[{"hash":"917253857567141291","title":"Cell Cycle and Telomere Maintenance","description":"The top GO terms cluster around core cell cycle processes (cell cycle, cell division) and telomere maintenance/capping (telomere capping, maintenance via telomerase), with related regulation of CDK activity and associated proteostasis (proteasome assembly) and RNA processing. While some terms are peripheral (muscle stretch, adipocyte differentiation), the dominant theme ties to cell proliferation and genomic stability through telomere biology.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0070682","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0032212","count":3}]},{"hash":"1312199042386710864","title":"Cardiac differentiation and RNA-based regulation","description":"This cluster shows a clear focus on cardiovascular development, with terms like ventricular cardiac muscle cell differentiation, ductus arteriosus closure, and negative regulation of cardiac muscle cell apoptosis. It\u2019s complemented by RNA-centric regulatory processes (regulatory ncRNA-mediated gene silencing and mRNA splicing via spliceosome) and protein sumoylation, suggesting coordinated gene expression and post-translational regulation during cardiac differentiation. Overall, the dominant theme is cardiac development coupled with RNA- and protein-level regulation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":3},{"id":"GO:1900222","count":3},{"id":"GO:0016925","count":3},{"id":"GO:0055012","count":3}]},{"hash":"615653071162642734","title":"Membrane Transport and Developmental Signaling","description":"The terms reveal membrane-associated processes (iron export, nitrite transport, phospholipid catabolism) alongside signaling and developmental activities (Rho signaling, face morphogenesis, osteoclast differentiation) and regulatory ubiquitination. This combination points to a cluster focused on membrane transport combined with regulatory signaling that shapes developmental outcomes, rather than a single cohesive pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060586","count":2},{"id":"GO:0015707","count":2},{"id":"GO:1903988","count":2},{"id":"GO:0010252","count":2},{"id":"GO:0009395","count":2}]},{"hash":"359658773641789534","title":"Signaling and Cytoskeletal Remodeling with RNA Processing","description":"The top GO terms point to signaling pathways (insulin/IGF receptor signaling, GPCR-related signaling), cytoskeletal dynamics (filopodium assembly, cell migration, mechanical response), protein ubiquitination, and RNA processing (splicing, mRNA export). This suggests a functional module linking signal transduction to cytoskeletal remodeling and transcriptional/post-transcriptional regulation. The presence of mitochondrial inheritance hints at coordinated organelle distribution during remodeling. Some terms are obsolete and there are no edges, so the label represents a best-fit theme rather than a tightly connected module.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0051489","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0071260","count":3}]},{"hash":"1628505235465356893","title":"Ubiquitin-Proteasome\u2013Mediated Proteolysis and Cell Cycle Regulation","description":"Proteins in this cluster are dominated by ubiquitin-dependent degradation pathways (SCF-dependent proteasomal ubiquitin-dependent catabolism, polyubiquitination, autoubiquitination) with ties to cell-cycle control and spindle dynamics (meiotic spindle assembly, microtubule processes). This points to a coherent theme of regulated proteolysis governing cell-cycle progression, with some signals of stress response (cadmium). Overall, the core function appears to be targeted protein degradation via the ubiquitin-proteasome system linked to cell-cycle regulation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0042787","count":14},{"id":"GO:0000209","count":10},{"id":"GO:0071276","count":9},{"id":"GO:0030433","count":8}]},{"hash":"851312747796833124","title":"Ubiquitin-dependent transcription regulation","description":"The cluster shows strong enrichment for deubiquitination (K29- and K48-linked), regulation of ubiquitin ligase activity, and histone H2B deubiquitination, all pointing to ubiquitin signaling that modulates transcription and chromatin state, with additional links to transcriptional regulation and DNA-templated transcription.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006415","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1901026","count":1},{"id":"GO:0035523","count":1},{"id":"GO:0048149","count":1}]},{"hash":"2302469926310795665","title":"Mechanotransduction and cytoskeletal dynamics","description":"The top GO terms point to sensing/responding to mechanical stimuli, cytoskeletal remodeling (lamellipodium assembly, axon extension), along with core growth and protein-handling processes (cell cycle, ribosome biogenesis, intracellular transport, ubiquitination). This combination suggests a cluster centered on mechanotransduction intertwined with proliferation and cytoskeletal dynamics, with some tissue-context modifiers (bone mineralization, angiogenesis regulation). Therefore, the label is representative, though not exclusive to a single narrow function.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0016525","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0030500","count":2}]},{"hash":"1860172066543798330","title":"Mitotic Chromatin Regulation and Cytoskeleton Dynamics","description":"The top GO terms cluster around mitotic processes (APC-dependent catabolic process, sister chromatid cohesion, spindle assembly, meiotic division regulation) and chromatin modification (histone acetylation), with supporting cytoskeletal dynamics (actin depolymerization) and growth signaling (TORC1). This suggests a cohesive theme of cell division coordination with chromatin state and cytoskeleton.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043981","count":4},{"id":"GO:0043982","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0043966","count":3},{"id":"GO:0070306","count":3}]},{"hash":"792676353156526502","title":"Rho GTPase\u2013driven actin remodeling and migration","description":"The cluster is dominated by GO terms tied to Rho-family GTPase signaling, lamellipodium assembly, and actin cytoskeleton organization, all central to cell migration and motility. Positive regulation of GTPase activity and small GTPase\u2013mediated signaling reinforce a cohesive theme of actin remodeling and adhesion-dependent spreading. IGF receptor signaling may modulate these processes, while an occasional term like B cell affinity maturation could reflect broader signaling roles or annotation overlap, but the core signal is cytoskeletal dynamics leading to migration.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0030032","count":5},{"id":"GO:0007264","count":5},{"id":"GO:0048009","count":5},{"id":"GO:0030036","count":5}]},{"hash":"212319137470117270","title":"Differentiation and Proliferation Regulation","description":"Top terms cluster around differentiation (fat cell, oligodendrocyte differentiation), cell migration, and RNA processing, with additional signals related to telomere maintenance and CDK activity regulation. This suggests a general theme of differentiation and proliferation control rather than a single pathway. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1904355","count":9},{"id":"GO:0032212","count":9},{"id":"GO:0006397","count":9},{"id":"GO:0045736","count":9},{"id":"GO:0035994","count":9}]},{"hash":"1055251465221292349","title":"Immune receptor signaling and lymphocyte activation","description":"The cluster shows enrichment in immune receptor signaling and lymphocyte activation, including B cell receptor signaling, Fc receptor pathways, and T cell activation. Tyrosine autophosphorylation and ubiquitination reflect common post-translational events in receptor-initiated signaling, while PDGF and Wnt terms may reflect broader signaling cross-talk. Overall, the strongest theme is adaptive immune signaling.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038083","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0050853","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0009395","count":4}]},{"hash":"676212732987593664","title":"Unknown","description":"The terms span apoptosis under ER stress, development, immune defense, transcription, protein degradation, DNA replication, and tissue-specific processes, with no dominant shared function. The cluster has no edges, indicating no clear interconnected pathway, so a single coherent label cannot be inferred.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070059","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0006351","count":3}]},{"hash":"621141814849315049","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":13,"triangles":1,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0000184","count":6},{"id":"GO:0000480","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0000398","count":5}]},{"hash":"2087600171706098860","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms for ubiquitination and ubiquitin-dependent protein catabolic processes (including autoubiquitination and various ubiquitin linkages), pointing to a set of proteins involved in tagging substrates for degradation, likely via the proteasome/ERAD pathways; a few other terms appear but do not override the ubiquitin-centric theme.","confidence":"High","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:0016567","count":11},{"id":"GO:0051865","count":11},{"id":"GO:0070936","count":10},{"id":"GO:0085020","count":9}]},{"hash":"2254525597994517603","title":"Unknown","description":"The terms show immune defense, neural and lens development, and core cell-cycle/biogenesis processes, with no single dominant function; with only a single edge and no triangles, the proteins do not form a cohesive functional cluster.","confidence":"","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0031146","count":3}]},{"hash":"1607518866395925174","title":"Organelle Protein Import and Membrane Insertion","description":"The top GO terms are dominated by protein import into mitochondria and chloroplasts and associated membrane insertion steps (mitochondrial matrix import, mitochondrial inner membrane insertion, chloroplast stromal import), which together define a clear theme of targeting and inserting proteins into organelles. Other terms appear as miscellaneous or legacy annotations, offering noise rather than a cohesive alternative theme. Given the low connectivity (one edge, no triangles), this label best captures the core function represented by the cluster.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0032088","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0045039","count":2}]},{"hash":"877071488284652302","title":"Cytoskeleton Assembly and Cell Division","description":"This cluster is dominated by terms for assembling structural components (sperm/axoneme, terminal web, actin crosslinking) and for the mitotic cell cycle, suggesting a core of cytoskeleton-driven assembly and division. Fungal reproductive terms (karyogamy, ascospore formation) indicate mating-related cytoskeletal remodeling, while proton transport and vacuolar acidification relate to general organelle function; a few terms (visual perception, endothelial proliferation) are outliers. Overall, the theme centers on cytoskeletal organization and cell division rather than a single pathway.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007288","count":2},{"id":"GO:1902896","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0051764","count":2}]},{"hash":"1278780919688396095","title":"Ribosome biogenesis and chromosome condensation during cell division","description":"Several top terms center on ribosome biogenesis and chromosome condensation\u2014both meiotic and mitotic\u2014along with a general cell division term, suggesting the cluster links protein synthesis capacity with chromosome dynamics during division. Peripheral terms such as tRNA gene clustering, vesicle transport, GTPase regulation, and bacteriocin immunity do not strongly redefine the core theme. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:1903342","count":3},{"id":"GO:0070058","count":3},{"id":"GO:0010032","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2106307340364544261","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0000398","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0000466","count":4}]},{"hash":"1745175939170317353","title":"Lipid metabolism: biosynthesis and catabolism","description":"The cluster shows a strong tilt toward lipid-related processes, including triglyceride catabolic, monoacylglycerol catabolic, phospholipid dephosphorylation, and phosphatidylserine catabolic processes, as well as regulation of endocannabinoid signaling, which ties to lipid signaling. Additionally, there are biosynthetic terms (antibiotic, biotin, menaquinone biosynthesis) that reflect broader metabolic capabilities often linked with lipid-associated pathways. Overall, the dominant theme is lipid metabolism with related biosynthetic activities.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":7},{"id":"GO:0009234","count":6},{"id":"GO:0019433","count":6},{"id":"GO:2000124","count":6}]},{"hash":"1468684618024663243","title":"Developmental morphogenesis and Wnt-regulated signaling","description":"Top GO terms point to developmental processes such as multicellular growth, CNS development, angiogenesis, and stem cell differentiation, along with cell adhesion (adherens junction organization) and planar cell polarity. The presence of Wnt signaling\u2013related terms and cytoskeletal/trafficking processes (microtubule severing, ER-to-Golgi transport) suggests coordinated morphogenesis and tissue patterning driven by signaling and adhesion networks. This makes a coherent theme of development-focused morphogenesis.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0048863","count":2},{"id":"GO:0034332","count":2}]},{"hash":"904008841552085464","title":"Unknown","description":"The listed GO terms span muscle/sarcomere development, neuronal spine formation, kidney morphogenesis, immune germinal center formation, circadian rhythm regulation, and even ubiquitination and tRNA modification, with no single cohesive theme tying them together. Without a clear unifying function, a specific label isn\u2019t justifiable.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0060996","count":2},{"id":"GO:0048741","count":2},{"id":"GO:1990390","count":2},{"id":"GO:0042752","count":2}]},{"hash":"1227559768455513337","title":"Ion Transport and Membrane Potential Regulation","description":"This cluster centers on ion transport and membrane potential regulation: potassium and sodium export, intracellular potassium homeostasis, and stabilization of membrane potential. A few terms (sperm capacitation, cell migration) indicate broader contexts where ion flux and membrane dynamics matter; overall the proteins likely participate in ion homeostasis and membrane potential maintenance.","confidence":"Medium","size":26,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":4},{"id":"GO:0048240","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0097623","count":3}]},{"hash":"1541141808721243692","title":"Lipid and small-molecule biosynthesis","description":"This cluster is rich in lipid-related biosynthetic terms (fatty acid biosynthesis and medium-chain fatty-acyl-CoA metabolism) and also includes several other small-molecule biosynthetic pathways (menaquinone, siderophore, retinol, phenylpropanoid) along with some catabolic processes. The common thread appears to be metabolism and production of lipids and diverse small molecules, rather than a single, tightly defined pathway, justifying a label focused on lipid and small-molecule biosynthesis.","confidence":"Medium","size":26,"edges":239,"triangles":1165,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0019518","count":7},{"id":"GO:0042572","count":6},{"id":"GO:0090410","count":5}]},{"hash":"304294117460507044","title":"Mitochondrial translation and ribosome biogenesis","description":"The dominant GO terms are mitochondrial translation and ribosome biogenesis, indicating proteins involved in mitochondrial protein synthesis and assembly of ribosomes. There is also linkage to cell cycle processes, suggesting coordination between mitochondrial function and cell proliferation; a few stress-related or obsolete terms reflect broader regulatory context but do not redefine the core theme. High","confidence":"","size":26,"edges":62,"triangles":30,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":2},{"id":"GO:0051384","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2154178837963444347","title":"Unknown","description":"The terms include RNA processing and translation-related processes (tRNA processing, translation, RNA-templated DNA biosynthetic process, CTD phosphorylation regulation), but also a mix of unrelated terms (cobalamin biosynthesis, myelin-related processes, phosphatidylinositol dephosphorylation). The lack of a single cohesive biological theme across the cluster suggests no clear common function, so I label it Unknown.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0006278","count":2},{"id":"GO:0031642","count":2}]},{"hash":"1962974564615493188","title":"Brain development and dopamine metabolism","description":"The cluster includes cerebral cortex development and pituitary gland development, plus dopamine catabolic process, which together point to neural and neuroendocrine functions; other terms are immune or stress-related or obsolete, but the brain-related terms provide the main theme.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0019835","count":9},{"id":"GO:0032496","count":7},{"id":"GO:0016575","count":7},{"id":"GO:0021987","count":7}]},{"hash":"767554698866940699","title":"Mitochondrial Transport and Membrane Potential","description":"This cluster is dominated by GO terms for transmembrane transport of metabolites (phosphate, NAD, CoA) and regulation of the mitochondrial membrane potential, along with mitochondrial-specific processes like apoptotic changes and genome maintenance. Together these terms point to a cohesive role in mitochondrial transport and energy regulation, with some broader signals (liver regeneration, pregnancy) potentially reflecting systemic energy needs.","confidence":"High","size":26,"edges":21,"triangles":2,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035435","count":6},{"id":"GO:0000002","count":5},{"id":"GO:0008637","count":5},{"id":"GO:0070542","count":5},{"id":"GO:0097421","count":5}]},{"hash":"703514251598320566","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":307,"triangles":2209,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0000463","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0006351","count":5}]},{"hash":"136232578603162725","title":"Genome maintenance and DNA damage response","description":"The most represented terms are about DNA replication (primer synthesis, DNA topology changes) and DNA damage response (SOS, UV protection), plus RNA quality control (nonsense-mediated decay). Together these point to a module focused on preserving genome integrity under stress; a few development terms may be annotations from broader roles or cross-species data, but the core signal fits genome maintenance.","confidence":"High","size":26,"edges":69,"triangles":64,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000184","count":17},{"id":"GO:0006268","count":16},{"id":"GO:0009432","count":16},{"id":"GO:0006269","count":12},{"id":"GO:0006265","count":12}]},{"hash":"944922470141372428","title":"Cell signaling, RNA processing, and trafficking","description":"Top terms point to signaling pathways (Wnt, PDGF, Fc receptor) and cytoskeletal dynamics (lamellipodium), while other terms highlight post-transcriptional control (splicing, mRNA stability) and protein processing/trafficking. The cluster therefore seems to integrate signal transduction with regulation of gene expression and protein trafficking, rather than a single narrow function.","confidence":"Medium","size":26,"edges":210,"triangles":1093,"max_degree":25,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0090263","count":4},{"id":"GO:0000381","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0006412","count":3}]},{"hash":"2291474701749360231","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":37,"triangles":18,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":7},{"id":"GO:0042273","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0000466","count":6},{"id":"GO:1902626","count":5}]},{"hash":"317451911318646052","title":"Ribosome biogenesis and nucleocytoplasmic transport","description":"The top GO terms are dominated by ribosome biogenesis and export of ribosomal subunits from the nucleus, along with mRNA export and translation preinitiation complex formation, indicating a coherent module of ribosome assembly and nucleocytoplasmic trafficking. Vesicle transport terms (ER-Golgi) appear ancillary but do not redefine the main theme. This supports a label focused on ribosome assembly and nuclear-cytoplasmic transport.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000055","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0006890","count":3}]},{"hash":"919068497481800217","title":"RNA Methylation and Biosynthetic Enzymes","description":"Top GO terms cluster around RNA (guanine-N7)-methylation and rRNA methylation, with multiple biosynthetic processes (antibiotic biosynthetic process, biotin biosynthesis, vitamin E biosynthesis) also enriched. This points to a group of enzymes involved in RNA modification and various secondary/essential biosynthesis pathways. Some terms (response to amine, interleukin-1, tellurium ion, nodulation) appear peripheral but do not define a single coherent process, so the label emphasizes the core RNA modification and biosynthesis functions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036265","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0014075","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0070555","count":4}]},{"hash":"1858026440240074352","title":"Postsynaptic density and synaptic plasticity","description":"The top terms cluster around building and modulating the postsynaptic apparatus\u2014postsynaptic density assembly, AMPA receptor clustering, and long-term synaptic depression\u2014supported by related cytoskeletal remodeling (lamellipodium assembly). While there are some growth factor signaling terms and an immune-focused term, the dominant pattern points to synaptic structure and plasticity, justifying a synaptic-focused label.","confidence":"High","size":26,"edges":25,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":3},{"id":"GO:0071364","count":3},{"id":"GO:0097107","count":2},{"id":"GO:1903286","count":2},{"id":"GO:1904717","count":2}]},{"hash":"1901794841930928139","title":"TLR signaling and interferon production","description":"The cluster is dominated by innate immune signaling terms: TLR2 and TLR9 pathways, detection of bacterial lipopeptide, and positive regulation of interferon-\u03b1 and chemokine production, pointing to Toll-like receptor\u2013driven innate immune activation and type I interferon responses. Some other terms (CAMKK-AMPK signaling, manganese ion response) may reflect broader metabolic or stress-related regulation, and a few development-related terms appear incidental, but the strongest theme is TLR-mediated pathogen sensing and interferon/chemokine output.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071287","count":3},{"id":"GO:2000172","count":3},{"id":"GO:0032722","count":3},{"id":"GO:0034134","count":3},{"id":"GO:1905289","count":3}]},{"hash":"2202982550695880674","title":"Developmental cell proliferation and gene expression","description":"This cluster is dominated by GO terms for mitotic cell cycle, DNA replication, and DNA-templated transcription, along with development-related terms such as forebrain development, neural tube closure, and multicellular organism development. This suggests a core theme around cell proliferation and gene expression during development, with some stress/immune-related terms present as potential context-dependent connections. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":15},{"id":"GO:0006260","count":15},{"id":"GO:0050830","count":14},{"id":"GO:0001843","count":14},{"id":"GO:0006349","count":14}]},{"hash":"502959170878300248","title":"Exocyst-mediated vesicle trafficking","description":"This cluster is dominated by GO terms tied to the exocyst complex and vesicle transport to the plasma membrane (exocyst localization, exocyst assembly, exocytosis, Golgi to plasma membrane transport). While other terms touch on signaling and adhesion, the strongest signal centers on exocytic trafficking machinery guiding secretion and surface delivery, justifying a label focused on exocyst-driven vesicle trafficking.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":3},{"id":"GO:0050798","count":3},{"id":"GO:0048013","count":3},{"id":"GO:0034446","count":3},{"id":"GO:0071300","count":3}]},{"hash":"2158349015928625616","title":"Mitotic cell cycle regulation and kinetochore localization","description":"Dominant signals are cell cycle and mitosis: several terms reference the mitotic cell cycle checkpoint, spindle pole separation, and, notably, protein localization to the kinetochore in assembly and function. Ubiquitination also appears as a key regulator of mitosis. A few other terms (carbohydrate/ganglioside metabolism) are present but much less frequent, suggesting they are background noise. Overall, the cluster centers on mitotic regulation and kinetochore dynamics.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0005975","count":1},{"id":"GO:0051692","count":1}]},{"hash":"155496851983480174","title":"Neural development and morphogenesis","description":"The cluster is dominated by GO terms tied to nervous system development (GO:0007399), neural tube closure (GO:0001843), dendrite morphogenesis (GO:0048813), and general morphogenesis (GO:0000902), as well as embryonic cranial skeleton morphogenesis. Combined with DNA replication, transcription, and mitotic cell cycle terms, this suggests a population of proliferating neural progenitors undergoing neurodevelopmental morphogenesis. The presence of an intrinsic apoptotic signaling pathway in response to ER stress may reflect developmental stress responses. Overall, the most coherent theme is neural development and morphogenesis.","confidence":"High","size":25,"edges":11,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":21},{"id":"GO:0048701","count":18},{"id":"GO:0006351","count":17},{"id":"GO:0000278","count":17},{"id":"GO:0007275","count":16}]},{"hash":"24042009888273069","title":"Unknown","description":"The top GO terms are very diverse: DNA replication, ER-Golgi transport, metabolism, development, and stress responses. Several entries are marked obsolete, and there is little shared functional theme across the proteins. With such scattered annotations and only one edge, a single cohesive label isn't supported; thus Unknown is appropriate.","confidence":"","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0010288","count":3}]},{"hash":"611480302526960879","title":"Amino acid catabolism and central metabolism","description":"Most of the top GO terms point to catabolic pathways for several amino acids (L-alanine, L-lysine, L-leucine) and L-kynurenine, together with core energy metabolism processes (glycolytic process, tricarboxylic acid cycle, oxaloacetate metabolic process). While Notch signaling appears among the top terms, the overall pattern centers on amino acid degradation feeding into central carbon metabolism and energy production, with some regulatory cues suggested by cAMP response. This supports a coherent theme of amino acid catabolism linked to energy metabolism.","confidence":"Medium","size":25,"edges":299,"triangles":2277,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":11},{"id":"GO:0042853","count":11},{"id":"GO:0007219","count":11},{"id":"GO:0019878","count":10},{"id":"GO:0006099","count":10}]},{"hash":"1280483950363921210","title":"Rho/Rap Signaling and Intracellular Transport","description":"Proteins in this cluster are enriched for Rho and Rap GTPase signaling, intracellular protein transport, and kinase regulation, with neural context hints (forebrain development and memory). The common theme ties signaling pathway regulation to transport processes, suggesting a coordinated cellular signaling/trafficking role, including neural-related functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0032486","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0060335","count":2}]},{"hash":"1511956693196092491","title":"Membrane Transport and Lipid Biosynthesis","description":"The cluster's top GO terms are dominated by membrane-related processes: lipopolysaccharide biosynthetic process, phospholipid translocation, and transmembrane transport of ions, plus retrograde vesicle transport between Golgi and ER. These suggest a common theme around membrane composition and trafficking, rather than a single catalytic function. Some terms like DNA replication/cell cycle may reflect broader multifunctionality or annotation noise, but the overall signal centers on lipid handling and membrane transport.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0045332","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0099133","count":3},{"id":"GO:0046677","count":3}]},{"hash":"2301537939116404521","title":"Plasma membrane signaling and trafficking","description":"The terms cluster around membrane-associated processes: receptor clustering and PI3K/AKT signaling point to membrane signaling; endocytic recycling and adherens junction assembly indicate trafficking and cell\u2013cell contact at the surface; lipid signaling (endocannabinoid regulation) and GTPase activation suggest coordinated membrane dynamics and cytoskeletal remodeling. While some terms are peripheral, the dominant theme is plasma membrane signaling and receptor turnover.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043113","count":3},{"id":"GO:0043491","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0019433","count":3},{"id":"GO:2000124","count":3}]},{"hash":"207637421078449959","title":"Lymphocyte development and cytokine signaling","description":"The cluster shows strong enrichment for immune-related processes: B cell affinity maturation, NK T cell differentiation, interleukin-4 production, interleukin-7 response, and hemopoiesis, alongside related signaling and protein turnover (including JNK regulation and proteasomal ubiquitin-dependent degradation). While a couple terms (like forebrain development or general transcription) are broader, the dominant pattern points to lymphocyte development and cytokine-mediated signaling.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0098761","count":5},{"id":"GO:0002344","count":5},{"id":"GO:2001275","count":5},{"id":"GO:0032436","count":5}]},{"hash":"1826914529408142994","title":"GTPase-driven neuronal vesicle trafficking and actin remodeling","description":"Top GO terms point to nervous system development, small GTPase signaling, regulation of synaptic vesicle exocytosis, and actin dynamics (filopodium and formin-nucleated actin). Together they suggest a cohesive role for GTPase-controlled cytoskeletal rearrangements and vesicle trafficking in neurons, with broader trafficking processes appearing in the dataset. This label captures the central theme of GTPase-regulated neuronal actin remodeling linked to vesicle transport.","confidence":"High","size":25,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0007264","count":6},{"id":"GO:0051301","count":6},{"id":"GO:2000300","count":6},{"id":"GO:0032258","count":6}]},{"hash":"2073030915211898335","title":"Unknown","description":"The top terms cover a wide range of processes (GTPase regulation, dendrite extension, bile acid secretion, nuclear transport, T cell regulation, mRNA/tRNA export, VEGF signaling, and dolichyl phosphate biosynthesis) with no clear single theme or pathway dominating. This suggests the proteins do not reflect a cohesive, well-defined functional module, so the cluster is best labeled Unknown.","confidence":"","size":25,"edges":11,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:1903861","count":4},{"id":"GO:0032782","count":3},{"id":"GO:0000060","count":3},{"id":"GO:0046642","count":3}]},{"hash":"777602273136337884","title":"Immune signaling and phagocytosis regulation","description":"The GO terms emphasize regulation of apoptosis and key signaling pathways (Rho, Ras, PI3K) along with regulation of phagocytosis and B cell differentiation, suggesting a cohesive theme around immune cell signaling and effector functions; a stray term like exploration behavior is likely noise.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0002316","count":2}]},{"hash":"1378004483826646596","title":"Ribosome Biogenesis and Protein Translation","description":"This cluster is dominated by GO terms for ribosome biogenesis, cytoplasmic translation, translation, and tRNA modification, indicating a core theme around ribosome assembly and protein synthesis. Related terms about ribosomal subunit export from the nucleus reinforce this focus, with a few cell-cycle-related terms likely reflecting growth coordination. Overall, the set centers on ribosome production and function.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":10},{"id":"GO:0002181","count":9},{"id":"GO:0006412","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0000747","count":7}]},{"hash":"1781378024869705329","title":"Chloroplast ribosome assembly and photosynthesis proteins","description":"This cluster\u2019s top GO terms are dominated by photosynthesis and ribosomal large subunit assembly, pointing to plastid/Chloroplast functions related to translating organellar genes and driving photosynthetic processes. Other terms (ER stress-related translation initiation, ubiquitination, and protein complexes) are more general, but the strongest signal centers on chloroplast gene expression and photosynthetic machinery. Confidence: Medium.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0051348","count":2},{"id":"GO:0036494","count":2}]},{"hash":"1285451904265915801","title":"Steroid and fatty acid biosynthesis","description":"The top GO terms cluster around lipid and steroid metabolism: testosterone biosynthetic process and androgen metabolic process point to steroid hormone production, while fatty acid elongation and very long-chain fatty acid biosynthetic processes indicate lipid biosynthesis. Dolichol-linked oligosaccharide biosynthesis relates to isoprenoid/lipid pathways, and male genitalia development aligns with androgen signaling. Overall, this suggests a lipid-centric module with steroid hormone biosynthesis as a core theme, rather than a single, narrow function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030539","count":2},{"id":"GO:0030497","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0006488","count":2},{"id":"GO:0042761","count":2}]},{"hash":"2224554420805975788","title":"Neuroimmune Signaling","description":"The cluster shows strong representation of innate immune terms (innate immune response, LPS response/signaling, defense against bacteria) alongside neural development and signaling terms (axonogenesis, corpus callosum development, dopamine response, pain-related behavior). This pattern suggests proteins with roles in neuroimmune communication or dual involvement in immune responses and neural development.