathway, and cell polarity maintenance, pointing to a cohesive theme of intracellular vesicle trafficking and secretory control; some terms are peripheral, but the dominant signal is vesicle trafficking-related functions.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0008333","count":1},{"id":"GO:1990456","count":1},{"id":"GO:1903307","count":1},{"id":"GO:0043652","count":1}]},{"hash":"1282616849564254871","title":"cGMP signaling with sensory and immune responses","description":"Based on the top GO terms, the cluster centers on cGMP-related signaling (receptor guanylyl cyclase pathway and cGMP response) and includes sensory perception (smell) and immune signaling (T cell receptor signaling, GM-CSF/M-CSF stimuli). This suggests a broader theme of signaling pathways that mediate cellular responses to diverse extracellular cues, with a particular emphasis on cGMP signaling.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010754","count":5},{"id":"GO:0071321","count":5},{"id":"GO:0007608","count":5},{"id":"GO:0050852","count":4},{"id":"GO:0071222","count":4}]},{"hash":"14123123306031777","title":"Embryonic Development and Organogenesis","description":"The GO terms point to development and morphogenesis across multiple tissues (embryonic organ development, in utero embryonic development, spinal cord and skin development, seminiferous tubule development) plus overall growth and proliferation, indicating a module centered on embryonic organ formation and tissue differentiation. A DNA repair term is present but does not override the central developmental theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":3},{"id":"GO:0007568","count":2},{"id":"GO:0072520","count":2},{"id":"GO:0048568","count":2},{"id":"GO:0035264","count":2}]},{"hash":"1080369053301569673","title":"Neurovascular signaling and synaptic regulation","description":"This cluster centers on neural signaling and synaptic regulation, with terms for positive regulation of synaptic plasticity, gephyrin clustering at the postsynaptic density, and serotonergic neuron axon guidance. It also includes angiogenesis-related terms (VEGF production, endothelial tip cell fate) and Notch target transcription, which can tie neural development to neurovascular patterning. A couple of outliers (marginal zone B cell differentiation, apoptotic processes in luteolysis) exist, but the dominant theme points to neural and neurovascular signaling. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031915","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0097116","count":2},{"id":"GO:0007221","count":2},{"id":"GO:0007154","count":2}]},{"hash":"1730637538599706364","title":"Unknown","description":"The terms are too heterogeneous to assign a single cohesive function: transcription regulation and a broad set of diverse biosynthetic and metabolic processes (PHB, BH4, retinol, sphingolipid, mycolic acid, androgen/estrogen biosynthesis), plus redox and catabolic activities. A concise, representative label cannot be derived.","confidence":"","size":12,"edges":14,"triangles":5,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0042619","count":4},{"id":"GO:0006729","count":4},{"id":"GO:0042572","count":4},{"id":"GO:0055114","count":4}]},{"hash":"1878756450714269544","title":"Unknown","description":"The top GO terms are very diverse, spanning oxidative stress response, carbohydrate phosphorylation, cilium-centrosome related functions, metal ion response, various post-translational modifications, and signaling. There isn\u2019t a single coherent biological theme connecting these terms, so a specific, representative label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0060296","count":1},{"id":"GO:0030850","count":1},{"id":"GO:0010288","count":1}]},{"hash":"108489365809054802","title":"Neural signaling and circadian regulation","description":"These proteins cluster around neural communication and rhythmic control: calcium entry facilitating neurotransmitter release, acetylcholine and GABA signaling, sensory processing (sound), startle reflex, and responses to nicotine and cocaine, along with circadian sleep/wake regulation. The collection consistently centers on neuronal signaling and sensory-circadian functions, with some amyloid-beta response context, which fits a neural signaling/sleep-regulation theme.","confidence":"High","size":12,"edges":19,"triangles":8,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0098703","count":6},{"id":"GO:0045188","count":6},{"id":"GO:0001964","count":6},{"id":"GO:0051971","count":5},{"id":"GO:0095500","count":5}]},{"hash":"1010200684335429873","title":"ER glycosylation and protein trafficking","description":"The top GO terms predominantly reflect protein glycosylation (including N- and O-linked pathways) and ER-related processes such as retention in the ER lumen and general protein transport. Immune signaling terms appear but are much less represented, suggesting the core function is glycoprotein maturation and secretory pathway trafficking with some incidental immune associations.","confidence":"High","size":12,"edges":17,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":2},{"id":"GO:0018279","count":1},{"id":"GO:0035269","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0010204","count":1}]},{"hash":"1357096326323422189","title":"tRNA modification and translational control","description":"The cluster features several translation-related GO terms (translation, translational elongation, translation initiation regulation by tRNA modification) and a wobble uridine modification term, pointing to a functional theme around protein synthesis and tRNA modification that modulates translation. A few other terms (antibiotic response, viral replication) appear peripheral or incidental. Overall, translation coupled with tRNA modification best explains the group.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0001172","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0006414","count":1},{"id":"GO:0043547","count":1}]},{"hash":"1524114328894194217","title":"Unknown","description":"The top GO terms span very disparate processes\u2014from iron-sulfur cluster assembly and unfolded protein response to fungal cell wall biosynthesis and DNA replication\u2014without a clear single theme linking the proteins. There is no coherent function that characterizes this cluster, so an Unknown label is appropriate.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":1},{"id":"GO:1903382","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0070880","count":1}]},{"hash":"604804685740253830","title":"Mitochondrial Redox and Energy Metabolism","description":"The cluster centers on redox balance and mitochondrial function, with terms for cell redox homeostasis, regulation of mitochondrial membrane potential, and various metabolic processes (ferredoxin, formate, phenylacetate, methylamine) that tie to mitochondrial energy metabolism. While translation appears as a minor theme and some endothelial signaling terms seem peripheral, the dominant signature is mitochondrial metabolism and redox regulation. ","confidence":"Medium","size":11,"edges":53,"triangles":147,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0030416","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006124","count":1},{"id":"GO:0006814","count":1}]},{"hash":"888501881341475219","title":"GPCR signaling in neural-immune regulation","description":"The cluster\u2019s terms center on GPCR signaling and its regulation (Gi-coupled pathways, arrestin-related desensitization), coupled with GTPase activity and components of immune-neural communication (immunological synapse, dendritic cell homeostasis). Additional terms touch on behavior (feeding, fear) and renal sodium handling, suggesting a theme of GPCR-driven signaling coordinating neural, immune, and systemic (behavioral and renal) responses.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007197","count":3},{"id":"GO:2000522","count":3},{"id":"GO:0060160","count":3},{"id":"GO:0035815","count":3}]},{"hash":"1549324292389625469","title":"Endosomal trafficking and autophagy regulation","description":"The terms point to endosome/lysosome localization, vesicle transport between plasma membrane, endosomes, and Golgi, and regulation of autophagosome maturation, all tied to Rab/Rap signaling and microtubule-based vesicle movement. This cohesive theme suggests a cluster focused on endosomal trafficking with autophagy control.","confidence":"High","size":11,"edges":17,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043553","count":1},{"id":"GO:0032486","count":1},{"id":"GO:0034499","count":1},{"id":"GO:0032483","count":1},{"id":"GO:1901097","count":1}]},{"hash":"1636084016506749217","title":"Neural development and axon guidance signaling","description":"This cluster centers on developmental signaling and neural wiring, with multiple terms tied to hedgehog signaling (Smoothened), axon guidance, and neuron migration, plus paranode localization. BMP signaling and other developmental pathways reinforce a neural-patterning theme, while a few terms like mast cell degranulation or muscle contraction may reflect broader signaling contexts. Overall, the proteins appear tied to neural development and axon pathfinding.","confidence":"Medium","size":11,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":3},{"id":"GO:0007432","count":2},{"id":"GO:0043303","count":2},{"id":"GO:0001764","count":2},{"id":"GO:0007411","count":2}]},{"hash":"2051545332067223936","title":"Unknown","description":"The top GO terms are diverse, spanning biosynthetic processes (biotin and menaquinone), antibiotic biosynthesis, general growth and stress response, host-symbiont dormancy, and even mammalian-specific terms like vasopressin secretion and cardiac membrane depolarization. With no shared, cohesive function and no network edges, there isn't a clear common biological role tying these proteins together.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0085014","count":3},{"id":"GO:0006950","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0009102","count":2}]},{"hash":"1801727039195945766","title":"Membrane organization and cell junction regulation","description":"Cluster terms consistently point to processes that organize membrane domains and cell\u2013cell interfaces, including tight junction assembly, endothelial barrier establishment, membrane raft polarization, eisosome assembly, and transcytosis, as well as regulation of adhesion and signaling pathways like PKC. While a couple of terms touch neural specifics (myelination, synaptic plasticity) and hearing, the dominant pattern is membrane/domain organization and barrier function across cell types, making this a coherent Membrane organization and cell junction regulation cluster.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034115","count":1},{"id":"GO:0090038","count":1},{"id":"GO:0007605","count":1},{"id":"GO:0042552","count":1},{"id":"GO:0045056","count":1}]},{"hash":"1155301300504725623","title":"Multi-substrate transmembrane transporters","description":"The top GO terms are dominated by transmembrane transport activities for a variety of substrates (nitrite, galactose, arabinose, 4-hydroxyphenylacetate, phosphate, nitrate assimilation, xenobiotics, etc.), with a metabolism term also present (fucose). This pattern strongly points to proteins that function as transporters with broad substrate specificity, rather than a single, narrow function.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":4},{"id":"GO:0015757","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0015751","count":3},{"id":"GO:0006855","count":3}]},{"hash":"599215824610622674","title":"Mitotic spindle and microtubule dynamics","description":"The cluster is dominated by GO terms tied to mitotic spindle function and microtubule behavior\u2014kinetochore attachment, plus- and minus-end directed movements, and microtubule depolymerization, all pointing to spindle assembly/disassembly and microtubule-based transport. A few terms reflect broader plant cytoskeletal roles (root development, chloroplast movement), but the common thread is microtubule dynamics during cell division. ","confidence":"High","size":10,"edges":35,"triangles":60,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0099607","count":10},{"id":"GO:0033624","count":10},{"id":"GO:0031534","count":10},{"id":"GO:0072383","count":10},{"id":"GO:0070462","count":10}]},{"hash":"1013141952147564876","title":"Unknown","description":"The top terms span both prostate gland development and epithelial differentiation, but also include mitotic spindle assembly, V(D)J recombination, NF-kappaB activation, and histone modification, indicating a highly mixed set of processes. With no edges or coherent functional module linking these terms, there isn't a single representative function for the cluster to name meaningfully, so Unknown is appropriate.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":2},{"id":"GO:0060528","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0060743","count":2},{"id":"GO:0033151","count":1}]},{"hash":"2181295442695025431","title":"Ribosome biogenesis and cell cycle machinery","description":"This cluster centers on fundamental growth and protein-synthesis processes, with strong signals for ribosome assembly (ribosome biogenesis, SSU-rRNA maturation, translation preinitiation complex) and genome duplication/division (DNA replication, mitotic sister chromatid cohesion, cell cycle). A few terms reflect stress/protein quality control (cadmium response, ERAD), but the dominant theme is core proliferation machinery. ","confidence":"High","size":10,"edges":43,"triangles":104,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1214204918431872379","title":"Unknown","description":"This set shows a mix of RNA metabolism-related terms (translation, transcription antitermination, exonuclease activity) and various development or signaling terms (cell morphogenesis, cardiac development, myelin assembly, TLR signaling, lipid metabolism) without a clear, unified function linking all proteins. With no dominant shared theme and edges unrelated, a confident, concise label is not possible.