[{"hash":"2127902417517116405","title":"Pexophagy and phagophore assembly","description":"This cluster is dominated by autophagy-related terms: peroxisome autophagy, cytoplasm-to-vacuole targeting, and localization to the phagophore assembly site, pointing to a core theme of autophagic vesicle formation and peroxisome turnover. Some terms related to neural development and adhesion appear, but they are less central to the primary autophagy-focused signal. Thus, the label emphasizes the strongest shared function among the proteins.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030242","count":5},{"id":"GO:0032258","count":5},{"id":"GO:0034497","count":5},{"id":"GO:0034446","count":3},{"id":"GO:0097155","count":3}]},{"hash":"760835123021619696","title":"Neuronal signaling and sensory development","description":"The top GO terms cluster around neural signaling and sensory processing\u2014presynaptic assembly, sensory neuron axon guidance, and visual perception\u2014with additional signals for pheromone and UV-B responses, indicating a theme of neuronal communication and sensory pathway regulation. A few terms related to GTPase activity and mitotic cell cycle suggest some multifunctional proteins bridging signaling and cell cycle, but the dominant signal is neural signaling and sensory development. ","confidence":"Medium","size":29,"edges":86,"triangles":111,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":26},{"id":"GO:0019236","count":25},{"id":"GO:0000278","count":25},{"id":"GO:0007601","count":25},{"id":"GO:0010224","count":24}]},{"hash":"1568700496638778943","title":"Heterochromatin formation and DNA replication initiation","description":"The top GO terms point to heterochromatin formation (silent mating-type cassette, subtelomeric heterochromatin) and DNA replication processes (DNA strand elongation, replication initiation, replication initiation in mitosis). This suggests a cohesive role in chromatin state maintenance during replication and genome stability. Some terms may be incidental noise, but the dominant theme is chromatin silencing/heterochromatin and replication control.","confidence":"High","size":29,"edges":33,"triangles":14,"max_degree":10,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0030466","count":7},{"id":"GO:1902450","count":6},{"id":"GO:0006271","count":6},{"id":"GO:0071466","count":6},{"id":"GO:0042127","count":6}]},{"hash":"2283635541909740082","title":"Prokaryotic lipid and amino acid biosynthesis","description":"The cluster shows strong enrichment for lipid-related pathways (fatty acid biosynthesis, lipoteichoic acid biosynthesis, menaquinone biosynthesis) and several amino acid biosynthetic/catabolic processes, pointing to a bacterial metabolism-focused group involved in membrane/envelope components and amino acid production. Confidence: High","confidence":"","size":29,"edges":188,"triangles":481,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0019518","count":7},{"id":"GO:1902987","count":6},{"id":"GO:0009234","count":6}]},{"hash":"1570379336965919050","title":"Mitotic division and ER-Golgi vesicle trafficking","description":"The cluster is enriched for mitotic cell cycle and cell division terms, signaling a mitosis-focused module. It also shows strong COPII vesicle budding and Golgi-to-ER transport terms, indicating secretory pathway involvement. Together, these patterns point to proteins coordinating cell division with membrane trafficking.","confidence":"High","size":29,"edges":106,"triangles":208,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":14},{"id":"GO:0008283","count":14},{"id":"GO:0033144","count":14},{"id":"GO:0090114","count":14},{"id":"GO:0006890","count":14}]},{"hash":"155470576468303680","title":"Neuronal development and vesicle trafficking","description":"This cluster is dominated by neural development terms (nervous system development, brain development, dendritic spine development) and trafficking processes (Golgi-to-ER transport, endosome transport, protein localization), suggesting a cohesive theme of neuronal maturation coordinated with intracellular transport critical for synapse formation and function.","confidence":"High","size":29,"edges":282,"triangles":1449,"max_degree":26,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0060999","count":8},{"id":"GO:0007399","count":7},{"id":"GO:0006890","count":7},{"id":"GO:0034629","count":7}]},{"hash":"728070955907834376","title":"APC/C-Dependent Ubiquitin Proteolysis","description":"This cluster is dominated by GO terms for anaphase-promoting complex\u2013dependent catabolic processes and K11-linked ubiquitination, plus ubiquitin-dependent protein degradation pathways, indicating a core role in APC/C-driven proteolysis. Additional terms for innate immune and antiviral responses may reflect stress-related regulation but the strongest signal is ubiquitin-mediated, APC/C-controlled protein turnover during cell cycle progression.","confidence":"High","size":29,"edges":27,"triangles":1,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0070979","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2}]},{"hash":"1511432048143075717","title":"Ubiquitin-Dependent Protein Degradation","description":"Dominant theme is ubiquitin-mediated protein turnover: SCF-dependent and general ubiquitination leading to proteasomal degradation (polyubiquitination, K6-linked ubiquitination). Some terms touch on stress responses (cadmium) and growth regulation, but the core signal is ubiquitin-dependent protein catabolism.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":10},{"id":"GO:0042787","count":9},{"id":"GO:0000209","count":7},{"id":"GO:0071276","count":6},{"id":"GO:0008285","count":5}]},{"hash":"1372643911436837504","title":"Developmental growth and transcriptional regulation","description":"These proteins show strong representation of developmental processes (neural tube closure, forebrain development, skeletal system development, multicellular organism development) alongside mitotic cell cycle and DNA-templated transcription, indicating coordinated growth and gene expression programs. The presence of stress-related terms (ER stress\u2013induced apoptotic signaling, cellular response to cadmium) suggests accompanying stress-responsive regulation that can occur during development or proliferation. Overall, the cluster seems to reflect developmental regulation via transcriptional control and cell-cycle activity, with ancillary stress responses.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0001843","count":6},{"id":"GO:0070059","count":6},{"id":"GO:0007275","count":6}]},{"hash":"2225620824392539278","title":"Cell growth signaling and ribosome biogenesis","description":"This cluster appears to center on growth and division signaling, with components that regulate GTPase activity and serine/threonine kinase activity, and promote mitosis and cell proliferation. It also includes processes tied to ribosome biogenesis, including maturation of rRNA species, which is essential for increased protein synthesis during growth. Some hypoxia response features align with stress adaptation seen in proliferative states. Thus, the label \u201cCell growth signaling and ribosome biogenesis\u201d captures the main theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0031954","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0051028","count":5}]},{"hash":"103753115254330324","title":"ER protein folding and COPI trafficking","description":"The cluster is driven by ER-centric functions: protein folding in the ER, retention of proteins in the ER lumen, COPI-coated vesicle budding/coating, and regulation of ER exit, all pointing to ER quality control and ER-to-Golgi transport. Additional terms like cholesterol homeostasis and oxidative detoxification suggest broader stress-related roles but do not override the core ER trafficking theme.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":2},{"id":"GO:0042632","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0034975","count":2}]},{"hash":"1683459195994784118","title":"Ubiquitin-Proteasome Pathway","description":"This cluster centers on ubiquitin-dependent protein catabolism, including SCF-dependent proteasomal degradation and ERAD, with widespread protein ubiquitination. The presence of innate immune and antiviral defense terms suggests links to antiviral regulation via ubiquitination as well.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0042787","count":8},{"id":"GO:0045087","count":8},{"id":"GO:0051607","count":8},{"id":"GO:0030433","count":8}]},{"hash":"17588599045035163","title":"Embryonic Neurodevelopment with Stress Responses","description":"This cluster centers on embryogenesis and neural development, as shown by terms like in utero embryonic development and positive regulation of neuron projection development, along with apoptosis. It also shows stress/immune and chemical response signals (response to lipopolysaccharide and response to xenobiotic stimulus), suggesting a group of proteins involved in developmental processes coupled with environmental stress responses. The low edge connectivity indicates a loosely connected set, but the core theme remains developmental neuroscience with stress signaling.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0032496","count":4},{"id":"GO:2000648","count":4},{"id":"GO:0042135","count":4},{"id":"GO:0043046","count":4}]},{"hash":"1136749212131085002","title":"Steroid and hormone biosynthesis","description":"The cluster centers on biosynthetic and metabolic processes for steroidal hormones. Brassinosteroid biosynthesis and homeostasis point to plant hormone production, while testosterone, prostaglandin, and progesterone biosynthetic/metabolic terms indicate animal hormone pathways; together with xenobiotic and glutathione metabolism, the proteins likely participate in general lipid/hormone biosynthesis and related redox/detox steps. ","confidence":"Medium","size":29,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0016132","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0001516","count":2}]},{"hash":"1688299397524094298","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0072520","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0000209","count":2}]},{"hash":"1083984035372183791","title":"Cell-cycle and telomere maintenance","description":"Top GO terms center on cell cycle and chromosome/telomere-related processes, suggesting a nuclear/chromosome maintenance theme. Some terms (e.g., chloroplast import and differentiation) appear ancillary or noisy, but the core enrichment points to cell-cycle regulation and telomere-associated chromosomal dynamics.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0045038","count":3},{"id":"GO:0070198","count":3},{"id":"GO:0050966","count":3}]},{"hash":"1471267145009255821","title":"Cilium/axoneme assembly and motility","description":"This cluster is dominated by GO terms related to cilium and flagellum function\u2014axoneme assembly, cilium movement, flagellated sperm motility, and microtubule modification (polyglycylation/polyglutamylation)\u2014pointing to a cohesive theme of ciliary/flagellar structure and movement, with a possible ancillary note on signaling pathways like Wnt that can intersect ciliogenesis.