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0071222","count":5},{"id":"GO:0071372","count":5},{"id":"GO:0014068","count":5},{"id":"GO:1903351","count":5}]},{"hash":"807488094315523330","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning bacterial lipoteichoic acid biosynthesis and Gram-positive defense, plus diverse eukaryotic processes (development, signaling, neural and muscle functions). With no cohesive shared function or pathway across the cluster and no interactions observed, there isn't a clear, single theme to name this cluster.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070395","count":4},{"id":"GO:0050830","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0002063","count":3}]},{"hash":"55382828296206021","title":"DNA replication and development","description":"The cluster centers on DNA replication and mitotic processes (DNA replication, mitotic DNA replication, sister chromatid cohesion, microtubule severing) and also includes several developmental terms (skeletal system development, brain development, neural tube closure). This mix suggests proteins involved in cell cycle progression and embryonic development, possibly nuclear factors coordinating replication with developmental pathways. Some terms are obsolete, which may reflect older annotations, but the overall theme points to a link between cell division and development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0032508","count":2},{"id":"GO:1902969","count":2},{"id":"GO:0007064","count":2}]},{"hash":"326398015333912874","title":"Translation and aminoacyl-tRNA charging","description":"This cluster shows a core enrichment for translation and tRNA aminoacylation (methionyl- and leucyl-tRNA charging), pointing to protein synthesis machinery as the main theme. The presence of metabolic and stress-related terms is less central to the cluster's primary function.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006915","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1912038785352964711","title":"Unknown","description":"The Top Terms are a mix of obsolete GO terms and unrelated processes (oxidation-reduction, regulation of translational initiation, GTPase regulation, ERAD pathway, aminoadipic acid biosynthesis, oligodendrocyte development, methionine salvage, and responses to nitric oxide and ethylene). This lack of a cohesive shared function prevents a meaningful, specific label for the cluster. Therefore the appropriate name is Unknown.","confidence":"","size":24,"edges":14,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006446","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0019878","count":3}]},{"hash":"387616278035774574","title":"Nuclear transport and ribosome biogenesis","description":"The top GO terms cluster around nucleocytoplasmic transport and ribosome-related processes (nuclear import of ribosomal proteins and NLS-bearing proteins, mRNA export, nuclear pore assembly), with additional links to DNA replication and cell division\u2014all pointing to nucleus-centric functions. This suggests the proteins function together in coordinating nuclear transport and ribosome biogenesis. ","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0000060","count":7},{"id":"GO:0051292","count":7},{"id":"GO:0006610","count":7},{"id":"GO:0006607","count":7}]},{"hash":"1870896779068113341","title":"Keratinocyte differentiation and apoptosis signaling","description":"This cluster centers on epithelial cell fate and programmed cell death, with recurrent signals related to keratinocyte differentiation, Wnt and Hippo pathway regulation, and growth/survival signaling (ERK, GTPase activity). Some terms touch neurons or T-cell regulation, but the dominant pattern points to keratinocyte differentiation intertwined with apoptotic and growth-control signaling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006915","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0030216","count":5},{"id":"GO:0035329","count":5}]},{"hash":"1910065970249876622","title":"RNA processing and translation regulation","description":"This cluster centers on RNA processing (splicing) and translation initiation/ regulation, with terms for mRNA splicing, formation of the preinitiation complex, and regulation of translational initiation, as well as IRES-dependent translation initiation. While apoptosis and redox-related terms appear, the strongest signal is control of gene expression at RNA processing and translation steps.","confidence":"Medium","size":24,"edges":10,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0075522","count":3},{"id":"GO:0000398","count":3}]},{"hash":"120688481508343183","title":"Chromatin-modifying transcription regulators","description":"The cluster centers on DNA-templated transcription and chromatin state, with histone demethylation and related post-translational modifications, plus regulatory roles in development (myoblast differentiation, vasculogenesis) and signaling (Notch) and hypoxia responses\u2014consistent with a group of transcription regulators linked to chromatin modification during development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0034720","count":8},{"id":"GO:0070544","count":8},{"id":"GO:0042265","count":6},{"id":"GO:0061428","count":6}]},{"hash":"1725414717718192837","title":"Redox Detoxification and Metabolic Stress","description":"This cluster centers on redox-related processes: cellular oxidant detoxification, glutathione metabolic process, and cellular redox homeostasis, indicating a core role in managing oxidative stress. Prostaglandin biosynthesis and toxin catabolic process further suggest lipid signaling and detox pathways interconnected with stress responses. The additional terms related to starvation response and calcium-linked muscle regulation likely reflect broader metabolic adaptation contexts. Overall, a concise label would be Redox Detoxification and Metabolic Stress.","confidence":"Medium","size":24,"edges":118,"triangles":165,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0006749","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0042594","count":5}]},{"hash":"2021116306602725240","title":"RNA processing and ribosome biogenesis","description":"This cluster centers on RNA processing: multiple terms point to mRNA splicing via the spliceosome (including positive regulation of splicing) and regulatory ncRNA\u2013mediated gene silencing. It also includes multiple terms related to ribosome biogenesis and maturation of rRNA components (large and small subunit maturation), suggesting a shared theme of RNA maturation and ribosome assembly. Although a couple of obsolete terms appear, the core signals converge on RNA processing and ribosome formation.","confidence":"Medium","size":24,"edges":13,"triangles":0,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":16},{"id":"GO:0031047","count":15},{"id":"GO:0000398","count":14},{"id":"GO:0042273","count":11},{"id":"GO:0000463","count":11}]},{"hash":"635467477543055383","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048009","count":2},{"id":"GO:0048709","count":2},{"id":"GO:0071392","count":2},{"id":"GO:0031659","count":2},{"id":"GO:0000294","count":1}]},{"hash":"1631086841844875648","title":"Leukocyte Adhesion and Migration Signaling","description":"The top GO terms cluster around immune cell adhesion and movement: leukocyte tethering/rolling, integrin-mediated signaling, heterophilic/heterotypic cell\u2013cell adhesion, substrate-dependent cell migration, and T cell activation via antigen recognition. This points to a cohesive theme of immune cell adhesion and trafficking, with some developmental context terms present but not overriding the main function.","confidence":"High","size":24,"edges":52,"triangles":20,"max_degree":17,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0035987","count":16},{"id":"GO:0045123","count":15},{"id":"GO:0006929","count":15},{"id":"GO:0034113","count":15},{"id":"GO:0002291","count":15}]},{"hash":"1710060046745033896","title":"Heart and vascular development","description":"Top terms center on heart and blood vessel formation (venous endothelial differentiation, cardiac morphogenesis, Notch signaling in heart field) and vascular regulation (positive regulation of blood coagulation, cellular response to mechanical stimulus). Transcriptional control during development (DNA-templated transcription, transcription by RNA polymerase II) complements these themes. Overall, the cluster appears enriched for cardiovascular development and endothelial differentiation, with supporting transcriptional and mechanotransduction signals.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060843","count":2},{"id":"GO:0030194","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0021654","count":2}]},{"hash":"1954709125067487817","title":"Chromatin remodeling and transcription regulation","description":"Most terms cluster around chromatin dynamics (chromatin organization, heterochromatin formation, chromatin remodeling) and transcriptional control (DNA-templated transcription, histone modification references). A few unrelated terms (platelet aggregation, collagen catabolic process) are likely noise. This supports labeling the cluster as chromatin remodeling and transcription regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034724","count":1}]},{"hash":"2019339444400273091","title":"Gametogenesis and Developmental Signaling","description":"This cluster is dominated by GO terms tied to reproductive signaling (cellular responses to peptide hormones and FSH stimulus), sperm maturation (sperm capacitation), and broad development (multicellular organism development, cell morphogenesis), with supporting signals from cell-cycle control and metabolism (mitotic cell cycle, fatty acid oxidation). An outlying dsRNA response term is present but does not define the group; overall, the proteins appear to coordinate hormone-driven development and gamete maturation with metabolic and proliferative processes. ","confidence":"Medium","size":23,"edges":135,"triangles":330,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043330","count":8},{"id":"GO:0071333","count":8},{"id":"GO:0071375","count":8},{"id":"GO:0071372","count":8},{"id":"GO:0006977","count":8}]},{"hash":"1450722317046271577","title":"Proliferation and developmental signaling control","description":"Cluster shows strong signals for regulating cell cycle, proliferation, and apoptosis, alongside cell migration and development (root development) and modulation of Wnt signaling. The combination suggests a cohesive module coordinating growth, differentiation, and movement during development, with supporting hints from nuclear import and proteasome localization indicating regulation of protein turnover and trafficking. ","confidence":"High","size":23,"edges":190,"triangles":854,"max_degree":22,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0015991","count":10},{"id":"GO:0006607","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0007050","count":9},{"id":"GO:0008285","count":9}]},{"hash":"317403449265177024","title":"Retroviral DNA replication and genome integration","description":"Top terms center on reverse transcription (RNA-templated DNA synthesis), DNA replication and recombination, DNA integration, and viral entry/latency in the host nucleus, all hallmarks of a retroviral life cycle. The explicit mentions of integrated proviral latency and viral nuclear entry strongly support this theme, with a minor contribution from DNA repair terms likely reflecting host responses to viral DNA. ","confidence":"High","size":23,"edges":122,"triangles":279,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0006310","count":9},{"id":"GO:0039651","count":8},{"id":"GO:0006278","count":8},{"id":"GO:0015074","count":8}]},{"hash":"813647146250228645","title":"Immune Signaling Regulation and Ubiquitination","description":"This cluster centers on immune signaling control, with terms for negative regulation of T cell receptor signaling and ERK cascades, plus positive regulation of interferon-beta production. It also emphasizes ubiquitin-related protein regulation, including K63-linked ubiquitination and MVB sorting. A few terms (glial differentiation, prolactin signaling) are broader or less directly tied, but overall the pattern points to immune signaling modulation and ubiquitin-mediated protein turnover.","confidence":"Medium","size":23,"edges":252,"triangles":1750,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0050860","count":20},{"id":"GO:0000200","count":20},{"id":"GO:0070373","count":20},{"id":"GO:0035549","count":15},{"id":"GO:1902523","count":15}]},{"hash":"2168220327985855045","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006281","count":5},{"id":"GO:0000467","count":3},{"id":"GO:0031047","count":3},{"id":"GO:1904355","count":2}]},{"hash":"1953702769578438568","title":"Cell Cycle and Division","description":"The cluster is mainly enriched for cell-cycle and mitotic processes, suggesting proteins involved in cell division; a few terms also indicate cytoskeletal remodeling and neurite development, but the dominant signal remains cell-cycle machinery.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0031175","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0046839","count":3}]},{"hash":"907324795414001373","title":"Ribosome biogenesis and translation machinery","description":"This cluster is dominated by GO terms tied to protein synthesis and ribosome assembly, including translation, ribosome biogenesis, rRNA and tRNA processing, and translation initiation complex formation. While there are additional gene-expression terms like transcription termination, the strongest and most consistent signals point to the core protein synthesis machinery and RNA processing needed for ribosome function and translation, with some growth-related terms suggesting coordination with cell division.","confidence":"High","size":23,"edges":19,"triangles":0,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0006364","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":2}]},{"hash":"1237559339383717583","title":"Unknown","description":"The listed GO terms span highly diverse processes (response to lead ion, morphine and other drug responses, T cell homeostasis, DNA replication, neuron and lung epithelial differentiation, unfolded protein response, histone dephosphorylation, and glucocorticoid signaling). There isn\u2019t a clear, single biological function or pathway tying all proteins together, suggesting heterogeneity or lack of a cohesive theme in this cluster. ","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010288","count":4},{"id":"GO:0043029","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0043278","count":4},{"id":"GO:0030182","count":4}]},{"hash":"1521461416270787834","title":"GTPase Signaling in Neural and Vascular Development","description":"Based on the top GO terms, the cluster is dominated by small GTPase signaling and its regulation (GO:0007264, GO:0043547) and includes neural development (hippocampus development, neuron apoptotic process) and vascular/angiogenic processes (endothelial tube lumen extension, sprouting angiogenesis, ephrin receptor signaling). This suggests a cohesive theme around GTPase-driven signaling impacting neural and vascular development, with additional trafficking and immune signaling terms reflecting broader signaling roles. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0043525","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0090051","count":3}]},{"hash":"445506435449242427","title":"Mitotic Cell Cycle and Transcription","description":"This cluster is dominated by GO terms tied to cell division and mitosis (mitotic cell cycle, cell division, APC-dependent catabolic process) and DNA-templated transcription, indicating core involvement in mitotic regulation and transcriptional activity during cell cycle. Additional terms point to regulatory signaling (Rho GTPase signaling) and stress-related responses (cadmium response, defense response to virus), suggesting peripheral regulatory and stress-related connections that may accompany mitotic processes. Overall, the dominant theme is mitosis with supportive transcriptional and regulatory context.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0031145","count":3},{"id":"GO:0043547","count":3},{"id":"GO:2001162","count":3}]},{"hash":"1163633067458782954","title":"Unknown","description":"The top GO terms span transcription regulation, RNA processing, protein transport, signaling, immune response, development, and ubiquitin-related protein modification, indicating a highly diverse set of functions with no clear, single theme tying the cluster together. This makes it hard to assign a specific, coherent label to the whole group.","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006397","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0002677","count":2}]},{"hash":"467150973788408493","title":"Centrosome and Microtubule Organization","description":"The cluster is dominated by GO terms related to centrosome duplication, mitotic cell cycle, tubulin complex assembly, and microtubule organization/nucleation, indicating a coherent module governing centrosome function and spindle/microtubule dynamics during cell division. Some terms reference neuronal development or innate immunity, but the strongest signals center on microtubule organization. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051298","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0021695","count":2},{"id":"GO:0007021","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1544430239360288679","title":"Chromatin Assembly and Histone Modification","description":"Dominant GO terms are nucleosome assembly and histone H3-K4 trimethylation, indicating chromatin organization. A few membrane transport and salt-stress terms are present but less represented, suggesting incidental annotations; overall the core signal is chromatin-related proteins.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0080182","count":2},{"id":"GO:1902600","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0097623","count":1}]},{"hash":"358268395418835579","title":"Membrane trafficking and neuronal signaling","description":"The GO terms point to vesicle trafficking (exocytosis; GTPase activity regulation), protein quality control/ER-associated transport (ER to cytosol transport; ERAD), and neural signaling (long-term synaptic depression; myelination in PNS; PDGF response). While some terms (tight junctions, potassium channel regulation) are broader, the recurring theme centers on membrane trafficking and signaling in neural contexts. Confidence: Medium.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0030970","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006887","count":2},{"id":"GO:0034260","count":2}]},{"hash":"504200660269190594","title":"Ubiquitin-Dependent Proteolysis and Antiviral Immunity","description":"The top GO terms center on ubiquitin-dependent protein catabolism (ERAD, SCF-mediated degradation, autoubiquitination) and various ubiquitin linkages (K48, K63, K6), pointing to a core function in tagging substrates for proteasomal degradation. The presence of innate immune response and defense against virus terms suggests these proteins also participate in antiviral defense, a common role for ubiquitin signaling in regulating immune pathways. The peroxisome import term is less central but may reflect broader proteostasis-related functions. Overall, the cluster seems driven by ubiquitin-mediated proteolysis with an antiviral defense association.","confidence":"High","size":22,"edges":30,"triangles":9,"max_degree":7,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0030433","count":9},{"id":"GO:0051865","count":9},{"id":"GO:0031146","count":9},{"id":"GO:0070936","count":8}]},{"hash":"1794885028320912770","title":"Unknown","description":"This cluster shows a broad mix of GO terms from very different biological contexts\u2014development, sensory processes, DNA damage, cell signaling, and mineralization. There is no clear, single function or pathway common to most proteins, and one term is obsolete, making a cohesive interpretation unlikely. Therefore, no specific, concise label fits better than Unknown.","confidence":"","size":22,"edges":154,"triangles":607,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007118","count":22},{"id":"GO:0009636","count":19},{"id":"GO:0007601","count":19},{"id":"GO:1990802","count":19},{"id":"GO:1904355","count":19}]},{"hash":"224541915109647175","title":"ER protein quality control and stress response","description":"This cluster\u2019s top GO terms cluster around the endoplasmic reticulum\u2019s protein handling and stress responses: unfolded protein response, ER-associated degradation, regulation of translation initiation during ER stress, and chaperone-dependent refolding. Together they define a coherent theme of ER protein quality control and adaptive stress signaling. Some other terms (cell cycle and innate immunity) appear less prominently, suggesting secondary associations rather than core functions. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0036494","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0051661","count":4},{"id":"GO:0070389","count":4}]},{"hash":"679301392536572666","title":"Cytoskeleton dynamics and signaling regulation","description":"The top GO terms cluster around actin filament assembly, focal adhesion regulation, and cellular responses to growth factors, which together indicate cytoskeletal remodeling linked to signaling. Additional terms on vesicle trafficking, GTPase activation, and cilium regulation support a broader theme of coordinated membrane\u2013cytoskeleton dynamics and signaling regulation. While a few terms are more divergent (e.g., virus-related activation, septation signaling), the prevailing pattern points to cytoskeleton-centered regulation of signaling and trafficking.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0051895","count":2},{"id":"GO:0032889","count":1},{"id":"GO:0090630","count":1}]},{"hash":"921100194856961696","title":"Developmental Kinase Signaling and Proliferation","description":"This cluster is enriched for kinase signaling terms (positive regulation of autophosphorylation and serine/threonine kinase activity) and regulators of GTPase activity, plus cell cycle, proliferation, and development terms (mitotic cell cycle, multicellular and skin development). The presence of hypoxia response and mRNA transport suggests coordinated signaling and gene expression changes during growth and differentiation. Together, these terms point to a cohesive theme of developmental signaling driving proliferation and differentiation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031954","count":7},{"id":"GO:0071456","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0071902","count":6}]},{"hash":"497745488694394892","title":"Cytoskeleton remodeling and junction assembly","description":"The cluster is dominated by GO terms tied to actin cytoskeleton organization and regulation of Rho/GTPase signaling, plus localization to adherens and tight junctions and establishment of endothelial barriers, pointing to coordinated cytoskeletal dynamics and junction assembly. Insulin receptor signaling and protein dephosphorylation further reflect regulatory signaling that modulates these processes; a few neural terms are present but do not define the overall theme. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":5},{"id":"GO:0030036","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0006470","count":3},{"id":"GO:0071625","count":3}]},{"hash":"1851418091033193736","title":"Ribosome biogenesis and translation","description":"This cluster centers on ribosome assembly and protein synthesis, with key terms for ribosome biogenesis, formation of the translation preinitiation complex, rRNA and snRNA pseudouridine synthesis, and overall translation. Additional terms about rRNA maturation and translation reinitiation reinforce a module focused on ribosomal production and use.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0001731","count":5},{"id":"GO:0031120","count":5},{"id":"GO:0031118","count":5},{"id":"GO:0006412","count":5}]},{"hash":"1114990868884611490","title":"Ubiquitination and ADP-ribosylation Regulators","description":"The top GO terms are strongly centered on post-translational modifications, especially protein ubiquitination (GO:0016567) and protein poly-ADP-ribosylation (GO:0070212). Other terms touch on cell growth, CDK activity regulation, and differentiation, suggesting a module of proteins involved in modifying and regulating signaling and cell-cycle processes rather than a single, tight pathway. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:2001275","count":6},{"id":"GO:0016049","count":6},{"id":"GO:0071260","count":6},{"id":"GO:1904355","count":5}]},{"hash":"568080493291408580","title":"DNA replication and genome maintenance","description":"The cluster is dominated by nuclear processes: DNA replication, DNA-templated transcription, mitotic cell cycle, and telomere maintenance, pointing to roles in genome integrity and cell division. Proteostasis-related terms (proteasome assembly, ERAD) may reflect coordinated protein turnover accompanying these processes, reinforcing a genome maintenance theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006351","count":6},{"id":"GO:2001275","count":6},{"id":"GO:0016477","count":6},{"id":"GO:0030433","count":5}]},{"hash":"439003471709330319","title":"DNA Replication and Transcription Stress Response","description":"The cluster is dominated by nucleic-acid related processes (DNA-templated transcription, DNA replication, SOS response, viral genome replication) with supplementary metabolic biosynthetic terms, suggesting a theme around genome stability and DNA metabolism. Some terms (host autophagy activation, obsolete GO terms) introduce noise, but the core signal points to DNA-related processes and stress responses.","confidence":"Medium","size":21,"edges":187,"triangles":960,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0055114","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0019518","count":5},{"id":"GO:0042866","count":5}]},{"hash":"1694788248716186846","title":"Fe-S Cluster Biogenesis and Organelle Translation","description":"The cluster centers on iron-sulfur cluster assembly/transfer and mitochondrial translation, with a note of ER stress\u2013associated translation initiation and organelle-related processes. This suggests a coherent theme around the biogenesis of Fe-S cofactors essential for organelle protein synthesis and function, with auxiliary signals reflecting related metabolic contexts (photosynthesis, nitrogen fixation) in Fe-S\u2013dependent systems. Despite some divergent terms, the core linkage appears to be Fe-S cluster biogenesis coupled to organelle translation.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0009399","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0016226","count":2}]},{"hash":"925074836609613755","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":196,"triangles":1088,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":7},{"id":"GO:0042866","count":6},{"id":"GO:0006564","count":6},{"id":"GO:0044571","count":6},{"id":"GO:0018283","count":6}]},{"hash":"1971230459162328404","title":"Post-transcriptional RNA splicing and stability regulation","description":"The top GO terms converge on RNA processing and post-transcriptional control\u2014regulation of splicing via the spliceosome, alternative splicing control, mRNA stabilization, and translation initiation factor assembly\u2014together with ncRNA-mediated gene silencing, indicating a coherent theme of RNA-level regulation of gene expression.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":15},{"id":"GO:0048026","count":15},{"id":"GO:1901407","count":11},{"id":"GO:0010610","count":10},{"id":"GO:0006378","count":10}]},{"hash":"2301971098488686264","title":"Mitosis and microtubule dynamics in development","description":"The cluster is dominated by GO terms for mitotic spindle assembly, actomyosin contractile ring formation, cytokinesis, and microtubule dynamics (minus-end and plus-end activities), plus links to development and tissue organization, indicating a cohesive role in cytoskeletal remodeling during cell division and developmental processes.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":20},{"id":"GO:0000915","count":20},{"id":"GO:0090307","count":20},{"id":"GO:0031534","count":20},{"id":"GO:0001560","count":20}]},{"hash":"401800516619925463","title":"Signaling and Intracellular Trafficking","description":"These terms cluster around cellular signaling responses to various stimuli (toxic substances, peptide hormones, PDGF, immune cues) and processes that move or regulate proteins between compartments (nucleus export, Golgi-to-plasma membrane transport, centrosome-related functions). This suggests a group of proteins that mediate signal transduction and coordinate intracellular trafficking, rather than a single narrowly defined process.","confidence":"Medium","size":21,"edges":19,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0042997","count":2},{"id":"GO:0002774","count":2}]},{"hash":"406356604535748817","title":"Ribosome biogenesis and mRNA quality control","description":"This cluster is dominated by translation and ribosome-related processes: translation, translational termination, and maturation/processing of rRNA, plus mRNA decay pathways (no-stop and no-go). Together they suggest a group involved in ribosome biogenesis and mRNA surveillance. Some unrelated terms (antibiotic biosynthesis; Wnt signaling; hematopoiesis) appear but are not representative of the main theme.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0070481","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000463","count":1}]},{"hash":"2274081260677844385","title":"Gram-negative envelope polysaccharide biosynthesis","description":"The GO terms are dominated by cell wall and polysaccharide biosynthesis activities, especially lipopolysaccharide and lipid A biosynthesis, along with UDP-glucose and GDP-L-fucose related sugar pathways, suggesting a shared role in assembling the bacterial outer membrane envelope and related sugar metabolism. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0005978","count":2},{"id":"GO:0009103","count":1},{"id":"GO:0006011","count":1},{"id":"GO:0009092","count":1}]},{"hash":"2113975721686961527","title":"Xenobiotic transport and fatty acid metabolism","description":"This cluster centers on membrane transport involving xenobiotics and drugs (xenobiotic export, daunorubicin transport, glycerophosphodiester transport) and fatty acid handling (long-chain fatty acid import into peroxisome, very long-chain fatty acid catabolism), suggesting a shared role in detoxification and lipid metabolism. Some antibiotic response terms appear but are likely ancillary to the core transport/metabolic theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0007584","count":3},{"id":"GO:0030153","count":3},{"id":"GO:0046618","count":3},{"id":"GO:0042760","count":3}]},{"hash":"92989248373594043","title":"Mechanotransduction and Cytoskeletal Motility","description":"The cluster is driven by GO terms related to cellular response to mechanical stimulus, actin filament bundle assembly, and cell migration, together with epithelial cell polarity establishment. These point to mechanosensing and cytoskeletal remodeling as a core theme, governing cell shape, movement, and polarity, with additional regulatory processes like ubiquitination and PARylation. While a few terms (e.g., oligodendrocyte differentiation, telomere capping) are less directly tied, the dominant signal is cytoskeleton- and polarity-associated motility.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":5},{"id":"GO:0016567","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0090162","count":4}]},{"hash":"143285826296354384","title":"Epithelial Development and Cell Adhesion","description":"The cluster is enriched for terms related to epithelial/tissue development (skin development, endodermal differentiation, nephron development) and for cell\u2011cell adhesion processes (heterophilic adhesion, integrin\u2011mediated adhesion) as well as calcium signaling. This suggests proteins coordinating epithelial morphogenesis and organogenesis, with adhesion interfaces and signaling guiding cell migration and differentiation. A few terms like exploration behavior and axonal defasciculation are less central but may reflect shared signaling modules that influence cell movement in other contexts.","confidence":"High","size":21,"edges":86,"triangles":134,"max_degree":20,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0010634","count":17},{"id":"GO:0035640","count":17},{"id":"GO:0043588","count":17},{"id":"GO:0035987","count":17},{"id":"GO:0010694","count":16}]},{"hash":"1660976508373664150","title":"NOD2-Mediated Innate Immune Signaling","description":"This cluster is best captured by its enrichment for NOD2-related signaling terms, including the NOD2 signaling pathway and muramyl dipeptide response, as well as links to NF-kappaB transcription factor activity, which together point to innate immune sensing of bacterial peptidoglycan and downstream NF-kB\u2013driven responses. While there are some metabolic transport terms in the list, the strongest and most specific theme centers on NOD2-dependent innate immunity rather than metabolism.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0071225","count":2},{"id":"GO:0042128","count":2}]},{"hash":"793836771702446708","title":"Ciliogenesis and neural development","description":"This cluster is dominated by GO terms related to cilium assembly and nervous system development (cNS development, innervation, GDNF receptor signaling, FGFR signaling regulation), suggesting a cohesive theme around cilia-associated processes in neural development and signaling. Some terms reflect broader developmental roles (e.g., chondrocyte development, smooth muscle contraction), but the central pattern points to ciliogenesis linked to neural development.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":3},{"id":"GO:0002063","count":2},{"id":"GO:0060384","count":2},{"id":"GO:0014846","count":2},{"id":"GO:0042425","count":2}]},{"hash":"1794799332246158090","title":"Cytoskeleton dynamics and spindle organization","description":"The cluster is enriched for microtubule-based movement, mitotic spindle assembly, filopodium assembly, and regulation of Rho signaling, all pointing to cytoskeletal dynamics and control of cell shape during development and division. Spinal cord development aligns with developmental cytoskeletal roles, while other terms like RNA methylation, sterol biosynthesis, immune defense, and growth hormone response may be context-specific or downstream effects. Overall, the strongest signal centers on cytoskeleton regulation and spindle function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0021510","count":4},{"id":"GO:0007018","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0046847","count":4},{"id":"GO:0036265","count":3}]},{"hash":"688324018360726490","title":"Mitochondrial Complex II Assembly","description":"The top GO term points to mitochondrial respiratory chain complex II assembly (succinate dehydrogenase assembly), suggesting the cluster comprises proteins involved in assembling complex II. Although there are no reported edges, the single specific annotation supports a cohesive theme of complex II assembly functions.