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055015","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0090503","count":2}]},{"hash":"2078874719780177818","title":"Integrin and Kit tyrosine kinase signaling","description":"This cluster is dominated by GO terms for integrin-mediated signaling, collagen-activated tyrosine kinase receptors, Kit signaling, peptidyl-tyrosine autophosphorylation, and PI3K-AKT\u2013related survival pathways, plus related processes like apoptotic cell clearance and anoikis regulation. Together these point to a cohesive theme of adhesion- and tyrosine kinase\u2013driven signaling that governs cell survival and immune-related functions, rather than a single metabolic or structural function. The term \u201cinnate immune response\u201d and environmental enrichment response support a broader immune-adaptive signaling context in this group.","confidence":"High","size":10,"edges":8,"triangles":0,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045087","count":8},{"id":"GO:0090648","count":7},{"id":"GO:0033138","count":7},{"id":"GO:0038063","count":7},{"id":"GO:0051897","count":7}]},{"hash":"866342069764734613","title":"Ribosome biogenesis and rRNA maturation","description":"This cluster is dominated by GO terms for maturation of SSU/LSU rRNA from tricistronic transcripts, 5.8S rRNA maturation, and large subunit preribosome assembly, indicating a core function in ribosome biogenesis and rRNA processing. A few terms are unrelated (e.g., embryonic morphogenesis, viral replication), but the ribosome-related terms are the strongest signal.","confidence":"High","size":10,"edges":40,"triangles":86,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0048701","count":3}]},{"hash":"2122668370500239347","title":"Embryonic Development and Organ Morphogenesis","description":"The top GO terms point to gastrulation (primitive streak formation), neural crest migration, and development across multiple organs (pancreas, retina, skeletal system, digestive tract, ureteric bud branching). This suggests a cohesive theme of embryonic morphogenesis and organ formation rather than a single tissue-specific function. A regulatory term is present but fits within broader developmental gene regulation. Overall, the cluster appears representative of general embryonic development and organ morphogenesis.","confidence":"High","size":10,"edges":28,"triangles":22,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090009","count":6},{"id":"GO:0031018","count":5},{"id":"GO:0001755","count":5},{"id":"GO:0090190","count":5},{"id":"GO:0048557","count":5}]},{"hash":"559420205436207078","title":"Myeloid inflammation and redox signaling","description":"These GO terms point to inflammatory signaling and oxidative stress regulation in the myeloid lineage: the presence of the cyclooxygenase pathway, negative regulation of TNF signaling and MCP-1 production, and regulation of nitric oxide and superoxide, together with a note on common myeloid progenitor proliferation. Although a few terms are obsolete, the core pattern is inflammatory/redox control in myeloid cells.","confidence":"Medium","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042178","count":1},{"id":"GO:1905804","count":1},{"id":"GO:0035732","count":1},{"id":"GO:0010804","count":1},{"id":"GO:0071638","count":1}]},{"hash":"1954724742571382673","title":"Chromatin modification and transcription regulation","description":"The top GO terms center on histone methylation (H3-K79 and H3-K4) and DNA-templated transcription, with protein homooligomerization also represented. This repeatedly points to a chromatin-regulated transcriptional control function as the cluster\u2019s core theme, with other terms (signaling, pattern formation) appearing as peripheral associations. Confidence is medium due to some heterogeneous terms outside chromatin/transcription.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034729","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051568","count":4},{"id":"GO:0072432","count":3}]},{"hash":"2230786490838962562","title":"Lipid Remodeling and T-Cell Signaling","description":"This cluster centers on lipid metabolism: ether lipid biosynthesis, phosphatidylcholine and cardiolipin remodeling, CDP-diacylglycerol biosynthesis, and triglyceride biosynthesis, suggesting a shared role in membrane lipid composition and lipid biosynthetic pathways. The presence of immune-related terms (interleukin-2 production and negative regulation of activation-induced T cell death) implies these lipid processes may influence T-cell signaling and survival. Some terms (like cutin biosynthesis and glandular epithelial maturation) seem less directly connected and may reflect broader annotation or cross-species noise. Overall, the dominant theme is lipid metabolism with potential immunomodulatory implications.","confidence":"Medium","size":10,"edges":23,"triangles":30,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0008611","count":4},{"id":"GO:2001246","count":4},{"id":"GO:0010143","count":4},{"id":"GO:0036151","count":4},{"id":"GO:0070236","count":4}]},{"hash":"1727162436081094608","title":"Multivesicular body sorting and vesicle formation","description":"Most of the top GO terms describe multivesicular body (MVB) assembly and sorting, intralumenal vesicle formation, membrane fission, and related ubiquitin-independent catabolic processes via the MVB pathway, pointing to endosomal trafficking and vesicle formation as the core function of this cluster. A few terms about spindle regulation/centriole elongation may reflect incidental cell-cycle links rather than the primary theme.","confidence":"High","size":10,"edges":11,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1901673","count":3},{"id":"GO:1902902","count":3},{"id":"GO:0036258","count":3},{"id":"GO:0090611","count":3},{"id":"GO:0071985","count":3}]},{"hash":"306178404931502135","title":"Monoamine Uptake and Brain Development","description":"The cluster\u2019s top GO terms are dominated by monoamine neurotransmitter handling, including dopamine uptake involved in synaptic transmission and serotonin uptake, along with a dopamine catabolic process and related neural signals (taurine transport also supports neural function). There are also development-related terms pointing to brain structures (thalamus development, adenohypophysis development) and a general growth regulation term, suggesting a broader neural-developmental theme. A couple of terms (pollen sperm cell differentiation, brown fat differentiation) appear as noise and do not fit the core neural theme. Overall, the data best align with a theme of monoamine neurotransmitter transport coupled with brain development processes.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048235","count":1},{"id":"GO:0050873","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0042420","count":1},{"id":"GO:0021984","count":1}]},{"hash":"171004951889837451","title":"Neuronal Synaptic Regulation and Plasticity","description":"The top GO terms cluster around neuronal synaptic function, including regulation of long-term synaptic plasticity, excitatory postsynaptic potential regulation, and postsynaptic density assembly, suggesting the proteins are primarily involved in synaptic signaling and organization. Some terms touch on immune or metabolic pathways, but the dominant signal is neuronal synaptic regulation and plasticity.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0048170","count":2},{"id":"GO:0043652","count":2},{"id":"GO:2000821","count":2},{"id":"GO:1902498","count":2}]},{"hash":"1778007195699733621","title":"Unknown","description":"The GO terms span a wide range of disparate developmental processes (kidney, heart, pancreas, muscle, nervous system) and even transcription-related terms, with no clear shared function or pathway linking the proteins. The lack of edges and several obsolete terms further suggest the cluster lacks a cohesive, interpretable biological theme.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0072289","count":1},{"id":"GO:0070898","count":1},{"id":"GO:0003308","count":1},{"id":"GO:0014718","count":1}]},{"hash":"954669419865131841","title":"Ubiquitin-regulated DNA repair and cell cycle","description":"Reasoning: The top GO terms center on ubiquitin signaling (K29- and K11-linked ubiquitination) coupled with nuclear processes like DNA repair, chromatin regulation, and cell-cycle transitions (exit from mitosis, meiotic telomere clustering, heterochromatin formation). Some peripheral terms (ABA response, fungal cell wall organization) exist but do not override the core theme. This suggests a cohesive cluster of ubiquitin-mediated control of genome maintenance and mitotic progression.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0042275","count":10},{"id":"GO:0035519","count":10},{"id":"GO:0060340","count":10},{"id":"GO:0090089","count":10},{"id":"GO:0009737","count":10}]},{"hash":"1604349994364995697","title":"Glycosylation and N-glycan processing","description":"The majority of top GO terms point to protein glycosylation, N-glycan processing, and related deglycosylation and mannose metabolism, suggesting a shared function in glycoprotein maturation; a few unrelated terms may reflect annotation noise.","confidence":"Medium","size":10,"edges":12,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":2},{"id":"GO:0016063","count":1},{"id":"GO:0035010","count":1},{"id":"GO:0006517","count":1},{"id":"GO:0006491","count":1}]},{"hash":"1905509116037899234","title":"Immune signaling and inflammatory response cluster","description":"This cluster is enriched for GO terms related to immune signaling (T cell receptor signaling, cellular response to lipopolysaccharide, GM-CSF stimulus) and inflammatory mediators (prostaglandin stimulus, GPCR desensitization). While there are also terms for DNA replication and mRNA processing, the strongest signals point to immune activation and inflammatory response, suggesting these proteins participate in immune communication and stress signaling rather than a single housekeeping process.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0050852","count":3},{"id":"GO:0071222","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0006915","count":3}]},{"hash":"294542932552934613","title":"Calcium signaling and membrane localization","description":"The GO terms point primarily to calcium ion response and transport, together with plasma membrane localization and phosphorylation regulation, suggesting a calcium-dependent signaling theme at the cell membrane. Some other terms (e.g., prostate gland development, immune cell processes) are less coherent with this core pattern, so the label focuses on the dominant calcium-membrane signaling context. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051592","count":2},{"id":"GO:0048146","count":2},{"id":"GO:0072661","count":1},{"id":"GO:0051290","count":1},{"id":"GO:0030850","count":1}]},{"hash":"441497408685681832","title":"Neural adhesion and synaptic organization","description":"The terms cluster around cell-cell adhesion in neural contexts (cadherin-mediated adhesion), postsynaptic organization (gephyrin clustering), and synaptic transmission, plus glial migration and axon guidance, implying a functional theme of neural adhesion, synapse assembly, and neuron\u2013glia interactions (with some ECM involvement suggested by collagen fibril organization).","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":2},{"id":"GO:0072661","count":1},{"id":"GO:0044331","count":1},{"id":"GO:0010804","count":1},{"id":"GO:0071307","count":1}]},{"hash":"712386009537818627","title":"Genome maintenance and DNA damage response","description":"The cluster is dominated by terms tied to genome maintenance: regulation of DNA recombination, helicase activity, DNA damage checkpoint signaling, and maintenance of repetitive elements, suggesting a role in genome stability and DNA repair. Other GO terms (viral process, embryonic development, immunoglobulin isotype switching) may reflect pleiotropic roles or context-specific functions, but do not redefine the core theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0008340","count":1},{"id":"GO:0043570","count":1},{"id":"GO:0048304","count":1},{"id":"GO:0048298","count":1}]},{"hash":"57917942785414531","title":"Actin-Driven Cell Polarity and Organelle Inheritance","description":"This cluster centers on actin cytoskeleton assembly and maintenance of cell polarity, with multiple terms for actin patch and filament bundle assembly and polarity-related shape control. It also includes inheritance of mitochondria and vacuoles, pointing to coordinated cytoskeletal dynamics and organelle distribution. Some terms (ascospore wall assembly, mesenchyme migration) are less directly tied but may reflect broader cytoskeletal or developmental roles; overall, the dominant pattern is actin-mediated organization alongside organelle inheritance.","confidence":"Medium","size":9,"edges":30,"triangles":57,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000147","count":3},{"id":"GO:0071963","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0000011","count":3},{"id":"GO:0043486","count":3}]},{"hash":"1360987638095660718","title":"Ciliogenesis and Neural Development with Cytoskeletal Remodeling","description":"Top GO terms point to ciliogenesis (motile and intraciliary transport) and neurogenesis, with supporting cues from synaptic target recognition and cytoskeletal organization (actin/microtubule). Although there are broader developmental terms (oogenesis, chaeta morphogenesis) the strongest signal centers on cilia-associated development and neural differentiation, implying a coherent cluster around ciliary functions linked to neural development and cytoskeletal remodeling.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0022008","count":8},{"id":"GO:0006915","count":8},{"id":"GO:0048477","count":7},{"id":"GO:0044458","count":7},{"id":"GO:0035735","count":7}]},{"hash":"1121792517288693456","title":"Immune signaling and metabolic regulation","description":"The GO terms point to immune signaling (positive regulation of T cell polarity, TLR3 signaling) and PKC pathways, while other terms involve cell adhesion/ECM remodeling and mitochondrial metabolism (SREBP signaling, inner mitochondrial membrane organization, mitochondrial DNA replication), suggesting a cluster where signaling, metabolism, and structural dynamics are co-regulated.","confidence":"Medium","size":9,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1903905","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2000049","count":2},{"id":"GO:0034141","count":2},{"id":"GO:0022617","count":2}]},{"hash":"1592854629838234078","title":"ER Stress Response and Protein Targeting","description":"The top GO terms highlight cellular response to unfolded protein and SRP-dependent cotranslational targeting to the ER, pointing to a core theme of managing protein folding and trafficking in the endoplasmic reticulum. A few terms (DNA replication, karyogamy, iron-sulfur cluster assembly) are less clearly related and may reflect broader cellular processes or annotation noise, but the dominant signal centers on ER-associated quality control and protein translocation.","confidence":"Medium","size":9,"edges":24,"triangles":27,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034620","count":2},{"id":"GO:0090084","count":1},{"id":"GO:1903382","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0000902","count":1}]},{"hash":"2143541110934101278","title":"Protein homeostasis and transcription regulation","description":"This cluster combines several themes around how cells manage and regulate proteins: translation (protein synthesis), post-translational modifications (deubiquitination and sumoylation), ER-associated degradation and ER stress\u2013related signaling, and control of transcription by RNA Pol II. Together these terms point to a cohesive function in maintaining proteostasis while coordinating gene expression, with additional connections to signaling pathways and developmental processes that may reflect broader regulatory roles. ","confidence":"Medium","size":9,"edges":29,"triangles":56,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0045648","count":7},{"id":"GO:0021888","count":6},{"id":"GO:0016579","count":6},{"id":"GO:0033132","count":6}]},{"hash":"318296299901238361","title":"Neural Embryogenesis and Protein Quality Control","description":"The top GO terms point to neural differentiation and embryonic development, indicating a developmental program toward neural lineages. Additional terms related to ubiquitination, aggresome formation, translation, and DNA replication suggest concurrent protein homeostasis and basic cellular processes supporting development. EMT regulation and TNF signaling imply interplay between signaling and morphogenesis. Taken together, the cluster centers on neural development and embryogenesis with supportive protein quality control mechanisms.