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0003351","count":1},{"id":"GO:0030516","count":1},{"id":"GO:0018094","count":1},{"id":"GO:0007288","count":1}]},{"hash":"528209851435907403","title":"Developmental morphogenesis and junctional regulation","description":"This cluster centers on processes of tissue morphogenesis and cell\u2013cell junction remodeling, including post-embryonic body morphogenesis, gastrulation-related cytoskeleton polarity, bicellular tight junction assembly, and negative regulation of cadherin-mediated adhesion, as well as photoreceptor development and GTPase signaling that drive cell shape and signaling during development. Copper homeostasis and cell division appear ancillary to this core theme. ","confidence":"Medium","size":28,"edges":63,"triangles":47,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006878","count":3},{"id":"GO:0070830","count":2},{"id":"GO:0042461","count":2}]},{"hash":"1172767951145835913","title":"RNA processing and splicing machinery","description":"The top GO terms cluster around RNA metabolism and processing: transcription termination of RNA Pol II, rRNA maturation, tRNA processing, mRNA splicing via the spliceosome, spliceosomal snRNP assembly, and nuclear import, with a related signal to P-body assembly. This points to a cohesive module centered on RNA processing, splicing, and RNA transport/metabolism; ABA response may reflect plant context but is not the primary theme.","confidence":"High","size":28,"edges":253,"triangles":1325,"max_degree":26,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006369","count":6},{"id":"GO:0070317","count":6},{"id":"GO:0030490","count":5},{"id":"GO:0008033","count":5},{"id":"GO:0045292","count":5}]},{"hash":"117933540633425102","title":"Kinetochore localization and mitotic progression","description":"The cluster is enriched for kinetochore localization, G1/S transition, DNA replication, and spindle assembly checkpoint signaling, indicating a shared function in mitosis and cell-cycle control.","confidence":"High","size":28,"edges":232,"triangles":1154,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":27},{"id":"GO:0060079","count":26},{"id":"GO:0051321","count":26},{"id":"GO:0014044","count":26},{"id":"GO:0000082","count":26}]},{"hash":"1678585855361103899","title":"Ribosome biogenesis and rRNA maturation","description":"The top GO terms cluster around maturation of SSU/LSU rRNA and ribosomal subunit biogenesis (SSU/5.8S/LSU rRNA maturation, ribosome biogenesis), indicating proteins involved in ribosome assembly and RNA processing. Additionally, there are RNA splicing-related terms (spliceosome-mediated splicing and its regulation) and ncRNA-mediated gene silencing, which fit RNA processing activities in the same nuclear/nucleolar context. While a few terms touch broader developmental processes, the dominant theme is ribosome biogenesis and rRNA maturation, with supporting RNA processing roles, justifying this label as representative of the cluster\u2019s function.","confidence":"High","size":28,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000462","count":8},{"id":"GO:0000466","count":8},{"id":"GO:0042273","count":8},{"id":"GO:0000463","count":8},{"id":"GO:0000398","count":8}]},{"hash":"1348812849943727591","title":"Plant photoreception and chlorophyll metabolism","description":"This cluster\u2019s top GO terms cluster around light detection and phototransduction (red/far-red light) and chlorophyll/tetrapyrrole-related processes (chlorophyll catabolic regulation, protein-tetrapyrrole linkage, detection of visible light). Together they suggest proteins involved in plant light sensing and chlorophyll metabolism/signaling, with secondary growth possibly tied to light responses. ","confidence":"High","size":28,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":2},{"id":"GO:0010271","count":2},{"id":"GO:0017006","count":2},{"id":"GO:0000160","count":2},{"id":"GO:0010201","count":2}]},{"hash":"747513984543220960","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":47,"triangles":17,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":4},{"id":"GO:0032092","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0002107","count":3}]},{"hash":"1995338077762433267","title":"Wnt signaling regulators in development","description":"The cluster is enriched for terms related to inhibiting canonical Wnt signaling, maintaining organ identity, controlling proliferation and migration, and promoting apoptosis, all of which point to developmental signaling and tissue growth regulation. Some peripheral terms (proton transport, DNA replication) appear but do not override the dominant developmental theme.","confidence":"Medium","size":28,"edges":72,"triangles":37,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090090","count":3},{"id":"GO:0048496","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0016477","count":3}]},{"hash":"1621938697329512053","title":"Peptide Hormone Processing","description":"The top GO terms are dominated by peptide/prohormone maturation and processing (insulin processing, enkephalin processing, peptide pheromone maturation), suggesting the proteins cluster around proteolytic processing and maturation of peptide hormones/neuropeptides. Some LDL receptor trafficking terms appear as minor signals, but the core theme is peptide processing.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030070","count":5},{"id":"GO:0030245","count":5},{"id":"GO:0034230","count":4},{"id":"GO:0032805","count":4},{"id":"GO:0032902","count":4}]},{"hash":"1573389312529906506","title":"Neuronal development and vesicle trafficking","description":"The cluster shows strong enrichment for brain development and synaptic vesicle exocytosis regulation, along with intracellular protein transport and endocytosis terms, all pointing to neuronal development and synaptic vesicle trafficking. Although there are some terms related to cell cycle and angiogenesis, the dominant signals are neuronal growth and vesicle trafficking processes, suggesting proteins in this cluster function together in neuronal development and synaptic vesicle regulation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":8},{"id":"GO:0010796","count":7},{"id":"GO:0031384","count":7},{"id":"GO:0006886","count":6},{"id":"GO:2000300","count":6}]},{"hash":"1300180775411062285","title":"Antibiotic Biosynthesis and Lipid/Steroid Metabolism","description":"The top GO terms indicate strong engagement in antibiotic biosynthesis and response, alongside a variety of lipid- and steroid-related biosynthetic processes (testosterone, glucocorticoids, fatty acid elongation, retinoic acid, phylloquinone, PHB, and 3-keto-sphinganine). This pattern points to a cluster of proteins involved in broad secondary metabolite and lipid/steroid biosynthesis rather than a single, narrow pathway.","confidence":"Medium","size":28,"edges":163,"triangles":516,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":18},{"id":"GO:0017000","count":18},{"id":"GO:0006666","count":17},{"id":"GO:0008207","count":17},{"id":"GO:0061370","count":17}]},{"hash":"248257352268473191","title":"Melanosome and Lysosome Vesicle Trafficking","description":"Reasoning: The top GO terms center on vesicle trafficking and fusion to lysosome-related organelles, including vesicle fusion with vacuole, phagosome-lysosome fusion, and vesicle tethering, plus eye pigment granule (melanosome) organization, indicating a cohesive theme of melanosome/lysosome trafficking rather than disparate processes.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902499","count":2},{"id":"GO:0030097","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0051469","count":1},{"id":"GO:0008057","count":1}]},{"hash":"1587546539584523923","title":"Unknown","description":"The top GO terms span vacuole fusion, cell proliferation, synaptic potentiation, osmotic stress response, plant cell wall biogenesis, viral processes, telomere protection, subtelomeric heterochromatin formation, and DNA repair regulation, which do not converge on a single clear function or pathway. This diversity suggests the cluster is functionally heterogeneous, making a concise, representative label difficult.","confidence":"","size":28,"edges":41,"triangles":16,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":3},{"id":"GO:0008284","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0006970","count":2},{"id":"GO:1901348","count":2}]},{"hash":"415456839290331497","title":"Cofactor and vitamin biosynthesis","description":"The cluster shows enrichment for biosynthetic processes across several essential cofactors and vitamins\u2014biotin, ubiquinone, cobalamin, and polyamines\u2014suggesting a shared functional theme around production of metabolic cofactors. While other terms like nodulation and angiogenesis appear, the strongest signal is biosynthesis-related, pointing to metabolic assembly lines. ","confidence":"Medium","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0009877","count":2},{"id":"GO:0009236","count":2}]},{"hash":"1980961368281776448","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045190","count":2},{"id":"GO:0051573","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0007406","count":2}]},{"hash":"1216986897719424856","title":"Erythrocyte and Megakaryocyte Differentiation Regulation","description":"The top GO terms are dominated by positive regulation of erythrocyte and megakaryocyte differentiation, including primitive erythrocyte differentiation, indicating the cluster centers on hematopoietic lineage specification. Other terms like response to lipopolysaccharide and xenobiotic stimulus may reflect broader stress or immune responsiveness, but the hematopoietic differentiation signals are strong and cohesive.","confidence":"High","size":28,"edges":32,"triangles":15,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045648","count":8},{"id":"GO:0045654","count":8},{"id":"GO:0010725","count":8},{"id":"GO:0032496","count":8},{"id":"GO:0009228","count":8}]},{"hash":"2021094668202273936","title":"DNA replication and ribosome biogenesis","description":"Many terms cluster around DNA replication and mitotic cell cycle, indicating a core role in cell proliferation. Additional terms on ribosome biogenesis and rRNA maturation suggest coordinated growth and protein synthesis during division. Some older, obsolete terms appear but do not alter the main theme of replication and ribosome production.