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1}]},{"hash":"1172373820340743606","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0048701","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0000480","count":6},{"id":"GO:0000472","count":6}]},{"hash":"2003105334144920715","title":"Diverse Biosynthetic Pathways","description":"The GO terms are dominated by biosynthetic processes spanning steroids, lipids, antibiotics, cofactors, and other metabolites, suggesting a cluster of proteins involved in various biosynthetic activities rather than a single, unified pathway. Some terms (lung development, sporulation) are less connected, but overall the theme centers on biosynthesis/metabolism. ","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045150","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0030324","count":4},{"id":"GO:0030435","count":4},{"id":"GO:0006703","count":3}]},{"hash":"601406684266502495","title":"Transcriptional Regulation and Stress Response","description":"The strongest shared function is DNA-templated transcription (4 proteins), pointing to regulation of gene expression. Additional terms (phosphorylation, oxidative stress response, cell division) suggest signaling and stress-responsive processes that can modulate transcription, with a few entries touching on metabolism and development. The cluster appears to group proteins involved in gene expression regulation under stress-related or signaling conditions, rather than a single cohesive pathway, hence a transcription-stress theme.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0016310","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0017000","count":2}]},{"hash":"1997968142361880783","title":"Glycan and lipid biosynthesis","description":"This cluster\u2019s top GO terms cluster around biosynthesis of carbohydrate polymers (glycogen, starch), glycan-related structures (GPI anchor, mannosylation), and lipid components (phospholipid, glycolipid), suggesting proteins involved in building glycan- and lipid-containing cellular components. Some terms like feeding behavior or water deprivation may reflect broader or misannotated associations, but the core theme is biosynthetic processes related to glycans and lipids.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0005978","count":5},{"id":"GO:0007631","count":4},{"id":"GO:0006506","count":4},{"id":"GO:0009744","count":4},{"id":"GO:0019252","count":4}]},{"hash":"2114142709063466106","title":"RNA processing and translation regulation cluster","description":"This cluster is dominated by GO terms for mRNA processing and stability (mRNA stabilization, regulation of alternative splicing, regulation of mRNA stability in response to stress) and for translation initiation factor complex assembly, suggesting a core function in post-transcriptional gene expression control. While a few terms touch signaling and cell cycle, the prevalent RNA-centric terms point to RNA metabolism and translation regulation as the cohesive theme.","confidence":"Medium","size":20,"edges":136,"triangles":487,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0000278","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0097010","count":3}]},{"hash":"671877853580182575","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0051013","count":3}]},{"hash":"1632984540353215535","title":"Rho/Rac GTPase\u2013driven cytoskeletal remodeling in immune cells","description":"This cluster centers on small GTPase signaling regulating actin dynamics (lamellipodium assembly, Rac/Rho pathways) and cell spreading, with additional immune-related processes such as dendritic cell chemotaxis and B cell maturation. The convergence on small GTPases and lamellipodium suggests a core theme of cytoskeletal remodeling guided by Rho/Rac signaling, while the immune terms indicate the context of immune cell migration and activation. The term \"myelin maintenance\" and \"IL-7 response\" are peripheral but do not override the dominant cytoskeletal/GTPase theme. Overall, a coherent label capturing GTPase-driven cytoskeletal remodeling in immune cells.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":2},{"id":"GO:1904424","count":2},{"id":"GO:0032287","count":2},{"id":"GO:0035020","count":2},{"id":"GO:0098761","count":2}]},{"hash":"1592759505226322745","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0000472","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0048568","count":3}]},{"hash":"2303363773296833276","title":"Synaptic vesicle trafficking and ERK signaling","description":"GO terms emphasize endocytosis, synaptic vesicle exocytosis, brain development, and ERK cascade regulation, indicating a set of proteins coordinating vesicle trafficking at synapses and related signaling pathways in neural development.","confidence":"Medium","size":20,"edges":53,"triangles":16,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031532","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0031384","count":5},{"id":"GO:0043547","count":5}]},{"hash":"410132087151912735","title":"Unknown","description":"The terms span diverse biological themes (proteolysis, sugar metabolism, apoptosis, neuronal projection, immune response to LPS, erythroid differentiation, neuromuscular control, fungal beta-glucan biosynthesis, N-glycan processing, vacuolar sequestration). There isn't a single unifying process or pathway that accounts for the majority of proteins, and the lack of edges implies weak connectivity. Therefore a cohesive, specific label cannot be reliably assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":4},{"id":"GO:0000023","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0010976","count":3},{"id":"GO:0032496","count":3}]},{"hash":"978916876719904819","title":"Cardiac signaling and cytoskeletal regulation","description":"The GO terms point to intracellular signal transduction with a notable emphasis on cardiac function (regulation of SA node cell action potential, cardiac muscle contraction) and cytoskeletal dynamics (regulation of Rho signaling, cell migration), along with endocytic processes (pinocytosis) and general stress response (heat). This suggests a cluster of proteins involved in cardiac signal transduction combined with cytoskeletal remodeling and related trafficking processes, rather than a single narrow pathway. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0048549","count":2},{"id":"GO:0008344","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0060048","count":2}]},{"hash":"976329290937241170","title":"Neurodevelopmental gene regulation","description":"The top GO terms point to neurodevelopment (forebrain development, neural tube closure) and broader organism development, with supporting signals of transcription, splicing, and translation initiation, plus chromatin modification. This suggests a cluster of proteins involved in regulating gene expression during neurodevelopment and development more generally, rather than a single isolated process.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0060528","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0016575","count":2}]},{"hash":"1929377379442402991","title":"Ion Transport and Salt Stress Response","description":"This cluster is dominated by GO terms for proton transmembrane transport, sodium and potassium ion movement across membranes, and vacuolar acidification, indicating a core role in ion homeostasis and osmotic stress response.","confidence":"High","size":19,"edges":13,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0097623","count":3},{"id":"GO:0007035","count":3},{"id":"GO:0036376","count":3}]},{"hash":"2050438036565156880","title":"Cofactor biosynthesis and RNA modification","description":"This cluster shows a strong representation of biosynthetic pathways for cofactors (biotin, menaquinone, pyrroloquinoline quinone, protoporphyrinogen IX) and enzymes involved in RNA modification (tRNA queuosine biosynthesis, tRNA methylation, rRNA base methylation). While there are other metabolic processes listed (e.g., energy metabolism), the most coherent theme tying the GO terms together is synthesis of essential cofactors and modification of RNA, suggesting a functional group focused on metabolic cofactor production and RNA maturation. ","confidence":"Medium","size":19,"edges":167,"triangles":903,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006120","count":2},{"id":"GO:0042426","count":2},{"id":"GO:0018189","count":2},{"id":"GO:0006782","count":2}]},{"hash":"772324930830339349","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0046373","count":2},{"id":"GO:0033050","count":1}]},{"hash":"1026576749239798320","title":"Keratinocyte differentiation and growth signaling","description":"This cluster centers on epidermal differentiation (keratinocyte differentiation) and key growth-regulatory signaling pathways (Hippo and Wnt) that modulate proliferation and organ size. The presence of terms for apoptotic processes, DNA replication, centrosome cycle, and receptor clustering supports a broader theme of coordinated cell cycle and signaling during development, including craniofacial morphogenesis. While not all terms map to a single pathway, the strongest theme is epidermal differentiation coupled with growth and developmental signaling.","confidence":"Medium","size":19,"edges":72,"triangles":96,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030216","count":16},{"id":"GO:0035329","count":16},{"id":"GO:0060044","count":16},{"id":"GO:0090263","count":16},{"id":"GO:0006915","count":16}]},{"hash":"2076396987142104787","title":"Cell cycle regulation and tissue development","description":"The cluster is driven by cell cycle and proliferation control terms (kinetochore localization, negative regulation of CDK activity, DNA replication, negative regulation of cell population proliferation), with additional development and signaling terms across brain and muscle (cerebellar cortex formation, Bergmann glial differentiation, insulin and T cell receptor signaling, cardiac muscle proliferation). This pattern suggests a broad network coordinating cell division and differentiation across tissues, rather than a single pathway, hence a label focusing on cell cycle regulation plus tissue development.","confidence":"Medium","size":19,"edges":113,"triangles":308,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":15},{"id":"GO:0045736","count":15},{"id":"GO:0050852","count":13},{"id":"GO:0060044","count":13},{"id":"GO:0008286","count":13}]},{"hash":"1318870103885422438","title":"Ubiquitin-Dependent Proteolysis and Chromatin Regulation","description":"The top GO terms cluster around ubiquitin-mediated degradation (ubiquitin-dependent proteolysis, ERAD, autoubiquitination, various ubiquitin linkages) and chromatin-related processes (histone catabolic/ubiquitination, histone modification regulation). While some terms (V(D)J recombination, X chromosome dosage compensation) are broader, the dominant signal points to ubiquitin-driven protein turnover and chromatin regulation. This makes a label focused on ubiquitin-mediated degradation and chromatin control appropriate and distinct from other clusters.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0030433","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0036205","count":6},{"id":"GO:0070535","count":6}]},{"hash":"768576277191948466","title":"Unknown","description":"The top GO terms span translation machinery and actin cytoskeleton dynamics, plus several development- and signaling-related processes, with no clear, single unifying function tying all terms together. The lack of edges also suggests the proteins may not form a cohesive functional module. Therefore no specific, representative label can be confidently assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007015","count":2},{"id":"GO:0030838","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0000027","count":1}]},{"hash":"1138931831634808287","title":"Unknown","description":"The top GO terms touch on diverse areas: cytoskeletal signaling (Rho regulation, lamellipodium assembly, JNK pathway regulation), GPCR signaling (tachykinin receptor), immune/growth factor responses (GM-CSF stimulus), lipid transport (ceramide transport), and development (placental glycogen cell differentiation). This lack of a single cohesive function makes it hard to assign a specific, representative label to the cluster beyond Unknown.","confidence":"","size":19,"edges":4,"triangles":0,"max_degree":4,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0097011","count":4},{"id":"GO:0060709","count":3},{"id":"GO:0035621","count":3},{"id":"GO:0060313","count":3}]},{"hash":"148433638103039994","title":"Growth signaling and development","description":"This cluster centers on signaling and growth processes, highlighted by TORC1 signaling, mitotic cell cycle regulation, and phosphorylation events (peptidyl-threonine and peptidyl-tyrosine) with positive regulation of GTPase activity. There are also developmental and organismal growth terms (multicellular growth, spinal cord development, cardiac contraction), suggesting broad roles in growth and development. The inclusion of an ascospore-related term is fungal-specific and reduces cohesion, but overall the terms point to growth signaling and development rather than a single specialized function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032120","count":5},{"id":"GO:0060048","count":4},{"id":"GO:0038202","count":4},{"id":"GO:0021510","count":4},{"id":"GO:0035264","count":4}]},{"hash":"896611938102834980","title":"DNA Damage Response and Repair","description":"Based on the GO terms, the predominant theme is DNA damage response and repair, including nonhomologous end joining, interstrand cross-link repair, telomere maintenance, and cellular responses to bleomycin and X-rays. The heart and forebrain development terms, and calcium transport, are less represented and may reflect multifunctional annotations or incidental associations.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0070588","count":2},{"id":"GO:1903087","count":2},{"id":"GO:0010833","count":1}]},{"hash":"1789802716380351388","title":"Muscle development and chromatin regulation","description":"The top terms show a clear emphasis on skeletal/striated muscle development and differentiation (e.g., skeletal muscle tissue regeneration, muscle cell differentiation, striated muscle tissue development) alongside chromatin/regulatory processes (histone acetylation and heterochromatin organization), suggesting a module where epigenetic regulation governs myogenesis. The presence of unrelated terms like ER targeting might be incidental, but the dominant theme points to muscle development linked with chromatin state control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043971","count":1},{"id":"GO:0043970","count":1},{"id":"GO:0044154","count":1},{"id":"GO:0070868","count":1},{"id":"GO:0048671","count":1}]},{"hash":"855648540393897418","title":"Immune system development and signaling","description":"This cluster is dominated by GO terms tied to immune system development and signaling: B cell affinity maturation, NK T cell differentiation, IL-7 response, IL-4 production, and hemopoiesis, with supporting terms on cell migration and signaling pathways such as GTPase activity and insulin receptor signaling. The outlier heart development term is less central but does not override the overall immune-development theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0098761","count":3},{"id":"GO:0002344","count":3},{"id":"GO:2001275","count":3}]},{"hash":"224145542796100996","title":"Unknown","description":"The GO terms span insulin signaling, retinoic acid response, cell cycle regulation, nucleotide biosynthesis, RNA splicing, and brain development, with no single cohesive function linking most proteins. This makes it hard to assign a specific, representative label beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0071300","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0006183","count":1}]},{"hash":"1098441677102617812","title":"Vitamin and coenzyme biosynthesis with cell remodeling","description":"The top GO terms point to vitamin/coenzyme biosynthesis (thiamine and thiamine diphosphate; ubiquinone) as prominent activities, suggesting a core metabolic theme. Additional terms such as proteolysis, tRNA modification, and processes related to cell wall organization, regulation of cell shape, and cell growth indicate broader metabolic and structural remodeling. The combination implies a cluster centered on vitamin and coenzyme biosynthesis with associated cellular remodeling and metabolism, hence the chosen label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0002098","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0008360","count":2}]},{"hash":"269483442397706035","title":"Unknown","description":"The top GO terms are very heterogeneous (telomere capping, PARPylation, endothelial differentiation, myeloid apoptosis, ephrin signaling, calcium release, IL-12 regulation, pain perception, intracellular signaling, and muscle regeneration), with no single dominant function tying the proteins together. The lack of a clear shared pathway and zero edges among proteins support treating this as a mixed set rather than a coherent functional cluster.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904355","count":3},{"id":"GO:0070212","count":3},{"id":"GO:0060843","count":3},{"id":"GO:0033028","count":3},{"id":"GO:1901187","count":3}]},{"hash":"1729262422009728760","title":"Nutrient sensing and metabolic regulation","description":"The top GO terms point to metabolism (carbohydrate metabolic process), growth signaling (positive regulation of PI3K/AKT), and stress/nutrient responses (amino acid starvation response, autophagosome regulation), with accompanying transport roles (urea and proline). A single, tissue-specific term (rhabdomere membrane biogenesis) is less aligned with the others, but the overall pattern supports a theme of metabolic control and nutrient-responsive signaling rather than a singular, narrow function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0016255","count":1},{"id":"GO:0045313","count":1},{"id":"GO:2000785","count":1}]},{"hash":"1213224807953819122","title":"Mitochondrial respiration and energy production","description":"The cluster shows strong representation of mitochondrial energy-related processes: aerobic respiration, TCA cycle, mitochondrial electron transport chain activity, and assembly of respiratory complexes, which together indicate a module focused on energy production and oxidative metabolism. Auxiliary terms like oxidative stress response and mitochondrial assembly support this theme, while a few outliers (translation and interleukin-4 response) may reflect broader cellular functions or annotation overlap but do not override the dominant mitochondrial signal.","confidence":"High","size":18,"edges":151,"triangles":784,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0033617","count":1},{"id":"GO:0098869","count":1}]},{"hash":"711082513037773212","title":"Central metabolism and quinone biosynthesis","description":"This cluster shows strong signals from core energy metabolism pathways (glycolysis, TCA cycle, beta-oxidation) and cofactors/quinone biosynthesis (menaquinone, phylloquinone), suggesting a shared role in energy production and redox balance. The presence of antibiotic biosynthetic process hints at secondary metabolism components, but the dominant theme is central metabolism and quinone-related biosynthesis. ","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0006635","count":6},{"id":"GO:0006096","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009234","count":5}]},{"hash":"1190656236968048013","title":"Neural development and carbohydrate metabolism","description":"The cluster is enriched for brain development and brain segmentation, along with carbohydrate metabolic processes and glycosylation pathways, suggesting proteins involved in neural development that also participate in carbohydrate processing. Additional terms related to signaling (cellular response to cAMP) and apoptosis indicate broader regulatory roles in neural contexts. Overall, the theme appears to be neural development linked with carbohydrate metabolism and glycosylation.","confidence":"Medium","size":18,"edges":16,"triangles":3,"max_degree":6,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0005978","count":2}]},{"hash":"1497274655147413982","title":"Cell signaling and transcription regulation","description":"The cluster centers on regulatory functions spanning transcription (DNA-templated transcription) and multiple signaling pathways (ephrin receptor signaling, T cell receptor signaling, excitatory postsynaptic potential), plus cell-cycle-related processes (mitotic cell cycle, mitotic spindle assembly). The mix of transcriptional control and diverse signaling cues suggests a broad regulatory role rather than a single cohesive pathway, justifying a label around signaling and transcription regulation as the most representative theme.","confidence":"Low","size":18,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007601","count":2}]},{"hash":"763821982083675588","title":"Cytoskeletal remodeling and cell migration","description":"Based on the prevalence of actin filament bundle assembly, cell migration, and epithelial polarity establishment, the cluster centers on cytoskeletal dynamics and movement, with accompanying regulatory processes (ubiquitination, signaling, cell fate decisions). While there are broader regulatory terms (apoptosis, cell cycle), the strongest and most cohesive theme is cytoskeletal remodeling tied to movement and polarity.","confidence":"Medium","size":18,"edges":13,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060988","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0033146","count":3}]},{"hash":"1436271119241846658","title":"Mitotic Cell Cycle and Cytoskeletal Regulation","description":"The proteins are enriched for mitotic cell cycle and cell division terms, and include several cytoskeletal/motility-related terms (pseudopodium assembly, cell spreading, cellular response to mechanical stimulus, migration regulation). This suggests a cohesive theme where cell division processes intersect with cytoskeletal remodeling and adhesion/migration dynamics, possibly via protein complex formation (heterooligomerization) that coordinates signaling and structural changes. ","confidence":"High","size":18,"edges":112,"triangles":378,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":11},{"id":"GO:0051301","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0090051","count":11},{"id":"GO:1900026","count":11}]},{"hash":"1638463961368471529","title":"GTPase-regulated Golgi\u2013endosome trafficking","description":"Most terms point to vesicle trafficking, notably establishment of Golgi localization, endosome-to-postsynaptic membrane transport, and small GTPase\u2013mediated signaling with activity regulation. Endothelial lumen extension and angiogenic regulation also align with trafficking processes during vessel formation. Some cell cycle terms may be less informative noise, but the common theme is GTPase-driven vesicle trafficking related to Golgi and endosomes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0051683","count":2},{"id":"GO:0098887","count":2},{"id":"GO:0090051","count":2}]},{"hash":"962795453400029615","title":"Embryonic Eye Development and Morphogenesis","description":"This cluster is dominated by GO terms related to embryonic and eye development (camera-type eye development, embryonic eye morphogenesis, in utero embryonic development) and transcriptional regulation (RNA polymerase II transcription, regulation of transcription), suggesting a cohesive group of proteins involved in eye formation and developmental gene regulation. Some metabolic and stress terms appear ancillary and less central to the main theme.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0043010","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0048048","count":3},{"id":"GO:0001701","count":3}]},{"hash":"2168483522702498224","title":"Embryonic morphogenesis and cell adhesion","description":"This cluster centers on developmental processes shaping tissues and organs, with strong emphasis on cell adhesion (integrin- and heterophilic adhesion), epithelial and smooth muscle differentiation, and morphogenetic events such as axis elongation and nephron development. Calcium signaling and TGF-beta production hint at coordinating pathways and ALP activity ties to differentiation contexts, supporting a theme of embryonic tissue morphogenesis and adhesion.","confidence":"High","size":18,"edges":30,"triangles":24,"max_degree":12,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0010694","count":18},{"id":"GO:0007414","count":18},{"id":"GO:0007157","count":18},{"id":"GO:0033631","count":18},{"id":"GO:0007204","count":18}]},{"hash":"1243462421560163380","title":"Growth and Nutrient Transport Regulation","description":"Based on the GO terms, the proteins cluster around growth-related processes (angiogenesis, lateral root branching, pseudohyphal and invasive growth) and nutrient handling (ammonium transport, nitrogen utilization, iron homeostasis), plus translation. This points to a broader theme of coordinating growth with nutrient uptake/metabolism across different organisms rather than a single, cohesive pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:2001137","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0072488","count":1},{"id":"GO:0080181","count":1}]},{"hash":"2105719301224512121","title":"Cytokinesis and spindle assembly dynamics","description":"The GO terms point to core cell division machinery and cytoskeletal remodeling: mitotic spindle assembly, microtubule dynamics (plus- and minus-end activities), actomyosin contractile ring assembly, and cytokinesis (including plant cell plate formation). A secondary context includes epidermal stem cell homeostasis and root development, suggesting developmental regulation during growth. Overall, the cluster seems best described by cytoskeletal and division processes with some developmental context.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0048364","count":1},{"id":"GO:0000915","count":1},{"id":"GO:0031534","count":1}]},{"hash":"1323393536175750072","title":"Ribosome Biogenesis and Translation Machinery","description":"This cluster is dominated by translation and ribosome-related functions. The top GO term is translation (14 proteins), with supporting terms for ribosome biogenesis, ribosomal large subunit assembly, and maturation of SSU-rRNA, as well as initiation and termination of translation. A minority of terms point to antibiotic response and regulation of translation initiation, consistent with a translation-centric group; a single item on heterochromatin regulation appears incidental. Overall, the cluster represents components involved in ribosome assembly and protein synthesis.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0042254","count":4},{"id":"GO:0006415","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006413","count":2}]},{"hash":"1716406511615310465","title":"Insulin/IGF and Small GTPase Signaling","description":"The top GO terms center on insulin receptor and IGF receptor signaling, cellular responses to insulin, and small GTPase\u2013mediated pathways (Ras and Rho), with additional notes on extracellular matrix signaling. This points to a cluster of proteins involved in growth-factor\u2013driven signaling and regulation of small GTPases, rather than a single, narrow pathway. While there are some immune signaling terms present, the dominant theme is growth factor\u2013 and GTPase-mediated signaling.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0038028","count":4},{"id":"GO:0038095","count":4},{"id":"GO:0032869","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0007264","count":4}]},{"hash":"1564146813865071022","title":"Cellular redox homeostasis and detoxification","description":"The cluster is dominated by GO terms tied to redox balance and detoxification (cellular oxidant detoxification, cell redox homeostasis, response to toxic substances, ethanol, and ascorbic acid), with supporting signals in stress-related regulatory pathways (NF-kappaB and IL-1\u03b2 signaling) and related insulin signaling and oligodendrocyte development contexts. This suggests a coherent theme of oxidative stress response and detoxification mechanisms.","confidence":"High","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":14},{"id":"GO:2000255","count":10},{"id":"GO:0045454","count":9},{"id":"GO:0009636","count":9},{"id":"GO:0045471","count":9}]},{"hash":"1825143468830410442","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for translation and ribosome assembly, including cytoplasmic translation, maturation of SSU-rRNA, and ribosome biogenesis, plus ribosomal subunit biogenesis, indicating proteins involved in ribosome production and protein synthesis. While a few terms touch on signaling or cell cycle, the core signal is ribosome-related.","confidence":"High","size":17,"edges":11,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000462","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1211200659475001399","title":"Transsulfuration and H2S biosynthesis","description":"The cluster is dominated by GO terms tied to sulfur-containing amino acid metabolism: hydrogen sulfide biosynthesis, transsulfuration, L-homocysteine catabolic process, and L-cysteine biosynthetic process via L-cystathionine, indicating a cohesive theme around cysteine/homocysteine metabolism and H2S production. Some other terms (GTPase regulation, gluconeogenesis, glycine betaine transport) are less directly connected and may reflect broader metabolic context or annotation noise, but the sulfur metabolism signals are the strongest. ","confidence":"High","size":17,"edges":129,"triangles":591,"max_degree":16,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0043547","count":10},{"id":"GO:0070814","count":8},{"id":"GO:0051289","count":8},{"id":"GO:0045722","count":8},{"id":"GO:0043418","count":8}]},{"hash":"316777568017221590","title":"Unknown","description":"The top GO terms point to a mix of distinct cellular processes (transcription regulation, redox, growth, ubiquitination, mechanotransduction, endocytosis, and meiosis-related events) with no clear, single functional theme tying the 17 proteins together. The lack of interactions (edges/triangles = 0) further impedes identifying a cohesive cluster function, so a single representative label cannot be confidently assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2}]},{"hash":"432680320161908646","title":"Cell Signaling and Stress Responses","description":"The top GO terms point to phosphorylation events and cellular responses to stressors like toxins and radiation, suggesting a signaling-centric cluster. While a few terms relate to development and trafficking, the common thread appears to be signal transduction and stress response pathways across contexts.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":17},{"id":"GO:0007601","count":17},{"id":"GO:1990802","count":17},{"id":"GO:1904355","count":17},{"id":"GO:0071479","count":17}]},{"hash":"2134410643638471213","title":"Nuclear RNA processing and splicing machinery","description":"The cluster is dominated by spliceosome- and RNA processing-related terms (mRNA splicing via spliceosome, spliceosomal snRNP assembly, transcription termination, SSU-rRNA maturation, histone mRNA metabolism) and nuclear import, indicating a coherent theme of nuclear RNA processing and related regulatory activities; a few terms touch on cell cycle and stress responses, but the core signal is splicing and RNA maturation in the nucleus.","confidence":"High","size":17,"edges":122,"triangles":497,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":9},{"id":"GO:0006369","count":6},{"id":"GO:0000387","count":5},{"id":"GO:0009737","count":5},{"id":"GO:0009414","count":5}]},{"hash":"56648583278080698","title":"Ubiquitin-Proteasome System and APC/C-Mediated Proteolysis","description":"The top GO terms center on ubiquitin processing and proteasomal degradation, including deubiquitination, proteasome core assembly, and APC/C-dependent proteolysis, indicating a strong link to regulated protein turnover and cell-cycle control. Additional terms related to stress responses (salt, cadmium, zinc) suggest roles in stress-associated proteolytic regulation, potentially intersecting with transcriptional responses. Despite some obsolete annotations, the dominant theme is proteostasis via the ubiquitin-proteasome system and APC/C pathways. ","confidence":"High","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":10},{"id":"GO:0080129","count":7},{"id":"GO:0010499","count":7},{"id":"GO:0051437","count":7},{"id":"GO:0009651","count":7}]},{"hash":"1851433217887042558","title":"Ion and carbohydrate transport","description":"Most of the top GO terms point to transmembrane transport of ions (potassium, sodium) and sugars (galactose), along with related metabolic processes (glucose metabolism, nitrate assimilation). This suggests a core theme around membrane transport and carbohydrate-related metabolism, with a few outlier terms (placenta development, response to cocaine, chemotaxis) that may reflect broader or misannotated annotations in the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0045793","count":3},{"id":"GO:0006006","count":3}]},{"hash":"1099641918930368292","title":"Cell proliferation and developmental growth","description":"Most of the top GO terms relate to cell division, mitotic cell cycle, and organismal growth (brain development, multicellular growth, cell population proliferation), indicating this cluster is centered on proliferative development. A subset of terms involve translation initiation/reinitiation and endosomal sorting, which may reflect broader cellular housekeeping and trafficking roles for proteins during growth; however the dominant signal is proliferation and development.","confidence":"Medium","size":17,"edges":20,"triangles":4,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0008283","count":3}]},{"hash":"1422033914195895286","title":"Steroid Hormone and Pigment Biosynthesis","description":"GO terms show enrichment for steroid hormone biosynthesis (glucocorticoid, androgen, C21-steroid) and pigment biosynthesis (melanin), plus phylloquinone biosynthesis and other biosynthetic processes. This suggests a coherent theme around biosynthesis of hormones and pigments, though some terms (phylloquinone, antibiotics, PHB) reflect broader metabolic biosynthesis within the cluster.","confidence":"Medium","size":17,"edges":63,"triangles":88,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0042619","count":12},{"id":"GO:0030324","count":11},{"id":"GO:0045150","count":11},{"id":"GO:0006704","count":11}]},{"hash":"2218881210150561249","title":"Chromatin-Linked DNA Replication and Cell Cycle","description":"The cluster shows strong representation of DNA replication initiation and elongation, replication fork protection, and mitotic DNA replication, alongside chromatin-related processes such as heterochromatin formation and telomere silencing, plus cell-cycle and meiotic recombination components. This points to proteins that coordinate DNA synthesis with chromatin state and cell-cycle progression.","confidence":"High","size":17,"edges":48,"triangles":71,"max_degree":14,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030466","count":8},{"id":"GO:0048478","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0042140","count":5}]},{"hash":"1862989199487368534","title":"RNA Pol II Transcription Regulation in Development","description":"The cluster is dominated by GO terms related to transcription by RNA polymerase II, including both positive and negative regulation, suggesting a core theme of transcriptional control. Additional development-related terms (rhombomere 5 development, brain segmentation) point to vertebrate neural development as a key context, with some ancillary immune and proteolytic processes that may reflect broader regulatory roles. Overall, the main signal is regulation of RNA Pol II\u2013mediated transcription in developmental settings, making this label representative.","confidence":"Medium","size":17,"edges":43,"triangles":30,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:2000347","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0045348","count":3},{"id":"GO:0010499","count":2},{"id":"GO:0061418","count":2}]},{"hash":"1139653403605069194","title":"Developmental growth and tissue differentiation","description":"The top GO terms cluster around organismal development and tissue differentiation (skin, forebrain, multicellular development/growth), indicating a developmental or differentiation-focused group. Additional terms point to epithelial differentiation and signaling regulation (GTPase activity, protein autophosphorylation) that often accompany developmental processes, with hypoxia response reflecting broader stress-adaptation within developing tissues. Overall, the cluster appears to reflect developmental maturation and differentiation programs rather than a single specialized pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071456","count":4},{"id":"GO:0043588","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0031954","count":3}]},{"hash":"677804226931913619","title":"Unknown","description":"The GO terms are highly diverse (RNA silencing and mRNA destabilization; cell cycle checkpoint; neural differentiation and neuromuscular processes; tissue homeostasis; IGF signaling; metabolism and ER organization) with no clear shared function or pathway linking the proteins. There are no edges or strong groupings to suggest a cohesive theme, so a single representative label cannot be reliably assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016441","count":1},{"id":"GO:0061157","count":1},{"id":"GO:0031571","count":1},{"id":"GO:0021522","count":1},{"id":"GO:0048873","count":1}]},{"hash":"159370786685211872","title":"Vacuolar and Endosomal Vesicle Transport","description":"The top GO terms cluster around intracellular vesicle trafficking and fusion, including intracellular protein transport, Golgi to endosome transport, endosome to lysosome transport, vesicle tethering, and vesicle fusion with the vacuole, as well as regulation of vacuole fusion and activation of GTPase activity\u2014pointing to a cohesive endomembrane system function toward the vacuole/lysosome. Some terms (platelet degranulation, cardiac muscle contraction) reflect secretory processes in other contexts but are compatible with vesicle exocytosis, reinforcing a vesicle-transport theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":3},{"id":"GO:0032889","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0008333","count":2}]},{"hash":"739128800280203939","title":"Cell Signaling and Calcium Regulation","description":"The top GO terms are dominated by receptor-mediated signaling (GPCR and ephrin pathways) and calcium dynamics (release of sequestered calcium into cytosol), suggesting a general signaling-focused cluster. Additional terms touch on immune modulation, endothelial differentiation, and other regulatory processes, indicating a broad but cohesive theme around signaling rather than a single precise pathway. Hence, a label reflecting overall signaling with calcium involvement is appropriate.