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0051865","count":2},{"id":"GO:0048745","count":2},{"id":"GO:0006412","count":2}]},{"hash":"871845165158987490","title":"Chromatin Regulation & Transcription Control","description":"This cluster centers on DNA-templated transcription, heterochromatin formation/maintenance, nucleosome density, and histone deacetylation, indicating epigenetic regulation of chromatin state; additional terms appear as broader process links but do not change the core theme.","confidence":"Medium","size":9,"edges":33,"triangles":65,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:2000648","count":3},{"id":"GO:0060303","count":3},{"id":"GO:0045820","count":3},{"id":"GO:0000183","count":3}]},{"hash":"231015984023940512","title":"Intercellular adhesion and signaling across tissues","description":"This cluster centers on terms related to cell-cell adhesion, signaling, and communication (including heterophilic adhesion, synapse assembly regulation, and GABA secretion) spanning neural, immune, and cardiac contexts. While bone ossification and host\u2013cell entry appear less directly linked, the dominant theme is intercellular communication and adhesion across diverse tissues, rather than a single tissue-specific process.","confidence":"Medium","size":9,"edges":11,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":3},{"id":"GO:0086072","count":3},{"id":"GO:0051963","count":3},{"id":"GO:0043318","count":3},{"id":"GO:0007157","count":3}]},{"hash":"598154029360451728","title":"Heart development and cardiac conduction","description":"This cluster is strongly linked to heart formation and electrical activity, with GO terms such as regulation of SA node cell action potential, regulation of atrial cardiac muscle cell action potential, and outflow tract morphogenesis pointing to cardiac development and electrophysiology. Other terms like DNA replication or protein folding are general cellular processes, but the cardiac-specific terms dominate the theme, supporting a cohesive label around heart development and cardiac conduction. ","confidence":"High","size":9,"edges":23,"triangles":26,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0090084","count":3},{"id":"GO:1900035","count":3}]},{"hash":"1872439854151061376","title":"Skeletal muscle contraction and regeneration signaling","description":"The top GO terms are dominated by skeletal muscle functions: diaphragm contraction, fast/slow fiber transition, and satellite cell activation in skeletal muscle regeneration, along with regulation by cAMP and epinephrine signaling. While a few terms (like phototransduction) are less related, the overall pattern centers on muscle contraction and its regulation and regeneration.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051591","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0071872","count":3},{"id":"GO:0002086","count":2},{"id":"GO:0036368","count":2}]},{"hash":"720551528695768788","title":"Plant development and cytoskeleton signaling","description":"Top terms include plant-specific adaxial/abaxial pattern formation, actin filament depolymerization and Arp2/3 regulation, and microtubule-based movement, alongside general signaling and cell-cycle related terms (G1 checkpoints, nutrient/glucose signaling). This suggests a cluster centered on plant development features intertwined with cytoskeletal dynamics and basic signaling, rather than a single narrow function. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0072432","count":6},{"id":"GO:0007200","count":6},{"id":"GO:2000011","count":6},{"id":"GO:0070317","count":6},{"id":"GO:0007584","count":6}]},{"hash":"102644409768000537","title":"RNA processing and spliceosome activity","description":"This cluster is dominated by GO terms related to RNA metabolism and spliceosome function: transcription termination by RNA polymerase II, mRNA splicing via the spliceosome, spliceosomal complex assembly, maturation of rRNA, and tRNA processing. These indicate a cohesive set of proteins involved in RNA processing and gene expression regulation. Some peripheral terms (sncRNA-mediated silencing, histone mRNA metabolism, abscisic acid response, hair cycle) may reflect broader regulatory connections but do not override the central RNA-processing theme.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006369","count":6},{"id":"GO:0045292","count":6},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0008334","count":4}]},{"hash":"1347140633871812947","title":"Macrophage phagocytosis and innate immunity","description":"The top GO terms cluster around innate immune response, apoptotic cell clearance, foam cell differentiation (a macrophage-related process), IL-4 regulation, and cell-matrix/vascular interactions, which together point to macrophage activation and phagocytic activity with endothelial context. Some terms (nuclear transcription and visual perception) are less specific to this theme, but the macrophage-immune signal is the strongest.","confidence":"Medium","size":9,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046826","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043277","count":2},{"id":"GO:0007160","count":2},{"id":"GO:0032753","count":2}]},{"hash":"2180198548494684245","title":"Core Translation Initiation and Termination Machinery","description":"The top GO terms are centered on translation, including translation itself, initiation, termination, formation of the preinitiation complex, and translation reinitiation, with additional signals of translational fidelity regulation. A few terms touch on RNA processing (spliceosome-regulated splicing and mRNA export), suggesting some coordination between RNA processing and translation. Overall, the cluster seems to represent proteins involved in the core translation machinery, with ancillary RNA processing links.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006413","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0000381","count":2}]},{"hash":"473521285982269204","title":"RTK-MAPK Signaling in Development","description":"This cluster is enriched for receptor tyrosine kinase signaling (cell surface receptor tyrosine kinase signaling pathway; peptidyl-tyrosine autophosphorylation) and MAPK cascade regulation, alongside several differentiation/development terms across tissues (urogenital system development, photoreceptor differentiation, NK cell differentiation). The common thread suggests RTK-driven signaling influencing developmental processes in diverse contexts.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0001655","count":4},{"id":"GO:0030513","count":4},{"id":"GO:0038083","count":4},{"id":"GO:0043277","count":4},{"id":"GO:0001751","count":4}]},{"hash":"1031377241557622505","title":"Axon Guidance and Neural Development","description":"It centers on neuronal development: GO terms include axon guidance, nervous system development, and Roundabout signaling (ROBO), with positive regulation of ERK/MAPK signaling contributing to neuronal growth and connectivity. While some terms relate to broader developmental processes (ossification, spermatid development, wound healing), the dominant theme is neural patterning and guidance.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0002551","count":3},{"id":"GO:0035385","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0043931","count":3}]},{"hash":"286825120522596314","title":"Developmental Morphogenesis Across Tissues","description":"Top GO terms consistently describe morphogenesis of diverse tissues and organs (semicircular canal, outflow tract, hindlimb, eye, placenta, prostate, habenula). This suggests a shared theme of developmental tissue formation across multiple systems, justifying the label with a broad yet specific focus on morphogenesis across tissues.","confidence":"High","size":9,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048752","count":2},{"id":"GO:0036091","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0060527","count":2}]},{"hash":"987559005038593338","title":"Mitochondrial transport and fission","description":"The cluster is dominated by mitochondrial-related functions, including mitochondrial membrane fission and iron import into mitochondrion, plus transport of various cofactors and ions (pyridoxal phosphate, thiamine pyrophosphate, phosphate, glycine) across membranes. This points to a group of proteins involved in mitochondrial metabolite transport and mitochondrial dynamics. Some systemic terms (liver regeneration, IGF stimulus) appear but are less central to the core theme.","confidence":"Medium","size":9,"edges":9,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":3},{"id":"GO:0031921","count":2},{"id":"GO:0090149","count":2},{"id":"GO:0030974","count":2},{"id":"GO:0007565","count":2}]},{"hash":"262128225863996190","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097310","count":1},{"id":"GO:0019062","count":1},{"id":"GO:0039694","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0000453","count":1}]},{"hash":"1096030371609024766","title":"Translation and Transcription Machinery","description":"The cluster is strongly enriched for translation-related GO terms: translation, ribosomal large subunit assembly, cytoplasmic translation, and translational termination, plus tRNA wobble uridine modification, pointing to the core protein synthesis machinery. There are also signals of transcription-related activity (DNA-templated transcription and its regulation), suggesting a broader link to gene expression. A few terms (response to antineoplastic agent, interleukin-4 response) may reflect context-dependent roles or annotation noise, but the dominant theme is translation/gene expression machinery.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000027","count":4},{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006415","count":1}]},{"hash":"1314249111325576359","title":"Embryonic development and organ morphogenesis","description":"This cluster includes GO terms across visual perception, neural differentiation and migration, skeletal and digit morphogenesis, skeletal muscle development, axis specification, and ureteric bud formation, indicating a broad theme of embryonic tissue morphogenesis and organ development. Some terms appear noisy or cross-annotated (e.g., plant hormone biosynthesis), but the dominant signal is developmental morphogenesis across multiple organ systems.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0048706","count":1},{"id":"GO:0009798","count":1},{"id":"GO:0061296","count":1},{"id":"GO:0010371","count":1}]},{"hash":"1112693941867983242","title":"Muscle Metabolism and Stress Signaling","description":"The terms center on muscle-related processes (fast/slow fiber transition; actomyosin contractile ring assembly), energy metabolism (glycogen metabolism), and cellular stress responses (unfolded protein response; chromatin regulation; mitochondrial DNA repair), suggesting a theme of muscle cell metabolism coupled with stress signaling, with some broader developmental and drug-response contexts reflected in overlapping pathways.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":8},{"id":"GO:0070940","count":8},{"id":"GO:0014883","count":8},{"id":"GO:0005977","count":8},{"id":"GO:0030324","count":8}]},{"hash":"754347211603121219","title":"Dopaminergic signaling and axonogenesis network","description":"The cluster centers on GO terms related to dopamine response, axonogenesis/axon extension, and regulation of phosphorylation and JNK signaling, which together point to dopamine-influenced neuronal growth and axon formation via MAPK/JNK pathways, with developmental context suggested by hippocampus development. Some terms (like T cell receptor signaling and abscisic acid signaling) seem peripheral or noisy, but the dominant pattern is neuronal signaling and axon growth.","confidence":"Medium","size":8,"edges":9,"triangles":2,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903351","count":6},{"id":"GO:0033138","count":6},{"id":"GO:0045773","count":6},{"id":"GO:0046330","count":6},{"id":"GO:0010800","count":6}]},{"hash":"78010872107406702","title":"Embryonic neural development and patterning","description":"The top GO terms cluster around early embryogenesis and neural development: primitive streak formation, axis specification, neuronal fate commitment (forebrain), and organogenesis (pituitary gland, skeletal system, digits). Despite some broad or cross-taxon terms, the dominant theme is embryonic development with emphasis on neural patterning and tissue formation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0090009","count":3},{"id":"GO:0021983","count":3},{"id":"GO:0048935","count":3},{"id":"GO:0048706","count":2}]},{"hash":"1425809005751062215","title":"Unknown","description":"The set includes diverse GO terms spanning reproduction (sperm capacitation), muscle development, lipid biosynthesis regulation, RNA processing, prostaglandin signaling, GPCR desensitization, environmental response, centrosome localization, and DNA damage response, with no single cohesive function linking them. This lack of a common theme makes it inappropriate to assign a specific, high-confidence label.","confidence":"","size":8,"edges":13,"triangles":5,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":6},{"id":"GO:0007519","count":5},{"id":"GO:0090153","count":5},{"id":"GO:0006397","count":5},{"id":"GO:0071380","count":5}]},{"hash":"36270129356064198","title":"Heart development and cardiac conduction signaling","description":"The enriched terms cluster around heart development and regulation of electrical conduction in the heart, with supporting muscle and cytoskeletal processes (diaphragm contraction, actin crosslinking, fiber-type switching) and signaling regulation (GTPase activity, kinase activity, methylation). These collectively point to a cohesive theme of cardiac muscle formation and the signaling that governs contraction and electrical coupling.