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0016575","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1467954177773379544","title":"T Cell Receptor Signaling and ERK Cascade","description":"This cluster centers on T cell receptor signaling (GO:0050852) and ERK1/ERK2 cascades (GO:0070374, GO:0070371), with supporting hints from ephrin receptor signaling and beta selection, pointing to immune receptor\u2013driven ERK pathway activity. While a PDGF response appears, the dominant theme is T cell\u2013specific signaling and ERK pathway activation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036120","count":3},{"id":"GO:0007257","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0048013","count":3}]},{"hash":"1625436015059589638","title":"Ubiquitin-Proteasome System","description":"The top GO terms are dominated by ubiquitination and proteasome-related processes (protein ubiquitination, polyubiquitination, ERAD, and proteasome regulatory particle assembly), indicating a cluster centered on ubiquitin-dependent protein turnover. Some additional terms touch on peroxisomal import and cell division, likely reflecting broader roles of ubiquitination, but the core theme remains degradation via the ubiquitin-proteasome system.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0000083","count":6},{"id":"GO:0033280","count":6}]},{"hash":"775607094310362305","title":"Developmental growth and cell cycle proteins","description":"The cluster features several developmental terms (brain development, kidney development, skeletal system development) alongside cell division and mitotic cell cycle terms, and includes ER-to-Golgi vesicle transport and proteolysis, suggesting a cohesive group of proteins involved in development and proliferative processes with roles in intracellular trafficking and signaling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0010255","count":3},{"id":"GO:0007420","count":3}]},{"hash":"1481371767927178557","title":"Transmembrane Transporters for Nutrients and Xenobiotics","description":"The top GO terms are dominated by various transmembrane transport activities, including xenobiotic, nitrate, potassium ion, arabinose, galactose, sialic acid, and vitamin transport, plus a lipid metabolic process. This points to a cluster of membrane transporter proteins that mediate uptake and efflux of diverse substrates. Some unrelated terms (sebaceous gland differentiation, myelin maintenance) may reflect contextual annotations but do not override the transport-centric theme.","confidence":"High","size":28,"edges":26,"triangles":0,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3}]},{"hash":"166133894486165529","title":"Unknown","description":"The GO terms span muscle, neural, immune, renal, and viral-related processes with no single shared function or pathway uniting the proteins, suggesting a highly heterogeneous set rather than a cohesive cluster.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":3},{"id":"GO:0000742","count":2},{"id":"GO:0007269","count":2},{"id":"GO:0007412","count":2},{"id":"GO:0060292","count":2}]},{"hash":"1130885134787089929","title":"Unknown","description":"The top terms show a highly heterogeneous mix of processes (xenobiotic response, renal water transport, redox homeostasis, hemolysis in another organism, phosphatidylinositol dephosphorylation, base-excision repair, DNA catabolic processes, and cellular response to cAMP) with some obsolete annotations. There isn\u2019t a coherent, single functional theme tying the proteins together, so no intuitive, specific label can be assigned beyond Unknown.","confidence":"","size":28,"edges":21,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:2001153","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0044179","count":2},{"id":"GO:0046856","count":2}]},{"hash":"1768222747889337696","title":"Fungal cell wall remodeling and biofilm formation","description":"The cluster is dominated by fungal-type cell wall processes (disassembly, beta-glucan and mannan metabolism, ergosteryl glycoside catabolism) and biofilm formation on both inanimate and host substrates, with accompanying plant cell wall\u2013degrading activities (cellulose/xylan), pointing to coordinated fungal cell wall remodeling and biofilm lifestyle. An IL-6 regulation term may reflect host interaction but does not define the core theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0045493","count":3},{"id":"GO:0055114","count":2},{"id":"GO:1904541","count":2},{"id":"GO:0070879","count":2}]},{"hash":"992161866142953811","title":"Rac GTPase Signaling","description":"The top GO terms point to regulation and activation of GTPase activity, especially Rac signaling, indicating the proteins function in Rac-mediated signal transduction and cytoskeletal remodeling. The presence of tissue morphogenesis terms (midbrain, heart structures) suggests Rac pathways also participate in developmental morphogenesis, but the core shared function across the cluster is Rac GTPase signaling. Confidence: High","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:1904693","count":3},{"id":"GO:2000973","count":3},{"id":"GO:0007296","count":3},{"id":"GO:0003344","count":3}]},{"hash":"1227071054389013017","title":"Neural development and calcium-dependent synaptic signaling","description":"The top terms center on brain development and glutamatergic synaptic transmission, with a notable reference to ryanodine-sensitive calcium release and calcium signaling\u2014pointing to neural development and calcium-dependent synaptic function. Some terms are obsolete, but the core signals consistently invoke neural/synaptic biology.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:2001015","count":2},{"id":"GO:0000335","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006970","count":2}]},{"hash":"1574767232887897653","title":"N-terminal and peptidyl acetylation","description":"The top GO terms are dominated by various acetylation processes (N-terminal acetylation and multiple peptidyl acetylations, including lysine N6, serine, and glutamic acid). This points to a cohesive theme of protein acetylation and related post-translational modifications, with other terms (sporulation, transcription, angiogenesis) appearing as less-connected outliers. Confidence in this being the core function cluster is moderate due to some heterogeneity but a clear acetylation signal is present.","confidence":"Medium","size":27,"edges":16,"triangles":4,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030435","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006526","count":5},{"id":"GO:0017198","count":4},{"id":"GO:0018003","count":4}]},{"hash":"957063997681015757","title":"Mitosis and Ciliogenesis Regulators","description":"This cluster is dominated by GO terms for mitotic cell cycle, chromosome passenger complex localization to kinetochore, and cilium assembly, pointing to proteins involved in cell division and ciliogenesis. Other terms (pheromone/UV-B response, Hippo signaling, presynaptic assembly) are more peripheral but do not override the core mitotic/ciliary theme.","confidence":"High","size":27,"edges":312,"triangles":2152,"max_degree":26,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":26},{"id":"GO:0010224","count":26},{"id":"GO:0000278","count":26},{"id":"GO:1905608","count":26},{"id":"GO:1905490","count":26}]},{"hash":"56461232182309129","title":"Phosphorylation-driven signaling and cell cycle control","description":"This cluster is dominated by GO terms centered on protein phosphorylation and signaling (peptidyl-threonine phosphorylation, tyrosine kinase signaling, general phosphorylation-related processes) along with mitotic checkpoint signaling (spindle assembly checkpoint, intra-S DNA damage checkpoint) and actin cytoskeleton dynamics. While some terms touch on development or immune responses, the core theme appears to be phosphorylation-based signaling that regulates cell cycle progression and cytoskeletal organization. ","confidence":"Medium","size":27,"edges":333,"triangles":2532,"max_degree":26,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007037","count":27},{"id":"GO:1904531","count":27},{"id":"GO:0007094","count":27},{"id":"GO:1902002","count":27},{"id":"GO:0001806","count":27}]},{"hash":"513417469520318761","title":"Mitochondrial metabolism and membrane dynamics","description":"This cluster is dominated by mitochondrial-related processes: genome maintenance and membrane fission, regulation of mitochondrial membrane potential, and responses to metabolic cues such as amino acid starvation and insulin/glucose signaling. It also includes transport of cofactors and metabolites (heme, thiamine pyrophosphate, thiosulfate), pointing to integrated mitochondrial energy metabolism and nutrient sensing.","confidence":"Medium","size":27,"edges":29,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":17},{"id":"GO:0090149","count":17},{"id":"GO:0034198","count":16},{"id":"GO:0051881","count":16},{"id":"GO:0032869","count":16}]},{"hash":"1176339156015018973","title":"Neural development and vesicle exocytosis","description":"This cluster is enriched for brain development, cochlea morphogenesis, and regulation of synaptic vesicle exocytosis, with supporting hints from intracellular protein transport and Rap signaling. While some terms relate to general cell division, the strongest signals center on neural differentiation and synaptic vesicle trafficking, suggesting proteins involved in neural development and synaptic function. ","confidence":"Medium","size":27,"edges":5,"triangles":0,"max_degree":3,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":8},{"id":"GO:0010796","count":7},{"id":"GO:0031384","count":7},{"id":"GO:2000300","count":6},{"id":"GO:0006886","count":6}]},{"hash":"1746942555053232777","title":"Purine nucleotide salvage and catabolism","description":"This cluster is dominated by GO terms for purine metabolism, including inosine/guanosine/deoxyguanosine catabolism, nucleotide salvage (AMP, UMP, nicotinate nucleotide salvage), and nucleotide interconversion, indicating a shared role in purine turnover. A single midbrain development term is present but does not override the clear metabolic theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006148","count":4},{"id":"GO:0046115","count":4},{"id":"GO:0044209","count":4},{"id":"GO:0030901","count":3},{"id":"GO:0019686","count":3}]},{"hash":"150149950605720098","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":62,"triangles":64,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0000398","count":8},{"id":"GO:0000462","count":6},{"id":"GO:0000466","count":6}]},{"hash":"1584733637592605736","title":"GTPase signaling and vesicle transport regulators","description":"This cluster shows enrichment in intracellular signaling and trafficking processes: positive regulation of GTPase activity and regulation of Rho signaling point to cytoskeletal regulation; ER to Golgi vesicle transport and peroxisome autophagy indicate trafficking and turnover of organelles; additional terms like cytokinesis, pigmentation, and fat cell differentiation suggest broader cell-state regulation. The most coherent theme links small GTPase\u2013mediated signaling with vesicle trafficking and related cellular processes, though the set spans several related yet distinct functions.