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":7},{"id":"GO:0098907","count":6},{"id":"GO:1904355","count":5},{"id":"GO:0070212","count":5},{"id":"GO:0060843","count":5}]},{"hash":"1809572817313722277","title":"Sphingolipid and phospholipid metabolism","description":"Most of the listed GO terms center on lipid metabolism, especially sphingolipid and phosphatidylserine pathways, including enzymes like serine palmitoyltransferase and phosphatidylserine transferase. This suggests the protein cluster participates in membrane lipid biosynthesis/remodeling that underpins processes such as myelination and membrane protrusions (filopodia). A few terms (virus detection, ER stress-induced apoptosis, proteolysis) are broader cellular responses that may relate indirectly to membrane integrity. Overall, the cohesive theme is lipid metabolism in membranes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904219","count":1},{"id":"GO:0006665","count":1},{"id":"GO:0006658","count":1},{"id":"GO:0009597","count":1},{"id":"GO:1904222","count":1}]},{"hash":"1936857737902530378","title":"Muscle development and neuromuscular signaling","description":"The terms cluster around muscle tissue development and function (skeletal muscle development, regulation of heart contraction, muscle cell homeostasis, neuromuscular posture control) and neuromuscular signaling, with supporting hints from nervous system development. A few outliers (e.g., B cell receptor signaling) are less connected, but the dominant theme is muscle/neuromuscular biology.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0007399","count":2}]},{"hash":"1734870636061341113","title":"DNA Damage Response and Genome Maintenance","description":"The strongest signals are around DNA replication, DNA repair, telomere maintenance, and responses to DNA damage (e.g., positive regulation of mismatch repair, positive regulation of telomere capping, cellular response to ionizing radiation), suggesting a coherent theme of genome stability and DNA damage response. A few development-related terms appear but are less central to the core function of the cluster.","confidence":"Medium","size":16,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0009636","count":1},{"id":"GO:0007601","count":1},{"id":"GO:1990802","count":1}]},{"hash":"2221093442118035812","title":"Zinc ion homeostasis and detoxification","description":"The cluster\u2019s top GO terms center on zinc biology: intracellular zinc ion homeostasis, detoxification and response to zinc ion, and cadmium detoxification. Translation appears but is likely incidental (ribosomal proteins), while a couple of immune-response terms seem less central. Taken together, the dominant theme is zinc ion management and detoxification across the proteins.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0008277","count":1},{"id":"GO:0061090","count":1},{"id":"GO:0010312","count":1},{"id":"GO:0010043","count":1}]},{"hash":"1046705470002565243","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":118,"triangles":532,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0042254","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0000461","count":2}]},{"hash":"1336300901301831985","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":107,"triangles":401,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0016311","count":4},{"id":"GO:0071400","count":3},{"id":"GO:0007494","count":3},{"id":"GO:0044205","count":3}]},{"hash":"1044588448911651676","title":"Ribosome biogenesis and translation","description":"The top GO terms are centered on protein synthesis: translation itself, translation initiation/elongation/termination, and ribosome biogenesis. Selenocysteine incorporation and deadenylation-dependent decay further point to translation-related regulation. Some terms like glial cell proliferation and cell division are broader cellular contexts but do not override the dominant translation/ribosome theme.","confidence":"High","size":16,"edges":113,"triangles":475,"max_degree":15,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0046677","count":6},{"id":"GO:0000288","count":5},{"id":"GO:0045901","count":5},{"id":"GO:0006415","count":5}]},{"hash":"1336307586431485379","title":"RNA processing and translation with mitochondrial tRNA charging","description":"The cluster\u2019s most represented terms are mRNA processing and translation, plus mitochondrial tRNA aminoacylation (charging), which together point to gene expression and mitochondrial protein synthesis as a cohesive theme. Other terms (angiogenesis, vacuole fusion regulation, and GTPase activation) are less central and could reflect ancillary signaling or trafficking roles, but the dominant pattern centers on RNA processing and mitochondrial translation functions.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0001570","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0070183","count":1}]},{"hash":"804232009151450417","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":2},{"id":"GO:0006526","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0006098","count":1}]},{"hash":"2175678096640744977","title":"Cell Division and Polarity Signaling","description":"This cluster combines terms tied to cell division processes (DNA replication, cytokinesis-related membrane addition, vesicle docking), cell polarity and shape maintenance, and signaling pathways (Wnt, T cell receptor) with transcriptional regulation. This pattern suggests a module where division, polarity establishment, and signaling coordination are functionally linked, with transcriptional control as a shared layer; some immune and neuronal signaling terms may reflect broader signaling components converging on these core processes.","confidence":"Medium","size":16,"edges":11,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":6},{"id":"GO:0045944","count":6},{"id":"GO:0071963","count":5},{"id":"GO:0006904","count":5},{"id":"GO:0007107","count":5}]},{"hash":"208734870232221164","title":"Signaling Complex Assembly and Regulation","description":"This cluster's top GO terms are largely about protein\u2013protein interactions and the formation or regulation of signaling complexes (protein heterooligomerization, GPCR signaling regulation, steroid receptor complex assembly, ubiquitination). A few terms like cell division and photosynthesis reflect broader cellular roles of these complexes. Overall, the theme is multiprotein complex assembly that modulates signaling and regulatory processes.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0015979","count":6},{"id":"GO:0051348","count":6},{"id":"GO:0036494","count":6},{"id":"GO:0051291","count":6}]},{"hash":"1031022066456040511","title":"Unknown","description":"The top GO terms span very different biological areas (visual perception, cellular response to ionizing radiation, DNA damage processing, development of trachea, bone mineralization, intracellular transport, immune signaling, and protein phosphorylation), with one obsolete term, indicating there isn't a clear, single functional theme linking these proteins. A cohesive label is not supported by the data, so the cluster is best described as Unknown.","confidence":"","size":16,"edges":60,"triangles":88,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":16},{"id":"GO:0007601","count":16},{"id":"GO:1990802","count":16},{"id":"GO:1904355","count":16},{"id":"GO:0071479","count":16}]},{"hash":"695818327694262207","title":"Translation initiation and RNA processing","description":"The GO terms cluster around translation machinery (initiation complex formation, reinitiation, eIF4F assembly, general translation) and RNA processing events (splicing regulation, polyadenylation, RNA methylation, mRNA stabilization). This points to a cohesive function in initiating and regulating protein synthesis intertwined with RNA maturation pathways; a peripheral defense-term appears incidental. Confidence: High","confidence":"","size":16,"edges":6,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0000381","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0036265","count":3}]},{"hash":"1419355235606013105","title":"DNA Damage Response and Apoptosis","description":"The cluster is enriched for GO terms related to DNA replication, response to ionizing radiation, apoptotic processes, and telomere maintenance, which together point to DNA damage signaling and cell fate decisions. Some trafficking-related terms appear but are likely secondary or annotation noise, so the dominant theme is DNA damage response and apoptosis.","confidence":"Medium","size":16,"edges":14,"triangles":5,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:2000641","count":11},{"id":"GO:0006915","count":11},{"id":"GO:0009636","count":10},{"id":"GO:0007601","count":10}]},{"hash":"1704967567804595950","title":"Cytoskeleton-driven morphogenesis and muscle assembly","description":"The top GO terms cluster around actin-based processes (vesicle transport along actin, cell polarity, budding growth) and muscle-related assembly/contraction (skeletal muscle contraction regulation, cardiac myofibril assembly), indicating a common theme of cytoskeletal dynamics guiding cell shape and tissue-specific muscle structure. Some terms (mRNA capping, xenobiotic response, magnesium ion response) are broader cellular processes that accompany these functions but do not override the primary cytoskeletal/morphogenesis signal.","confidence":"Medium","size":16,"edges":25,"triangles":9,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006370","count":4},{"id":"GO:0071963","count":4},{"id":"GO:0030050","count":4},{"id":"GO:0007605","count":4},{"id":"GO:0007118","count":4}]},{"hash":"1407576900280541222","title":"Unknown","description":"The top GO terms are diverse\u2014telomere maintenance and capping, tyrosine phosphorylation, mRNA processing, Schwann cell development, and amino acid starvation response\u2014showing no single shared function or pathway. The cluster has no edges, suggesting a lack of cohesive interactions, so there isn't a clear, representative label we can assign. Therefore, Unknown with no confidence.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1904355","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0051389","count":3},{"id":"GO:0038083","count":3},{"id":"GO:0034198","count":3}]},{"hash":"829985344447612190","title":"Unknown","description":"The GO terms span telomere maintenance, PARylation, endothelial differentiation, immune cell apoptosis, ephrin signaling regulation, calcium signaling, IL-12 production, pain perception, general intracellular signaling, and muscle regeneration. They do not point to a single cohesive biological process or pathway, making a specific, concise cluster label inappropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904355","count":2},{"id":"GO:0070212","count":2},{"id":"GO:0060843","count":2},{"id":"GO:0033028","count":2},{"id":"GO:1901187","count":2}]},{"hash":"1288606483657509132","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0000447","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000480","count":3}]},{"hash":"375216857177744125","title":"Unknown","description":"Mix of genome maintenance terms (meiotic cell cycle, DNA replication, telomere capping, radiation response) and broad developmental/sensory terms (heart development, left/right symmetry, visual perception). There is no single cohesive function tying all terms together, so a confident, specific label cannot be assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051321","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0007368","count":2},{"id":"GO:0006897","count":2}]},{"hash":"1078365224215219139","title":"ER-Golgi trafficking and secretion","description":"Most of the top GO terms describe steps and components of the ER-to-Golgi secretory pathway (ER retention, COPI-coated vesicles, Golgi ribbon formation, and ER exit). The term for regulation of Wnt protein secretion also fits into this secretory context. A few development-related terms appear but the dominant signal is vesicular trafficking and secretion through the ER-Golgi axis. This makes the name representative of the cluster's function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001893","count":4},{"id":"GO:0048042","count":3},{"id":"GO:0090161","count":3},{"id":"GO:0070863","count":3},{"id":"GO:0032525","count":3}]},{"hash":"514000548477534840","title":"Retina Development and Cholinergic Synaptic Signaling","description":"Proteins in this cluster are enriched for retina development and various synaptic functions, especially cholinergic signaling, synaptic transmission regulation, and synapse organization. The acetylcholine catabolic process, negative regulation of cholinergic transmission, receptor internalization, and neuron adhesion terms all point to both developmental processes in retinal neurons and the maintenance of cholinergic synapses, with learning as a neural plasticity readout. The combined signals suggest a cohesive theme of retinal neuron development coupled with specialized synaptic signaling.","confidence":"High","size":16,"edges":114,"triangles":480,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":6},{"id":"GO:0098942","count":5},{"id":"GO:0001507","count":5},{"id":"GO:0032223","count":5},{"id":"GO:0007612","count":5}]},{"hash":"713357088259991986","title":"Unknown","description":"The top GO terms are highly diverse, ranging from RNA processing to various differentiation and signaling processes, with no clear, single linking function for all proteins. While RNA processing appears, many other terms (telomere regulation, oligodendrocyte and venous endothelial differentiation, ephrin signaling, calcium release) suggest unrelated roles, so a cohesive label is not supported.","confidence":"","size":16,"edges":42,"triangles":35,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0006378","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0048709","count":2},{"id":"GO:0045736","count":2}]},{"hash":"1241146500251545984","title":"Vertebrate neural and cardiovascular development","description":"This cluster\u2019s top GO terms center on neural lineage differentiation (amacrine cell differentiation, oligodendrocyte development, floor plate development) and cardiac/vascular formation (cardiac neural crest\u2013driven outflow tract morphogenesis, endocardial cushion EMT, lung vasculature development, vascular wound healing). The co-occurrence of neural patterning and heart/vasculature formation terms suggests a cohesive theme of vertebrate embryonic development focusing on neural and cardiovascular systems.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":9},{"id":"GO:0035881","count":6},{"id":"GO:0060426","count":6},{"id":"GO:0001756","count":6},{"id":"GO:0033504","count":6}]},{"hash":"23652466236529161","title":"Unknown","description":"The Top Terms span DNA replication, mismatch repair, and chromatin modification, alongside metabolism, stress response, and signaling, with no single cohesive function dominating. This breadth suggests there isn\u2019t a clear, representative biological theme linking all proteins in this cluster.","confidence":"","size":16,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0006298","count":1},{"id":"GO:0006261","count":1}]},{"hash":"716003229040460482","title":"Unknown","description":"The GO terms span nervous system development (myelination), sensory perception, cardiac development/hypertrophy, B cell differentiation, DNA repair regulation, calcium detection, and multiple signaling pathways (GTPase/Rho, Wnt). This broad, tissue- and process-diverse set lacks a single cohesive function to define a specific cluster label, so an Unknown designation is most appropriate.","confidence":"","size":16,"edges":14,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0014898","count":3}]},{"hash":"1343310004245963925","title":"EGF-Responsive Integrin Signaling and Cytoskeletal Remodeling","description":"The terms cluster around growth factor (EGF/EGFR)\u2013linked signaling, integrin-mediated adhesion, podosome assembly, and small GTPase\u2013driven cytoskeletal dynamics in response to mechanical cues, with negative regulation of EGFR activity. This suggests a cohesive module where growth factor signaling interfaces with adhesion and cytoskeletal remodeling, rather than disparate processes.","confidence":"High","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":2},{"id":"GO:0008625","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0071803","count":2},{"id":"GO:0007264","count":2}]},{"hash":"1331173315990838617","title":"Growth Factor Signaling and RNA Processing","description":"The top terms show a clear pattern of cellular responses to growth factors such as epidermal growth factor (EGF) and fibroblast growth factor (FGF), plus positive regulation of cell growth, indicating a growth-signaling theme. In addition, several RNA-related processes (snoRNA splicing, deadenylation-dependent decay, and miRNA-mediated silencing) suggest RNA processing/regulation functions, which may co-occur with growth signaling in these proteins. Some immune-related and cilium-related terms appear but are less central. Overall, the cluster seems to couple growth-factor signaling with RNA regulatory activities.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":3},{"id":"GO:0030307","count":2},{"id":"GO:0044458","count":1},{"id":"GO:0045657","count":1},{"id":"GO:0000288","count":1}]},{"hash":"1395547406991047302","title":"Nuclear RNA processing and chromatin organization","description":"The top GO terms are strongly centered on RNA-related nuclear processes (translation, maturation of SSU-rRNA, spliceosomal snRNP assembly, histone mRNA metabolism) and nuclear import, plus chromatin-related events (pericentric heterochromatin formation). This suggests a cluster focused on ribonucleoprotein assembly and RNA processing within the nucleus, with chromatin organization as a related theme; some stress hormone responses appear less directly connected.  ","confidence":"Medium","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0030490","count":6},{"id":"GO:0000387","count":5},{"id":"GO:0009737","count":5},{"id":"GO:0009414","count":5}]},{"hash":"383177974998489076","title":"Unknown","description":"The GO terms span diverse metabolic processes (retinol/retinal, fructose, ascorbate, farnesol-related) plus some development-related terms (renal system and collecting duct development) and a general anti-apoptotic signal; there isn\u2019t a single cohesive function linking these terms, so a unified label is not apparent.","confidence":"","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":10},{"id":"GO:0046370","count":9},{"id":"GO:0042574","count":8},{"id":"GO:0043066","count":7},{"id":"GO:1901653","count":7}]},{"hash":"1799775474491364198","title":"Core Metabolism and Stress Responses","description":"The cluster shows signals of central metabolism (tricarboxylic acid cycle and protoporphyrinogen IX biosynthesis) suggesting mitochondrial-associated metabolism. It also includes stress- and signaling-related terms (response to morphine, response to lead ion, and ER stress\u2013related translation initiation), indicating involvement in cellular stress responses. The mix points to a broad metabolic-stress functional grouping rather than a single specific pathway, so the label reflects both aspects.","confidence":"Medium","size":15,"edges":12,"triangles":1,"max_degree":6,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0019878","count":4},{"id":"GO:0043278","count":4},{"id":"GO:0006099","count":3},{"id":"GO:0006782","count":3},{"id":"GO:0009089","count":3}]},{"hash":"835698399842826087","title":"Mitochondrial metabolite transport and energy signaling","description":"This cluster centers on transport of key metabolic cofactors (NAD, CoA, ADP, heme) across membranes and the regulation of mitochondrial membrane potential/permeability, coupled with insulin signaling and amino acid starvation responses\u2014indicating a cohesive theme of mitochondrial transport/metabolism and energy regulation. Some tissue-specific terms (liver, pregnancy) may reflect physiological contexts rather than core function. ","confidence":"High","size":15,"edges":29,"triangles":17,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034198","count":10},{"id":"GO:0035349","count":10},{"id":"GO:0051881","count":10},{"id":"GO:0007565","count":10},{"id":"GO:0097421","count":10}]},{"hash":"926127723502295786","title":"Embryonic Neural Development and Transcriptional Regulation","description":"This cluster shows a strong emphasis on developmental biology and neural formation, with key terms like multicellular organism development, neural tube closure, dendritic spine morphogenesis, and DNA-templated transcription. The combination suggests a module of transcriptional regulators driving embryonic neural development and related tissue formation, while also touching on neuron-specific functions (behavioral responses) and cellular stress/apoptosis pathways that can intersect during development. A single immune-defense term appears but does not override the central neural-development transcriptional theme.","confidence":"Medium","size":15,"edges":16,"triangles":0,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":14},{"id":"GO:0006349","count":13},{"id":"GO:0006351","count":13},{"id":"GO:0001501","count":13},{"id":"GO:0050830","count":13}]},{"hash":"1979367215957613145","title":"Cerebellar neural development and synapse formation","description":"The top GO terms cluster around cerebellar and neural development\u2014Bergmann glial differentiation, cerebellar cortex formation, dendritic spine morphogenesis, and regulation of axon regeneration\u2014suggest a functional theme of cerebellar neuron maturation and synaptic development. Some insulin receptor signaling and T cell receptor signaling appear as broader signaling contexts but don't override the cerebellar development signal.","confidence":"Medium","size":15,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060020","count":9},{"id":"GO:2001275","count":9},{"id":"GO:0050852","count":9},{"id":"GO:0021697","count":9},{"id":"GO:0060997","count":8}]},{"hash":"1039220562860659440","title":"Ubiquitin-driven development and signaling","description":"This cluster centers on ubiquitination-related processes (protein ubiquitination and autoubiquitination regulation) and includes signaling-related and developmental features (Wnt signalosome assembly, branching morphogenesis, epithelial polarity), along with cell cycle and apoptosis terms, suggesting a theme of ubiquitin-mediated regulation coordinating development, cell fate decisions, and tissue organization.","confidence":"Medium","size":15,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0033028","count":2},{"id":"GO:0007049","count":2},{"id":"GO:2000171","count":2}]},{"hash":"515074088625514682","title":"GTPase-regulated adhesion and receptor signaling","description":"The cluster shows strong representation of small GTPase\u2013mediated signaling and regulation of GTPase activity, along with adhesion-related processes (substrate adhesion-dependent spreading, tight junction and podosome assembly) and multiple receptor signaling pathways (EGFR, ephrin, T cell receptor). This combination points to coordinated control of cytoskeletal dynamics, cell\u2013cell/ECM adhesion, and receptor-driven signaling across epithelial and immune contexts, including related phagocytic activity.","confidence":"High","size":15,"edges":15,"triangles":1,"max_degree":14,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:1900026","count":10},{"id":"GO:0007264","count":10},{"id":"GO:0070830","count":9},{"id":"GO:0051835","count":9},{"id":"GO:0071803","count":9}]},{"hash":"1689640699557397857","title":"Ubiquitin-Related Signaling and PTMs","description":"The cluster centers on protein modification and signaling, with frequent terms for ubiquitination, ubiquitin-dependent ERAD, and poly-ADP-ribosylation, as well as NF-kB and NOD2-mediated signaling. While a few terms touch on cell differentiation and electrophysiology, the dominant GO terms point to post-translational modification and ubiquitin-regulated signaling, suggesting these proteins function in stress- and immune-related signaling networks rather than a single specialized process.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":4},{"id":"GO:0032088","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0098907","count":4},{"id":"GO:0071260","count":4}]},{"hash":"1445467830768426558","title":"Unknown","description":"The top GO terms span diverse areas (xenobiotic response, regulation of stem cell differentiation, protein targeting and translocation, DNA replication, heat response, chaperone activity, actin organization, insulin signaling, and segment specification) with no clear common function or cohesive pathway. Additionally, there are no edges connecting the proteins, suggesting the group may be functionally heterogeneous or not a single functional module. Therefore, a cohesive, interpretable label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:1902037","count":2},{"id":"GO:0090084","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0006260","count":2}]},{"hash":"640360789187365307","title":"Endothelial cytoskeleton remodeling and angiogenesis","description":"These proteins cluster around Rho and small GTPase signaling, actin cytoskeleton organization, and endothelial morphogenesis, including sprouting angiogenesis and lumen extension, suggesting a core role in cytoskeletal dynamics driving blood vessel formation. Other terms like ER-Golgi ceramide transport and metabolic regulation appear ancillary and do not define a single cohesive function, so the dominant theme is endothelial signal transduction linked to cytoskeletal remodeling and angiogenesis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0007264","count":3},{"id":"GO:0048009","count":3},{"id":"GO:0030036","count":3},{"id":"GO:0035621","count":2}]},{"hash":"240158647005837670","title":"ER stress response and transcription regulation","description":"The terms cluster around ER-associated functions (protein folding in ER, ER lumen retention) and transcription-related processes (transcription regulation, DNA binding). Redox homeostasis is also linked to ER stress, suggesting a theme of ER quality control intertwined with transcriptional regulation and stress signaling. While some terms are obsolete and there are no edges, the common thread appears to be ER-related protein handling coupled to transcriptional control.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0043388","count":3}]},{"hash":"1893421643677739680","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"This cluster is dominated by GO terms related to actin cytoskeleton reorganization, Rho signaling, ruffle assembly, and fibroblast migration, all core aspects of cytoskeleton-driven shape changes and movement. Although there are ancillary terms touching on innate immunity, development, and cell cycle transitions, the convergent theme is actin dynamics enabling migration and related signaling, which justifies a label centered on cytoskeleton remodeling and migration.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0010761","count":2},{"id":"GO:0097178","count":2}]},{"hash":"290700685279807903","title":"Neuronal signaling and sensory perception","description":"Based on the GO terms, most entries point to neural signaling and sensory processing (visual perception, detection of calcium ion, detection of stimulus involved in sensory perception, phosphatidylinositol signaling in neurons, and PNS myelination), with a few outlier terms like nitrate assimilation and an obsolete calcium channel regulation entry. Overall, the cluster appears to reflect neural signaling and sensory functions rather than a single metabolic pathway.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:1901841","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0005513","count":1},{"id":"GO:0048015","count":1}]},{"hash":"2007578864683712116","title":"Nuclear Transport and Transcription Regulation","description":"The top GO terms center on transcription initiation and regulation (DNA-templated transcription, RNA Pol II promoter initiation) and on nuclear-cytoplasmic trafficking (protein import/export, Golgi-to-ER transport), suggesting a core theme of coordinating transcription with nuclear/cytoplasmic transport and intracellular trafficking. A few terms (ribophagy, light absorption, imaginal disc growth regulation) appear ancillary or annotation-noise, but don\u2019t override the main theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006367","count":2},{"id":"GO:0034517","count":1},{"id":"GO:0016037","count":1},{"id":"GO:0045571","count":1}]},{"hash":"317459706428264365","title":"Rho and JNK Signaling Regulation","description":"Top GO terms emphasize regulation of Rho protein signal transduction and regulation of the JNK cascade, pointing to a core theme of signaling pathway control. Other terms (ER organization, peroxisome/nuclear pore assembly, sensory perception) are more diverse and may reflect broader cellular organization roles or annotation noise. Overall, the cluster seems to represent regulators of signaling pathways with ancillary organelle-associated functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:2000821","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0050916","count":1},{"id":"GO:0071786","count":1}]},{"hash":"772716046123225170","title":"Unknown","description":"The GO terms span metabolism (cholesterol biosynthesis; ATP synthesis via electron transport), transcriptional regulation (galactose-induced RNAPII activity), cell migration and growth factor signaling, and multiple environmental response processes (antibiotics, morphine, toxic substances) plus visual perception. This broad and disparate mix does not reveal a single coherent function or pathway to define a concise cluster label, so Unknown with no confidence is appropriate.","confidence":"","size":14,"edges":16,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":3},{"id":"GO:0000435","count":3},{"id":"GO:0010763","count":3},{"id":"GO:0035729","count":3},{"id":"GO:0042773","count":2}]},{"hash":"74287108868905242","title":"RNA processing and protein modification","description":"This cluster centers on RNA metabolism (rRNA processing and mitochondrial tRNA methylation) and protein modification processes (arginine methylation and ubiquitination), indicating a shared function in RNA handling coupled with regulation of protein activity. Additional terms touch on stress responses (response to cold, cellular senescence) and signaling (NOD2 pathway), suggesting broader regulatory roles. Some terms (cobalamin biosynthesis) appear as distant associations, likely reflecting component annotations rather than core cluster function.","confidence":"Medium","size":14,"edges":8,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":5},{"id":"GO:0009409","count":4},{"id":"GO:0006364","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0032088","count":3}]},{"hash":"2012082136621663447","title":"Actin cytoskeleton dynamics and lamellipodium assembly","description":"The cluster is defined by actin cytoskeleton organization, lamellipodium assembly, actin filament polymerization, and dendritic spine morphogenesis, pointing to actin remodeling driving motility and shape changes. Peripheral terms like heart development or vasodilation may reflect contextual roles rather than core function.","confidence":"High","size":14,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0060997","count":2}]},{"hash":"1368828021048006053","title":"Glycolysis and redox-balanced central metabolism","description":"The top GO terms cluster around glycolysis, central carbon metabolism (2-oxoglutarate), folate and amino acid metabolism, nitrate assimilation, redox homeostasis, and membrane potential regulation. The common theme is metabolic pathways that generate energy and maintain cellular redox balance, pointing to a cohesive metabolic cluster rather than a single signaling or structural function.","confidence":"Medium","size":14,"edges":70,"triangles":183,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0006096","count":7},{"id":"GO:0042128","count":6},{"id":"GO:0000305","count":6},{"id":"GO:0006550","count":6}]},{"hash":"1269482635122598450","title":"Ubiquitin-Proteasome System","description":"The cluster is dominated by GO terms for ubiquitination (K48-, K6-linked, autoubiquitination), SCF-dependent proteasomal degradation, ERAD, and neddylation, indicating a cohesive ubiquitin-proteasome\u2013mediated protein turnover program; peroxisomal import and NF-kappaB regulation terms reflect downstream regulatory roles tied to ubiquitin signaling.","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070936","count":14},{"id":"GO:0016032","count":14},{"id":"GO:0016558","count":14},{"id":"GO:0045116","count":14},{"id":"GO:0070911","count":14}]},{"hash":"1668352416451338839","title":"Post-transcriptional mRNA processing and export","description":"This cluster centers on RNA maturation and post-transcriptional control: splicing regulation (via spliceosome), mRNA stability and export from the nucleus, and assembly of the translation initiation machinery (eIF4F), with additional ncRNA-mediated regulation, indicating a cohesive role in post-transcriptional gene expression regulation rather than transcriptional control.","confidence":"Medium","size":14,"edges":68,"triangles":161,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":9},{"id":"GO:0048026","count":8},{"id":"GO:0031047","count":8},{"id":"GO:0097010","count":6},{"id":"GO:0048255","count":6}]},{"hash":"995132304234025533","title":"TORC1 signaling and ribosome biogenesis","description":"The top terms cluster around TORC1 signaling and its positive regulation, plus ribosome-related processes (LSU rRNA maturation and translation preinitiation complex formation), suggesting a cohesive theme of growth and protein synthesis regulation. Some other terms appear divergent (viral mRNA export, development), but the core signal points to TOR-driven growth and ribosome assembly.