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0031954","count":6},{"id":"GO:0051764","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0071902","count":6}]},{"hash":"717103406421134051","title":"Ubiquitin-dependent protein degradation","description":"This cluster is strongly characterized by ubiquitination-related GO terms: protein ubiquitination, ubiquitin-dependent protein catabolic process, and protein autoubiquitination, pointing to a core role in tagging and degrading proteins. The other annotated terms (transcriptional regulation, oxidative stress response, metabolic regulation, behavior, and cell adhesion) may reflect broader regulatory connections but do not outweigh the central ubiquitination theme. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0070301","count":2}]},{"hash":"1427114416159735360","title":"LDL receptor metabolism and trafficking","description":"The GO terms are dominated by LDL receptor\u2013related processes (catabolic regulation, receptor catabolic activity, receptor binding, and receptor recycling), indicating a cluster centered on LDL receptor metabolism and trafficking. Additional terms about insulin processing and secretory pathway protein processing appear as related ancillary processes, but the most consistent theme is LDL receptor regulation and receptor trafficking.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032805","count":1},{"id":"GO:0032804","count":1},{"id":"GO:0030070","count":1},{"id":"GO:1905596","count":1},{"id":"GO:0007323","count":1}]},{"hash":"1216611269093504189","title":"RNA Modification and Translation","description":"This cluster centers on RNA processing, with strong signals for pseudouridine synthesis in rRNA and snRNA alongside cytoplasmic translation, suggesting a role in RNA maturation and protein synthesis. Minor terms like DNA repair and chromatin organization appear less related and may reflect background signals.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0031118","count":2},{"id":"GO:0031120","count":2},{"id":"GO:0006281","count":1},{"id":"GO:0071549","count":1}]},{"hash":"1880244591269962629","title":"Circadian Neuronal Signaling","description":"This cluster centers on neuronal signaling and excitability, highlighted by circadian regulation of sleep/wake cycles and multiple neurotransmission pathways (GABA and acetylcholine signaling), along with ion transport (K+ and Ca2+), sensory processing (sound perception, startle response), and behavioral responses (to cocaine, amyloid-beta). Together, these terms suggest a cohesive theme of circadian-influenced neural signaling and sensory processing.","confidence":"High","size":8,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045188","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0001964","count":5},{"id":"GO:0098703","count":5},{"id":"GO:0051971","count":3}]},{"hash":"16509107083101030","title":"Rho-driven actin remodeling","description":"The top GO terms show strong enrichment for actin cytoskeleton organization, filopodium and crosslink formation, and regulation of Rho signaling, plus activation of GTPase activity. This points to a core function in cytoskeleton dynamics governed by Rho-family GTPases. Some terms (mitochondrial fission, endosome-Golgi transport, COP9 signalosome assembly, thrombin receptor signaling) suggest broader GTPase-regulated signaling and trafficking, but the dominant theme is actin remodeling driven by Rho signaling.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000266","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0070493","count":2}]},{"hash":"373245178514533339","title":"Plasmodesmata transport and cell wall synthesis","description":"This cluster centers on plant-specific processes: plasmodesma organization, regulation of plant-type cell wall cellulose biosynthesis, and cell wall modification, along with protein secretion/transport and ER retention. Together they suggest proteins involved in trafficking to the cell wall/plasmodesmata and in wall synthesis/remodeling, with a minor signal of immune-related signaling that may be incidental. ","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009831","count":1},{"id":"GO:0009663","count":1},{"id":"GO:2001009","count":1},{"id":"GO:0009306","count":1},{"id":"GO:0010204","count":1}]},{"hash":"375652074213751241","title":"Embryonic organogenesis and morphogenesis","description":"The GO terms cluster around diverse developmental processes across multiple organs (heart valve formation, metanephric kidney/nephron morphogenesis, somitogenesis, neuronal differentiation timing, nerve and bronchiole development, and body morphogenesis). This suggests a shared role in embryonic tissue morphogenesis and differentiation rather than a single tissue-specific function.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000802","count":2},{"id":"GO:0072162","count":2},{"id":"GO:0072282","count":2},{"id":"GO:0001756","count":2},{"id":"GO:2000820","count":2}]},{"hash":"1847814803374756269","title":"Embryonic organ morphogenesis","description":"The GO terms center on embryogenesis and organ morphogenesis across multiple tissues (pancreas, neural crest, kidney, digestive tract, lung, eye, etc.), suggesting a shared role in developmental patterning and morphogenesis rather than a single molecular function.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0031018","count":4},{"id":"GO:0001755","count":4},{"id":"GO:0090190","count":4},{"id":"GO:0048557","count":4}]},{"hash":"1174178765689402908","title":"Mitochondrial Translation and Respiration","description":"The cluster\u2019s GO terms center on mitochondrial protein synthesis (translation, rRNA maturation) and energy production (aerobic respiration, mitochondrial electron transport, proton-driven ATP synthesis, and complex III assembly), indicating a coherent module for mitochondrial gene expression paired with oxidative phosphorylation. A cilium localization term appears as a peripheral annotation but does not override the central mitochondrial theme.","confidence":"High","size":8,"edges":20,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0099132","count":1}]},{"hash":"1742340432850397070","title":"Proteostasis: ERAD and Nuclear QC","description":"The cluster centers on protein quality control processes, including handling of misfolded proteins, ubiquitin-dependent ER-associated degradation (ERAD), chaperone-assisted refolding, and nuclear quality control. The presence of terms for misfolded protein transport, ERAD, ubiquitin-proteasome\u2013mediated nuclear QC, and post-translational targeting to membranes suggests a cohesive proteostasis module, though there are a few development-related terms that appear ancillary.","confidence":"High","size":8,"edges":23,"triangles":31,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0032781","count":2}]},{"hash":"624063440840328390","title":"Cerebellar cortex development and Bergmann glia differentiation","description":"The top GO terms include Bergmann glial cell differentiation and cerebellar cortex formation, which point to a cerebellum-focused developmental role for this cluster. Other terms such as cell cycle regulation, insulin signaling, and RNA capping appear but do not form a cohesive theme, so the strongest signal is cerebellar neurodevelopment, with surrounding terms likely representing broader cellular processes that co-occur. Overall, a cerebellar development-themed label is appropriate, with some caveats due to noise from unrelated functions.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0048679","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0050852","count":2}]},{"hash":"656705487157570570","title":"Neuronal signaling and sensory processing","description":"This cluster centers on neural communication and sensory modalities, with strong representation for memory (long-term memory), synaptic activity (excitatory postsynaptic potential), and sensory transduction (phototransduction, cone photoresponse recovery), plus calcium transport which underpins neuronal signaling. The presence of amphetamine response and protein methylation/chromatin regulation suggests activity-dependent neural plasticity. A few terms related to muscle contraction and regeneration may be secondary noise. Overall, the theme is neural signaling and sensory perception.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035562","count":2},{"id":"GO:0007616","count":2},{"id":"GO:0006816","count":2},{"id":"GO:0001975","count":2},{"id":"GO:0060079","count":2}]},{"hash":"1134691041127299414","title":"Neuronal Axon Guidance and Neurodevelopment","description":"This cluster shows enriched GO terms centered on neural development and axon pathfinding, including dopaminergic/serotonergic neuron axon guidance and synapse assembly, with supporting terms for planar polarity and inner ear development. A non-neural term related to B cell differentiation is likely incidental, not changing the overall neural development theme. ","confidence":"High","size":8,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090251","count":4},{"id":"GO:0007626","count":4},{"id":"GO:0060490","count":4},{"id":"GO:0051965","count":4},{"id":"GO:0003273","count":4}]},{"hash":"1437844322762004183","title":"Excitable-tissue signaling in muscle and retina","description":"Based on the top GO terms, the cluster shows a pattern centered on muscle function (diaphragm contraction; satellite cell activation in muscle regeneration; fiber type switching) and retinal/visual system processes (cone photoresponse recovery; phototransduction; retinal bipolar neuron differentiation), with an additional note of cardiac electrical coupling. This suggests proteins involved in signaling and differentiation across excitable tissues such as muscle, retina, and heart. Some terms are more general (xenobiotic transport, protein methylation, cytokinesis regulation) but do not overpower the overall theme.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0002086","count":1},{"id":"GO:0036368","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0014718","count":1}]},{"hash":"36961468333788493","title":"Cellular stress responses and metabolic regulation","description":"This cluster features terms related to proteostasis (unfolded protein response), genome maintenance (mitotic intra-S checkpoint signaling, mitochondrial double-strand break repair), chromatin regulation, metabolism (glycogen metabolic process), and developmental pathways (lung development, muscle fiber transition). The common thread appears to be cellular stress response and maintenance of cellular homeostasis that intersects metabolism and development, with some cell-cycle control elements also present.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":7},{"id":"GO:0070940","count":7},{"id":"GO:0014883","count":7},{"id":"GO:0005977","count":7},{"id":"GO:0030324","count":7}]},{"hash":"919237561951637413","title":"Developmental Signaling and Differentiation","description":"The cluster features GO terms tied to signaling pathways (positive regulation of GTPase activity; glucose-mediated signaling; blue light signaling; forskolin response) and developmental/differentiation processes (embryonic digit morphogenesis; regulation of melanocyte differentiation). This suggests a cohesive theme around signaling-driven development and pigment cell differentiation, with mitochondrial membrane organization indicating a supportive cellular context. Some terms are marked obsolete, but the core signals point to developmentally focused signaling roles.","confidence":"Medium","size":7,"edges":17,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0055108","count":3},{"id":"GO:1904322","count":3},{"id":"GO:0042733","count":3},{"id":"GO:0045634","count":3}]},{"hash":"1116949763048478739","title":"DNA replication and nucleotide-excision repair cluster","description":"This cluster is dominated by GO:0006260 (DNA replication) and GO:0006289 (nucleotide-excision repair), indicating a core function in genome maintenance. Additional signals for embryonic development, hair cell differentiation, hypoxia response, and RNA processing suggest broader regulatory or context-specific roles, but the dominant theme remains DNA replication and repair.","confidence":"Medium","size":7,"edges":7,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0048568","count":2},{"id":"GO:0033683","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0006289","count":2}]},{"hash":"489426083407217385","title":"Neural and Sensory System Development","description":"The top GO terms cluster around nervous system and sensory organ development\u2014inner ear, cerebellum, retinal ganglion cell axon guidance, motor neuron axon guidance, and general nervous system development\u2014suggesting the proteins are involved in neural/sensory patterning and connectivity. While some terms (heart, placenta, skeletal muscle development) touch broader embryogenesis, the dominant signal is neural and sensory development and axon guidance.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0048839","count":4},{"id":"GO:0007519","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0021549","count":3}]},{"hash":"1161871188815142927","title":"Unknown","description":"The Top Terms span hair follicle maturation, cardiac muscle development, secretory granule localization, actin regulation, hearing, thrombin signaling, microvillus organization, brain development, cytokinesis membrane addition, and unidimensional cell growth. There is no clear shared function or pathway linking these terms, and the graph shows no edges or triangles, indicating a lack of cohesive biological theme. Consequently, no specific, descriptive label can be confidently assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048820","count":1},{"id":"GO:0048739","count":1},{"id":"GO:0032252","count":1},{"id":"GO:1903919","count":1},{"id":"GO:0007605","count":1}]},{"hash":"582646785398789173","title":"Unknown","description":"The top GO terms span very different processes (DNA damage response, GPCR-PLC signaling, plant patterning, cell-cycle transitions, nutrient and glucose signaling, actin/microtubule dynamics, ribosomal RNA maturation). This diversity provides no single coherent function tying all 7 proteins together, so there isn\u2019t a clear label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072432","count":2},{"id":"GO:0007200","count":2},{"id":"GO:2000011","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0007584","count":2}]},{"hash":"62714219265612075","title":"Multisystem Stress Response","description":"These GO terms span endocrine (vasopressin secretion, cortisol biosynthesis), cardiovascular (SA node regulation), immune (T cell signaling regulation, macrophage protein production), sensory (thermoception), and osmotic stress signaling. The common thread is a systemic stress-response across tissues rather than a single molecular function, suggesting a cross-system adaptation theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030103","count":2},{"id":"GO:0051928","count":2},{"id":"GO:0016340","count":2},{"id":"GO:0034651","count":2},{"id":"GO:0008627","count":2}]},{"hash":"466754593289182435","title":"RNA Methylation and Ribosome Biogenesis","description":"The top GO terms are dominated by RNA modification activities (tRNA methylation, tRNA wobble uridine modification, RNA guanine-N7 methylation) and a ribosome-related process (ribosomal small subunit export from nucleus), suggesting a core theme around RNA processing/modification and ribosome biogenesis. The remaining terms (cobalamin, vitamin E, and sterol biosynthesis) seem more peripheral or noisy in this cluster. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000056","count":4},{"id":"GO:0035690","count":4},{"id":"GO:0030488","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0006972","count":3}]},{"hash":"914599295273977053","title":"Vertebrate Embryogenesis and Neurodevelopment","description":"These proteins are enriched for vertebrate embryogenesis and neurodevelopment processes, including primitive streak formation, axis specification, skeletal system development, pituitary formation, and neuronal differentiation, suggesting a coherent developmental program rather than a single pathway.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090009","count":4},{"id":"GO:0021983","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0048935","count":4},{"id":"GO:0055114","count":3}]},{"hash":"1613332170030932306","title":"Unknown","description":"The GO terms span diverse biology\u2014from cell cycle and neural differentiation to cardiac signaling, hormone secretion, innate immune signaling, RNA processing, plant defense signaling, and protein localization\u2014without a common, dominant function tying the proteins together. This breadth suggests no coherent theme for this cluster, so the label Unknown with no confidence is appropriate.","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:1900827","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0030103","count":2},{"id":"GO:0051017","count":2}]},{"hash":"894055438060086329","title":"Unknown","description":"The GO terms are scattered across multiple unrelated developmental and cellular processes (kidney, heart, pancreas, glands, neuroblast division, transcription initiation, immune signaling) with no clear shared function or pathway, and there are no interactions in the cluster. This lack of a cohesive theme warrants an Unknown label with no confidence.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072289","count":1},{"id":"GO:0070898","count":1},{"id":"GO:0003308","count":1},{"id":"GO:0014718","count":1},{"id":"GO:0044334","count":1}]},{"hash":"2304444157732169705","title":"Unknown","description":"The top terms span diverse processes (aging, xenobiotic response, DNA repair, skin development, redox homeostasis, and lipid signaling) with no single dominant function, so there is no coherent unifying theme to name the cluster beyond Unknown.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0080111","count":2},{"id":"GO:0044179","count":2},{"id":"GO:0006284","count":2}]},{"hash":"493869762896456760","title":"Neurodevelopment and Sensory Signaling","description":"The terms cluster around neural development (neural crest/Wnt signaling and globus pallidus development), sensory perception (touch and pain), circadian neural regulation, and modulation of signaling pathways (Rho, oligomerization). A few cardiac-related terms are present, but the dominant theme is neural development and sensory signaling, with broader regulatory processes.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":1},{"id":"GO:0044335","count":1},{"id":"GO:0060372","count":1},{"id":"GO:0021759","count":1},{"id":"GO:0035024","count":1}]},{"hash":"869797789213922326","title":"Mitochondrial respiration and ATP synthesis","description":"The dominant GO terms are mitochondrial electron transport, aerobic respiration, and ATP synthesis, pointing to a core role in mitochondrial energy production. While there are incidental immune signaling terms represented at low frequencies, they do not define the cluster\u2019s primary function. This makes mitochondrial energy metabolism a solid, representative label.","confidence":"High","size":7,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0042776","count":1},{"id":"GO:0002296","count":1},{"id":"GO:0071638","count":1}]},{"hash":"995536105345061854","title":"Proteostasis and protein quality control","description":"The GO terms cluster around handling misfolded proteins, ERAD, ubiquitin-proteasome\u2013mediated quality control, chaperone-assisted refolding, and nuclear quality control, with elements of protein export and membrane targeting\u2014together pointing to a proteostasis network maintaining protein folding and turnover.","confidence":"High","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":5},{"id":"GO:0070843","count":5},{"id":"GO:0030433","count":5},{"id":"GO:1901621","count":5},{"id":"GO:0032781","count":5}]},{"hash":"776933914026103662","title":"Ubiquitin/SUMO control of ER stress and protein homeostasis","description":"The cluster\u2019s top GO terms cluster around post-translational modification and protein quality control: ubiquitin-dependent ERAD, deubiquitination, and sumoylation, as well as regulation related to ER stress and protein handling. Additional terms touch on nuclear transport and transcription, which can be connected to protein trafficking and gene regulation in the context of homeostasis. The recurring theme is ubiquitin/SUMO pathways governing protein fate and ER stress responses, making a combined label more informative than any single term. ","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0090204","count":4},{"id":"GO:0021888","count":4},{"id":"GO:0016579","count":4},{"id":"GO:0033132","count":4}]},{"hash":"1880198437354966147","title":"Unknown","description":"The terms span hormone biosynthesis (abscisic acid), RNA processing, chromatin modification, vesicle transport, and transcriptional regulation, with many unrelated GO terms. This dispersion suggests no single cohesive function for the cluster; thus a precise, representative label is not apparent.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0035196","count":2},{"id":"GO:0033624","count":2}]},{"hash":"1574383008117665792","title":"Nucleotide salvage and catabolism","description":"The top GO terms cluster around salvage and breakdown of nucleotides (UMP salvage, purine ribonucleoside salvage, inosine and deoxyguanosine catabolism, urate biosynthesis), suggesting a coherent theme of nucleotide metabolism; other terms are present but less central, making the nucleotide salvage focus the best-supported label.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006148","count":2},{"id":"GO:0034418","count":2},{"id":"GO:0044206","count":2}]},{"hash":"816626400723330855","title":"Neural and muscular differentiation and signaling","description":"The GO terms point to differentiation and maturation of neural tissues (retinal bipolar neurons, astrocyte differentiation) and muscle systems (diaphragm contraction, fast/slow fiber transitions, cardiac conduction signaling) along with related calcium signaling and phototransduction processes. A few terms (e.g., fungal prospore membrane formation) seem less connected, suggesting some noise, but the dominant theme is neural and muscular development and signaling.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002086","count":6},{"id":"GO:0006479","count":6},{"id":"GO:0007602","count":6},{"id":"GO:0014883","count":6},{"id":"GO:0032465","count":6}]},{"hash":"2002040972063774712","title":"Muscle development and retinal signaling","description":"Several top GO terms cluster around skeletal muscle biology (diaphragm contraction; positive regulation of satellite cell activation involved in skeletal muscle regeneration; transition between fast and slow fiber) and retinal signaling (cone photoresponse recovery; phototransduction; retinal bipolar neuron differentiation). While there are outliers related to general processes (protein methylation; regulation of cytokinesis) and cardiac conduction, the strongest signal ties to signaling in excitable tissues\u2014muscle and retina. Thus the label reflects the core themes of muscle development and retinal signaling in the cluster.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002086","count":5},{"id":"GO:0036368","count":5},{"id":"GO:0006479","count":5},{"id":"GO:0014718","count":5},{"id":"GO:0007602","count":5}]},{"hash":"436081871436776608","title":"Peptidoglycan Synthesis and Cell Division","description":"These proteins cluster around core bacterial growth processes: peptidoglycan biosynthesis, cell wall organization, regulation of cell shape, and cell division. While a few metabolism and development terms appear, the dominant signal is assembly of the cell wall and cytokinesis, supporting a cohesive theme of bacterial growth and division.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009252","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0005978","count":2}]},{"hash":"619868725930251700","title":"Unknown","description":"The top GO terms cover a wide range of processes\u2014from immune signaling (negative regulation of TLR2) to calcium transport, behavior, translation initiation, cytoskeleton (actin bundle, ruffle assembly), cell junction localization, B cell differentiation, and development (uterus). The proteins show no edges or consistent functional theme, so there is no cohesive cluster function to name. Therefore this cluster is Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034136","count":2},{"id":"GO:1905664","count":2},{"id":"GO:2000821","count":2},{"id":"GO:1903679","count":2},{"id":"GO:0051017","count":2}]},{"hash":"1309703286554325260","title":"Unknown","description":"The top GO terms span lipid regulation, cell polarity, sporulation, intracellular pH changes, vitamin transport and metabolism, placenta development, and lysosome organization, which reflect multiple unrelated biological areas rather than a single coherent function. With no clear shared pathway or process across the six proteins, there isn\u2019t a concise label that captures the cluster\u2019s function.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001246","count":1},{"id":"GO:2000114","count":1},{"id":"GO:0043942","count":1},{"id":"GO:0051452","count":1},{"id":"GO:0051180","count":1}]},{"hash":"1287889585506126605","title":"Embryonic organogenesis and neural morphogenesis","description":"This cluster's GO terms span heart valve morphogenesis, metanephric nephron/tubule development, somitogenesis, neural differentiation timing, trochlear nerve development, and synapse maturation, indicating a cohesive theme of developmental patterning and organogenesis across multiple tissues, with temporal regulation elements.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032922","count":5},{"id":"GO:2000802","count":4},{"id":"GO:0072162","count":4},{"id":"GO:0072282","count":4},{"id":"GO:0001756","count":4}]},{"hash":"115981224117304940","title":"Methylation of proteins, RNA, and chromatin","description":"Top terms across the proteins center on various methylation reactions: arginine and lysine methylation on proteins, rRNA and tRNA methylation, RNA guanine-N7 methylation, and histone methylation. This points to a cohesive theme of methylation-based regulation affecting both ribonucleic acids and chromatin-associated proteins, with downstream effects on transcription, growth, and senescence. The cobalamin biosynthetic process may reflect methyl transfer chemistry involving cofactors, further tying the cluster to methylation activity. Overall, the cluster represents diverse methylation processes connected to gene regulation and chromatin state.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019919","count":5},{"id":"GO:0009236","count":5},{"id":"GO:0031167","count":5},{"id":"GO:0043985","count":4},{"id":"GO:0016049","count":4}]},{"hash":"923355738907616962","title":"Cardiomyocyte and neuronal signaling regulators","description":"The Top Terms show a mix of cardiac-focused processes (calcium ion transport, regulation of cardiac muscle relaxation, cardiac muscle cell growth and apoptosis, angiotensin signaling) and neuronal aspects (regulation of synaptic plasticity, dendrite morphogenesis). The convergence suggests proteins in this cluster participate in signaling pathways that coordinate heart muscle function with neural regulation, possibly at the neuro-cardiac interface, rather than a single isolated process.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048168","count":1},{"id":"GO:0038166","count":1},{"id":"GO:0006816","count":1},{"id":"GO:1901897","count":1},{"id":"GO:0035022","count":1}]},{"hash":"211026644021341665","title":"Immune Receptor and Integrin Signaling Regulation","description":"The terms point to modulation of immune-receptor pathways (TLR2, Fc receptor) and integrin-related signaling, including receptor internalization and tyrosine phosphorylation, along with adhesion dynamics. While some terms are structural (microvillus organization) or DNA-damage related, the strongest common theme is regulation of membrane signaling networks involved in immune response and cell adhesion.","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034136","count":6},{"id":"GO:0033629","count":6},{"id":"GO:0000077","count":6},{"id":"GO:0038063","count":6},{"id":"GO:0002092","count":6}]},{"hash":"119183704652099179","title":"Regulation of translation initiation and stress response","description":"Core theme is regulation of translation initiation and associated translational control, including preinitiation complex formation, IRES-dependent initiation, and reinitiation. The cluster also shows links to mRNA stability and cytoplasmic stress granule localization, consistent with translational control during stress. A lone term about transcription by RNA Pol II likely reflects a secondary function of some members rather than the cluster\u2019s main role.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2}]},{"hash":"189393382901416005","title":"Glutamatergic Synaptic Transmission","description":"The cluster is characterized by GO terms centered on excitatory neurotransmission at glutamatergic synapses, including synaptic transmission and ionotropic glutamate receptor signaling, plus vesicle fusion regulation, receptor internalization, and calcium transport\u2014key aspects of glutamatergic signaling and synaptic plasticity. Some terms (e.g., memory, social behavior) reflect brain function rather than direct molecular processes, and a few outliers (peptidoglycan metabolism, lateral line development) may be annotation noise. Overall, the dominant theme is glutamatergic synaptic activity, so this label is representative.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":2},{"id":"GO:0031623","count":1},{"id":"GO:0006816","count":1},{"id":"GO:0035235","count":1},{"id":"GO:0072375","count":1}]},{"hash":"2138383654590707416","title":"RNA Pol II transcription control in neuron maturation","description":"Top GO terms indicate regulation of RNA polymerase II\u2013driven transcription and neuron maturation, with retinoic acid response supporting a neuronal differentiation context. While a few terms pertain to other developmental processes, the shared theme is transcriptional regulation underlying neuronal development, making this a coherent cluster despite some outliers.