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0032465","count":2},{"id":"GO:0000413","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0030242","count":2}]},{"hash":"1693436383130822354","title":"B cell maturation and genome maintenance","description":"The proteins are enriched for immunoglobulin gene diversification (isotype switching and somatic hypermutation) alongside DNA-related processes (chromosome segregation, deoxyribonucleotide biosynthesis) and redox/homeostasis, pointing to a cluster that links B cell maturation with genome maintenance and oxidative stress handling.","confidence":"Medium","size":27,"edges":66,"triangles":60,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0045190","count":2},{"id":"GO:0016446","count":2},{"id":"GO:0007059","count":2},{"id":"GO:0034599","count":1}]},{"hash":"395858236176215394","title":"Dendritic Spine Morphogenesis and Actin Dynamics","description":"Proteins are enriched for neuronal spine development and actin cytoskeleton dynamics, with GO terms on dendritic spine morphogenesis, lamellipodium/ruffle assembly, and Rac signaling. This points to actin-driven remodeling in neurons (hippocampus development), supporting a label focused on dendritic spine morphogenesis and cytoskeletal regulation.","confidence":"High","size":27,"edges":43,"triangles":14,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":8},{"id":"GO:0051301","count":8},{"id":"GO:0045792","count":8},{"id":"GO:0097178","count":8},{"id":"GO:0061001","count":8}]},{"hash":"363497883746375472","title":"Golgi-ER Vesicle Trafficking and Exosome Secretion","description":"This cluster centers on Golgi and ER vesicle transport (ER-to-Golgi, intra-Golgi, retrograde endosome-to-Golgi) and vesicle fusion, with an additional link to exosome secretion, indicating a cohesive role in Golgi-mediated trafficking and regulated secretion.","confidence":"High","size":27,"edges":2,"triangles":0,"max_degree":2,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006457","count":3},{"id":"GO:0006891","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0042144","count":2}]},{"hash":"753309103352029402","title":"Isoprenoid biosynthesis","description":"This cluster is dominated by GO terms for terpenoid and isoprenoid biosynthesis, including farnesyl and geranylgeranyl diphosphate biosynthesis, cholesterol and monoterpene biosynthesis, and quinone production, all of which share precursors from acetyl-CoA and the TCA cycle. The recurring emphasis on prenyl diphosphate\u2013mediated pathways suggests a coherent theme around isoprenoid/terpenoid biosynthesis.","confidence":"High","size":27,"edges":14,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0006085","count":4},{"id":"GO:0019679","count":4},{"id":"GO:0019629","count":4},{"id":"GO:1901663","count":3}]},{"hash":"1089407729601008745","title":"Lipid metabolism and innate immune signaling","description":"The cluster shows strong enrichment for lipid metabolic processes (phosphatidylcholine and cholesterol metabolism) alongside immune-related regulatory processes (IL-17 signaling and chemokine production), plus host antiviral responses (suppression of viral release) and RNA regulation (miRNA processing/silencing). While some GO terms are less tightly connected (e.g., peptide amidation), the dominant theme appears to be lipid metabolism linked to immune signaling, with RNA-mediated regulation as a secondary facet, justifying this label.","confidence":"Medium","size":27,"edges":34,"triangles":13,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046470","count":9},{"id":"GO:1903883","count":9},{"id":"GO:0018032","count":9},{"id":"GO:0035278","count":9},{"id":"GO:0001519","count":9}]},{"hash":"2279910292757663350","title":"Ribosome Biogenesis and Cell Cycle","description":"The top GO terms cluster around ribosome biogenesis and related processes (ribosome assembly, ribosomal subunit biogenesis, ribosomal export from nucleus, tRNA modification) alongside core cell cycle and division activities (cell division, cell cycle, mitotic sister chromatid cohesion, septum assembly). This suggests a coherent theme of coordinating protein synthesis machinery with cell growth and division, despite a few outlier terms. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0007064","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000747","count":3}]},{"hash":"587099347811095122","title":"Multisystem developmental gene regulation","description":"This cluster shows enrichment in tissue-specific developmental processes (heart development, Schwann cell development, axonogenesis, visual perception) together with transcriptional regulation (DNA-templated transcription) and signaling-related processes, suggesting a set of proteins involved in coordinating developmental gene expression across multiple tissues.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0007507","count":8},{"id":"GO:0007601","count":8},{"id":"GO:0007409","count":7}]},{"hash":"1148835858327933290","title":"ER Stress Response and Protein Folding","description":"The top GO terms are dominated by endoplasmic reticulum stress and protein folding-related processes\u2014unfolded protein response, chaperone-assisted refolding, ERAD\u2014indicating a focus on ER quality control and protein folding. Other terms (chromatin remodeling, various signaling pathways, immune-related terms) may reflect broader regulatory links, but the strongest signal is ER stress response and protein folding.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0009736","count":3}]},{"hash":"1896201460454998623","title":"Peripheral nerve development and signaling","description":"This cluster is enriched for terms related to Schwann cell development, peripheral nervous system myelination, and excitatory synaptic signaling, pointing to a theme of nerve formation and neural communication in the PNS. Occasional terms like DNA replication and ascospore formation likely reflect background processes or noise rather than core function.","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0014044","count":7},{"id":"GO:0060079","count":7},{"id":"GO:0022011","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0033173","count":6}]},{"hash":"289099182462582340","title":"cGMP signaling in sensory transduction","description":"Grouping supported by GO terms pointing to cyclic GMP signaling and sensory processes: cellular response to cGMP, regulation of guanylyl cyclase signaling, sensory perception of smell, and retinal cone cell development. Together these indicate a theme of cGMP-driven signal transduction in sensory systems (smell and vision), with allied terms like xenobiotic response and cardiac regulation reflecting broader NO/cGMP pathways. Some terms are peripheral or noisy, but the core theme links to cGMP-mediated sensory signaling.","confidence":"Medium","size":27,"edges":32,"triangles":21,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0009405","count":5},{"id":"GO:0086004","count":4},{"id":"GO:0010754","count":4},{"id":"GO:0071321","count":4}]},{"hash":"1055194784191999002","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0044339","count":1},{"id":"GO:0000022","count":1},{"id":"GO:0051533","count":1},{"id":"GO:0045694","count":1}]},{"hash":"576166381354103039","title":"Neuronal development and protein trafficking","description":"The terms cluster around neural development (nervous system and photoreceptor development, dendritic spine development) and intracellular transport/localization (Golgi to plasma membrane transport, protein-containing complex localization). While cell cycle terms appear, the dominant theme is neural differentiation and synaptic connectivity supported by trafficking processes, suggesting a neuronal development and protein trafficking group. ","confidence":"Medium","size":27,"edges":13,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046909","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0043001","count":3}]},{"hash":"845767478125928387","title":"Unknown","description":"The GO terms span very different biological areas\u2014eye development/visual perception, meiosis/cytokinesis, Rho signaling, ubiquitination, xenobiotic response, and carbohydrate metabolism\u2014without a unifying process. With no edges among the proteins, there isn't a coherent functional theme to bind the cluster, so a single representative function cannot be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035025","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0031397","count":2},{"id":"GO:0060041","count":2}]},{"hash":"260688198653670953","title":"Gene Expression Machinery","description":"This cluster is enriched for core gene expression processes: mRNA splicing, translation initiation/reinitiation, transcription, and rRNA maturation, indicating a focus on RNA processing and translation. The presence of development terms appears ancillary, so the dominant theme remains general gene expression machinery rather than a specific developmental pathway.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":11},{"id":"GO:0001731","count":10},{"id":"GO:0002188","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0007584","count":8}]},{"hash":"449605598900953230","title":"Neural development and signaling regulation","description":"This cluster is enriched for neural development terms, notably peripheral nervous system myelination and spinal cord development, suggesting a primary role in neural formation. The presence of GO terms on regulation of GTPase activity and signaling pathways (Wnt and MAPK) indicates involvement in signaling control during neural development, with some auxiliary processes (DNA repair, translation initiation) that are less central to the theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0022011","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0035414","count":2}]},{"hash":"2003114009620658128","title":"Transcription Regulation and Chromatin Modification","description":"This cluster is characterized by GO terms centered on transcription control and chromatin state, such as regulation of DNA-templated transcription, DNA-templated transcription, negative regulation of transcription by RNA polymerase II, and histone H4-R3 methylation, indicating a core theme of transcriptional regulation and epigenetic modification; a few other terms related to metabolism appear incidental.