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0046784","count":2},{"id":"GO:0021510","count":2}]},{"hash":"874804794801910653","title":"Regulation of receptor signaling and vesicle trafficking","description":"This cluster centers on terms related to controlling signaling pathways (e.g., negative regulation of NF-kappaB and Rac signaling) and vesicle trafficking processes (endocytic recycling, pinocytosis, Golgi localization, and neurotransmitter receptor transport from endosome to postsynaptic membrane). Although some terms are broader or obsolete, the shared theme appears to be regulation of intracellular signaling through trafficking and receptor localization, justifying a label focused on signaling and vesicle dynamics.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0060313","count":1},{"id":"GO:0035021","count":1}]},{"hash":"1710378120508899483","title":"Neural and vascular differentiation signaling","description":"These proteins pull together themes of cell differentiation (oligodendrocyte and venous endothelial differentiation) and signaling pathways (ephrin signaling, calcium release, immune signaling via IL-12 regulation) with a note on post-translational modification (poly-ADP-ribosylation) that modulates signaling. The cluster appears to reflect coordinated differentiation and communication in neural and vascular contexts, with supporting immune and signaling aspects.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0050679","count":4},{"id":"GO:1904355","count":3},{"id":"GO:0048709","count":3},{"id":"GO:0070212","count":3},{"id":"GO:0060843","count":3}]},{"hash":"1088325777963435901","title":"Rho-regulated cytoskeletal signaling","description":"The cluster centers on regulation of Rho signaling and lamellipodium assembly, indicating a focus on actin cytoskeleton dynamics and cell migration. Additional GO terms (TGF-beta and insulin responses, calcium release, PI biosynthesis) reflect interconnected signaling pathways that modulate cytoskeletal reorganization and transcriptional responses, supporting a cohesive theme of signaling-driven cytoskeletal remodeling.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0032869","count":3},{"id":"GO:0042518","count":3}]},{"hash":"368601482490626562","title":"Nuclear transcription and telomere maintenance","description":"Based on the top GO terms, the cluster centers on nuclear gene expression and genome integrity: DNA-templated transcription and mRNA processing, mitotic cell cycle, and key telomere maintenance/capping processes. While some stress-related terms (cadmium response and defense to Gram-positive bacteria) appear, the dominant theme is transcriptional activity coupled with telomere maintenance, suggesting these proteins function in gene expression regulation and genome stability. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0071276","count":5},{"id":"GO:1904355","count":4},{"id":"GO:0006349","count":4}]},{"hash":"659391448674071674","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0034349","count":4},{"id":"GO:0002534","count":4},{"id":"GO:0070306","count":4},{"id":"GO:0031175","count":4}]},{"hash":"1117094247356533793","title":"Rac GTPase signaling and cytoskeletal dynamics","description":"The top GO terms show regulation of GTPase activity and Rac signaling, along with podosome assembly and cytoskeletal regulation, plus related membrane trafficking processes like endocytic recycling. While a few terms touch on transcription or development, the core pattern points to signaling modulation that governs actin-based structures and cell movement. The absence of interaction edges suggests the proteins share functional roles rather than forming a single complex.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0071800","count":2},{"id":"GO:0006368","count":1},{"id":"GO:0007474","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1078228730680294925","title":"Stress-Response Signaling Proteins","description":"This cluster centers on cellular stress responses and phosphorylation-driven signaling, with terms for response to toxic substances, ionizing radiation, and DNA damage processing, plus protein trans-autophosphorylation and Fc receptor signaling. Some terms touch on development, but the dominant theme is signaling networks governing stress responses and damage repair. ","confidence":"Medium","size":13,"edges":71,"triangles":217,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":13},{"id":"GO:0007601","count":13},{"id":"GO:1990802","count":13},{"id":"GO:1904355","count":13},{"id":"GO:0071479","count":13}]},{"hash":"1034333543643733761","title":"Transcriptional Regulation and Chromatin Remodeling","description":"The top GO terms center on regulation of RNA polymerase II transcription, preinitiation complex assembly, and chromatin-related processes like histone acetylation and nucleosome mobilization, indicating a cohesive function in controlling gene expression at the chromatin level. Some terms refer to photomorphogenesis and metabolic regulation, which may reflect context-specific regulation in plants or broader regulatory networks; however the core theme remains transcriptional control.","confidence":"Medium","size":13,"edges":20,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043457","count":2},{"id":"GO:0043966","count":1},{"id":"GO:0042766","count":1},{"id":"GO:2000306","count":1},{"id":"GO:0000436","count":1}]},{"hash":"320104033812733463","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":10,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009103","count":2},{"id":"GO:0009242","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0019305","count":2}]},{"hash":"1631644589741484756","title":"Unknown","description":"The top GO terms cover disparate processes (DNA replication, cytoskeleton dynamics, chromatin assembly, vesicle trafficking, protein quality control, transformation competence, and SCF complex activity) with no clear unifying function, so a cohesive label cannot be assigned.","confidence":"","size":13,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990171","count":2},{"id":"GO:0006272","count":2},{"id":"GO:0003341","count":2},{"id":"GO:0030420","count":2},{"id":"GO:0090261","count":2}]},{"hash":"769010971288189309","title":"Developmental signaling and growth control","description":"This cluster centers on multicellular development and skin development, with accompanying regulatory signals such as positive regulation of kinase activity and GTPase activity, and links to cell proliferation and the mitotic cell cycle, suggesting involvement in signaling pathways that coordinate growth and tissue differentiation; a few terms (karyogamy, hypoxia response) are less directly aligned but do not override the dominant developmental signaling theme.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0043588","count":3}]},{"hash":"969321354180705174","title":"Unknown","description":"The cluster mixes GO terms for photosynthesis with mammalian development and metabolism, with only broad cellular processes like transport and translation present as well. There is no unambiguous common function tying these terms together, making it unclear what specific biological role the protein set shares.","confidence":"","size":13,"edges":58,"triangles":116,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0019684","count":2},{"id":"GO:0006810","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0014823","count":1},{"id":"GO:0060612","count":1}]},{"hash":"359916548246636541","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":53,"triangles":92,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0030488","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0031167","count":4}]},{"hash":"639818069654505302","title":"Chromatin remodeling and RNA processing","description":"This cluster shows a pattern of nuclear processes: chromatin remodeling and nucleosome dynamics, DNA unwinding in replication, rRNA maturation, mRNA catabolic processes, and protein import. Taken together, they suggest a core theme of chromatin organization coupled with RNA biogenesis and turnover in the nucleus, with a few developmental or stress annotations that may be secondary associations.","confidence":"Medium","size":13,"edges":48,"triangles":72,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":3},{"id":"GO:0042766","count":2},{"id":"GO:0006268","count":2},{"id":"GO:0071042","count":2},{"id":"GO:0043044","count":2}]},{"hash":"298265155779851441","title":"Developmental growth and vesicle trafficking","description":"The Top Terms include brain development, multicellular organism growth, and cell proliferation, signaling a developmental/growth theme. They also include COPII-coated vesicle budding, ER to Golgi transport, and protein transmembrane transport, indicating a robust secretory pathway component. Additionally, mitotic cell cycle and mitotic spindle assembly point to cell division. The overlap suggests a cluster of proteins participating in development-driven growth that relies on vesicle trafficking and mitotic machinery.","confidence":"Medium","size":13,"edges":47,"triangles":74,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0090114","count":6},{"id":"GO:0035264","count":6},{"id":"GO:0006888","count":6}]},{"hash":"1866258795631677505","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071035","count":3},{"id":"GO:0000390","count":3},{"id":"GO:0034476","count":3},{"id":"GO:0006268","count":2},{"id":"GO:0042766","count":2}]},{"hash":"981268106439844157","title":"ER Stress and Proteostasis","description":"The strongest signal among the GO terms centers on ER stress response and proteostasis: protein folding in the endoplasmic reticulum, unfolded protein response, and translation initiation regulation in response to ER stress. Redox homeostasis and glycolysis suggest metabolic adjustment during stress, while other terms (DNA replication, nitrate assimilation) are less central. Overall, the cluster appears to lump proteins involved in managing protein folding quality control under stress, with ancillary metabolic ties.","confidence":"Medium","size":13,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0036494","count":2},{"id":"GO:0006260","count":2}]},{"hash":"672015372000947624","title":"Growth Factor Signaling and Secretory Trafficking","description":"These proteins show enrichment for IGF receptor signaling, EGF/EGFR stimulus, estradiol response, and PI3K signaling, along with calcium-dependent exocytosis and endosome-to-lysosome transport. The common thread appears to be signaling-driven regulation of vesicle trafficking and secretion, rather than a single metabolic or immune function. Some terms (ultradian rhythm, myeloid apoptosis) are less central but do not override the core theme.","confidence":"Medium","size":13,"edges":11,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0014065","count":3},{"id":"GO:0048009","count":3},{"id":"GO:0045725","count":3},{"id":"GO:0071364","count":3},{"id":"GO:0071392","count":3}]},{"hash":"337628942035142015","title":"Unknown","description":"The top GO terms span diverse functions: biosynthesis (biotin, menaquinone, L-cysteine), metabolism (fatty acid oxidation, sulfate assimilation), transport (magnesium ion transport), and signaling/immune-related processes (immunoglobulin production, prostaglandin secretion, hydrogen peroxide\u2013mediated programmed cell death). There is no single cohesive theme or pathway linking these terms, and the cluster shows no edges, making a precise, representative label inappropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:0002377","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0090346","count":1},{"id":"GO:0009234","count":1}]},{"hash":"17292140195202478","title":"RNA processing and translation initiation","description":"The top GO terms cluster around mRNA maturation and regulation of translation, including spliceosome-mediated alternative splicing, mRNA stabilization and export, mRNA modification, and the formation of the translation preinitiation complex. This points to a cohesive unit coordinating RNA processing with translation initiation, potentially linked to stress responses.","confidence":"High","size":13,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0097010","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0010610","count":2},{"id":"GO:1902625","count":2}]},{"hash":"737869615708616393","title":"Protein Regulation and Signaling","description":"The terms cluster around mechanisms that regulate protein production, modification, assembly, and signal transduction\u2014such as ER-stress\u2013driven translation initiation, ubiquitination, protein complex assembly, and GPCR/steroid receptor signaling. While a couple of terms reflect broader cellular processes (e.g., photosynthesis, cell division), the common thread is control of protein function and communication pathways, suggesting a label focused on protein regulation and signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0015979","count":1},{"id":"GO:0051348","count":1},{"id":"GO:0036494","count":1}]},{"hash":"1368176783052382153","title":"Neural development and innervation","description":"These proteins are annotated with GO terms that cluster around nervous system development and nerve formation (CNS development, innervation, glial signaling) and associated signaling regulation (FGFR pathway). While a few terms touch on other tissues, the dominant theme is neural development and innervation, justifying a label that emphasizes nerve formation and signaling processes. ","confidence":"Medium","size":13,"edges":32,"triangles":34,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0002063","count":1},{"id":"GO:0060384","count":1},{"id":"GO:0014846","count":1},{"id":"GO:0042425","count":1},{"id":"GO:0035860","count":1}]},{"hash":"1835334953270291171","title":"Plant ion transport and salt-stress response","description":"This cluster is dominated by membrane ion transport terms (sodium import/export, potassium export, proton transport) and a salt-stress response, plus vacuolar acidification, pointing to plant ion homeostasis and pH regulation. While there are a couple of other plant-specific terms (cell wall biogenesis, transcription), the core theme centers on ion transport and salt response in plants.","confidence":"High","size":12,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1902600","count":1}]},{"hash":"1064292328328149713","title":"Unknown","description":"The top GO terms cover lipid catabolism, aerotaxis, lymph vessel morphogenesis, metanephric tubule morphogenesis, ion transport, and signaling via cAMP/cGMP and NO biosynthesis. These represent diverse, not clearly related processes rather than a shared cellular function, so there isn't a coherent theme to name a specific cluster function.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":3},{"id":"GO:0009454","count":2},{"id":"GO:0036303","count":2},{"id":"GO:0072237","count":2},{"id":"GO:0098719","count":2}]},{"hash":"638075661861526753","title":"Embryonic tissue and organ differentiation","description":"The proteins here are associated with development and differentiation across diverse tissues (muscle, heart, neural crest derivatives, oligodendrocytes, liver, kidney, and nerves), indicating a broad organogenesis/lineage specification theme rather than a single pathway. Transcription by RNA polymerase II is also a general regulatory process linked to these differentiation events.","confidence":"Medium","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":7},{"id":"GO:2001016","count":6},{"id":"GO:0061309","count":5},{"id":"GO:0014003","count":5},{"id":"GO:0003199","count":5}]},{"hash":"114023541157959109","title":"Cell division and signaling proteins","description":"The top GO terms center on core cell cycle events (cell division; mitotic spindle assembly) and growth-related processes (ribosome biogenesis; signaling via GTPases and tyrosine phosphorylation). Additional terms about xenobiotic and nutrient responses, and peripheral nervous system myelination, suggest broader regulatory or developmental roles but still fit a general theme around proliferation and intracellular signaling. Overall, the cluster appears to be proteins involved in cell cycle progression and signaling rather than a single specialized pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0042220","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0000747","count":2}]},{"hash":"294973290640185494","title":"Unknown","description":"The top GO terms are highly diverse (DNA repair and meiotic recombination; calcium ion detection; transcription termination; lipid A biosynthesis; lung development; mitotic chromosome regulation; locomotion; metal ion response; myelination), spanning unrelated processes and tissues. There isn\u2019t a single coherent function or pathway that ties these terms together for this cluster, so a single representative label isn\u2019t supported.","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010791","count":10},{"id":"GO:0005513","count":10},{"id":"GO:0030846","count":10},{"id":"GO:0009245","count":10},{"id":"GO:0030324","count":10}]},{"hash":"1331254863257698976","title":"Developmental transcription and morphogenesis","description":"This cluster is dominated by GO terms tied to multicellular development (forebrain development, neural tube closure, skeletal system development, general multicellular organism development) and DNA-templated transcription, suggesting proteins involved in developmental gene regulation and morphogenesis. A few terms touch on immune response and ER-stress apoptosis, but the central theme is development and transcriptional control.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":8},{"id":"GO:0007275","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0001501","count":8},{"id":"GO:0050830","count":8}]},{"hash":"44732320401849892","title":"Unknown","description":"The cluster contains a mix of neural signaling terms (long-term synaptic depression, glutamate secretion, sensory perception of light) and broad cellular responses (response to hyperoxia, mechanical stimulus, interferon-alpha), plus gene expression and some development/apoptosis terms. This wide, non-overlapping set provides no single cohesive function or pathway linking the proteins, suggesting unknown or dispersed roles rather than a defined module.","confidence":"","size":12,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060292","count":2},{"id":"GO:0051660","count":2},{"id":"GO:0071455","count":2},{"id":"GO:0010467","count":2},{"id":"GO:0097284","count":2}]},{"hash":"18450948956925920","title":"Mitochondrial dynamics and signaling","description":"The strongest signals come from GO terms related to mitochondria: inner mitochondrial membrane organization, regulation of mitochondrial DNA replication, mitochondrial membrane potential, and mitochondrion morphogenesis. This points to a core theme around mitochondrial organization and energetic signaling. The other terms (root development, extracellular matrix disassembly, excretion, interleukin-2 production, dopaminergic synaptic transmission) may reflect broader, context-dependent annotations rather than a unifying function of the cluster. Overall, the proteins seem to form a module centered on mitochondrial dynamics and function.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":5},{"id":"GO:0007007","count":5},{"id":"GO:0022617","count":5},{"id":"GO:0090297","count":5},{"id":"GO:0045861","count":5}]},{"hash":"59216363274926700","title":"Acetylation and Acetyl-CoA Metabolism","description":"This cluster is dominated by GO terms tied to acetylation (peptidyl-lysine N6-acetylation, N-terminal propionylation, spermine acetylation, histone H4 acetylation) and acetyl-group metabolism (glucosamine and N-acetylglucosamine pathways, acetoin catabolism, melatonin biosynthesis), suggesting a shared theme around acetyltransferase activity and acetyl-CoA\u2013dependent processes. The inclusion of leaf formation regulation and angiogenesis likely reflects downstream effects of acetylation on gene expression and signaling, spanning developmental contexts. Overall, the cluster appears to center on acetylation-related metabolism and regulation.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006041","count":9},{"id":"GO:0018003","count":9},{"id":"GO:0032919","count":9},{"id":"GO:2000025","count":9},{"id":"GO:0045150","count":9}]},{"hash":"1463441154816692239","title":"Developmental regulation and chromatin modification","description":"Top terms indicate neural and germline development (cerebellum morphogenesis; seminiferous tubule development; male germ-line stem cell asymmetric division) plus chromatin modification (histone acetylation/deacetylation, heterochromatin). The presence of endosome organization hints at trafficking-related signaling that modulates these developmental programs. Together, the cluster seems to reflect developmental regulation via chromatin state.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007032","count":2},{"id":"GO:0021587","count":2},{"id":"GO:0061186","count":1},{"id":"GO:1900404","count":1},{"id":"GO:0043966","count":1}]},{"hash":"2087531547960434307","title":"Synaptic signaling with actin remodeling","description":"The cluster centers on signals that regulate the actin cytoskeleton (positive regulation of GTPase activity, actin crosslink formation) and calcium/phosphoinositide signaling, with strong ties to synaptic plasticity (long-term potentiation) and sensory perception. While some terms like heart development and mitotic cell cycle are less directly connected, the dominant pattern points to neuronal signaling and cytoskeletal remodeling that underlie synaptic strength changes.","confidence":"Medium","size":12,"edges":32,"triangles":38,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0051764","count":7},{"id":"GO:0060291","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0000278","count":7}]},{"hash":"1401664523010588602","title":"Ciliary Hedgehog signaling and vesicle trafficking","description":"The cluster centers on cilium-related processes (motile cilium assembly, Smoothened/Hedgehog signaling) and vesicular trafficking (ER-to-Golgi transport, Golgi localization, endosome-to-postsynaptic membrane transport, and GTPase-regulated signaling), suggesting a cohesive module of ciliary signaling integrated with intracellular transport pathways. Some vascular/angiogenesis terms appear but do not define the core theme.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0044458","count":2},{"id":"GO:0007224","count":2},{"id":"GO:0051683","count":2},{"id":"GO:0098887","count":2},{"id":"GO:0090051","count":2}]},{"hash":"518061200746776694","title":"Antigen presentation and T cell activation","description":"This cluster shows clear immune signaling signals: antigen processing and presentation via MHC class II, positive regulation of IL-2 and IL-12 production, and positive regulation of T cell proliferation, along with NF-kappaB-related transcription factor activity. These aspects together suggest a role in adaptive immune activation and cytokine-mediated communication. A couple developmental GO terms appear, which may reflect annotation noise rather than a core theme. Overall, the dominant pattern points to antigen presentation and T cell\u2013mediated immune responses.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0001843","count":1},{"id":"GO:0007370","count":1},{"id":"GO:0042102","count":1},{"id":"GO:0051092","count":1}]},{"hash":"2120673404585988558","title":"Plant cell wall polysaccharide biosynthesis and glycosylation","description":"The predominant GO terms point to plant cell wall biogenesis and polysaccharide synthesis (homogalacturonan, glucuronoxylan, mucilage, cell wall organization, plant-type cell wall biogenesis) and protein O-linked glycosylation, indicating a cluster of proteins involved in cell wall matrix construction and glycosylation. A single unrelated term (skeletal muscle tissue regeneration) does not override the overall plant-focused theme.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016266","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0010289","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0035269","count":2}]},{"hash":"1807578740315283187","title":"NF-kappaB signaling and proteostasis regulation","description":"The cluster shows multiple terms tying to NF-kappaB pathway regulation (positive regulation of NF-kappaB activity, I-kappaB phosphorylation) and protein turnover (proteasomal ubiquitin-dependent degradation, ufmylation), with some hints of hormone signaling and stress responses. This suggests a theme around signaling regulation coupled with protein homeostasis rather than a single, narrow function. ","confidence":"Medium","size":12,"edges":18,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0033146","count":2},{"id":"GO:0032436","count":2},{"id":"GO:1903721","count":1},{"id":"GO:1905636","count":1}]},{"hash":"1584365864923032308","title":"Rho GTPase signaling and TORC1 growth control","description":"The cluster centers on regulation of Rho GTPase signaling and GTPase activity, with notable inclusion of TORC1 pathway activation, plus cytoskeletal and vesicle trafficking processes (microtubule movement, endosomal fusion) and nutrient response. This pattern suggests a cohesive theme of cytoskeletal dynamics integrated with nutrient-sensing growth signaling, rather than disparate functions. Immune-related terms appear as less dominant signals rather than defining the cluster.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0034058","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1783935856935905062","title":"Sugar and lipid biosynthesis","description":"The terms cluster around carbohydrate metabolism and lipid biosynthesis (feeding behavior; response to sucrose; starch biosynthetic process; phospholipid and glycolipid biosynthetic processes) with an additional bacillithiol biosynthetic term, and a couple glycosylation terms that are marked obsolete; overall this points to a metabolic biosynthesis theme rather than a single, specific signaling pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007631","count":3},{"id":"GO:0006506","count":3},{"id":"GO:0009744","count":3},{"id":"GO:0019252","count":3},{"id":"GO:0008654","count":3}]},{"hash":"640414288275901940","title":"Synaptic vesicle trafficking and exocytosis","description":"The terms cluster around vesicle life cycle steps in secretory pathways, especially in neurons: endosome-to-lysosome transport, Golgi-to-endosome transport, synaptic vesicle maturation, vesicle tethering/docking, SNARE regulation, and neurotransmitter/dense core vesicle exocytosis. This points to a cohesive theme of neuronal vesicle trafficking and exocytosis, with some overlap into general secretory processes such as insulin secretion and vesicle turnover via autophagy.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":3},{"id":"GO:0016188","count":3},{"id":"GO:0099022","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0006904","count":2}]},{"hash":"2195825366273821127","title":"Membrane Ion Transport and Calcium Signaling","description":"The dominant GO terms center on ion transport across the plasma membrane (potassium and sodium), intracellular calcium homeostasis with ER calcium regulation, and lipid-related processes such as phospholipid translocation and phospholipid metabolism. Together, these suggest a cluster of proteins involved in maintaining membrane ion gradients and calcium-dependent signaling, with linked lipid dynamics. Some outliers (lipopolysaccharide biosynthesis, testosterone response) may reflect broader functional associations or annotation noise rather than a core theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":5},{"id":"GO:0097623","count":4},{"id":"GO:0009103","count":3},{"id":"GO:0032470","count":3},{"id":"GO:0006564","count":3}]},{"hash":"872386443398469420","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":32,"triangles":60,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000480","count":10},{"id":"GO:0000398","count":10},{"id":"GO:0042273","count":10},{"id":"GO:0000463","count":10},{"id":"GO:0000462","count":10}]},{"hash":"651501025680799092","title":"DNA repair and cell-cycle regulation","description":"The cluster shows strong signals for DNA repair (UV-damage excision repair; DNA repair) and mitotic spindle orientation checkpoint signaling, pointing to genome maintenance and cell-cycle control as the core theme. Additional terms on vesicle trafficking, GTPase activity, and cilium assembly may reflect broader regulatory roles or pleiotropy, but the primary association appears with DNA repair and cell-cycle regulation.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0046726","count":3},{"id":"GO:0031578","count":3},{"id":"GO:0070914","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0032889","count":2}]},{"hash":"1645996915937745330","title":"Unknown","description":"The top GO terms are a mix of obsolete nuclear processes (nucleosome mobilization, histone exchange) and an assortment of unrelated functions (platelet aggregation; pollen exine formation; exploration behavior; protein import; various catabolic processes; methanol response). This lack of a common, cohesive biological theme suggests no single interpretable function ties the cluster together, so an Unknown label with None confidence is appropriate.","confidence":"","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":3},{"id":"GO:0043486","count":3},{"id":"GO:0070527","count":3},{"id":"GO:0035640","count":2},{"id":"GO:0017038","count":2}]},{"hash":"852567968349041297","title":"Synaptic plasticity and signaling regulation","description":"This cluster is driven by GO terms related to synaptic regulation and neuronal signaling, including regulation of synaptic plasticity via receptor localization to the synapse, ephrin receptor signaling, and cerebellar granule cell differentiation, suggesting a focus on neuronal communication and development. Ubiquitination and mRNA stability appear as broader regulatory mechanisms that can affect synaptic components, while a few terms (like endothelial differentiation or telomere capping) are less directly related, contributing to some noise in the set. Overall, the pattern supports a neuronal signaling/plasticity theme with regulatory breadth.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900383","count":6},{"id":"GO:0016567","count":6},{"id":"GO:1901187","count":6},{"id":"GO:2001275","count":6},{"id":"GO:0071260","count":6}]},{"hash":"2115183275263844913","title":"Unknown","description":"The GO terms for this cluster show a highly diverse mix\u2014translation elongation, plant cannabinoid biosynthesis, bacterial immunity, mitochondrial peptide export, various transport and vesicle-related processes, and unrelated drug and reproductive terms. There is no clear, single biological theme tying these proteins together, making a coherent label difficult to justify.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006414","count":2},{"id":"GO:1901697","count":1},{"id":"GO:1901696","count":1},{"id":"GO:0030153","count":1},{"id":"GO:0090374","count":1}]},{"hash":"1175928537258928227","title":"Tissue remodeling and organ morphogenesis","description":"The cluster centers on ECM and tissue remodeling across multiple organs: bone formation/remodeling (intramembranous ossification, bone resorption), basement membrane disassembly, lung branching morphogenesis, decidualization, thyroid hormone responsiveness, and immune interactions (T cell cytotoxicity). Bradykinin catabolism and extracellular Wnt signaling hints support an ECM-context and developmental remodeling theme. Taken together, the proteins likely participate in broad tissue remodeling and morphogenesis rather than a single dedicated pathway.","confidence":"Medium","size":11,"edges":28,"triangles":36,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":7},{"id":"GO:0035593","count":6},{"id":"GO:0001957","count":6},{"id":"GO:0097067","count":6},{"id":"GO:0045453","count":6}]},{"hash":"269286953632388366","title":"Ribosome Biogenesis and RNA Export","description":"This cluster is dominated by GO terms tied to ribosome production and RNA trafficking: ribosome biogenesis, translation, ribosomal small subunit assembly, rRNA export from the nucleus, and tRNA export from the nucleus. A few development-related terms (oogenesis, placenta development, neurogenesis) appear among the top terms, which may reflect broader pleiotropy or annotation noise, but the core theme centers on ribosome assembly/ RNA processing and transport. ","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019233","count":2},{"id":"GO:0048477","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1941224613237833039","title":"Secondary metabolite biosynthesis","description":"The Top Terms include verruculogen biosynthetic process, ectoine biosynthetic process, antibiotic biosynthetic process, and related biosynthetic/metabolic terms, pointing to a shared role in production of secondary metabolites. While some terms are unrelated or obsolete, the strongest signal is the biosynthesis of secondary metabolites (antibiotics, ectoine, toxins), which justifies the label. The cluster shows low connectivity, suggesting annotation-based grouping around biosynthetic functions rather than tight physical interactions.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034720","count":3},{"id":"GO:0070544","count":3},{"id":"GO:1902181","count":3},{"id":"GO:0097089","count":3},{"id":"GO:0042400","count":3}]},{"hash":"1911488969899759153","title":"Golgi vesicle trafficking and organization","description":"The cluster is dominated by GO terms tied to Golgi-related vesicle transport and organization: ER-to-Golgi transport, intra-Golgi transport, Golgi-to-vacuole transport, Golgi vesicle fusion, and Golgi ribbon formation, indicating a coherent function in Golgi trafficking and structural organization. Some co-occurring terms are unrelated (e.g., pregnancy, mitochondrial potential), but they appear less central to the cluster\u2019s core theme. ","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":4},{"id":"GO:0006891","count":4},{"id":"GO:0090161","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0006896","count":4}]},{"hash":"355444538874883067","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1234465081461241791","title":"Cellular Stress Response and Genome Maintenance","description":"The cluster is enriched for redox homeostasis, DNA damage tolerance/processing, and xenobiotic response terms, with supporting terms for lipid droplet organization and epidermal development pointing to broader stress-adaptation roles. Taken together, these proteins likely participate in managing oxidative stress, DNA damage, and detoxification.","confidence":"Medium","size":11,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0070987","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0034389","count":2},{"id":"GO:0006308","count":2}]},{"hash":"806973014825962592","title":"Neuronal vesicle trafficking and synaptic signaling","description":"The top terms cluster around endocytosis, retrograde vesicle transport (Golgi to ER), and endosome-to-melanosome trafficking, plus excitatory postsynaptic potential, pointing to vesicle dynamics and synaptic function in neurons. Some development terms (substantia nigra, oligodendrocyte differentiation) appear related but ancillary to the core trafficking/synaptic theme.