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0042551","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1904179","count":2},{"id":"GO:0071300","count":2}]},{"hash":"1545889691340023680","title":"Ubiquitin-regulated DNA repair and chromatin dynamics","description":"The terms show a strong emphasis on ubiquitination (K29- and K11-linked) and DNA repair (error-free postreplication), plus chromatin-associated processes (heterochromatin formation, meiotic telomere clustering) and cell-cycle exit, suggesting a module where ubiquitin signals coordinate genome maintenance with chromatin state and mitosis. Some terms (interferon signaling, abscisic acid response, fungal cell wall organization) are less coherent with this core theme and may reflect broader stress responses or annotation overlap, but the primary theme fits ubiquitin-driven genome integrity and chromatin regulation.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0042275","count":6},{"id":"GO:0035519","count":6},{"id":"GO:0060340","count":6},{"id":"GO:0090089","count":6},{"id":"GO:0009737","count":6}]},{"hash":"2265972908354355244","title":"Unknown","description":"The terms span glycolysis regulation, redox/immune-related responses, xenobiotic and metal ion responses, and tissue-specific development/apoptosis signals, suggesting a heterogeneous set of functions rather than a single cohesive theme. Therefore a confident, specific label cannot be assigned.","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045730","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0060576","count":1},{"id":"GO:0045820","count":1},{"id":"GO:1904024","count":1}]},{"hash":"2216915449860888589","title":"Developmental Morphogenesis and Neural Guidance","description":"The proteins touch on neural development (axon guidance, neuron migration, collateral sprouting) and core developmental signaling (BMP pathway, tissue morphogenesis like salivary gland boundary specification and pigmentation), with additional broad development/differentiation roles (immune-related and cuticle patterning terms). This suggests a theme of developmental signaling and morphogenesis, with a notable emphasis on neural guidance.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007432","count":2},{"id":"GO:0043303","count":2},{"id":"GO:0048070","count":2},{"id":"GO:0001764","count":2},{"id":"GO:0002320","count":2}]},{"hash":"1441123647648788267","title":"Unknown","description":"The top GO terms come from diverse and largely unrelated processes (DNA replication, cell morphogenesis, Golgi maintenance, GTPase regulation, protein refolding, iron-sulfur cluster assembly, and even an obsolete fungal cell wall term), with no clear unifying function for the cluster. Several items are outdated, making a cohesive label inappropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0051684","count":2},{"id":"GO:0043547","count":2}]},{"hash":"37390356106343100","title":"Fatty acid transport and metabolism","description":"The Top Terms prominently feature long-chain fatty acid import across the plasma membrane and long-chain fatty acid import into the cell, along with related lipid-processing terms (medium-chain fatty-acyl-CoA metabolic process, carnitine metabolic process). Together these indicate a cohesive theme of fatty acid uptake and metabolism, with plant-associated secondary metabolism hints (phenylpropanoid) in the broader context. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0019427","count":1},{"id":"GO:0010030","count":1},{"id":"GO:0019542","count":1},{"id":"GO:0009698","count":1}]},{"hash":"1356005730716381361","title":"Viral entry, replication, and host microtubule manipulation","description":"The cluster\u2019s top GO terms point to viral processes (entry via membrane permeabilization, rolling hairpin viral DNA replication, symbiont-mediated host cell cycle arrest) and interactions with host microtubules (plus/minus end transport, spindle/kinetochore dynamics, microtubule depolymerization). This suggests a cohesive theme of viruses hijacking host cell machinery for entry, genome replication, and manipulation of the cytoskeleton and cell cycle.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0039592","count":1},{"id":"GO:0039685","count":1},{"id":"GO:0039665","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0099607","count":1}]},{"hash":"1009802616083219169","title":"Cytoskeleton remodeling and cell cycle signaling","description":"The cluster combines actin dynamics (actin filament depolymerization; regulation of Arp2/3 nucleation) with microtubule-based movement and cell cycle controls (G1 DNA damage checkpoint signaling; negative regulation of G0 to G1 transition), plus GPCR-triggered signaling and nutrient/glucose responses that can influence growth and cytoskeletal remodeling. This suggests a cohesive theme around cytoskeletal regulation linked to cell cycle progression and metabolic signaling.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0072432","count":3},{"id":"GO:0007200","count":3},{"id":"GO:2000011","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0007584","count":3}]},{"hash":"1437115200404430470","title":"Neuronal Morphogenesis and Synaptic Regulation","description":"The cluster\u2019s top GO terms point to neural development and synaptic function, including corticospinal tract morphogenesis, sensory perception of sound, positive regulation of synapse assembly, and long-term synaptic plasticity (with related presynaptic regulation). Although a few terms are unrelated (transcriptional regulation, T cell costimulation, nephric duct morphogenesis), the dominant theme centers on neuronal development and synaptic connectivity, supporting the label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021957","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0016049","count":2}]},{"hash":"861543055044587783","title":"Golgi-ER trafficking during mitosis","description":"This cluster shows GO terms for COPII-coated vesicle budding and retrograde Golgi-to-ER transport alongside mitotic processes (mitotic spindle assembly, mitotic cell cycle, cell division, cell proliferation), suggesting a theme that links vesicle trafficking with progression through mitosis. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1948297624687300191","title":"Neural development and ion transport","description":"This cluster\u2019s GO terms cluster around nervous system functions (sensory perception of pain, visual learning), development (multicellular organism development, skeletal muscle tissue development), and membrane ion transport (potassium and sodium flux), suggesting proteins involved in neural development and signaling with ion channel/pump activity. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0008542","count":3}]},{"hash":"1753184101130604729","title":"Translation machinery and regulation","description":"These proteins are tied to core translation processes, with GO terms spanning cytoplasmic and mitochondrial translation, translation initiation and reinitiation, ribosome disassembly, and maintenance of translational fidelity, plus regulation of translation. The consistent emphasis on ribosome-associated functions and control of protein synthesis suggests a cluster centered on translation machinery and its regulation.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0070126","count":1},{"id":"GO:1990145","count":1}]},{"hash":"805860421532456484","title":"Potassium Transport and Membrane Potential Regulation","description":"Top GO terms center on membrane excitability and potassium handling: regulation of resting membrane potential, stabilization of membrane potential, potassium ion transmembrane transport, and membrane repolarization in cardiac muscle cells. This suggests a functional theme around potassium-dependent control of membrane potential. Some transcription-related terms and a mechanosensory term are present but do not fit the core membrane-excitability theme, so they may reflect incidental annotations. Overall, the cluster is best described as potassium transport and membrane potential regulation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":1},{"id":"GO:0060075","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0030322","count":1},{"id":"GO:0098914","count":1}]},{"hash":"313243439597316093","title":"Synaptic transmission and neurotransmitter regulation","description":"The cluster\u2019s GO terms converge on neural communication and synaptic function: receptor internalization, neuromuscular synaptic transmission, calcium ion transport, ionotropic glutamate receptor signaling, and regulation of synaptic vesicle fusion\u2014all central to neurotransmitter release and signaling. Additional terms for serotonin metabolism and behavioral responses (ethanol, memory, social behavior) reinforce a theme of how synaptic activity translates to behavior. A fish-specific development term is present but relates to neural sensory systems, fitting within the broader neurosignaling context. Overall, these terms coherently point to synaptic signaling and neurotransmitter control as the cluster\u2019s core function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031623","count":1},{"id":"GO:0007274","count":1},{"id":"GO:0042428","count":1},{"id":"GO:0006816","count":1},{"id":"GO:0035235","count":1}]},{"hash":"488964424779231721","title":"Rab-Mediated Vesicle Transport and Cilium Assembly","description":"The proteins show a cohesive pattern around vesicle trafficking (ER to Golgi, recycling endosome to Golgi) and Rab signaling, with a connection to cilium assembly, suggesting a role in trafficking-supporting ciliogenesis. Some terms appear more developmental or cell-cycle oriented but do not override the core trafficking/ciliogenesis theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":1},{"id":"GO:0018192","count":1},{"id":"GO:1902953","count":1},{"id":"GO:0032483","count":1},{"id":"GO:0031030","count":1}]},{"hash":"648398623452423502","title":"Cell Cycle and Epithelial Polarity Signaling","description":"The top terms cluster around cell cycle progression and epithelial polarity components (tight junction assembly and apical protein localization), with additional cAMP-related signaling (forskolin response and adenylate cyclase activation) linking proliferation to polarity. While some terms are more developmental or sensory, the core theme is cell-cycle control coupled to epithelial polarity via cAMP pathways.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0070830","count":2},{"id":"GO:0045176","count":2},{"id":"GO:0007124","count":1},{"id":"GO:1904322","count":1}]},{"hash":"1494247610517070348","title":"Chromatin organization and transcription regulation","description":"This cluster prominently features nucleosome assembly, heterochromatin formation, and chromatin localization, plus regulation of RNA polymerase II\u2013driven transcription, indicating a core theme of chromatin structure shaping gene expression. Related terms about estradiol response and mRNA decay suggest wider regulatory context but don't outweigh the chromatin-centric pattern.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1904815","count":2},{"id":"GO:0071392","count":2},{"id":"GO:0070481","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0030466","count":2}]},{"hash":"378384945594231737","title":"RNA export and stress-responsive mRNA stability","description":"Based on the GO terms, the strongest signals are mRNA export from nucleus and regulation of mRNA stability in response to stress, indicating a core RNA processing/stress response function. The remaining terms (SCF disassembly under cadmium, ATP biosynthesis regulation, fatty acid catabolism, etc.) are diverse and likely reflect secondary activities or background noise, so the label emphasizes the dominant RNA processing/stress theme.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0010610","count":2},{"id":"GO:1990171","count":1},{"id":"GO:2001171","count":1}]},{"hash":"148921751632174001","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0016925","count":1},{"id":"GO:0034087","count":1},{"id":"GO:0006283","count":1},{"id":"GO:0035753","count":1}]},{"hash":"1331213036340356172","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031053","count":1},{"id":"GO:0045071","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0031442","count":1}]},{"hash":"2295937182885993910","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0016049","count":2}]},{"hash":"207372826965916183","title":"Embryonic organogenesis and patterning","description":"The proteins map broadly to diverse embryonic development processes across multiple tissues\u2014heart, skeletal system, digits, neurons, bronchioles, and kidney-related structures\u2014along with axis specification. This suggests a general role in embryogenesis and tissue patterning rather than a single tissue-specific function.","confidence":"High","size":5,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0048706","count":3},{"id":"GO:0009798","count":3},{"id":"GO:0061296","count":3},{"id":"GO:0021902","count":3}]},{"hash":"665948420040664063","title":"Embryonic Tissue Morphogenesis","description":"This cluster features diverse embryonic development terms spanning skeletal, neural, and organ morphogenesis (e.g., skeletal development, axis specification, neuron migration, digit morphogenesis, bronchiole and ureteric bud formation, uterus development). The common thread is embryonic tissue morphogenesis rather than a single tissue-specific process, justifying a broad 'embryonic tissue morphogenesis' label.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":5},{"id":"GO:0048706","count":3},{"id":"GO:0009798","count":3},{"id":"GO:0061296","count":3},{"id":"GO:0021902","count":3}]},{"hash":"1510319566431409730","title":"Membrane Ion Transport and Homeostasis","description":"The top GO terms cluster around transmembrane transport of ions (calcium, zinc, cadmium, sodium), maintenance of ion gradients, and intracellular calcium homeostasis, pointing to a shared role in ion balance across membranes and calcium signaling. A few outlier terms (lipopolysaccharide biosynthesis, pheromone-induced conjugation) are less related but do not negate the overarching theme of ion transport and homeostasis. This label best captures the common functional thread among the majority of terms.