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0030245","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0009236","count":3}]},{"hash":"1697545847597583754","title":"Cytoskeleton Dynamics and Organelle Inheritance","description":"The top terms center on actin cortical patches, cell polarity and shape, and inheritance of mitochondria and vacuoles, indicating a core theme around cytoskeletal control of organelle distribution, with developmental contexts (muscle and brain) reflecting morphogenesis aspects.","confidence":"Medium","size":26,"edges":187,"triangles":727,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048741","count":12},{"id":"GO:0021762","count":12},{"id":"GO:0042766","count":10},{"id":"GO:0043486","count":10},{"id":"GO:0000147","count":9}]},{"hash":"1109590462079227504","title":"Cytoskeletal Dynamics and Cell Division","description":"The top GO terms cluster around actomyosin contractile ring assembly, spindle elongation, centrosome separation, and microtubule dynamics (axonemal depolymerization), along with DNA replication and several developmental processes. This points to a shared theme of cytoskeletal organization and mitotic/cellular division machinery, with developmental contexts supporting these processes. Therefore the label reflects cytoskeletal regulation during division and growth.","confidence":"Medium","size":26,"edges":175,"triangles":548,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048741","count":10},{"id":"GO:0021762","count":10},{"id":"GO:0007100","count":8},{"id":"GO:0000742","count":8},{"id":"GO:0006260","count":7}]},{"hash":"608721441172723708","title":"Neural development and morphogenesis","description":"The cluster\u2019s top GO terms are dominated by nervous system and brain development, dendrite morphogenesis, and regulation of axonogenesis, indicating a neural development theme. While there are also terms related to general cell proliferation and vesicle trafficking, the neural development signals are the strongest and best represent the cluster\u2019s likely function.","confidence":"High","size":26,"edges":30,"triangles":10,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0033138","count":4},{"id":"GO:0003334","count":4},{"id":"GO:0050771","count":4},{"id":"GO:0000278","count":4}]},{"hash":"630258349785768592","title":"Nervous and Musculoskeletal Development","description":"This cluster is dominated by GO terms for nervous system development, heart and skeletal system development, axon regeneration, and signaling (Rho pathway and calcium-dependent exocytosis), pointing to a module of neural and muscular tissue development and communication; cholesterol biosynthesis and transcription terms support membrane formation and gene regulation during development, while pseudohyphal growth appears as an outlier.","confidence":"High","size":26,"edges":59,"triangles":21,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007399","count":7},{"id":"GO:0006695","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0006939","count":6},{"id":"GO:0048680","count":6}]},{"hash":"14012784026510196","title":"RNA Processing and Transcription Regulation","description":"The top GO terms cluster around nuclear RNA metabolism and chromatin-related processes: chromatin organization, transcription termination, mRNA splicing, tRNA processing, and rRNA maturation, pointing to a core role in RNA processing and gene expression control. Some terms like collagen catabolic process and chemotaxis are less central and may reflect annotation noise. Overall, the cluster appears to reflect RNA processing and transcription regulation.","confidence":"Medium","size":26,"edges":273,"triangles":1727,"max_degree":25,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0034724","count":4},{"id":"GO:0034396","count":4},{"id":"GO:0035551","count":4},{"id":"GO:0030574","count":4},{"id":"GO:0008033","count":4}]},{"hash":"1003828573663817957","title":"Potassium Ion Transport and cAMP/cGMP Signaling","description":"Based on the top GO terms, the proteins are enriched for potassium ion import/export, transmembrane transport, and intracellular potassium homeostasis. Additional terms for cellular responses to cAMP and cGMP and regulation of guanylyl cyclase signaling suggest linked membrane signaling. Sodium and manganese transport occur but are less dominant. Thus the cluster centers on potassium handling with supporting cyclic-nucleotide signaling.","confidence":"High","size":26,"edges":65,"triangles":30,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":6},{"id":"GO:0030007","count":5},{"id":"GO:0097623","count":5},{"id":"GO:0071320","count":5},{"id":"GO:0071805","count":5}]},{"hash":"1980858056238863756","title":"Cardiac Development and Fibroblast Migration","description":"The terms cluster around heart development and cardiac muscle differentiation, with related signaling and adhesion processes (integrin-mediated signaling, cellular response to PDGF, and positive regulation of fibroblast migration). This points to a shared theme of cardiac tissue formation involving fibroblast behavior and cell-matrix interactions, with transcriptional regulation as part of developmental programs. Despite no network edges, the GO annotations converge on cardiac development and fibroblast signaling/migration.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0034446","count":6},{"id":"GO:2000811","count":6},{"id":"GO:0036120","count":6},{"id":"GO:0007229","count":6}]},{"hash":"1180287111415913403","title":"Golgi Trafficking and Organization","description":"Several top GO terms point to Golgi organization and vesicle transport (Golgi to plasma membrane, retrograde Golgi-ER), indicating a core function in Golgi trafficking and protein localization; additional terms about nervous system development may reflect neuronal roles but do not override the Golgi-focused signal.","confidence":"High","size":26,"edges":68,"triangles":30,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":13},{"id":"GO:0060789","count":13},{"id":"GO:0071701","count":13},{"id":"GO:0046909","count":13},{"id":"GO:0007030","count":13}]},{"hash":"411965981311644843","title":"Neural migration and adhesion signaling","description":"The proteins cluster around adhesion and migration processes (substrate adhesion-dependent spreading, focal adhesion regulation, tangential migration in neural development, and sprouting angiogenesis), together with ephrin signaling and synapse assembly regulation, which together point to a developmental program coordinating cell movement, adhesion, and neural connectivity. Protein heterooligomerization and cell division also fit into complex assembly and growth during development.","confidence":"High","size":26,"edges":55,"triangles":62,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0034446","count":3},{"id":"GO:0002042","count":3},{"id":"GO:0051965","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0048013","count":3}]},{"hash":"1912796486623250489","title":"Nuclear transcription regulation and export control","description":"The cluster is enriched for transcription-related terms (negative regulation of transcription by RNA polymerase II and DNA-templated transcription) and a nuclear transport term (negative regulation of protein export from the nucleus), suggesting a theme of gene expression control within the nucleus. Redox/detoxification terms are present but less central, and midbrain development appears as a weaker signal. Overall, the name captures the strongest, cohesive theme of nuclear transcription regulation with export regulation.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0046826","count":2},{"id":"GO:0006508","count":2}]},{"hash":"660927404697610527","title":"Mitosis and ubiquitin-mediated proteolysis","description":"This cluster centers on mitosis and ubiquitin-driven proteolysis: terms like mitotic cell cycle, APC/C-dependent catabolic process, and cell division, together with polyubiquitination and ERAD, point to coordinated protein degradation essential for mitotic progression. Brain development and innate immune terms are present but less central to the core theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0030433","count":3}]},{"hash":"552085120952347260","title":"Unknown","description":"The terms span hair follicle maturation, Wnt-related osteoblast differentiation, mitotic spindle elongation, post-translational protein modification regulation, redox/oxidation-reduction processes, intracellular oxygen homeostasis, peptidyl-proline hydroxylation, positive regulation of cell growth, mRNA export from the nucleus, and regulation of presynapse assembly, with no single cohesive function tying them together. Because there are no clear connections among the terms and the cluster lacks edges indicating a shared pathway, there isn\u2019t a well-defined label to assign.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048820","count":2},{"id":"GO:0044339","count":1},{"id":"GO:0000022","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0055114","count":1}]},{"hash":"797677291943954720","title":"Immune Receptor Signaling and NF-\u03baB Activation","description":"Based on the top GO terms, the cluster is enriched for receptor-mediated signaling in immune cells (B cell and T cell receptor pathways) and related serine/threonine kinase signaling, with NF-\u03baB transcription factor activity suggesting downstream transcriptional responses. Although DNA replication and repair terms are present, the dominant theme is receptor-driven signaling in immune contexts, making this label a concise summary of the cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0008286","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0033138","count":2}]},{"hash":"1865650336231762034","title":"Nuclear DNA replication and chromosome maintenance","description":"The cluster\u2019s top GO terms are dominated by nuclear, genome-maintenance processes: DNA replication, mitotic cell cycle (including sister chromatid cohesion), and homologous recombination repair, with additional signals for ribosome biogenesis and nuclear pore localization. This points to a cohesive set of proteins involved in nuclear genome maintenance and cell-cycle progression, with some auxiliary nucleolar functions; the neuronal-related terms appear as noise relative to the core theme. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0000724","count":2},{"id":"GO:1900454","count":2}]},{"hash":"1986979116389775570","title":"Cell division and vesicle trafficking with ubiquitin turnover","description":"The cluster centers on intracellular transport (ER-Golgi vesicle transport, intracellular protein transport), protein turnover (ubiquitin-dependent proteolysis), and core cell division activities (cell division, meiotic spindle elongation, chromosome movement). Activation of GTPases and Rap signaling likely regulate these trafficking and mitotic/meiotic processes, supporting a cohesive module for division-linked trafficking and protein homeostasis. Some developmental or differentiation terms are peripheral but do not override the main theme.","confidence":"High","size":26,"edges":8,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0051232","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2131945702976222810","title":"Immune signaling and apoptosis","description":"The GO terms cluster around immune system functions: spleen development, T follicular helper cell differentiation, and IL-17\u2013mediated signaling, plus responses to lipopolysaccharide and apoptosis. While a few terms are obsolete or less directly related, the predominant theme is immune response regulation and signaling, with apoptosis as a related process. This supports a coherent, specific label rather than a general or unrelated grouping.