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0060079","count":2}]},{"hash":"1015498594310410688","title":"Unknown","description":"The top GO terms cover neural signaling (glutamate secretion, vocalization behavior, light stimulus perception), cell adhesion (zonula adherens and adherens junction localization), intracellular signaling (protein dephosphorylation, GTPase activation, Wnt regulation), and cellular organization (Golgi localization) with no single unifying function. Because the terms span disparate processes without a cohesive theme, there isn\u2019t a clear concise label that represents the cluster as a whole.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014047","count":1},{"id":"GO:0050953","count":1},{"id":"GO:0045186","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0030111","count":1}]},{"hash":"2146735950463473462","title":"Plant cytokinesis and root epidermal development","description":"The cluster is heavily enriched for plant-specific processes: cell plate\u2013mediated cytokinesis, actomyosin ring and microtubule dynamics, mitotic spindle assembly, plus root development and epidermal stem cell homeostasis, indicating a cohesive module linking cell division with root epidermal maintenance.","confidence":"High","size":11,"edges":35,"triangles":49,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000742","count":7},{"id":"GO:0048364","count":6},{"id":"GO:0000915","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0031534","count":6}]},{"hash":"496379634933183341","title":"Nervous system signaling and sensory perception","description":"This cluster centers on neuronal function: visual perception, detection of calcium ions and sensory stimuli, phosphatidylinositol signaling in neurons, autonomic regulation of heart rate, and peripheral nervous system myelination, plus regulation of dendrite morphogenesis. The combination points to a cohesive theme of neuronal signaling and sensory processing, with development and maturation aspects (dendrite morphogenesis, myelination) as well as some broader or ancillary terms (transcriptional regulation, toxin response) that can accompany neural proteins.","confidence":"High","size":11,"edges":8,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050774","count":4},{"id":"GO:1901841","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0005513","count":3},{"id":"GO:0048015","count":3}]},{"hash":"355872878732052946","title":"Unknown","description":"These 11 proteins are annotated with GO terms spanning multiple distinct biological themes, including amino acid biosynthesis and catabolism (lysine, tyrosine, aspartate), heme and sphingomyelin biosynthesis, central metabolism (oxaloacetate), insulin signaling, transcription, and a fruit ripening term. There is no single cohesive pathway or function that all terms prominently reflect, so the cluster does not map to a specific, interpretable biological function.","confidence":"","size":11,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0033512","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0006107","count":1}]},{"hash":"1998501470465665943","title":"Mitochondrial transport and energy metabolism","description":"The GO terms cluster around mitochondrial membrane potential regulation, apoptotic mitochondrial changes, and transmembrane transport of key metabolites (ADP, NAD, CoA), with linked energy- and stress-responsive processes (insulin signaling, amino acid starvation). This points to a cohesive theme of mitochondrial transport coupled with energy metabolism and membrane integrity.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":6},{"id":"GO:0034198","count":5},{"id":"GO:0035349","count":5},{"id":"GO:0051881","count":5},{"id":"GO:0007565","count":5}]},{"hash":"1127332715854259938","title":"Neural crest and oligodendrocyte development with Wnt signaling","description":"The dominant GO terms point to vertebrate neural development, especially neural crest cell migration and oligodendrocyte differentiation, with Wnt signaling as a central pathway. Additional terms reflect broader signaling roles (JAK-STAT, PI3K-AKT) and some unrelated processes, but the core theme remains neural development and Wnt pathway involvement.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048709","count":2},{"id":"GO:0001755","count":2},{"id":"GO:0030238","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0048919","count":1}]},{"hash":"1740081897174224615","title":"Golgi-to-plasma membrane transport and signaling","description":"The top GO terms point to vesicle trafficking from the ER/Golgi to the plasma membrane (GO:0006888, GO:0043001, GO:0090316), with additional enrichment for intracellular transport and several signaling pathways (ERK cascade, Wnt, Ephrin, TCR) and related contexts such as synaptic potentiation and beta selection. This suggests a cohesive role for proteins in membrane trafficking coupled with signaling, justifying a label focused on both processes.","confidence":"Medium","size":10,"edges":6,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0090316","count":4},{"id":"GO:0043001","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0048013","count":4}]},{"hash":"556818574871696619","title":"Broad organ development and morphogenesis","description":"The GO terms indicate development and morphogenesis across multiple organs and tissues (midgut, hindbrain, optic cup, blood vessels, pituitary, ureter) and symmetry formation, suggesting a cohesive theme of embryonic organogenesis rather than a single pathway.","confidence":"High","size":10,"edges":43,"triangles":105,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007494","count":9},{"id":"GO:0035799","count":9},{"id":"GO:0009855","count":9},{"id":"GO:0030902","count":9},{"id":"GO:0021983","count":9}]},{"hash":"1133431962836188012","title":"Plant carbohydrate biosynthesis and cell wall metabolism","description":"The top GO terms are dominated by carbohydrate biosynthesis (starch and glycogen) and plant cell wall metabolism (cellulose and related polysaccharides), indicating a theme of synthesis of plant-based carbohydrates and cell wall components. Some non-specific terms (DNA replication, mRNA decay, olfactory development) appear but do not overshadow the main plant carbohydrate/cell wall signal.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070481","count":2},{"id":"GO:0045190","count":2},{"id":"GO:0019252","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0006260","count":2}]},{"hash":"411854390012172604","title":"Organelle protein targeting and RNA processing","description":"GO terms indicate organelle targeting (peroxisome matrix import, mitochondrial inner membrane insertion) and RNA metabolism (mRNA export, stress granule disassembly), pointing to a theme of organizing organelles and RNA handling under stress. Some terms (vesicle formation, oxidative/proteolytic processes) are broader or less directly linked, reflecting annotation breadth. Overall, the cluster aligns with organelle targeting plus RNA processing.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016562","count":2},{"id":"GO:0032979","count":2},{"id":"GO:0070414","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0035617","count":2}]},{"hash":"1954401536981343460","title":"Diverse biosynthesis and regulatory processes","description":"The terms span sterol biosynthesis, various regulatory processes (negative regulation, regulation of myelination), cell morphogenesis, and foundational biosynthetic/biogenesis activities (iron-sulfur cluster assembly, DNA replication, post-translational targeting). This indicates a cluster of proteins involved in multiple biosynthetic and regulatory roles rather than a single cohesive pathway, justifying a broad label rather than a specific function.","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":2},{"id":"GO:0031641","count":2},{"id":"GO:0090084","count":1},{"id":"GO:1902037","count":1},{"id":"GO:0000902","count":1}]},{"hash":"273799207607654938","title":"Growth plate cartilage growth and angiogenesis","description":"This cluster centers on skeletal development, with terms like growth plate cartilage chondrocyte growth and regulation of bone mineralization, plus angiogenesis-related terms such as positive regulation of angiogenesis and cellular response to PDGF stimulus. While a couple of immune-related terms appear, the dominant theme is bone growth and vascular remodeling in the growth plate context.","confidence":"High","size":10,"edges":8,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042997","count":7},{"id":"GO:0002774","count":7},{"id":"GO:0030500","count":7},{"id":"GO:0036120","count":7},{"id":"GO:0045766","count":7}]},{"hash":"1181465714581709453","title":"Cell-cycle control and developmental signaling","description":"The cluster strongly centers on cell proliferation machinery (DNA replication, centrosome cycle, nuclear export) and developmental signaling pathways (Wnt, Hippo) with differentiation/morphogenesis terms (keratinocyte differentiation, cranial skeleton morphogenesis). This suggests proteins coordinating cell cycle progression with growth and tissue development, including epidermal differentiation and craniofacial morphogenesis.","confidence":"High","size":10,"edges":43,"triangles":104,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007118","count":7},{"id":"GO:0048701","count":5},{"id":"GO:0007098","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0010571","count":5}]},{"hash":"170920404728998506","title":"Nutrient and Ion Transmembrane Transporters","description":"The top GO terms show a clear emphasis on transmembrane transport for a variety of substrates (galactose, fucose, vitamins, phosphate, sodium, xenobiotics, 4-hydroxyphenylacetate), suggesting these proteins mainly function as membrane transporters handling nutrient and ion uptake/efflux. Some metabolism terms are incidental or obsolete, but the unifying theme is transport across membranes.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0015757","count":2}]},{"hash":"853584248232737851","title":"Unknown","description":"The terms are highly heterogeneous, spanning various sugar and amino sugar catabolic processes alongside unrelated topics like transcription, oligodendrocyte differentiation, and otic vesicle formation. With edges missing and no clear, single biological theme tying the proteins together, there is no coherent function to label beyond Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0019877","count":1},{"id":"GO:0046176","count":1},{"id":"GO:0019470","count":1},{"id":"GO:0042838","count":1}]},{"hash":"1200929442339427849","title":"ER stress proteostasis and protein trafficking","description":"The top GO terms cluster around mechanisms of protein quality control in the endoplasmic reticulum and associated trafficking: regulation of translation initiation during ER stress, post-translational targeting to membranes, transport of misfolded proteins, and maintenance of redox homeostasis in folding environments. While a few terms (DNA replication, hormone signaling, neural patterning) are less connected and may reflect broader or unrelated roles of some proteins, the dominant theme points to proteostasis and ER-related trafficking.","confidence":"Medium","size":10,"edges":8,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0036494","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0045454","count":2}]},{"hash":"130614444014831263","title":"mRNA processing and translation initiation","description":"The top GO terms cluster around mRNA processing and translation initiation, including eIF4F complex assembly, preinitiation complex formation, mRNA export, stabilization, and splicing regulation, suggesting a module coordinating mRNA maturation with translation initiation.","confidence":"High","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097010","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0010610","count":2},{"id":"GO:1902625","count":2}]},{"hash":"991746086692869424","title":"Cellular stress response and redox homeostasis","description":"This cluster is dominated by oxidative stress-related terms (removal of superoxide radicals, redox homeostasis) and ER stress response, indicating a core role in managing cellular stress. Additional terms touch on cytoskeletal remodeling and polarity (Cdc42 signaling, cell shape maintenance, hemocyte migration), and structural organization (melanosome and anatomical structure arrangement), suggesting stress-associated remodeling rather than a single specialized pathway. Overall, the GO profile aligns with a stress-response module focused on redox balance, with ancillary cytoskeletal and trafficking aspects.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1903206","count":2},{"id":"GO:0034976","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0019430","count":2}]},{"hash":"1182714048177970946","title":"Fatty acid and cholesterol metabolism and transport","description":"The top GO terms point to fatty acid catabolism and peroxisomal import, cholesterol homeostasis, and a broad set of transport processes (lipids, xenobiotics, and small molecules). This suggests a coherent theme of lipid handling intertwined with molecule transport/detox pathways, with some terms (like bacteriocin immunity) being less directly connected. Overall, the pattern supports a lipid metabolism and transport-focused cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030153","count":1},{"id":"GO:0046618","count":1},{"id":"GO:0042760","count":1},{"id":"GO:0001407","count":1},{"id":"GO:0045796","count":1}]},{"hash":"532011014300304085","title":"Platelet-Endothelial Immune Signaling","description":"The top GO terms point to platelet activation and signaling (platelet degranulation; Fc receptor inhibitory signaling), leukocyte diapedesis across endothelium, and endothelial/vascular responses to stimuli (shear stress, PDGF) and immune cell activation. Together, these suggest a theme of communication between platelets, immune cells, and the vascular endothelium, rather than a single, cohesive enzymatic pathway. Some terms (germ cell development, insulin response) are less clearly connected to this axis, possibly reflecting broader annotations in the protein set. Overall, the label Platelet-Endothelial Immune Signaling captures the core connectivity among the included processes.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007281","count":2},{"id":"GO:0042997","count":2},{"id":"GO:0002774","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0040014","count":2}]},{"hash":"768342366109778234","title":"Diverse Biosynthetic and Metabolic Pathways","description":"The top GO terms show multiple biosynthetic processes (PHB, estrogen, glucocorticoid, mycolic acid, tetrahydrobiopterin, 3-keto-sphinganine) and related metabolism, along with a few broader or secondary processes (acetoin catabolism, redox, antibiotic response, lung development). This pattern points to a cluster of proteins broadly involved in metabolism and biosynthesis rather than a single specific function, so a general label like \"Diverse Biosynthetic and Metabolic Pathways\" best captures the theme. Some annotations may be cross-thematic or species-specific exceptions.","confidence":"Medium","size":10,"edges":8,"triangles":3,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0042619","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0006703","count":4},{"id":"GO:0030324","count":4}]},{"hash":"1744955139452852744","title":"Meiosis and chromosome segregation","description":"The top GO terms cluster around meiotic processes and chromosome dynamics (meiotic spindle midzone assembly, male meiosis sister chromatid cohesion, chromosome segregation), suggesting a shared role in meiotic cell division. Other terms like TOR signaling and GTPase regulation are broader and less defining, and the absence of edges among proteins adds uncertainty, but the strongest signals point to meiosis-related function.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":2},{"id":"GO:0051257","count":1},{"id":"GO:0071230","count":1},{"id":"GO:0007065","count":1},{"id":"GO:0007059","count":1}]},{"hash":"988946355500347694","title":"DNA Damage Response and Apoptosis","description":"The cluster centers on GO terms tied to genome maintenance and cellular stress responses, including apoptotic process, DNA replication/recombination, and cellular response to ionizing radiation, with a note on telomere capping regulation. These collectively point to a DNA damage response leading to cell fate decisions. Some terms (visual perception, trachea formation) appear unrelated and likely reflect annotation noise, but the core signal supports a DNA damage/apoptosis theme.","confidence":"Medium","size":9,"edges":31,"triangles":56,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071375","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0009636","count":2}]},{"hash":"790209246845449898","title":"Mitochondrial Electron Transport and ATP Synthesis","description":"The top GO terms are dominated by aerobic electron transport chain, oxidative phosphorylation, and respiratory chain complex IV assembly, plus proton transmembrane transport, all pointing to mitochondrial respiration and ATP production. A few outlier terms exist, but the core signal strongly supports ETC/energy metabolism.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:1902600","count":1},{"id":"GO:0019646","count":1},{"id":"GO:0008535","count":1},{"id":"GO:0006119","count":1}]},{"hash":"1369443402674443832","title":"Unknown","description":"The terms span steroid and lipid metabolism (steroid catabolic, estrogen and glucocorticoid biosynthesis, 3-keto-sphinganine, mycolic acid, phylloquinone), as well as development (lung development) and general processes (DNA-templated transcription, antibiotic biosynthesis, acetoin catabolism). This wide scatter suggests no single cohesive function characterizes the cluster, so a specific functional label is not assignable with confidence.","confidence":"","size":9,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006706","count":2},{"id":"GO:0006703","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045150","count":2}]},{"hash":"981599485380653243","title":"DNA Replication and Chromatin Assembly","description":"The cluster is dominated by GO terms tied to DNA replication (DNA replication; leading strand elongation) and chromatin assembly (CENP-A containing chromatin assembly). While some terms reflect broader cellular stress responses and protein handling, the strongest signals pertain to genome duplication and chromatin organization.","confidence":"Medium","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:1990171","count":3},{"id":"GO:0006272","count":3},{"id":"GO:0030420","count":3},{"id":"GO:0090261","count":3}]},{"hash":"1927564416572880962","title":"Immune signaling and vascular permeability regulation","description":"The proteins show enrichment for immune-related processes (neutrophil chemotaxis, monocyte differentiation, IL-2 production) and for regulation of vascular permeability (both positive and negative), suggesting a theme of inflammatory immune signaling coupled with dynamic control of vascular barriers. Other terms involve calcium signaling and metabolic processes that may reflect downstream signaling cross-talk. Overall, the cluster appears tied to immune activation with modulation of vascular permeability.","confidence":"Medium","size":9,"edges":10,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043117","count":3},{"id":"GO:0006198","count":3},{"id":"GO:0030593","count":3},{"id":"GO:0010880","count":3},{"id":"GO:0043116","count":3}]},{"hash":"1689491127431807594","title":"Developmental transcription and neural development","description":"The top GO terms point to developmental regulation and transcription (multicellular organism development, skeletal system development, forebrain development, neural tube closure, DNA-templated transcription), suggesting these proteins cohesively govern gene expression during development and neural formation. Some terms reflect broader stress or immune responses, but the dominant signal is developmental transcriptional control.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0001501","count":6},{"id":"GO:0050830","count":6}]},{"hash":"232867229166802988","title":"Neuronal signaling and endosomal trafficking","description":"The cluster features strong neural-related signaling and development terms (ephrin receptor signaling, excitatory postsynaptic potential, dopamine response, hippocampus development) along with endosomal trafficking terms (early-to-late endosome transport, endosome-to-melanosome transport) and synaptic regulation; these point to proteins that function in neuronal signaling and intracellular endosomal trafficking. Some terms (T cell receptor signaling, mast cell degranulation regulation) may reflect broader signaling overlaps or annotation noise, but the dominant theme is neural signaling and trafficking.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048013","count":3},{"id":"GO:0045022","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0035646","count":3}]},{"hash":"69179614314025779","title":"Developmental proliferation and migration signaling","description":"The terms cluster around cell cycle and DNA replication (proliferation), cytoskeletal and signaling processes (Rho regulation and cell migration), and development of vascular and neural lineages, with supporting roles for PARylation and telomere regulation. This mix points to a coordinated program of proliferation, movement, and differentiation during development rather than a single pathway.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0070212","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0016477","count":3}]},{"hash":"249917180111781864","title":"Mitosis and DNA replication","description":"Enriched GO terms cluster around cell cycle progression and DNA synthesis (G1/S and G2/M transitions, mitotic cell cycle, DNA replication). While potassium ion transport and neural development terms appear, the dominant signal is mitosis-related processes, supporting a label focused on cell-cycle control and DNA replication.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006813","count":6},{"id":"GO:0034501","count":5},{"id":"GO:0000086","count":5},{"id":"GO:0000082","count":5},{"id":"GO:0045773","count":5}]},{"hash":"582610233305924595","title":"Mitotic Chromosome Segregation","description":"The cluster's frequent GO terms center on mitosis and chromosome handling: mitotic cell cycle, mitotic sister chromatid segregation, CENP-A containing chromatin assembly, and microtubule severing, all pointing to chromosome dynamics during cell division. A couple of terms refer to vesicle transport and peroxisomal import, which are less central here and may reflect broader cellular roles or annotation noise.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":2},{"id":"GO:0000070","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2102325568839700680","title":"Platelet-immune signaling and leukocyte diapedesis","description":"This cluster centers on platelet activation/degranulation and Fc receptor\u2013related immune signaling, with concurrent links to endothelial/vascular responses and leukocyte transmigration (diapedesis). The term set suggests a cohesive theme of immune-platelet crosstalk in vascular contexts, including signaling that regulates immune and mast cell activity and leukocyte movement through vessel walls.","confidence":"Medium","size":9,"edges":10,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042997","count":6},{"id":"GO:0002774","count":6},{"id":"GO:0032869","count":6},{"id":"GO:0040014","count":6},{"id":"GO:0050904","count":6}]},{"hash":"147701705180888957","title":"Mitochondrial respiration and protein complex assembly","description":"The top GO terms point to mitochondrial functions: proton transmembrane transport, aerobic respiration, and protein targeting/assembly within mitochondria (protein heterooligomerization and homotetramerization). While some terms are tissue-specific and less directly linked, the core signal centers on mitochondrial energy metabolism and formation of protein complexes. ","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006675","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0009060","count":3}]},{"hash":"368073193673196838","title":"Cardiac development and actin cytoskeleton signaling","description":"This cluster is dominated by GO terms for heart development and cardiac muscle contraction, and is strongly connected to actin cytoskeleton dynamics (lamellipodium assembly, cell spreading) and small GTPase signaling (Rac/Rho). While there are a couple of immune-related terms present, the core pattern points to cardiac development accompanied by cytoskeletal remodeling and GTPase-mediated signaling, which often coordinate tissue formation and contractile function.","confidence":"High","size":9,"edges":8,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0002606","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0035020","count":2},{"id":"GO:0098761","count":2}]},{"hash":"2282178780764665248","title":"Cell signaling and protein regulation","description":"Top GO terms indicate involvement in cellular signaling (response to morphine, GPCR signaling, steroid hormone receptor complex assembly) and protein regulation processes (ubiquitination, protein heterooligomerization, translation initiation in ER stress). While photosynthesis appears as an outlier, the dominant theme is regulation of signaling pathways and protein interactions, suggesting a coherent functional cluster around cellular signaling and protein regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0043278","count":6},{"id":"GO:0015979","count":5},{"id":"GO:0051348","count":5},{"id":"GO:0036494","count":5},{"id":"GO:0051291","count":5}]},{"hash":"1171966002681400675","title":"ER Stress\u2013Driven Protein Folding and Quality Control","description":"ER Stress\u2013Driven Protein Folding and Quality Control is suggested by terms like positive regulation of translation initiation in response to ER stress, post-translational targeting to membranes, misfolded protein transport, ER-associated degradation pathways, and redox homeostasis, all pointing to the cellular machinery that handles protein folding, maturation, and quality control under stress. Some terms (e.g., tRNA import, DNA replication, and developmental signaling) are less directly connected and may reflect broader cellular states or annotation noise, but the dominant theme is ER-associated protein homeostasis and quality control.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036494","count":7},{"id":"GO:0031204","count":7},{"id":"GO:0045454","count":7},{"id":"GO:0035719","count":7},{"id":"GO:0097428","count":7}]},{"hash":"466884409695408188","title":"RNA Splicing and mRNA Stability Regulation","description":"These proteins cluster around RNA processing and regulation of gene expression. The top GO terms emphasize spliceosome-mediated mRNA splicing and regulation of splicing, coupled with mRNA stability and stress-responsive regulation of mRNA stability. Related terms include transcription termination and rRNA processing, suggesting involvement in broader RNA metabolism. Overall, the module appears to reflect post-transcriptional control and RNA maturation rather than just transcription. ","confidence":"High","size":9,"edges":13,"triangles":5,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0006378","count":3}]},{"hash":"2139344918532393744","title":"Unknown","description":"The top GO terms are mixed across platelet activation, phagolysosome assembly, integrin regulation, T cell death, fertilization, neural development, histone acetylation, and microtubule movement, with no clear shared function. The cluster has no edges, indicating little cohesive biology linking the proteins, so no single interpretable theme emerges.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010572","count":2},{"id":"GO:0001845","count":2},{"id":"GO:0033623","count":2},{"id":"GO:0006924","count":2},{"id":"GO:0007338","count":2}]},{"hash":"1217413542018639791","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0031222","count":2},{"id":"GO:0085030","count":2},{"id":"GO:0046373","count":2},{"id":"GO:0045493","count":2}]},{"hash":"713295896241495080","title":"NOD2-driven innate immune signaling","description":"The cluster\u2019s top GO terms point to innate immune signaling, notably NOD2 signaling and NF-\u03baB\u2013related regulation, plus immune cytokine regulation (negative regulation of IL-12). Calcium signaling and broader cell signaling terms (ephrin signaling) are compatible with immune pathways, while a few terms (telomere capping, venous endothelial differentiation) are less directly connected but can intersect with immune or stress signaling. Overall, the strongest recurring theme is innate immune/inflammatory signaling.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":2},{"id":"GO:0032088","count":2},{"id":"GO:1904355","count":1},{"id":"GO:0070212","count":1},{"id":"GO:0060843","count":1}]},{"hash":"1355811098383695080","title":"Organogenesis and tissue morphogenesis","description":"These terms emphasize development and morphogenesis across multiple organs (skin, heart, kidney) and related tissue-specific processes (cardiac action potentials, calcium signaling), suggesting a general role in organ formation rather than a single signaling pathway.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0097050","count":2},{"id":"GO:0035502","count":2},{"id":"GO:0098910","count":2}]},{"hash":"1115287422896296389","title":"Photoreceptor signaling and second-messenger pathways","description":"The cluster includes GO terms for light detection and visual perception, along with cGMP biosynthesis and signaling-related terms such as adenylate cyclase activation and forskolin response. This points to photoreceptor\u2013driven signaling and involvement of second messengers (cGMP, cAMP), with metabolic terms likely peripheral. ","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033317","count":2},{"id":"GO:0050908","count":2},{"id":"GO:0032026","count":2},{"id":"GO:0019375","count":1},{"id":"GO:0009405","count":1}]},{"hash":"372682738033437467","title":"Unknown","description":"The terms are heterogeneous: plant-development terms (leaf morphogenesis; positive regulation of flower development) coexist with metabolic and regulatory processes (glycoside and glycosylceramide catabolism; carbohydrate metabolism; regulation of nitric oxide synthase; dexamethasone response; intestinal epithelial differentiation; transcription by RNA polymerase II). There is no single, cohesive biological process tying all proteins together, making a clear, specific cluster label unlikely. Therefore, Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046477","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0016139","count":1},{"id":"GO:0009965","count":1},{"id":"GO:0051001","count":1}]},{"hash":"541714761931825754","title":"Translation Initiation and mRNA Transport","description":"The cluster is dominated by terms for initiating translation and moving mRNA (formation of translation preinitiation complex, translation reinitiation, mRNA transport), indicating a module centered on post-transcriptional control of protein synthesis. Additional terms hint at regulatory signaling (positive regulation of GTPase and serine/threonine kinase activity) and stress responses (nutrient and hypoxia), suggesting these proteins also participate in signaling that modulates translation, while some terms like spinal cord development and mitotic cell cycle reflect broader roles of the included proteins.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0071456","count":3}]},{"hash":"1619326111705608492","title":"Rho GTPase\u2013driven lamellipodium formation","description":"This cluster is dominated by lamellipodium assembly and Rho-dependent signaling, with terms for GTPase activity regulation pointing to actin cytoskeleton remodeling driven by Rho-family GTPases. Other terms suggest broader developmental signaling, but the cytoskeletal remodeling theme best ties the proteins together.","confidence":"High","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0007399","count":2}]},{"hash":"580388319680836888","title":"Unknown","description":"The terms cover a mix of DNA replication, chromatin assembly, stress responses, protein trafficking, and cytoskeletal remodeling, with no clear single function tying all eight proteins together.","confidence":"","size":8,"edges":19,"triangles":23,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1990171","count":7},{"id":"GO:0006272","count":7},{"id":"GO:0030420","count":7},{"id":"GO:0090261","count":7},{"id":"GO:0061641","count":7}]},{"hash":"1253160149024450939","title":"Energy Metabolism and Lipid Biosynthesis","description":"The top GO terms cluster around metabolic biosynthesis and utilization\u2014glycogen biosynthesis, carnitine biosynthesis/metabolism, fatty-acyl-CoA biosynthesis, and fatty acid beta-oxidation\u2014suggesting a shared theme of energy metabolism and lipid processing. Some terms (e.g., heart development, response to cold) are less central to core metabolism and may reflect broader annotations, but the dominant signal points to metabolism-related functions. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0005978","count":3},{"id":"GO:0045329","count":3},{"id":"GO:0019254","count":2},{"id":"GO:0009409","count":2}]},{"hash":"1396403655987707588","title":"Redox homeostasis and carbon metabolism","description":"This cluster is enriched for GO terms related to maintaining cellular redox balance (GO:0045454) and carbon metabolism, notably the pentose-phosphate shunt (GO:0006098) and one-carbon metabolism (GO:0006730), along with serine and tyrosine biosynthesis and a hypoxia response. The common theme appears to be metabolic adaptation under oxidative stress, with NADPH generation and redox regulation guiding carbon flux through these pathways.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006098","count":1},{"id":"GO:0006564","count":1},{"id":"GO:0098706","count":1}]},{"hash":"1431102825268446285","title":"Neuronal development and signaling","description":"This cluster centers on nervous system development and nerve morphogenesis (branching morphogenesis of a nerve, nervous system development) and on signaling pathways relevant to neurons (Wnt signalosome assembly, cellular response to dopamine, maintenance of cell polarity, and regulation of actin cytoskeleton for neurite outgrowth). While a few terms relate to broader immune signaling (NF-kappaB, protein ubiquitination, T cell receptor signaling), the dominant themes are neuronal development, synaptic signaling, and cytoskeletal remodeling that shapes neuronal morphology. ","confidence":"Medium","size":8,"edges":26,"triangles":44,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":5},{"id":"GO:0090338","count":4},{"id":"GO:2000172","count":4},{"id":"GO:1904887","count":4},{"id":"GO:0043124","count":4}]},{"hash":"1863145008032586589","title":"Developmental Epigenetic Regulation","description":"This cluster combines chromatin-modifying activities (peptidyl-arginine hydroxylation and histone H3K4/H3K36 demethylation) with a range of developmental and morphogenesis-related processes (lung epithelial branching, bone remodeling/osteoblast differentiation, Wnt signaling, thyroid hormone response, and neural precursor proliferation). The pattern suggests proteins that regulate development through epigenetic control and signaling pathways governing tissue morphogenesis.