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0070588","count":2},{"id":"GO:0031448","count":2},{"id":"GO:0006874","count":2},{"id":"GO:0000749","count":2}]},{"hash":"283643716280733550","title":"Immune regulation and proteostasis","description":"The cluster includes terms tied to immune signaling, such as B cell cytokine production and T cell\u2013mediated immune responses to tumors, suggesting active immune-related function. It also features protein quality control and mitochondrial protein handling terms\u2014detection of misfolded proteins, chaperone-assisted refolding, protein stabilization, and import into the mitochondrial intermembrane space\u2014indicating a proteostasis/stress-response angle. Some terms (e.g., scaRNA localization; pore complex assembly) are broader cellular processes that don\u2019t override the core theme but reflect ancillary functions within the same cellular stress context.","confidence":"Low","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071866","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0046931","count":4},{"id":"GO:0051085","count":4},{"id":"GO:0002368","count":4}]},{"hash":"182748099267164972","title":"Proteostasis and Immune Signaling","description":"The terms point to protein quality control and organelle proteostasis (misfolded-protein detection, chaperone-assisted refolding, protein stabilization, and mitochondrial intermembrane space import, plus pore complex assembly), with additional immune-related processes (B cell cytokine production and T cell\u2013mediated responses). A few terms are peripheral (response to cocaine, Cajal body RNA localization) but do not overwhelm the core theme. Overall, the cluster seems to fuse protein homeostasis with immune signaling pathways.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071866","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0046931","count":4},{"id":"GO:0051085","count":4},{"id":"GO:0002368","count":4}]},{"hash":"285766782613631609","title":"Ubiquitin-regulated antigen processing and immune signaling","description":"The cluster combines GO terms for deubiquitination and proteasomal protein catabolism with antigen processing/presentation via MHC I, as well as signaling pathways involved in immune responses (T cell receptor and Fc receptor signaling). This suggests a core theme of ubiquitin-controlled protein turnover influencing immune signaling and antigen presentation, even though additional terms touch on Wnt signaling and cell-cycle regulation.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0010499","count":3},{"id":"GO:0006521","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0090090","count":3}]},{"hash":"412771552171955898","title":"Unknown","description":"The GO terms are highly diverse (cell cycle regulation, protein folding, responses to cocaine and xenobiotics, telomerase/telomere maintenance, actin rod assembly, virion attachment), with no single coherent function tying all four proteins together. This makes it inappropriate to assign a specific, representative label.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0042220","count":1},{"id":"GO:0071318","count":1},{"id":"GO:2000010","count":1}]},{"hash":"285020618544349006","title":"Proteostasis and Heat Stress Response","description":"The cluster centers on protein quality control and degradation: ubiquitin-dependent ERAD, misfolded-protein transport, ubiquitin-mediated protein catabolism, and chaperone/refolding activities, with heat-stress response terms. This points to a module maintaining proteome integrity under stress. The DNA replication term appears as a minor or multifunctional annotation rather than a core theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0090084","count":1},{"id":"GO:0070843","count":1}]},{"hash":"1316741749996440242","title":"Neuronal protein quality control and transport","description":"These GO terms collectively point to neuron-focused processes of protein handling and localization (nuclear pore localization, ERAD, deubiquitination, sumoylation, ER stress\u2013related pathways), along with neuronal development and excitability (axonogenesis, transcription regulation). Together they suggest a cluster centered on neuronal protein quality control and trafficking.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090204","count":4},{"id":"GO:0021888","count":4},{"id":"GO:0016579","count":4},{"id":"GO:0033132","count":4},{"id":"GO:0030433","count":4}]},{"hash":"896039652695161349","title":"Translation initiation and RNA processing regulation","description":"Several terms point to translation start and initiation complex assembly (regulation of translational initiation; formation of translation preinitiation complex; IRES-dependent translational initiation), while others point to RNA processing (mRNA splicing via spliceosome) and protein turnover regulation (COP9 signalosome assembly; protein K63-linked deubiquitination; deubiquitination). This suggests a theme around how the cell orchestrates protein synthesis and RNA processing, with ubiquitin-mediated regulation as a common mechanism.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010387","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0070537","count":1},{"id":"GO:0070452","count":1}]},{"hash":"988202329402802328","title":"Spliceosome-Mediated RNA Processing and Stability","description":"The top GO terms cluster around splicing via the spliceosome, regulatory ncRNA-mediated silencing, and regulators of mRNA stability and translation initiation, with a note on transcription termination. This suggests a cohesive module centered on RNA processing and post-transcriptional gene regulation, rather than metabolic or signaling processes. Hence the label focuses on spliceosome-driven RNA processing and mRNA fate control.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006369","count":2},{"id":"GO:0048255","count":2}]},{"hash":"36571089211934643","title":"Unknown","description":"The GO terms span multiple distinct biological themes (actin cytoskeleton regulation; neural development/axonogenesis; various organ development processes; immune regulation; metabolism), and there are no interactions among the proteins (Edges: 0). There isn\u2019t a single coherent function that ties these terms together, so a reliable, representative label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030835","count":2},{"id":"GO:0021521","count":2},{"id":"GO:0046013","count":2},{"id":"GO:0008585","count":2},{"id":"GO:0045805","count":2}]},{"hash":"896204377169659681","title":"Neural development and axon guidance","description":"This cluster highlights neural-specific regulatory processes: positive regulation of long-term neuronal synaptic plasticity, positive regulation of axonogenesis, and fasciculation of sensory neuron axons indicate roles in neural growth and connectivity. Additional signaling terms (BMP and prolactin pathways) and organogenesis terms suggest broader developmental signaling context, but the strongest recurring theme centers on neural development and axon pathfinding.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048170","count":3},{"id":"GO:2000525","count":3},{"id":"GO:0072178","count":3},{"id":"GO:0007432","count":3},{"id":"GO:1904238","count":3}]},{"hash":"1601676659324180993","title":"Endosomal signaling and neuronal remodeling","description":"The top GO terms cluster around endosome-associated processes (exosomal secretion, localization to endosome, retrograde transport to Golgi, phagosome-lysosome fusion) with neuronal development and synaptic remodeling (dendrite development, modification of synaptic structure, wound healing). This suggests a cohesive theme where endosome-driven signaling and trafficking influence neuronal connectivity and structural changes.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048013","count":2},{"id":"GO:1990182","count":2},{"id":"GO:0036010","count":2},{"id":"GO:0070830","count":2},{"id":"GO:0016358","count":2}]},{"hash":"228855561482046365","title":"Cell Spreading and Trafficking Regulation","description":"The cluster shows enrichment in GO terms for cell spreading, wound healing, and epithelial polarity (GO:1900026, GO:0044319, GO:0090162), together with intracellular trafficking processes such as regulation of endosome-to-Golgi transport and phagosome-lysosome fusion (GO:1905279, GO:0090385). This points to a coordinated program of cell adhesion/movement and cargo routing, typical of tissue remodeling and membrane trafficking dynamics. While a few terms (cytotoxic T cell degranulation, hormone signaling) are less directly connected, the dominant theme among the proteins appears to be regulation of cell spreading and intracellular trafficking. Therefore the label reflects the core function of the cluster with moderate confidence.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033144","count":4},{"id":"GO:1900026","count":4},{"id":"GO:1905279","count":2},{"id":"GO:0044319","count":2},{"id":"GO:0045792","count":2}]},{"hash":"1394635013294124165","title":"Neural adhesion and development","description":"The terms center on neuron and neural tissue organization: neuron cell\u2013cell adhesion (GO:0007158), cadherin-mediated adhesion (GO:0044331), planar polarity localization (GO:0090251) and corticospinal tract morphogenesis (GO:0021957). Additional terms touch on neural-related functions such as sensory perception of sound (GO:0007605) and locomotory behavior (GO:0007626). While some terms are more general (deneddylation, I-kappaB phosphorylation), the dominant signal is neural development and adhesion.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060625","count":1},{"id":"GO:0007252","count":1},{"id":"GO:1902910","count":1},{"id":"GO:0044331","count":1},{"id":"GO:0090251","count":1}]},{"hash":"2281946273095406894","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":1},{"id":"GO:0071166","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0000480","count":1}]},{"hash":"1877551412139759578","title":"Mitochondrial protein import and inner-membrane insertion","description":"Most of the top GO terms point to proteins involved in targeting and importing other proteins into mitochondria, including matrix import and inner membrane insertion, with one term also referencing chloroplast stroma import. The remaining terms are more peripheral and less coherent, but the dominant signal supports a cluster related to organelle protein import and membrane insertion machinery. ","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0045037","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0032094","count":1}]},{"hash":"1451297146868153591","title":"Contraction and electrical signaling in excitable tissues","description":"The GO terms cluster around muscle contraction (diaphragm contraction, fast/slow fiber transitions, satellite cell\u2013mediated muscle regeneration) and neural/photoreceptor signaling (phototransduction, cone recovery, retinal bipolar neuron differentiation), plus cardiac electrical coupling. This suggests a common theme of excitable tissues that rely on contraction and electrical signaling across muscle, heart, and retina. Some terms are broader, but the dominant pattern supports this cohesive theme.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002086","count":1},{"id":"GO:0036368","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0014718","count":1},{"id":"GO:0007602","count":1}]},{"hash":"1723415426335303171","title":"Zinc ion transport and homeostasis","description":"The terms cluster predominantly around zinc import, transmembrane transport, and intracellular zinc homeostasis, with detoxification and starvation responses also represented; a distant limb-development term is incidental. This makes zinc handling the most representative theme for the cluster.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":1},{"id":"GO:0044749","count":1},{"id":"GO:0006882","count":1},{"id":"GO:0060173","count":1},{"id":"GO:0034224","count":1}]},{"hash":"925304500848310200","title":"Cell wall mannoprotein biosynthesis and O-mannosylation","description":"The cluster\u2019s top GO terms strongly point to cell wall mannoprotein biosynthesis and O-linked glycosylation via mannose, suggesting a shared role in constructing and glycosylating fungal cell wall proteins. Some additional terms relate to vacuolar acidification and proton transport, which may reflect membrane trafficking roles, but the central theme remains mannoprotein production and glycosylation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000032","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0060049","count":1}]},{"hash":"698915185575609704","title":"Embryonic tissue morphogenesis","description":"This cluster centers on embryonic development and morphogenesis across multiple tissues (skeletal, digits, neurons, muscle, kidney/ureteric bud, bronchioles, uterus, etc.), rather than a single tissue-specific function. The presence of axis specification alongside diverse organogenesis terms suggests a broad developmental program, justifying a general label of embryonic tissue morphogenesis.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048706","count":2},{"id":"GO:0009798","count":2},{"id":"GO:0061296","count":2},{"id":"GO:0021902","count":2},{"id":"GO:0042733","count":2}]},{"hash":"418452546601619467","title":"Retroviral entry, integration, and latency","description":"Most of the top GO terms point to steps in the retroviral life cycle: entry into the host cell and nucleus, DNA integration into the host genome, and establishment of proviral latency, along with reverse transcription (RNA-templated DNA synthesis) and DNA recombination. This suggests the cluster comprises proteins functioning in viral infection and proviral maintenance rather than typical host cellular processes. The presence of RNA silencing-related terms hints at interactions with host defenses. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0039651","count":4},{"id":"GO:0075732","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0075713","count":4}]},{"hash":"876326237068051638","title":"Nucleotide Salvage and NAD Biosynthesis","description":"The majority of GO terms describe salvage and catabolism of nucleotides and related metabolites (UMP salvage, purine ribonucleoside salvage, inosine and deoxyguanosine catabolism, nicotinamide riboside/NAD salvage), pointing to a shared role in maintaining nucleotide and NAD pools; a few terms (glucose starvation response, T cell differentiation, menaquinone biosynthesis) appear less central to this core theme.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0044206","count":2},{"id":"GO:0006148","count":1},{"id":"GO:0034418","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0046638","count":1}]},{"hash":"1269733136115687351","title":"Unknown","description":"The top GO terms span fungal sporulation, animal development, chromosomal movement, platelet aggregation, histone modification, and cytoskeleton-related processes, with no clear, single biological theme tying them together. This suggests there isn\u2019t a cohesive function for the cluster as a whole.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030476","count":3},{"id":"GO:0090131","count":3},{"id":"GO:0043486","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0051592","count":3}]},{"hash":"1166893031257170737","title":"Immune Signaling and Adhesion Regulation","description":"The cluster is driven by GO terms tied to immune signaling and cell\u2013cell interactions, notably positive regulation of T cell polarity and TLR3 signaling, plus cadherin-mediated adhesion and extracellular matrix remodeling. While some terms touch on mitochondria and metabolism, the strongest shared theme is immune cell signaling and adhesion.