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:1903762","count":2},{"id":"GO:0048536","count":2},{"id":"GO:0070535","count":2},{"id":"GO:0061470","count":2}]},{"hash":"477423408040318216","title":"Mitochondrial respiration & complex assembly","description":"The strongest GO signals point to mitochondrial energy metabolism: regulation of aerobic respiration, positive regulation of oxidative phosphorylation, and mitochondrial respiratory chain complex III assembly, suggesting a core theme around mitochondrial respiration and assembly. Other terms (protein processing, Golgi retention, transcription regulation, microtubule depolymerization, DNA repair) are present but less represented, indicating additional, but secondary, roles; overall the cluster seems best described by mitochondrial energy production and complex assembly.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":3},{"id":"GO:1903715","count":3},{"id":"GO:0031117","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0016485","count":2}]},{"hash":"895587946047598737","title":"Endothelial Tube Formation and Angiogenesis Regulation","description":"The top GO terms point to endothelial tube lumen extension and negative regulation of sprouting angiogenesis, indicating a vascular remodeling theme. Additional terms on heat response, ubiquitination, and kinase activity modulation suggest stress signaling and protein turnover that can influence angiogenic processes. Transport terms may reflect membrane proteins in endothelial cells but do not override the central vascular-focused functions. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0071901","count":2},{"id":"GO:0090051","count":2}]},{"hash":"1463968278377343467","title":"Calcium signaling and ER stress/ubiquitin pathways","description":"Most terms cluster around calcium signaling (cellular response to calcium ion; ryanodine-sensitive channel activity) and ER-stress\u2013related proteostasis (translation initiation in response to ER stress; ubiquitination and APC-dependent catabolic processes). While there are some noisy terms (e.g., chlorophyll-related), the core pattern suggests a theme linking calcium signaling to ER stress responses and ubiquitin-mediated protein turnover, with a secondary note on innate immune modulation. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0050689","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0070979","count":1}]},{"hash":"1863872466941158292","title":"Cardiac and neuronal signaling regulation","description":"The most represented GO terms relate to regulation of heart contraction and atrial action potential, mitochondrial calcium signaling, and neural processes (synaptic exocytosis and plasticity), together with cAMP response. This points to a cluster of proteins involved in signaling regulation in excitable tissues, spanning both cardiac and neural contexts.","confidence":"Medium","size":26,"edges":14,"triangles":4,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097274","count":10},{"id":"GO:0006469","count":7},{"id":"GO:0008016","count":6},{"id":"GO:2000300","count":6},{"id":"GO:0048168","count":6}]},{"hash":"2264811096842746989","title":"Membrane transport and antigen presentation","description":"The cluster shows strong signals for transmembrane transport of various substrates (nitrite, potassium ions, xenobiotics, aluminum cations), indicating a membrane transport theme. It also includes immune-related processes such as MHC class II biosynthesis and dendritic cell antigen processing/presentation, along with Th1 regulation, T cell cytokine production, and respiratory burst, suggesting a link between transport functions and antigen-processing/immune activation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0006855","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0015690","count":2}]},{"hash":"419441950402236959","title":"Budding yeast growth and cytokinesis regulation","description":"The terms point to budding and cell division processes (apical bud growth, septation signaling, septum digestion) and polarity/shape regulation, suggesting a module that controls yeast cell growth and cytokinesis. While metabolic terms are present, the division-related GO terms dominate, guiding the overall theme.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019628","count":1},{"id":"GO:0006144","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0019428","count":1},{"id":"GO:0007118","count":1}]},{"hash":"1254866433209525929","title":"Transmembrane nutrient and xenobiotic transport","description":"This cluster is dominated by GO terms for transmembrane transport of a wide range of nutrients and xenobiotics (vitamins, amino acids, thiamine, methionine, heme, cysteine, molybdate, xenobiotics), plus antibiotic and SOS response signals. The shared theme is membrane transport of diverse substrates, indicating a cohesive set of transporter proteins likely involved in nutrient uptake and detoxification.","confidence":"High","size":25,"edges":49,"triangles":15,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035461","count":24},{"id":"GO:0006855","count":24},{"id":"GO:0046677","count":20},{"id":"GO:0042883","count":19},{"id":"GO:0015888","count":19}]},{"hash":"2024375163112092406","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":259,"triangles":1671,"max_degree":24,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":18},{"id":"GO:0031047","count":17},{"id":"GO:0000467","count":12},{"id":"GO:0034475","count":12},{"id":"GO:0034476","count":12}]},{"hash":"2089157070630498339","title":"Retinoid metabolism and testosterone biosynthesis","description":"Based on the top GO terms, the cluster is enriched for retinol and retinal metabolic processes and regulation of retinoic acid receptor signaling, indicating a retinoid metabolism theme. There is also notable enrichment for testosterone biosynthesis and its regulation, suggesting a secondary hormonal biosynthesis axis. Additional terms like renal system development and endothelial apoptotic regulation are present but appear peripheral, not overriding the core retinoid and steroid biosynthesis signature.","confidence":"High","size":25,"edges":242,"triangles":1344,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":16},{"id":"GO:0042574","count":16},{"id":"GO:0055114","count":15},{"id":"GO:0072001","count":13},{"id":"GO:2000224","count":13}]},{"hash":"1613166126655660303","title":"Unknown","description":"Top GO terms are highly diverse (lens fiber cell morphogenesis, smooth muscle development, apoptotic process, cilium assembly, phototropism, immune regulation, etc.), with several terms unrelated or species-specific and no clear overarching biological process linking all 25 proteins. The lack of a coherent functional theme means a reliable single-label name cannot be assigned; hence Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070309","count":2},{"id":"GO:0048745","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0045497","count":1}]},{"hash":"2303531434880336080","title":"ECM Remodeling and Adhesion Signaling","description":"The top terms cluster around extracellular matrix biology and cell-matrix interactions: hyaluronan metabolism, integrin-mediated signaling, metallopeptidase activity, and protein heterotrimerization, all pointing to matrix remodeling and cell adhesion. Blood coagulation also ties into ECM remodeling contexts. While DNA replication and mitotic cell cycle appear, they are more general cellular processes and less specific to the core theme. Therefore, ECM remodeling and adhesion signaling best represents the group.","confidence":"High","size":25,"edges":159,"triangles":651,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030212","count":5},{"id":"GO:1905050","count":5},{"id":"GO:0007229","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0007596","count":5}]},{"hash":"980167552606805413","title":"Neuronal development and vesicle trafficking","description":"The cluster shows a strong emphasis on brain and nervous system development (brain development; nervous system development) alongside vesicle dynamics and intracellular transport (regulation of synaptic vesicle exocytosis; intracellular transport; Golgi-to-ER transport; membrane repair), suggesting proteins involved in neuronal maturation, presynaptic function, and membrane/organelle trafficking. Some terms are obsolete and less informative, but the overarching theme centers on neuronal development coupled with vesicle trafficking.","confidence":"High","size":25,"edges":159,"triangles":380,"max_degree":19,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0010796","count":12},{"id":"GO:0031384","count":12},{"id":"GO:0007420","count":10},{"id":"GO:2000300","count":9},{"id":"GO:0006886","count":8}]},{"hash":"696323727624203616","title":"Mitochondrial transport and energy regulation","description":"The top GO terms are centered on mitochondrial processes, including transport of various metabolites into and out of the mitochondrion (thiamine pyrophosphate, thiosulfate, heme, pyrimidine nucleotides, magnesium), and regulation of mitochondrial membrane potential, all pointing to mitochondrial transport and energy homeostasis. Related terms about nutrient response and insulin secretion further anchor the cluster to mitochondrial energy metabolism. Confidence High","confidence":"","size":25,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061179","count":13},{"id":"GO:0000002","count":12},{"id":"GO:0097274","count":12},{"id":"GO:0015886","count":12},{"id":"GO:0030974","count":12}]},{"hash":"1378697930019018464","title":"Proliferation and polarity with cytoskeletal remodeling","description":"The terms cluster around mitotic cell cycle and cell proliferation, and include many cytoskeleton- and polarity-related processes (lamellipodium assembly, Rac signaling, actin reorganization, spindle assembly). There are also hints of development and immune signaling, which can relate to cytoskeletal dynamics in those contexts. Overall, the proteins seem to link cell growth/division with changes in cell shape and movement, justifying a label focused on proliferation together with polarity and cytoskeletal remodeling.