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097067","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0045668","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0070544","count":2}]},{"hash":"249433277731037662","title":"Protein quality control under ER stress","description":"This cluster centers on ER-associated protein handling: negative regulation of kinase activity, translation initiation in response to ER stress, post-translational targeting to membranes, misfolded protein transport, and iron-sulfur cluster\u2013dependent maturation, all pointing to protein quality control during stress. Redox homeostasis supports this stress response. Some terms (DNA replication, parathyroid hormone signaling) are less connected and may reflect incidental associations. Overall, the theme is ER-related protein folding/maturation and trafficking.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0036494","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0035719","count":3}]},{"hash":"1786913051891877459","title":"Cardiac Calcium Signaling and Electrical Coupling","description":"The top GO terms center on calcium handling (release of Ca2+ from the sarcoplasmic reticulum, RyR channel regulation, intracellular calcium signaling) and electrical signaling in heart and neurons (cardiac conduction, neuronal action potential propagation), suggesting a cohesive function in excitation-contraction coupling and calcium-mediated signaling. A couple of outliers (cell cycle, steroid receptor assembly) are peripheral to this core theme, but overall the cluster maps to calcium-dependent electrical signaling in excitable tissues.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0086064","count":1},{"id":"GO:0014808","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0006463","count":1}]},{"hash":"2036338836225560790","title":"Ubiquitin-dependent proteolysis","description":"Most top terms point to ubiquitin-related protein turnover (K48 ubiquitination, ISG15 conjugation, proteasome quality control) and APC/C-mediated degradation, implying the cluster centers on regulated protein destruction. A few terms (peroxisome import, chromatin methylation) are less clearly connected, suggesting some functional noise. Overall, the dominant theme is ubiquitin-dependent proteolysis.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0051965","count":8},{"id":"GO:0016562","count":8},{"id":"GO:0031145","count":8},{"id":"GO:0032020","count":8},{"id":"GO:0051569","count":8}]},{"hash":"402949606590304338","title":"Neural calcium signaling and sensory perception","description":"These proteins cluster around nervous system signaling and sensory processing: visual perception, detection of calcium ions, calcium channel activity, PI-mediated signaling, peripheral nervous system myelination, and autonomic regulation of heart rate. While a few terms (transcription regulation, methylmercury response) may be ancillary, the dominant GO terms point to neuronal signaling and sensory function driven by calcium signaling.","confidence":"High","size":8,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1901841","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0005513","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0050906","count":2}]},{"hash":"919339664130081273","title":"Proteostasis and Immune Signaling Regulation","description":"This cluster shows enrichment for protein quality control and turnover (cellular response to misfolded protein, deubiquitination in ubiquitin-dependent protein catabolic process, regulation of ER to Golgi vesicle transport) alongside modulation of immune/inflammatory pathways (negative regulation of canonical NF-kappaB signaling, tolerance induction to LPS, negative regulation of leukocyte migration). While a couple of terms touch development, the strongest shared theme is coordination between proteostasis and inflammatory signaling in cellular contexts such as epithelia. ","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060576","count":1},{"id":"GO:0060628","count":1},{"id":"GO:0071243","count":1},{"id":"GO:0071218","count":1},{"id":"GO:0048662","count":1}]},{"hash":"422813581198200064","title":"Mitochondrial respiration and peroxisome turnover","description":"The GO terms cluster around mitochondrial energy metabolism (mitochondrial respiratory chain complex IV assembly, proton transmembrane transport, plasma membrane ATP synthesis coupled electron transport, transport) and organelle turnover (autophagy of peroxisome). Together they suggest a theme of energy production with related membrane transport and peroxisome dynamics, rather than a single narrow function. Some stress-response terms (response to freezing, response to toxic substance) also fit energy-demanding remodeling. ","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050826","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0006810","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0033617","count":1}]},{"hash":"1376055998820366866","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0010610","count":2},{"id":"GO:0044830","count":2},{"id":"GO:0006402","count":2},{"id":"GO:2000637","count":2}]},{"hash":"1038189690640854616","title":"mRNA processing and translation initiation","description":"This cluster centers on multiple RNA-processing steps (splicing, polyadenylation, mRNA export, stability) and the assembly of the translation initiation machinery, suggesting coordinated roles in mRNA maturation and the start of translation.","confidence":"High","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0045292","count":5},{"id":"GO:0097010","count":4},{"id":"GO:0048255","count":4},{"id":"GO:0000381","count":4}]},{"hash":"2261358444475096268","title":"Cell Polarity and Cytoskeleton-Driven Morphogenesis","description":"These proteins cluster around cell polarity establishment, cytoskeletal remodeling (Cdc42 signaling, formin-mediated actin assembly), and cell movement during development and tissue shaping. They also touch on organelle biogenesis (melanosomes) and calcium-regulated exocytosis, fitting polarity-dependent secretion and migration processes such as hemocyte migration, nerve branching, and sprouting angiogenesis. Overall, the terms point to a coherent theme of polarity-guided cytoskeletal dynamics coordinating morphogenesis and migration.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":2},{"id":"GO:0048532","count":2},{"id":"GO:0035099","count":2},{"id":"GO:0032488","count":2},{"id":"GO:1903232","count":2}]},{"hash":"361976080963659092","title":"RNA processing and translation initiation control","description":"The cluster's GO terms cluster around post-transcriptional regulation: mRNA processing, splicing regulation, miRNA processing, mRNA stabilization, and translation initiation (IRES-dependent and eIF4F assembly), suggesting proteins that govern RNA fate and translation rather than transcription.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0051533","count":1},{"id":"GO:0097010","count":1},{"id":"GO:0048255","count":1},{"id":"GO:0035196","count":1}]},{"hash":"1909900609919985917","title":"Rho/Rac GTPase Signaling and Lamellipodium Dynamics","description":"The cluster centers on small GTPase\u2013mediated signaling (Rac and Rho) and actin-driven lamellipodium assembly, tying together pathways like EGFR signaling, insulin-responsive signaling, and broader immune-related signals. This points to a cohesive theme of cytoskeletal remodeling driven by GTPase signaling across multiple contexts.","confidence":"High","size":8,"edges":16,"triangles":12,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032869","count":7},{"id":"GO:0030032","count":7},{"id":"GO:1904140","count":7},{"id":"GO:0035020","count":7},{"id":"GO:0098761","count":7}]},{"hash":"2075442918564907543","title":"Triglyceride and Phospholipid Catabolism","description":"Predominant signals point to lipid energy metabolism and membrane lipid remodeling, especially triglyceride catabolism and phospholipid turnover. The cluster also touches on endocannabinoid signaling regulation, consistent with lipid-derived signaling, and a modest link to PKA pathway regulation. A formaldehyde catabolic term appears as a minor outlier.","confidence":"High","size":8,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0006642","count":2},{"id":"GO:2000480","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0046338","count":2}]},{"hash":"703606405159094988","title":"Multisystem Embryonic Development","description":"These proteins are annotated with GO terms spanning development across multiple organ systems (nervous system, inner ear, lung epithelium, placenta, cartilage, kidney) and related differentiation processes, suggesting a broad embryogenic role rather than a single specific pathway. The mix of tissue-specific and general developmental terms supports a cross-tissue developmental cluster rather than a focused function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0042491","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0060428","count":1},{"id":"GO:0007050","count":1}]},{"hash":"1652539686857008225","title":"Developmental ECM Remodeling","description":"This cluster centers on tissue development and extracellular matrix dynamics: multiple terms point to organism and skeletal development, vascular development in the labyrinthine layer, and fibroblast migration, complemented by hyaluronan metabolism relevant to ECM remodeling. The DNA-templated transcription term suggests gene regulation underlying these processes, while cholesterol biosynthesis and glucose response reflect supporting metabolic activity. Overall, development-associated ECM remodeling best captures the common theme, with secondary metabolic signals present. ","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":3},{"id":"GO:0030212","count":3},{"id":"GO:0006695","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1661497362718382205","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":15,"triangles":16,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0006268","count":5},{"id":"GO:0071042","count":5},{"id":"GO:0000463","count":5}]},{"hash":"1280270288352300297","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":17,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0006283","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0071042","count":2}]},{"hash":"1804924855491758968","title":"Bacterial lipid and quinone biosynthesis","description":"The proteins show enrichment in fatty acid biosynthesis, lipid A biosynthesis, and menaquinone/phylloquinone biosynthesis, plus related cell wall organization, pointing to a cohesive theme of lipid and quinone metabolism in bacteria; antibiotic biosynthesis and minor catabolic terms are present but do not override this core signal.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0006633","count":3},{"id":"GO:0009245","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0009234","count":2}]},{"hash":"199245547403233612","title":"Neural differentiation and microtubule dynamics","description":"Driven by neuron differentiation (GO:0030182) and neuron migration (GO:0001764) with mechanosensory behavior (GO:1905792), plus cytoskeletal and mitotic microtubule processes (GO:0031122, GO:0051256, GO:1902408) that support neural development and cellular morphology.","confidence":"Medium","size":7,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":4},{"id":"GO:1905792","count":2},{"id":"GO:0031122","count":2},{"id":"GO:0051256","count":2},{"id":"GO:0071353","count":2}]},{"hash":"454477823281321078","title":"Mitochondrial Regulation of T Cell Activation","description":"The presence of T cell receptor signaling and interleukin-2 production terms, together with mitochondrial processes such as inner membrane organization, mtDNA replication, and membrane potential regulation, suggests a theme where mitochondrial function modulates T cell activation and cytokine production. Some other terms (ECM disassembly, excretion, dopaminergic transmission) are less cohesive with this core, but do not override the central immune\u2013mitochondrial link.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":2},{"id":"GO:0007007","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0090297","count":1},{"id":"GO:0045861","count":1}]},{"hash":"1186227439766466721","title":"Developmental signaling regulation","description":"Top GO terms point to modulation of signaling pathways (BMP/SMAD, NF-kappaB) and developmental processes (meristem maintenance, germ-line masculinization), with additional notes on dephosphorylation and nuclear export that influence signaling outcomes. This suggests a cohesive theme of regulatory control over development-related signaling, despite some heterogeneous or organism-specific terms; the proteins likely function as regulators rather than core metabolic components.","confidence":"Medium","size":7,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":5},{"id":"GO:0010991","count":5},{"id":"GO:0000173","count":5},{"id":"GO:0080005","count":5},{"id":"GO:0061191","count":5}]},{"hash":"1042456162720611206","title":"RTK-MAPK Signaling in Development and Immunity","description":"The GO terms point to receptor-driven signaling pathways (integrin signaling, ephrin receptor signaling, T cell receptor signaling) converging on downstream MAPK/ERK cascades, with regulation of serine phosphorylation and cytoskeletal reorganization. Developmental contexts (embryonic cranial skeleton morphogenesis, axonogenesis) alongside immune signaling indicate a shared role for RTK/MAPK pathways in coordinating adhesion, migration, and differentiation during development and immune responses.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":4},{"id":"GO:0050771","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0007229","count":4}]},{"hash":"98716525841997317","title":"Unknown","description":"The top GO terms include angiogenesis, endothelial migration, trachea formation, visual perception, sperm capacitation, DNA replication, and DNA damage response, which span several distinct biological themes. There isn't a single, coherent function that unites these processes across the protein set, so a concise, representative label can't be confidently assigned.","confidence":"","size":7,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001525","count":5},{"id":"GO:0043536","count":5},{"id":"GO:0048240","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0009636","count":4}]},{"hash":"30271161691468979","title":"Neural development and synaptic regulation","description":"The top GO terms cluster around neuronal processes: negative and positive regulation of neuron apoptotic processes, brain development, and regulation of synaptic vesicle exocytosis, with additional signals related to Wnt signaling and GTPase activity. This suggests the proteins in this cluster are involved in neural development and synaptic signaling rather than generic cell cycle functions, despite one or two broader terms.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043524","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0031384","count":4}]},{"hash":"1410062102269188214","title":"Oxidative stress response and redox homeostasis","description":"The cluster is dominated by GO terms related to managing reactive oxygen species and redox balance: cellular response to hydrogen peroxide, removal of superoxide radicals, and maintaining redox homeostasis, plus related processes like regulation of stress-activated MAPK cascade and peptidyl-cysteine oxidation. Some terms (male gonad development, NK cell mediated cytotoxicity) appear less cohesive, likely representing annotation noise. Overall, the shared theme is redox regulation and oxidative stress response.","confidence":"Medium","size":7,"edges":16,"triangles":16,"max_degree":6,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0008584","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0070301","count":5},{"id":"GO:0042267","count":4},{"id":"GO:0032872","count":4}]},{"hash":"668716507304136043","title":"Diverse biosynthesis and metabolism","description":"The top GO terms are dominated by biosynthetic processes (antibiotic biosynthesis, PHB biosynthesis, mycolic acid biosynthesis, steroid biosynthesis like estrogen/glucocorticoids) with a few outliers (DNA replication, lung development). This suggests the cluster captures a broad, high-level theme of biosynthesis and metabolic production rather than a single, cohesive pathway. Despite no detected interactions, the common thread is varied biosynthetic/metabolic capabilities.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0006703","count":2}]},{"hash":"203859109061505406","title":"Neuronal development and TGF-beta signaling","description":"The top GO terms center on neuronal development (substantia nigra development) and signaling pathways, especially TGF-beta/BMP signaling and its regulation (negative regulation of BMP, SMAD-related processes). Additional terms like response to morphine and lead ion, plus peptidyl-serine dephosphorylation and ER-to-Golgi transport, suggest a broader neuronal signaling and secretory trafficking context. Overall, the cluster seems to reflect neuronal development with modulation by growth factor signaling and related regulatory processes.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0071560","count":2},{"id":"GO:0010288","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0021762","count":2}]},{"hash":"2270897473741504190","title":"Developmental signaling and transcription","description":"Top GO terms cluster around development and differentiation (multicellular organism development, keratinocyte differentiation, skeletal system development) and transcriptional control (DNA-templated transcription), with signaling pathways (Hippo, JNK) and cell-cycle processes interwoven. This suggests a group of proteins that coordinate developmental signaling and regulation of gene expression; the immune-defense term is ancillary and does not define the cluster.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035329","count":3}]},{"hash":"2052519464238156875","title":"ER quality control and protein maturation","description":"The cluster is dominated by GO terms related to ER-associated processes: positive regulation of translation initiation in response to ER stress, post-translational protein targeting to membranes, misfolded protein transport, and (obsolete) ERAD pathways, all pointing to protein folding, processing, and degradation in the endoplasmic reticulum. Redox homeostasis also fits with the oxidative folding environment of the ER. A few terms like tRNA import into nucleus and DNA replication appear peripheral, but the core theme centers on protein maturation and quality control in the secretory pathway.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0035719","count":1},{"id":"GO:0097428","count":1}]},{"hash":"161193246478574747","title":"Rho/Rac GTPase\u2013driven cytoskeletal remodeling","description":"The cluster is enriched for small GTPase\u2013mediated signaling (Rho, Rac), with terms like lamellipodium assembly, positive regulation of Rac/Rho signaling, and cell spreading, which point to cytoskeletal remodeling and motility as the core function across multiple contexts (neuron projection development, PNS myelin maintenance). Immune-related terms (IL-7 response, B cell maturation) may reflect broader signaling roles but do not override the central cytoskeletal theme.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0010976","count":4},{"id":"GO:0030032","count":4},{"id":"GO:0032287","count":4},{"id":"GO:0035020","count":4}]},{"hash":"579233074560861813","title":"Telomere maintenance and telomere localization","description":"The top GO terms repeatedly point to telomere biology\u2014positive regulation of telomere capping, maintenance via telomerase, and localization to chromosome telomeric regions\u2014suggesting this cluster centers on telomere maintenance and chromosome telomere dynamics. A few other terms (pinocytosis, angiogenesis, phosphorylation) appear as less-connected annotations, but do not override the telomere-focused core.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010873","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0097498","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0070212","count":2}]},{"hash":"548426005145442170","title":"Rac/Rho-Driven Lamellipodium and Actin Dynamics","description":"The top terms point to actin cytoskeleton remodeling (lamellipodium assembly, actin cytoskeleton organization) and regulation by small GTPases Rac and Rho, indicating a cohesive theme of GTPase-controlled actin dynamics and cell spreading/migration. While some terms (insulin signaling, heart development, B cell maturation) appear, the core cluster is best described by Rac/Rho-mediated actin remodeling and lamellipodium formation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":4},{"id":"GO:0035020","count":4},{"id":"GO:0098761","count":4},{"id":"GO:0002344","count":4},{"id":"GO:0035023","count":4}]},{"hash":"848933173268076121","title":"Proteostasis and ERAD/Proteasome Regulation","description":"The top GO terms cluster around protein quality control and trafficking, including cellular response to misfolded proteins, proteasome assembly, K48-linked deubiquitination, ERAD pathway regulation, Golgi retention, and exosome assembly regulation. These indicate a coherent module focused on maintaining protein homeostasis and sorting/degrading proteins, with a few transcription-related terms appearing as secondary signals. A small amount of noise (e.g., stamen formation) may reflect annotation cross-talk rather than a core function of this cluster.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071218","count":1},{"id":"GO:0045053","count":1},{"id":"GO:0043248","count":1}]},{"hash":"721511907070588402","title":"Aromatic amino acid catabolism (phenylalanine/tyrosine)","description":"The top terms cluster around L-tyrosine and L-phenylalanine catabolic processes, including homogentisate and 4-hydroxyphenylacetate catabolism, with additional related aromatic compound degradation terms. This pattern points to enzymes involved in aromatic amino acid degradation pathways rather than general metabolism.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006572","count":2},{"id":"GO:0006559","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006527","count":1},{"id":"GO:1902000","count":1}]},{"hash":"1543274298632054918","title":"Plant carbohydrate metabolism and secondary cell wall biosynthesis","description":"Top GO terms are dominated by plant-specific carbohydrate biosynthesis and cell wall processes (starch, glycogen, sucrose biosynthesis; glucuronoxylan; pollen exine; plant-type secondary cell wall biogenesis). A few terms like DNA recombination appear less connected, but the overall theme centers on carbohydrate production and cell wall construction in plants, supporting this label.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0019252","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0005985","count":2},{"id":"GO:0050650","count":1}]},{"hash":"1253537930199585099","title":"Mitochondrial Transporters and Metabolic Regulation","description":"The GO terms cluster around transmembrane transport of key metabolites (ADP, NAD, CoA, heme) and regulation of mitochondrial membrane potential/permeability, indicating proteins focused on mitochondrial metabolite exchange and energy regulation. Contextual terms such as cellular response to insulin, amino acid starvation, liver regeneration, and pregnancy suggest metabolic adaptation where mitochondrial function is central. This cohesive pattern supports a mitochondrial transport/metabolism function.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":6},{"id":"GO:0035349","count":6},{"id":"GO:0051881","count":6},{"id":"GO:0007565","count":6},{"id":"GO:0097421","count":6}]},{"hash":"748246045192991448","title":"Unknown","description":"The GO terms cover a mix of stress/response, lipid signaling, neural structure, cell-cycle regulation, vascular functions, and basic metabolism, with no clear shared pathway or function linking the proteins, so no cohesive label can be assigned beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0097107","count":1},{"id":"GO:0031536","count":1},{"id":"GO:0043117","count":1}]},{"hash":"1653075021904367994","title":"Chromatin regulation and sarcomere organization","description":"The cluster shows nuclear processes (DNA replication, histone acetylation, nucleosome mobilization) alongside cytoskeletal and muscle assembly terms (Arp2/3-mediated actin nucleation, actin filament bundle assembly, sarcomere organization, skeletal muscle fiber development), suggesting a dual role in genome regulation and muscle cell architecture.","confidence":"Medium","size":6,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0043981","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0021762","count":2}]},{"hash":"40009101587388264","title":"Transmembrane Transport of Nutrients and Xenobiotics","description":"This cluster centers on membrane transport functions: multiple GO terms describe transmembrane transport of thiamine, molybdate, methionine, xenobiotics, and related phospholipid movement, suggesting a group of transporter proteins. Some terms about stem cell proliferation and antimicrobial responses appear as less direct connections.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015888","count":6},{"id":"GO:0045332","count":6},{"id":"GO:0015689","count":6},{"id":"GO:0006855","count":6},{"id":"GO:0072089","count":6}]},{"hash":"1245275888725560548","title":"Oxidative Stress and DNA Damage Response","description":"Proteins here are linked to cellular responses to oxidative and DNA-damaging stresses (nitroglycerin, sodium arsenite, diamide, singlet oxygen, gamma radiation) and to transcriptional regulation associated with stress, including DNA-templated transcription and regulation of transcription. This suggests a cohesive theme of stress-induced transcriptional programs coupled with DNA damage response, rather than a single isolated function.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900427","count":2},{"id":"GO:1900365","count":2},{"id":"GO:1904843","count":2},{"id":"GO:1903936","count":2},{"id":"GO:0001892","count":2}]},{"hash":"1076990180746184701","title":"Cofactor and antioxidant metabolism","description":"The cluster shows enrichment for metabolism of cofactors and redox-related molecules: tetrahydrofolate, lipoate, and glutathione metabolism, as well as a response to reactive oxygen species. Additional terms touch on nucleotide metabolism and development-related processes, which may be incidental annotations. Overall, the dominant theme is small-molecule cofactor turnover and redox balance.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000305","count":3},{"id":"GO:0046653","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0051572","count":3},{"id":"GO:0046098","count":3}]},{"hash":"925435750239324920","title":"Unknown","description":"The top GO terms cover a wide range of processes from nucleotide-sugar salvage and metabolism to ER targeting, endocytosis, lipid remodeling, and ion transport, with no clear single function tying the six proteins together. The sparse connectivity (2 edges, 0 triangles) supports a lack of cohesive biology in this cluster.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042352","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0045047","count":1},{"id":"GO:0006465","count":1},{"id":"GO:0009103","count":1}]},{"hash":"1538247465225633766","title":"Unknown","description":"The listed GO terms span diverse areas\u2014stress responses (toxic substance, ionizing radiation), signaling (autophosphorylation, Fc receptor signaling), transport regulation (Golgi to plasma membrane), and various developmental/tissue-specific processes (visual perception, trachea formation, bone mineralization)\u2014with no single unifying function. This lack of a coherent shared theme makes it difficult to assign a meaningful, specific label to the cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0007601","count":3},{"id":"GO:1990802","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071479","count":3}]},{"hash":"1985537748678790902","title":"Retroviral DNA replication and integration","description":"The Top Terms point to DNA replication, recombination, RNA-templated DNA biosynthesis (reverse transcription), and DNA integration, along with viral entry into the host nucleus and proviral latency. These collectively reflect the retroviral lifecycle: reverse transcription of viral RNA into DNA, integration into host DNA, and establishment of latency, with some terms also indicating pathogen-host interactions. ","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0006278","count":2},{"id":"GO:0015074","count":2}]},{"hash":"738294311644112810","title":"Neuronal development and synaptic signaling","description":"This cluster is enriched in neural growth and communication terms\u2014hippocampus development, dendrite morphogenesis, excitatory postsynaptic potential, and axon extension\u2014alongside ephrin receptor signaling and dopamine response, indicating a focus on neuronal development and synaptic signaling. Immune-related terms (T cell receptor signaling, mast cell degranulation) are present but less representative.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":5},{"id":"GO:0045956","count":4},{"id":"GO:0048013","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0043304","count":4}]},{"hash":"288103625477400866","title":"Ribosome biogenesis and translation","description":"The top GO terms cluster around translation (initiation, termination), ribosome biogenesis (ribosomal subunit assembly, rRNA maturation across SSU/LSU and 5.8S), and mRNA surveillance related to translation (no-go and nonstop decay). This suggests the proteins are involved in assembling and functioning ribosomes and ensuring proper translation, making a label focused on ribosome biogenesis and translation appropriate and representative.","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006413","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0070481","count":1}]},{"hash":"727285594432558022","title":"Hair Cell Development and DNA Repair Cluster","description":"The cluster shows enrichment for DNA replication and nucleotide-excision repair, alongside embryonic organ and hair cell differentiation terms, suggesting a theme where DNA maintenance links with sensory hair cell development.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048568","count":5},{"id":"GO:0035315","count":5},{"id":"GO:0001666","count":5},{"id":"GO:0006289","count":5}]},{"hash":"1924972632352170087","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0034349","count":1},{"id":"GO:0002534","count":1}]},{"hash":"135049470251962499","title":"RNA Decay and Translation Regulation","description":"The cluster shows enrichment for RNA metabolism and translation control terms (mRNA decay pathways like no-go and nonstop decay, RNA processing, ribosome disassembly, and translational termination regulation). A few developmental terms (endoderm development, EMT, BMP signaling) suggest broader roles in gene expression during development, but the dominant signal points to post-transcriptional regulation of gene expression. This supports a cohesive label around RNA decay and translation regulation.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051078","count":1},{"id":"GO:0070966","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0007492","count":1},{"id":"GO:0032790","count":1}]},{"hash":"1859162165579786341","title":"Mitochondrial Transport and Energy Regulation","description":"The top GO terms cluster around transport of energy-related molecules across membranes (NAD, CoA, ADP) and regulation of mitochondrial membrane potential and permeability, with supporting terms for insulin signaling and liver/pregnancy\u2013related processes. This suggests a cohesive theme of mitochondrial transport paired with metabolic regulation, justifying the label.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":3},{"id":"GO:0035349","count":3},{"id":"GO:0051881","count":3},{"id":"GO:0007565","count":3},{"id":"GO:0097421","count":3}]},{"hash":"821583678641533457","title":"Unknown","description":"The GO terms are a highly heterogeneous mix covering cofactor biosynthesis, tRNA modification, development (imaginal disc wing hair orientation, gastrulation adhesion), cytoskeletal organization, endocytosis, and signaling, with no single cohesive function dominating. This makes it unclear what common function unites the cluster.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006728","count":1},{"id":"GO:0008616","count":1},{"id":"GO:0006729","count":1},{"id":"GO:0043538","count":1},{"id":"GO:1902951","count":1}]},{"hash":"2244650873357392862","title":"Mitotic progression and spindle organization","description":"Based on the GO terms, the strongest signals are cell cycle, cell division, and spindle organization, with a specific note on G1/S transition. This points to a functional cluster of proteins involved in mitotic progression and spindle assembly, with some supporting signals for ubiquitin-dependent protein turnover and apoptosis that may reflect quality control during division. Overall, the theme is mitosis-related processes.","confidence":"High","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006405","count":1}]},{"hash":"512007897689916743","title":"Unknown","description":"GO terms cover viral entry and latency, plant development, ion transport, and immune-related processes with no clear unifying function, so there is no cohesive theme linking these proteins.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0019061","count":1},{"id":"GO:0050999","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0050900","count":1}]},{"hash":"1382927224644415860","title":"Neural signaling and sensory perception","description":"These proteins show enrichment for calcium signaling and ion-channel related terms (calcium transport, detection of calcium ion, clustering of voltage-gated potassium channels) along with nervous system functions (visual perception, retina layer formation, myelination in peripheral nervous system, regulation of heart rate, sensory stimulus detection). Together these indicate roles in neural signaling and sensory processing rather than a non-neural theme. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070588","count":2},{"id":"GO:1901841","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0005513","count":1},{"id":"GO:0050906","count":1}]},{"hash":"1991890397050823432","title":"Bacterial metabolism and cell envelope biosynthesis","description":"The top GO terms point to diverse bacterial metabolic activities, including catabolism of malonate and phenylacetate, menaquinone and siderophore biosynthesis, and various fatty acid metabolism processes, plus lipoteichoic acid biosynthesis which is tied to the cell envelope. This combination suggests a cluster centered on bacterial metabolism and cell-wall/envelope biosynthesis rather than a single plant or eukaryotic pathway.