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903905","count":3},{"id":"GO:0030433","count":3},{"id":"GO:2000049","count":3},{"id":"GO:0034141","count":3},{"id":"GO:0022617","count":3}]},{"hash":"1656897505564930418","title":"Unknown","description":"The top terms cover a mix of neuronal synaptic regulation, organ morphogenesis, immune signaling, sensory perception, and other unrelated processes. There is no single cohesive function linking these proteins, given the diverse GO terms and zero edges. As a result, a concise, representative label cannot be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048170","count":1},{"id":"GO:0021957","count":1},{"id":"GO:2000525","count":1},{"id":"GO:0072178","count":1},{"id":"GO:0007605","count":1}]},{"hash":"673961385960044872","title":"Membrane Targeting and Secretion","description":"Based on the prevalence of GO terms related to SRP-dependent cotranslational targeting to membranes, Sec complex\u2013mediated transport, post-translational membrane targeting, and general protein targeting and secretion, the cluster seems to group proteins involved in the secretory pathway and intracellular trafficking to membranes and organelles. A couple of outlier terms (chromatin organization, collagen catabolic process) exist but do not alter the dominant trafficking theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0009306","count":1}]},{"hash":"1679551545906644179","title":"Retinoid metabolism and neural development","description":"The dominant GO terms are retinol metabolism and cellular response to retinoic acid, with forebrain development, suggesting these proteins participate in retinoid signaling pathways that influence neural development. Some other metabolic terms appear, but the retinoid-related signals are the strongest hint of a cohesive function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901023","count":3},{"id":"GO:0009450","count":3},{"id":"GO:0019413","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0071300","count":3}]},{"hash":"506172325480332703","title":"Endomembrane trafficking and vesicle transport","description":"This cluster is dominated by GO terms related to vesicle movement within the endomembrane system, including retrograde transport between the Golgi and ER, endocytosis, and endosome-to-lysosome pathways, plus multivesicular body assembly and secretory pathway regulation. This cohesive set suggests a core function in membrane trafficking, despite a few unrelated terms present. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0008333","count":1},{"id":"GO:1990456","count":1},{"id":"GO:1903307","count":1}]},{"hash":"422533408577288275","title":"Unknown","description":"The GO terms span transcription regulation, lipid metabolism, signaling, immune response, and trafficking, with no single cohesive function tying the proteins together.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045943","count":1},{"id":"GO:0045723","count":1},{"id":"GO:0038026","count":1},{"id":"GO:0002432","count":1},{"id":"GO:0090153","count":1}]},{"hash":"2091345591227694585","title":"Neural development and cell adhesion","description":"This cluster\u2019s top GO terms center on neuron cell\u2013cell adhesion and cadherin-mediated adhesion, planar polarity establishment, and neural morphogenesis such as corticospinal tract formation; these themes point to roles in neural development and tissue organization. While a few terms touch on melanosome transport or signaling, the dominant pattern is neural development coupled with adhesion and polarity.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902910","count":3},{"id":"GO:0044331","count":3},{"id":"GO:0090251","count":3},{"id":"GO:0007158","count":3},{"id":"GO:0021957","count":3}]},{"hash":"224670059420681887","title":"Innate immune signaling and RNA processing","description":"The terms cluster around innate immune activation (innate immune response-activating signaling) and RNA processing (RNA splicing, mRNA processing, siRNA processing regulation), suggesting a shared theme of defense-linked RNA regulatory activities. Additional terms about symbiont entry, host apoptosis, and viral nuclear penetration reinforce a host-pathogen interaction context, though the core connection centers on immune signaling intertwined with nucleic acid metabolism. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010204","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0009870","count":1},{"id":"GO:0039651","count":1}]},{"hash":"207256376817264716","title":"Translation Initiation and Reinitiation","description":"Dominant terms relate to translation initiation and reinitiation (IRES-dependent viral initiation, preinitiation complex formation, and translation reinitiation), with minor signals of cell cycle and nutrient signaling.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1979242121129464037","title":"RNA processing and translation initiation control","description":"The GO terms cluster around post-transcriptional regulation: mRNA stability and stress-responsive regulation, splicing via the spliceosome, mRNA modification, and initiation of translation (preinitiation complex formation and IRES-driven initiation). This suggests a module dedicated to RNA processing and control of translation rather than transcriptional regulation.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":1},{"id":"GO:0010610","count":1},{"id":"GO:0006446","count":1},{"id":"GO:1901407","count":1},{"id":"GO:0001825","count":1}]},{"hash":"1706059265863781868","title":"Nucleosome Assembly and Chromatin Organization","description":"This cluster is dominated by GO terms for nucleosome assembly, establishment of protein localization to chromatin, and heterochromatin organization, pointing to a cohesive chromatin-structure\u2013related function. While a few ancillary terms (like mRNA decay) appear less central, the core terms consistently describe chromatin packaging and chromosomal organization, suggesting these proteins work together in chromatin assembly/organization processes.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":3},{"id":"GO:0071169","count":3},{"id":"GO:0070828","count":2},{"id":"GO:0098532","count":2},{"id":"GO:0097298","count":2}]},{"hash":"896974959035771152","title":"Unknown","description":"The GO terms span a mix of protein folding stress responses, iron metabolism, structural biosynthesis, protein targeting, DNA replication, and mating-related processes, with no clear, single biological theme linking the proteins. This makes it inappropriate to assign a specific functional label, so the cluster is Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":1},{"id":"GO:1903382","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0070880","count":1}]},{"hash":"1727419774943203266","title":"Golgi-associated neuronal development","description":"The top GO terms point to neural development (cerebral cortex development, neuron migration) and Golgi-related processes (Golgi reassembly, establishment of Golgi localization), with supporting neuron-function terms like membrane depolarization. Although a few terms touch insulin signaling or epidermal cell proliferation, the strongest signals describe neural differentiation and Golgi organization, suggesting a cluster of proteins involved in neuronal development linked to Golgi dynamics.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0001836","count":1},{"id":"GO:0010482","count":1},{"id":"GO:0071901","count":1},{"id":"GO:0090168","count":1}]},{"hash":"2197443696393077382","title":"Unknown","description":"The GO terms are a mix of unrelated processes (glycosylation, SCF complex dynamics under cadmium, ATP biosynthesis regulation, mitochondrial inner membrane insertion, defense to fungus, heat/stress related metabolism, oxidative stress responses, snoRNP assembly). With only 3 proteins and no coherent, single functional theme linking these terms, there isn\u2019t a clear common function to name the cluster beyond Unknown.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:1990171","count":1},{"id":"GO:2001171","count":1},{"id":"GO:0032979","count":1},{"id":"GO:2000072","count":1}]},{"hash":"1362639807057998619","title":"Unknown","description":"There are no GO terms associated with this cluster (Top Terms list is empty), and with only three proteins and two edges there is insufficient functional signal to identify a unifying theme.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"70835462576600994","title":"Notch-regulated developmental patterning","description":"The terms cluster around developmental processes and patterning, with a notable emphasis on Notch signaling regulation and segmentation/pattern specification across tissues, suggesting proteins with roles in Notch-guided development.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060576","count":1},{"id":"GO:0032092","count":1},{"id":"GO:0045747","count":1},{"id":"GO:0001541","count":1},{"id":"GO:0007386","count":1}]},{"hash":"1984171957450158069","title":"Vesicle trafficking and endocytosis","description":"The top GO terms cluster around vesicle transport between organelles (ER-Golgi), clathrin-coated vesicle cargo loading, and vesicle organization including synaptic vesicles and receptor internalization. While a few terms pertain to meiosis or chromatin, the dominant signal is vesicle trafficking and endocytosis, suggesting this cluster represents core vesicle transport machinery. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":1},{"id":"GO:1903342","count":1},{"id":"GO:0035652","count":1},{"id":"GO:0099590","count":1},{"id":"GO:0051307","count":1}]},{"hash":"266341082348195663","title":"Unknown","description":"The GO terms are highly diverse and span immune/inflammatory response, temperature stimulus, gonad development (male and female), cell-cycle regulation, p53-mediated DNA damage response, skeletal muscle differentiation, centrosome cycle, and vitamin D receptor signaling. With no clear shared pathway or dominant function linking these proteins, and no edges connecting them, there is no coherent single label to assign. Thus, Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071502","count":1},{"id":"GO:0002526","count":1},{"id":"GO:0048147","count":1},{"id":"GO:2000194","count":1},{"id":"GO:0071157","count":1}]},{"hash":"1506494452765835969","title":"BMP and WNT-mediated embryonic patterning","description":"These terms repeatedly point to embryonic development and tissue patterning, with BMP signaling active roles, WNT pathway regulation, and spatial axis specification (anterior/posterior, dorsal/ventral) as common themes. The wing disc and hindlimb morphogenesis terms suggest a conserved developmental program. Despite a couple of outliers, the dominant theme is BMP/WNT-driven pattern formation during embryogenesis, so BMP and WNT-mediated embryonic patterning seems an appropriate label.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009948","count":1},{"id":"GO:0046326","count":1},{"id":"GO:0008101","count":1},{"id":"GO:0035116","count":1},{"id":"GO:0060976","count":1}]},{"hash":"181662137656100459","title":"Unknown","description":"The GO terms cover neural growth factor signaling, secretory granule-related processes, immune/mast cell degranulation, dendrite morphogenesis regulation, broad developmental pathways, and various signaling cascades, which do not converge on a single clear function for this small cluster. The lack of a unifying theme makes a specific, representative label inappropriate.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0038180","count":1},{"id":"GO:0032252","count":1},{"id":"GO:0043303","count":1},{"id":"GO:0050774","count":1},{"id":"GO:0007296","count":1}]},{"hash":"949446702708798292","title":"Ubiquitin-Dependent Protein Degradation","description":"The dominant GO terms are ubiquitin-related proteolysis: ubiquitin-dependent protein catabolic process, autoubiquitination, and K63/K48-linked ubiquitination, indicating a primary role in ubiquitin-mediated protein degradation; the developmental terms are few and less coherent with this core signal, so the main theme is ubiquitin-dependent proteolysis.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0070936","count":2},{"id":"GO:0060536","count":1}]},{"hash":"1105463667709996590","title":"Cytoskeleton Remodeling and Cell Cycle Signaling","description":"Based on the prominent actin-related terms (actin filament depolymerization; negative regulation of Arp2/3; microtubule-based movement) and cell-cycle terms (G0 to G1 transition; G1/ DNA damage checkpoint signaling), the cluster appears to group proteins involved in cytoskeleton dynamics coupled to cell-cycle regulation. Additional GPCR/PLC signaling and a plant development term (adaxial/abaxial pattern formation) suggest broader signaling roles that intersect with cytoskeleton remodeling. Overall, this label captures the core shared functions. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072432","count":1},{"id":"GO:0007200","count":1},{"id":"GO:2000011","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0007584","count":1}]},{"hash":"584587949489568891","title":"Unknown","description":"The listed GO terms are highly diverse, with only a few pointing to bone-related processes (cementum mineralization, endochondral ossification, and vitamin D response). Most terms concern general metabolism and other unrelated processes, suggesting no cohesive functional theme for the cluster. Therefore, Unknown with no confidence (None).","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009264","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0006015","count":1},{"id":"GO:0071529","count":1},{"id":"GO:0006007","count":1}]},{"hash":"1388880130685485228","title":"Nuclear mRNA export and ER-Golgi vesicle trafficking","description":"The GO terms cluster around two linked themes: export and processing of RNA from the nucleus (mRNA export, nuclear mRNA surveillance, tethering of RNA pol II) and vesicle trafficking between the endoplasmic reticulum and Golgi, including intra-Golgi and retrograde transport, plus endosome-to-vacuole pathways. This suggests a cohesive function in nucleocytoplasmic transport coupled with secretory pathway trafficking. A few terms (notochord development, pancreatic juice secretion) are more distantly related but may reflect broader developmental/secretory contexts.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000973","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0071033","count":1},{"id":"GO:0030903","count":1},{"id":"GO:0032511","count":1}]},{"hash":"1773790855850793870","title":"Unknown","description":"The two top GO terms (aggrephagy and platelet formation) indicate unrelated biological processes, and there are no interactions or common functional themes among the three proteins. Without a coherent shared function, a meaningful cluster label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035973","count":1},{"id":"GO:0030220","count":1}]}]