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0008283","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0071963","count":4}]},{"hash":"2185493595835861420","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms on formation of translation preinitiation complex, translation reinitiation, ribosome biogenesis, and regulation of translational initiation, plus IRES-dependent viral initiation and termination-reinitiation. Together these indicate a module centered on ribosome assembly and control of protein synthesis, with supporting RNA processing and surveillance functions that relate to quality control of translation.","confidence":"High","size":25,"edges":195,"triangles":713,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0075522","count":4}]},{"hash":"876517424972100852","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001682","count":2},{"id":"GO:0034965","count":2},{"id":"GO:0045717","count":2},{"id":"GO:0071037","count":2},{"id":"GO:0071035","count":2}]},{"hash":"1781714976091834624","title":"Unknown","description":"The Top Terms span translation, heat response, post-translational deglutamylation, liver regeneration and hepatocyte regulation, insulin processing, brain development, and bradykinin catabolism, showing no single cohesive functional theme. With no edges or clear connectivity, a unified, meaningful label cannot be derived from this cluster.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0035611","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0010757","count":1}]},{"hash":"2240918227875643422","title":"RNA Transcription Machinery & Ribosome Biogenesis","description":"The top GO terms are heavily biased toward transcription by RNA polymerases II and III, including initiation, elongation, termination, and RNA-templated transcription, with ribosome biogenesis also represented. This suggests a cluster of proteins involved in transcriptional machinery and ribosome production rather than signaling or metabolism, despite a couple of unrelated terms that appear as minor noise.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0006354","count":1}]},{"hash":"1804410230611513449","title":"Unknown","description":"The top terms cover ubiquitination, GPCR signaling, chloroplast thylakoid import, telomere/chromosome localization, mechanosensation, telomeric cohesion regulation, brown fat differentiation, oligodendrocyte differentiation, ephrin signaling, and general intracellular signal transduction. They span plant and animal contexts with no single cohesive function, so the cluster has no clear representative theme.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0045038","count":3},{"id":"GO:0070198","count":3},{"id":"GO:0050966","count":3}]},{"hash":"1538624266759949162","title":"Developmental signaling and differentiation","description":"The GO terms cluster around developmental processes across multiple tissues: fat cell differentiation, heart development, neural tube closure, visual perception, along with transcriptional regulation and signaling modulation via GPCR desensitization and phosphorylation. This pattern suggests a module of proteins that coordinate developmental signaling and lineage differentiation rather than a single tissue-specific function, likely including transcription regulators and kinases that influence cardiac, neural, adipose, and sensory development. The label captures the shared theme of development and signaling, though it is broad and not tissue-specific.","confidence":"Medium","size":24,"edges":10,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045444","count":10},{"id":"GO:0002029","count":10},{"id":"GO:0007507","count":10},{"id":"GO:0018107","count":10},{"id":"GO:0006351","count":9}]},{"hash":"2244033312149200916","title":"Developmental signaling and morphogenesis","description":"This cluster centers on developmental processes (heart, skeletal, embryonic digit, and multicellular development) and associated signaling pathways (Rho, cAMP/PKA, and receptor-mediated signaling), plus transcriptional regulation, suggesting a cohesive theme of signaling guiding development and morphogenesis. Some terms like pseudohyphal growth or blue light signaling add breadth, but do not outweigh the core developmental and signaling focus.","confidence":"Medium","size":24,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0007124","count":3},{"id":"GO:0001501","count":3}]},{"hash":"133073131558042426","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":188,"triangles":818,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":5},{"id":"GO:0042273","count":5},{"id":"GO:1902626","count":5},{"id":"GO:0009432","count":5}]},{"hash":"1022046342209494329","title":"Plant transcription regulation and cytokinin signaling","description":"The cluster is driven by transcriptional control (regulation of DNA-templated transcription) and cytokinin-activated signaling, with associated translation initiation and intracellular signaling terms, suggesting a plant-specific module coordinating gene expression with hormone signaling.","confidence":"Medium","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0009736","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007601","count":2}]},{"hash":"310250617229788541","title":"Ribosome Biogenesis and Cell Cycle Regulation","description":"This cluster combines strong signals for ribosome biogenesis and translation machinery (ribosome biogenesis, rRNA maturation, translation initiation) with cell cycle control processes (cell division, APC/C-mediated ubiquitination, mitosis), suggesting a coordinated module linking protein synthesis capacity to cell proliferation. The presence of ubiquitination via K11-linked chains and APC/C-dependent catabolic processes further supports mitotic regulation as a core theme.","confidence":"High","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0008283","count":5},{"id":"GO:0000463","count":4}]},{"hash":"1052678646038573697","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0007175","count":1},{"id":"GO:0000494","count":1},{"id":"GO:1904744","count":1}]},{"hash":"291437446766170341","title":"DNA replication and genome maintenance","description":"Most prominent signals are DNA replication and DNA-templated replication, along with DNA repair and premeiotic replication, plus associated telomere maintenance. This points to a cluster of proteins involved in duplication and genome stability, with modest contributions from ribosome biogenesis and signaling.","confidence":"High","size":24,"edges":33,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006261","count":2}]},{"hash":"1871427271648602102","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0017004","count":2}]},{"hash":"1639805831963254637","title":"Cell Cycle and Vesicle Trafficking","description":"The top terms cluster around cell cycle processes (cell division, DNA replication, replication initiation) with supporting roles for microtubule dynamics and ubiquitination, hinting at mitotic regulation. Additional terms point to vesicle trafficking (SNARE disassembly, ER-to-Golgi transport) and general protein processing, suggesting a broader coordination between cell-cycle control and intracellular transport. Some transcriptional and metabolic regulation terms appear as supplementary regulatory layers, consistent with growth-state coordination during cell division. Overall, the cluster appears to center on cell-cycle\u2013related machinery with linked trafficking/regulatory processes.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0035494","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0016567","count":3}]},{"hash":"622300030536429785","title":"Sugar and vitamin transmembrane transport","description":"Top GO terms indicate transmembrane transport of sugars (arabinose, galactose, xylose), sialic acid, phosphate and organic anions, and vitamin transport/metabolism (including L-ascorbic acid), suggesting a shared role in nutrient uptake across membranes. A secondary term related to intestinal epithelial structure and osmotic stress is present but does not define the core function. Confidence: High","confidence":"","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0015753","count":2}]},{"hash":"918786327245904596","title":"Na+/K+ Ion Transport and Stress Response","description":"GO terms show membrane ion transport (sodium import, potassium export) coupled with diverse stress responses (cold, hypoxia, xenobiotic/toxic stimuli) and apoptosis, with occasional notes on development and chromatin regulation, suggesting ion homeostasis tied to cellular stress signaling.","confidence":"Medium","size":24,"edges":13,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0007275","count":2}]},{"hash":"2174639522038335742","title":"Cardiac Contractility Regulation","description":"The GO terms are dominated by regulation of cardiac muscle contraction, heart contraction strength, and heart development (including catecholamine signaling and hypertrophy), pointing to proteins involved in controlling cardiac contractility and related signaling. A single adipogenesis term appears incidental to the main cardiac theme. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0045988","count":2},{"id":"GO:0003108","count":2},{"id":"GO:0060394","count":2}]},{"hash":"1110379375148793744","title":"ER Folding and Membrane Transport","description":"The top GO terms show both ER-associated protein folding and multiple membrane transport activities for ions and small molecules, suggesting a functional link between protein maturation in the ER and transport processes across membranes. This cluster likely centers on proteins involved in ER folding and broad membrane transport roles, hence a label focusing on both aspects.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0008292","count":1},{"id":"GO:0071436","count":1},{"id":"GO:1904659","count":1}]},{"hash":"962603101365164787","title":"DNA replication and cell cycle proteins","description":"The top GO terms converge on cell-cycle and DNA metabolism functions (G1/S transition, DNA replication, DNA-templated transcription, and cell division), suggesting the cluster is enriched for proteins involved in DNA replication and cell-cycle regulation. Some metabolic catabolic terms appear as noise, but do not override the dominant cell-cycle signal.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000082","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006660","count":4},{"id":"GO:0030245","count":4}]},{"hash":"1793903928287106186","title":"Unknown","description":"The top terms are very diverse, including spermatogenesis, protein glycosylation, cell wall organization, triglyceride biosynthesis, regulation of mitochondrial membrane permeability, mitochondrial protein import, DNA replication, and cell cycle regulation. There is no single cohesive function or pathway clearly uniting these terms, beyond some scattered mitochondrial-related entries, so a precise, representative label cannot be determined.