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090410","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0019290","count":1},{"id":"GO:0009698","count":1}]},{"hash":"1294281597738674861","title":"Redox Homeostasis and Oxidative Stress Response","description":"Proteins here center on managing cellular redox state: detoxifying oxidants, maintaining redox balance, and responding to hydrogen peroxide, with deglutathionylation supporting redox control. Some minor signals include methylamine metabolism and nucleotide biosynthesis, but the dominant theme is redox regulation and oxidative stress defense.","confidence":"High","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0030416","count":2},{"id":"GO:0070301","count":2}]},{"hash":"2289196380533670061","title":"ER-stress linked translation and protein quality control","description":"This cluster centers on translation and its regulation under ER stress, including translation initiation regulation in response to ER stress and the handling of misfolded proteins through targeted transport and maturation pathways. The presence of terms related to membrane targeting, redox homeostasis, and Fe-S cluster\u2013dependent maturation supports a broader theme of protein homeostasis and maturation under stress. A few terms (DNA replication, Hedgehog pathway regulation) are less connected, but the core signals point to stress-related translation and protein quality control.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0035719","count":2}]},{"hash":"919839020026479718","title":"Ketone, lipid, and amino acid metabolism","description":"The set centers on various metabolic processes\u2014ketone body catabolism and biosynthesis, cholesterol metabolism, and catabolism of amino acids and aromatics\u2014plus several development-related GO terms (adipose tissue, brain, nephron development) that may reflect tissue-specific expression. A single apoptosis-related term also appears, but the dominant signal is energy and lipid-associated metabolism across tissues, hence the chosen label.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060612","count":3},{"id":"GO:0006550","count":3},{"id":"GO:0019619","count":3},{"id":"GO:0046952","count":3},{"id":"GO:1901029","count":3}]},{"hash":"141484737162900835","title":"Purine nucleotide metabolism","description":"This cluster is dominated by GO terms for AMP salvage, ADP and CDP biosynthesis, and purine ribonucleotide interconversion, plus ITP metabolism, pointing to a shared role in nucleotide metabolism and synthesis. Occasional transcription and development terms appear less central to the core function, so the main signal remains nucleotide metabolism.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":3},{"id":"GO:0044209","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0046940","count":2},{"id":"GO:0007420","count":2}]},{"hash":"1746897347563372228","title":"Unknown","description":"The terms include a partial emphasis on DNA damage response and transcription (DNA-templated transcription, cellular response to ionizing radiation, telomere capping), but there are several unrelated terms (visual perception, trachea formation, bone mineralization, Golgi transport, Fc signaling), making a single cohesive function hard to assign.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0007601","count":3},{"id":"GO:1990802","count":3},{"id":"GO:1904355","count":3}]},{"hash":"471081295030094559","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0032147","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0034349","count":1},{"id":"GO:0002534","count":1}]},{"hash":"290480384865301131","title":"Platelet Degranulation and Angiogenesis Signaling","description":"This cluster prominently features GO terms for platelet degranulation and angiogenesis, with additional ties to extracellular matrix organization and signaling pathways (Rho, calcium, calcineurin-NFAT, Fc-epsilon receptor). The convergence on platelet/immune activation, ECM remodeling, and vascular growth suggests a cohesive role in platelet-driven signaling during vascular remodeling. The presence of axonogenesis is less central but can overlap with angiogenic and nerve-vascular interactions, supporting a broad vascular signaling theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002576","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0030198","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006470","count":2}]},{"hash":"1050100343743865028","title":"Keratinocyte differentiation and innate immunity","description":"The top GO terms point to skin-related biology (keratinocyte differentiation, vitamin D response) together with innate immune signaling and stress responses (response to toxic substances, apoptosis, ubiquitination), suggesting a cluster centered on epidermal differentiation coupled with immune regulation. Some terms (visual perception, telomere capping) are less directly related, but the dominant pattern supports a keratinocyte-immune theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0035372","count":2}]},{"hash":"1615065403920950096","title":"Ubiquitin-proteasome-mediated degradation","description":"These proteins show a strong signal for protein turnover and quality control via ubiquitin pathways: K48-linked ubiquitination, ISG15-protein conjugation, cytoplasmic quality control by the ubiquitin-proteasome system, and APC-dependent proteolysis. Some terms related to meiosis and peroxisome import appear as less central or context-specific, but the dominant theme is ubiquitin-proteasome\u2013driven protein degradation. ","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0010845","count":5},{"id":"GO:0051965","count":3},{"id":"GO:0016562","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0032020","count":3}]},{"hash":"1792602280469567521","title":"Unknown","description":"The cluster contains a highly diverse set of GO terms (toxic substance response, visual perception, DNA damage processing, telomere capping, ionizing radiation response, trachea formation, Golgi-to-plasma membrane transport regulation, Fc receptor signaling, bone mineralization, and protein trans-autophosphorylation) with no clear shared function, and there are no edges or coherent grouping to imply a common biological process. Confidence: None","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":1},{"id":"GO:0007601","count":1},{"id":"GO:1990802","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071479","count":1}]},{"hash":"1773978410713312586","title":"Neuronal mitochondrial quality control and ROS regulation","description":"GO terms point to mitochondrial processes (membrane potential regulation, mitophagy), redox/ROS signaling, and neuron-specific survival pathways, with dopamine uptake indicating a neural context. This coherence supports labeling the cluster as neuronal mitochondrial quality control and ROS regulation.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":2},{"id":"GO:1903073","count":1},{"id":"GO:0010273","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0051583","count":1}]},{"hash":"2240846068402903250","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000494","count":1},{"id":"GO:0010087","count":1},{"id":"GO:0032211","count":1},{"id":"GO:0000390","count":1},{"id":"GO:0035196","count":1}]},{"hash":"1352789668854392694","title":"Ubiquitin-regulated signaling and adhesion","description":"The cluster prominently features GO terms for ubiquitin-related processes, including positive regulation of K63-linked ubiquitination and ubiquitin-dependent protein catabolic pathways via multivesicular body sorting. This points to post-translational control of signaling and protein turnover. Supporting terms involve signaling regulation (interferon-beta production, prolactin signaling) and cell adhesion structures (slit diaphragm assembly, homotypic cell-cell adhesion), suggesting a broader theme of regulating cell signaling and interactions through ubiquitin-mediated trafficking and degradation.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035549","count":1},{"id":"GO:1902523","count":1},{"id":"GO:0010633","count":1},{"id":"GO:0043162","count":1},{"id":"GO:0060020","count":1}]},{"hash":"1829615817034600919","title":"Proteasome-driven degradation and stress signaling","description":"Top GO terms indicate a core role in proteasome function (proteasome core complex assembly; ubiquitin-independent proteolysis) and in signaling pathways that depend on proteasomal processing (non-canonical NF-\u03baB signaling; APC/C-dependent catabolic process). Additional terms about stress responses to salt, cadmium, and zinc, along with inflammatory regulation, suggest the cluster coordinates protein turnover with environmental and inflammatory signals. Together, these points imply a proteasome-centric module coupling degradation with stress and cell-cycle\u2013related signaling.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0038061","count":4},{"id":"GO:0080129","count":3},{"id":"GO:0010499","count":3},{"id":"GO:0051437","count":3},{"id":"GO:0009651","count":3}]},{"hash":"45038346894750375","title":"Mitotic spindle assembly and chromosome segregation","description":"The top GO terms cluster around mitosis (spindle assembly, sister chromatid segregation/cohesion, APC/C-dependent catabolic process and related ubiquitination), indicating proteins function together in mitotic progression and chromosome segregation. A few items (lens differentiation, TORC1 signaling, viral mRNA export) appear as minor outliers but do not override the dominant mitotic theme.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:1902426","count":1},{"id":"GO:0070306","count":1},{"id":"GO:1904263","count":1},{"id":"GO:0070979","count":1}]},{"hash":"814889078526644668","title":"Inflammation and wound repair","description":"The proteins are enriched for immune and tissue remodeling processes (neutrophil chemotaxis, apoptotic cell clearance, wound healing, epithelial integrity), with supporting signs of platelet involvement. While some terms are tangential (lipid transport regulation, axonal aspects), the dominant signal points to inflammatory response paired with tissue repair/remodeling, rather than a single enzymatic pathway.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0032369","count":3},{"id":"GO:0043277","count":3},{"id":"GO:0030593","count":3},{"id":"GO:0035160","count":3},{"id":"GO:0035313","count":3}]},{"hash":"1043478061160899464","title":"TLR2-driven innate immunity and chemokine production","description":"This cluster centers on innate immune signaling, with terms such as toll-like receptor 2 signaling, defense response to Gram-positive bacteria, and regulation of chemokines (IL-8, chemokine production). Together these suggest a theme of inflammatory and immune regulatory functions. Some terms appear less related (synapse assembly, brassinosteroid detection), likely incidental GO annotations, but the strongest link is TLR2-mediated immune response and chemokine regulation.","confidence":"Medium","size":5,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904027","count":1},{"id":"GO:0045416","count":1},{"id":"GO:0051965","count":1},{"id":"GO:0090141","count":1},{"id":"GO:0009729","count":1}]},{"hash":"221661502999292961","title":"Terpenoid/isoprenoid biosynthesis and cholesterol formation","description":"The enriched terms cluster around production of prenyl diphosphates (geranyl, farnesyl, geranylgeranyl) and downstream terpenoid products (monoterpenes, quinones) as well as cholesterol biosynthesis, indicating a coherent isoprenoid/terpenoid biosynthesis theme with related sterol pathways. Other terms like protein transport/heterotetramerization are present but less central. This supports labeling the cluster asTerpenoid/isoprenoid biosynthesis and cholesterol formation.","confidence":"High","size":5,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0033386","count":2},{"id":"GO:0045337","count":2},{"id":"GO:0051290","count":2}]},{"hash":"1793456474215816484","title":"Unknown","description":"The GO terms are highly diverse, with endocytosis and actin cortical patch assembly suggesting membrane trafficking, but other terms refer to bacterial peptidoglycan turnover, various metabolic processes, transcription, and biosynthesis. There isn't a single coherent function uniting all four proteins, indicating no clear cluster theme. ","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000147","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0009254","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0006751","count":1}]},{"hash":"1856166450613018839","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070681","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0009062","count":1},{"id":"GO:0019876","count":1},{"id":"GO:0032543","count":1}]},{"hash":"597261894730851618","title":"Unknown","description":"The top GO terms cover a wide range of biological areas (fungal pseudohyphal growth, neuronal signaling and retinal development, epithelial tight junctions, immune cell apoptosis, vesicle trafficking, lipid biosynthesis, and glial scaffolding). There isn\u2019t a clear unifying function or pathway linking these terms, so a single cohesive label cannot be confidently assigned.","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":4},{"id":"GO:0007215","count":3},{"id":"GO:0042711","count":3},{"id":"GO:0070830","count":3},{"id":"GO:0009785","count":3}]},{"hash":"100140831427518204","title":"Unknown","description":"Top GO terms are highly diverse, spanning transcriptional regulation, RNA modification (rRNA/tRNA), vitamin E and antibiotic biosynthesis, metal/stress response, nodulation, and cellular senescence. With no shared pathway or functional theme and no edges linking the proteins, there isn\u2019t a coherent label to assign beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":1},{"id":"GO:0010189","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0046690","count":1}]},{"hash":"1931713343834655132","title":"Unknown","description":"The GO terms cover immune signaling (B cell cytokine production, T cell\u2013mediated tumor responses), redox stress (ROS biosynthetic regulation), telomere maintenance, nuclear pore and Cajal body organization, and general protein stabilization. These do not coalesce into a single coherent function for the four proteins, suggesting the cluster spans multiple unrelated roles rather than a specific pathway.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903427","count":2},{"id":"GO:0002368","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0046931","count":2},{"id":"GO:0050821","count":2}]},{"hash":"814753643465896485","title":"Neural signaling and exocytosis regulation","description":"The top GO terms point to neural communication and vesicle release, including positive regulation of calcium ion-dependent exocytosis, excitatory postsynaptic potential, and substantia nigra development, as well as ephrin receptor signaling. While there are immune-related signaling terms (T cell receptor signaling, mast cell degranulation) and broader pathways (JNK cascade), the strongest cohesive theme is signaling linked to neuronal exocytosis and synaptic activity, giving a neural-signaling flavor to the cluster. Confidence: Medium.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046330","count":3},{"id":"GO:0006919","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0016237","count":2},{"id":"GO:0048013","count":2}]},{"hash":"1377986550165912426","title":"Organelle dynamics and trafficking","description":"The GO terms indicate mitochondrial fission and distribution, Golgi retention, macroautophagy, and endocytic recycling, all pointing to intracellular organelle dynamics and turnover.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0090149","count":2},{"id":"GO:0048312","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0000002","count":2}]},{"hash":"1765770866432163617","title":"Organ development","description":"The GO terms cluster around developmental processes in different organs (plant root development; metanephros and renal development; brain region formation such as zona limitans intrathalamica), suggesting a shared theme of organogenesis. Some terms on cytoskeletal assembly, proteasome localization, and cell cycle regulation may reflect concurrent cellular remodeling during development, but the dominant signal is developmental patterning and organ formation rather than a single pathway. Therefore, labeling as Organ development captures the overarching function of the group.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":1},{"id":"GO:0003338","count":1},{"id":"GO:0086019","count":1},{"id":"GO:0045110","count":1},{"id":"GO:0031144","count":1}]},{"hash":"1301820834836646322","title":"Unknown","description":"The GO terms span very diverse biological themes, including visual perception, response to toxins and radiation, telomere regulation, bone mineralization, Golgi transport, Fc signaling, and protein phosphorylation, with no clear shared function tying all proteins together. This prevents a cohesive, specific label; Unknown best reflects the lack of a unifying theme in this cluster.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":4},{"id":"GO:0007601","count":4},{"id":"GO:1990802","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0071479","count":4}]},{"hash":"226035047257180903","title":"Unknown","description":"The GO terms span cold response, nitric oxide signaling, sperm capacitation, apoptosis, cerebral cortex development, visual perception, and telomere regulation, showing no single cohesive function across the four proteins. The diverse, nonoverlapping themes indicate a lack of a clear shared biological role for this cluster, so Unknown is the appropriate label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":2},{"id":"GO:0071732","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0006915","count":2}]},{"hash":"520047740344997980","title":"Nucleolar ribosome biogenesis","description":"The GO terms cluster around ribosome production and nucleolar RNA transcription, including ribosome biogenesis and small subunit biogenesis, Pol I\u2013driven rRNA transcription and Pol III\u2013driven tRNA transcription, plus nucleologenesis and RNA-templated transcription. This points to a cohesive function in ribosome assembly within the nucleolus, with transcriptional activity supporting rRNA/tRNA production as a core aspect.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0042274","count":2},{"id":"GO:0006366","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0031048","count":1}]},{"hash":"502210499849273399","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes\u2014cell cycle regulation, protein lipidation and other post-translational modifications, autophagy-related pathways, tRNA modification, vesicle targeting, and even thiamine biosynthesis. Because there is no single cohesive function that ties these terms together, the cluster likely reflects heterogeneous or unrelated roles, so it is best labeled Unknown with no confidence in a unifying theme.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051726","count":2},{"id":"GO:0006501","count":2},{"id":"GO:0007113","count":2},{"id":"GO:0018192","count":2},{"id":"GO:0000422","count":2}]},{"hash":"325440972164939194","title":"Immune signaling and nuclear transport","description":"Top GO terms include B cell cytokine production and positive regulation of T cell\u2013mediated immune response to tumor cells, indicating immune signaling. In addition, terms for pore complex assembly and Cajal body protein localization point to nuclear transport/RNA processing, with telomere maintenance and stress-related terms suggesting broader nuclear roles. Taken together, these proteins likely connect immune signaling with nuclear transport/organization rather than a single narrow pathway, hence the label Immune signaling and nuclear transport.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903427","count":4},{"id":"GO:0002368","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0046931","count":4},{"id":"GO:0050821","count":4}]},{"hash":"930914599698171234","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0034349","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0070306","count":1}]},{"hash":"457382480865234439","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904355","count":1},{"id":"GO:0006268","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0070417","count":1},{"id":"GO:0000480","count":1}]},{"hash":"154760036103543704","title":"Epigenetic Regulation of Muscle Development","description":"The GO terms cluster around chromatin-level regulation (histone deacetylation, nucleosome positioning, gene silencing, and transcription) and also include muscle-specific processes (regulation of skeletal muscle fiber development, response to denervation in muscle adaptation). This combination suggests a theme of epigenetic control of gene expression that modulates muscle development and adaptation, hence a cohesive label focusing on epigenetic regulation in muscle. ","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061186","count":2},{"id":"GO:0014894","count":2},{"id":"GO:1901300","count":2},{"id":"GO:0010978","count":2},{"id":"GO:0070932","count":2}]},{"hash":"1941826124497307907","title":"Regulation of actin cytoskeleton and cell migration","description":"This cluster is tied to cytoskeleton dynamics and movement regulation, exemplified by GO terms for actin cytoskeleton reorganization, Rho signaling, semaphorin-plexin signaling, axonogenesis, and cellular response to mechanical stimulus, plus biased representation of migration-related processes such as trophoblast migration. A couple of terms related to mRNA surveillance (nonsense-mediated decay, exon-exon junction complex disassembly) appear as outliers, suggesting some proteins may have multiple roles.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":1},{"id":"GO:1903259","count":1},{"id":"GO:0071526","count":1},{"id":"GO:1901164","count":1},{"id":"GO:0035023","count":1}]},{"hash":"192661311783128230","title":"Cdc42-Driven Polarity and Endocytosis","description":"The GO terms consistently highlight establishment/maintenance of cell polarity and endocytosis, with Cdc42 signaling and actin remodeling (including formin-mediated actin assembly) guiding polarized vesicle trafficking and membrane organization. This theme is reinforced by references to endosome-to-postsynaptic transport and related cytoskeletal dynamics (including melanosome assembly and neural morphogenesis), suggesting a cohesive cluster of polarity- and trafficking-related proteins.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0098887","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0048532","count":1}]},{"hash":"1027445812554587466","title":"Signaling and transcription regulation","description":"The GO terms show a focus on regulatory roles across signaling pathways (e.g., insulin receptor, Wnt) and transcriptional control (positive/negative regulation of transcription, CDK activity regulation), plus related developmental and stress responses. This suggests the proteins act broadly as regulators rather than a single, cohesive pathway, so a broad label emphasizing regulatory function is appropriate.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0010673","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0060749","count":1}]},{"hash":"1100390138945686012","title":"Triglyceride lipolysis and phospholipid catabolism","description":"The cluster\u2019s top GO terms center on breakdown and remodeling of lipids, especially triglycerides and major phospholipids (phosphatidylcholine and phosphatidylethanolamine), plus acyl-chain remodeling and enrichment for triglyceride mobilization and catabolic regulation. This points to a lipid metabolism module involved in lipolysis and phospholipid turnover, with a regulatory hint via negative regulation of PKA activity. Other terms (ATP synthesis, cell budding, synapse assembly) may reflect broader cellular energy or context but do not override the lipid-centric theme.","confidence":"High","size":4,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006642","count":2},{"id":"GO:2000480","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0046338","count":2}]},{"hash":"101608074937549539","title":"Unknown","description":"These terms cover liver homeostasis and regeneration, glucocorticoid and toxin responses, brain development, and histone methylation, with no single coherent function tying all four proteins together, so there isn't a clear cluster theme to name more specifically.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990654","count":1},{"id":"GO:0071549","count":1},{"id":"GO:0080182","count":1},{"id":"GO:1904772","count":1},{"id":"GO:0034771","count":1}]},{"hash":"1025723677952805373","title":"Unknown","description":"The top GO terms are highly diverse, ranging from telomere capping regulation to various differentiation processes (oligodendrocyte, venous endothelium, myeloid), together with signaling and regulatory processes (CDK activity inhibition, PARylation, ephrin signaling, calcium release, IL-12 production, and pain perception). This lack of a single, cohesive biological theme or shared pathway, along with no network connectivity among the proteins, suggests there is no common function defining this cluster. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904355","count":1},{"id":"GO:0048709","count":1},{"id":"GO:0045736","count":1},{"id":"GO:0070212","count":1},{"id":"GO:0060843","count":1}]},{"hash":"2142571691034157966","title":"Sugar catabolic pathways","description":"The top GO terms are dominated by various carbohydrate catabolic processes (e.g., D-glucuronate, L-fucose, rhamnose, L-arabinose, xylulose) and carbohydrate phosphorylation, indicating the proteins function in sugar breakdown and utilization; a quorum-sensing term and an immune response term are present but far less representative.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009372","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0019640","count":1},{"id":"GO:0042355","count":1},{"id":"GO:0019521","count":1}]},{"hash":"248406398597407567","title":"Actin Cytoskeleton Assembly and Sarcomere Organization","description":"This cluster centers on actin cytoskeleton dynamics and muscle architecture, with multiple GO terms for actin nucleation (Arp2/3), filament bundle assembly, sarcomere organization, and skeletal muscle fiber development. Some terms touch on broader cell polarity or neuronal development, but the strongest signal is actin-based organization and sarcomere formation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":3},{"id":"GO:0071963","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0048741","count":3}]},{"hash":"2209278445779633483","title":"Unknown","description":"The terms span transport, hypoxia and stimulus responses, and multiple organ developmental processes (lung/kidney), showing no single unifying function for the cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":1},{"id":"GO:0009454","count":1},{"id":"GO:0060428","count":1},{"id":"GO:0071910","count":1},{"id":"GO:0001964","count":1}]},{"hash":"1258678127951222852","title":"Immune signaling and nuclear maintenance","description":"The top GO terms include adaptive immune activity (B cell cytokine production; T cell mediated immune response to tumor cell) alongside nuclear and genome maintenance processes (telomere maintenance via telomerase; Cajal body localization; pore complex assembly; cell cycle; protein stabilization). This suggests a cluster of proteins involved in immune activation that are also linked to nuclear structure and genome stability, possibly reflecting proliferating immune cells requiring telomere maintenance and nuclear transport. Because the connection spans multiple broad functions rather than a single cohesive role, the label conveys the general theme without over-commitment.","confidence":"Low","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903427","count":3},{"id":"GO:0002368","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0046931","count":3},{"id":"GO:0050821","count":3}]},{"hash":"286038923825785109","title":"Embryonic Organogenesis","description":"These proteins appear linked to diverse developmental pathways across several organ systems: heart development (cardiac neural crest, endocardial cushion EMT), nervous system (oligodendrocyte development, oculomotor nerve development), pancreas (pancreatic PP cell fate), and kidney (nephron tubule morphogenesis, renal interstitial fibroblast development). The shared theme is embryonic organogenesis rather than a single tissue-specific function, so Embryonic Organogenesis is an appropriate, concise label.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061309","count":2},{"id":"GO:0014003","count":2},{"id":"GO:0003199","count":2},{"id":"GO:0070368","count":2},{"id":"GO:0072750","count":2}]},{"hash":"2296356692837740632","title":"Unknown","description":"The listed GO terms cover very diverse and largely unrelated processes (toxic response, vision, telomere regulation, radiation response, trachea formation, Golgi transport, Fc signaling, bone mineralization, protein autophosphorylation). The mix, plus an obsolete term and no shared pathway, suggests no coherent functional theme linking these proteins. Therefore, Unknown with no confidence.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0007601","count":3},{"id":"GO:1990802","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071479","count":3}]},{"hash":"253661551713297643","title":"Neuronal Endosomal Trafficking","description":"The top terms highlight endosome targeting and vesicle regulation (protein localization to endosome, regulation of synaptic vesicle exocytosis, multivesicular body size), plus phosphatidylinositol signaling and brain development. This points to a functional cluster of proteins involved in endosomal/vesicular trafficking with roles in neural signaling and development, despite some terms being less directly related.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010796","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0007420","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0036010","count":2}]},{"hash":"2169967524530181702","title":"ER-centric proteostasis and post-translational modifications","description":"This cluster is driven by GO terms pointing to ER-related protein processing and quality control (e.g., tail-anchored membrane protein insertion into the ER membrane, ER stress\u2013related apoptotic signaling, deglycosylation) and to protein turnover/modification processes (negative regulation of proteasomal degradation, sumoylation and PML body organization). Together these suggest a theme of maintaining protein homeostasis via ER-associated pathways and PTMs, even though a few terms (nucleotide-excision repair, chromatin-related processes, GnRH neuron development) are more peripheral. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":3},{"id":"GO:0006517","count":3},{"id":"GO:0030578","count":3},{"id":"GO:0071816","count":3},{"id":"GO:0021888","count":3}]},{"hash":"1167640847000703602","title":"Embryogenesis and Cell Proliferation","description":"This cluster is dominated by GO terms linked to embryonic development (in utero embryonic development, embryonic cleavage) and cell proliferation (cell population proliferation), pointing to a developmental program governing embryo formation and growth. Additional terms related to DNA damage response and cytoskeletal functions appear incidental and do not override the central developmental theme. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009640","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0044346","count":1},{"id":"GO:0070979","count":1}]},{"hash":"2191808707711080928","title":"Neural development and synapse formation","description":"These terms cluster around neural development, especially neurogenesis, forebrain/corpus callosum development, neuron migration, and synapse assembly, with additional notes on astrocyte differentiation and potassium channel clustering that relate to neuronal connectivity. While a couple of terms (endosome transport and T cell regulation) are less clearly tied, the dominant neural development theme justifies this label.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0022008","count":3},{"id":"GO:0006915","count":3},{"id":"GO:1902955","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0021885","count":2}]},{"hash":"2090391239384432287","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0034349","count":1},{"id":"GO:0002534","count":1}]},{"hash":"1232993521266227227","title":"Nuclear organization and chromatin regulation","description":"The terms cluster around nuclear processes: import into the nucleus, chromatin maintenance/silencing at telomeres, chromatin remodeling/chromosome puffing, and Pol II tethering at the nuclear periphery, with a note of spindle organization; together they point to nuclear architecture and chromatin regulation, with a few outliers in metabolism that are less represented.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035392","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0035080","count":2},{"id":"GO:0036228","count":2},{"id":"GO:0000973","count":2}]},{"hash":"2000948636134527972","title":"T cell receptor signaling and activation","description":"This cluster is dominated by GO terms tied to T cell receptor signaling, activated T cell proliferation, and Fc receptor\u2013mediated signaling, indicating a theme of T cell activation and immune signaling; additional terms on ephrin signaling and actin regulation provide supportive signaling contexts.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042997","count":2},{"id":"GO:0002774","count":2},{"id":"GO:0036120","count":2},{"id":"GO:0050798","count":2},{"id":"GO:0048013","count":2}]},{"hash":"199339893887793693","title":"Stress granule disassembly and translation regulation","description":"The top GO terms point to RNA stress response and translational control (stress granule disassembly and negative regulation of translation), suggesting a core theme around stress granule dynamics. The remaining terms are diverse and seem not to cohere into a single function, likely reflecting annotation noise or multifunctional proteins.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":2},{"id":"GO:0031221","count":1},{"id":"GO:0016266","count":1},{"id":"GO:0006683","count":1},{"id":"GO:0070278","count":1}]},{"hash":"690457809862736971","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":2},{"id":"GO:0034349","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0070306","count":1},{"id":"GO:0031175","count":1}]},{"hash":"2014623312332810436","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002755","count":1},{"id":"GO:0045410","count":1},{"id":"GO:0070935","count":1},{"id":"GO:0043123","count":1},{"id":"GO:0034145","count":1}]},{"hash":"1402510195046204830","title":"RNA Methylation and Transcription Regulation","description":"The top GO terms repeatedly highlight methylation events (RNA guanine-N7-methylation, rRNA N7 methylation, and N-terminal serine dimethylation) along with a clear link to transcriptional control (negative regulation of transcription by RNA Pol II). Other terms appear incidental, but the strongest shared theme is RNA modification coupled with transcription regulation.  ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019505","count":2},{"id":"GO:0070555","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0010189","count":2}]},{"hash":"1189469084026328837","title":"Unknown","description":"The GO terms are highly diverse, including stress responses (ethanol, cold, aluminum), various metabolic processes (folate metabolism, D-serine and dopamine catabolism), RNA modification, and endocrine regulation, with no clear shared function across the three proteins. This lack of a cohesive theme suggests an Unknown cluster with None confidence.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":1},{"id":"GO:0002097","count":1},{"id":"GO:0036088","count":1},{"id":"GO:0009409","count":1},{"id":"GO:0042420","count":1}]}]