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":3},{"id":"GO:0007283","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0010867","count":2}]},{"hash":"1914996631418170062","title":"Viral budding and ESCRT-mediated vesicle trafficking","description":"The top GO terms cluster around host-virus interactions and vesicle trafficking, notably viral life cycle, viral budding via host ESCRT, intralumenal vesicle formation, multivesicular body-lysosome fusion, and regulation of exosomal secretion, with suppression of viral release by host\u2014pointing to ESCRT-driven vesicle formation and viral budding/exosome dynamics as the core function. Some terms like nuclear membrane reassembly and cell division are ancillary. Confidence: High","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":4},{"id":"GO:0051301","count":4},{"id":"GO:1903541","count":3},{"id":"GO:0071454","count":3},{"id":"GO:0031468","count":3}]},{"hash":"778957511075239616","title":"Lipid and carbohydrate catabolism","description":"The cluster\u2019s top GO terms are dominated by various catabolic processes across lipids (triglyceride, diacylglycerol, phosphatidylserine, arachidonate) and carbohydrates (cellulose, pectin), plus a microautophagy term, suggesting a general theme of substrate breakdown and autophagic turnover rather than a single specific pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":6},{"id":"GO:0019433","count":6},{"id":"GO:0046340","count":6},{"id":"GO:0042136","count":6},{"id":"GO:0006660","count":5}]},{"hash":"1243293530330957332","title":"Blood Coagulation, Fibrinolysis, and ECM Remodeling","description":"The terms point to plasminogen activation, fibrinolysis, blood coagulation, tissue remodeling, and extracellular matrix disassembly, indicating a core theme of coagulation and ECM remodeling. Some transcription regulation terms are present, but they appear peripheral to the main function. Therefore, labeling the cluster as coagulation/fibrinolysis with ECM remodeling captures the primary functional group represented by these proteins.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0031639","count":3},{"id":"GO:0048771","count":3},{"id":"GO:0022617","count":3},{"id":"GO:0042730","count":3}]},{"hash":"230216524100900491","title":"N-terminal protein acetylation network","description":"The cluster is dominated by GO terms describing N-terminal acetylation of proteins (e.g., acetylation of serine, methionine, glutamic acid, lysine; also propionylation), suggesting a module of N-terminal acetyltransferases and related PTMs. Other terms like angiogenesis, melatonin biosynthesis, and glucosamine metabolism appear but are less central to the core signal.","confidence":"High","size":23,"edges":108,"triangles":410,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":14},{"id":"GO:0006526","count":14},{"id":"GO:0017198","count":13},{"id":"GO:0018003","count":13},{"id":"GO:0061606","count":13}]},{"hash":"1295506478366398465","title":"Light-regulated chlorophyll metabolism and cytokinin signaling","description":"This cluster centers on plant-specific processes where light perception (red/far-red phototransduction) influences chlorophyll turnover and tetrapyrrole/chromophore chemistry, alongside cytokinin-activated signaling and transcriptional regulation. The combination suggests a cohesive module linking light sensing to chloroplast gene/metabolism regulation and growth signaling.","confidence":"High","size":23,"edges":31,"triangles":11,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0080117","count":9},{"id":"GO:0010271","count":8},{"id":"GO:0009736","count":8},{"id":"GO:0034757","count":8}]},{"hash":"479794995344569014","title":"Cytokinin-Driven Cell Cycle Signaling","description":"This cluster is dominated by GO terms linking cytokinin-activated signaling with core cell cycle processes (cell division, mitotic cell cycle, phosphorelay signaling) and growth regulation (cell size). While a few terms touch on metabolism and stress responses, the central pattern points to cytokinin signaling coordinating cell proliferation and growth in plants, justifying a label centered on cytokinin-driven cell cycle control.","confidence":"High","size":23,"edges":6,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009736","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0051291","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006526","count":3}]},{"hash":"656442421372124450","title":"Steroid and oxylipin biosynthesis","description":"The top GO terms cluster around the biosynthesis and metabolism of lipid-derived signaling molecules, including prostaglandins, oxylipins via epoxygenase pathways, fatty acid omega-oxidation, and various steroids (brassinosteroids, ecdysone, testosterone). This points to a coherent theme of lipid-based signaling molecule production, with some additional xenobiotic/ozone-related metabolic roles that can intersect with lipid pathways. Confidence: Medium","confidence":"","size":23,"edges":30,"triangles":9,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010193","count":7},{"id":"GO:0019383","count":7},{"id":"GO:0031408","count":7},{"id":"GO:0010430","count":6},{"id":"GO:0002677","count":6}]},{"hash":"1281795250266522","title":"Embryonic heart and cartilage development","description":"The most represented GO terms cluster around developmental processes, notably post-embryonic development, heart development, and cartilage condensation, suggesting genes involved in embryonic/skeletal and cardiogenic development. Transcription-related terms support regulatory control, while metabolic and immune terms are secondary. Overall, the dominant theme is developmental programs with some metabolic/regulatory context.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009791","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0001502","count":5},{"id":"GO:0071226","count":5},{"id":"GO:0006111","count":5}]},{"hash":"1239085056189874112","title":"SNARE-Mediated Neuronal Vesicle Cycling","description":"The cluster shows strong representation of GO terms related to synaptic vesicle cycling and neurotransmitter release in neurons, including regulation of synaptic vesicle exocytosis, endocytic recycling, and SNARE complex disassembly. The presence of excitatory postsynaptic potential and substantia nigra development terms supports a neuronal context, suggesting these proteins participate in vesicle trafficking and exocytosis machinery underlying synaptic transmission.","confidence":"High","size":23,"edges":34,"triangles":12,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0097274","count":3},{"id":"GO:0060079","count":2},{"id":"GO:0021762","count":2},{"id":"GO:1900242","count":2}]},{"hash":"1415251799426705716","title":"ER-Golgi vesicle transport and microtubule movement","description":"The top GO terms cluster around intracellular transport\u2014especially ER-to-Golgi and Golgi-to-ER vesicle trafficking\u2014plus microtubule-based movement and related signaling (GTPase regulation). This points to a coherent theme of vesicle trafficking coordinated with cytoskeletal dynamics and cell division, with mitotic cycle terms reinforcing the cell-division angle. Some terms like brain development may reflect broader roles of trafficking machinery in neural development but do not override the main theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0032258","count":4}]},{"hash":"36570656574653288","title":"Amino acid and cofactor biosynthesis cluster","description":"The top terms cluster around biosynthetic processes for multiple amino acids (alanine, histidine, serine, lysine) and cofactors (biotin, protoporphyrinogen IX), plus related catabolic/biosynthetic pathways, indicating a metabolic module focused on amino acid and cofactor production. Occasional terms like Notch signaling and DNA-templated transcription appear as less central annotations but do not define the main theme. ","confidence":"Medium","size":23,"edges":66,"triangles":91,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0000105","count":5},{"id":"GO:0006564","count":4},{"id":"GO:0006782","count":4}]},{"hash":"1111970352962647553","title":"DNA Repair and Cellular Stress Response","description":"The cluster is dominated by terms related to DNA maintenance (base-excision repair, DNA catabolic process) and oxidative/stress signaling (redox homeostasis, xenobiotic response), suggesting a central theme of DNA repair coupled with general cellular stress responses. Some terms, like renal water transport and aging, appear inconsistent with this core and may reflect annotation noise or multifunctional proteins. Overall, the strongest signal points to DNA repair and stress-response functions.","confidence":"Medium","size":23,"edges":19,"triangles":2,"max_degree":9,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006284","count":8},{"id":"GO:0007568","count":8},{"id":"GO:0042493","count":8},{"id":"GO:2001153","count":7},{"id":"GO:0045454","count":7}]},{"hash":"324739466874160553","title":"Cell signaling and stress responses","description":"These proteins cluster around several signaling and stress-response processes: regulation of GTPase activity (cell signaling), thyroid hormone transport, cytokine production, and cellular responses to nitric oxide, ethylene, and amino-acid starvation. A few terms touch on development (oligodendrocyte development) and translation initiation, suggesting participation in broader regulatory networks rather than a single pathway. The varied GO terms collectively point to a theme of signaling and adaptive responses to stimuli.","confidence":"Medium","size":23,"edges":7,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0070327","count":3},{"id":"GO:0050663","count":3},{"id":"GO:0014003","count":2}]},{"hash":"1277500816495878267","title":"Amino acid and essential nutrient transporters","description":"This cluster is dominated by GO terms for transmembrane transport of amino acids (methionine, cysteine), vitamins (thiamine), and metal/organic cofactors (molybdate, heme), suggesting a shared function in nutrient uptake. Additional terms relate to antibiotic response and SOS signaling, which may reflect stress-responsive regulation of transport systems; a few terms like DNA replication and morphogenesis are less central, so the core theme is transport.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0000902","count":3},{"id":"GO:0042883","count":3},{"id":"GO:0015888","count":3}]},{"hash":"154730736887931379","title":"Nucleolar ribosome biogenesis and RNA processing","description":"The top GO terms cluster around ribosome biogenesis and rRNA maturation (e.g., maturation of LSU rRNA, maturation of 5.8S rRNA, ribosome biogenesis, formation of translation preinitiation complex) and DNA-templated transcription, with additional RNA processing (mRNA splicing) and cell division signals. This pattern suggests a nucleolar program focused on producing ribosomes and associated RNA maturation/processing steps, with some linked cell-cycle activity. Therefore, the label reflects the main functional theme of the cluster.","confidence":"High","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000463","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000466","count":4}]},{"hash":"387097855576925114","title":"Steroid hormone and lipid biosynthesis","description":"The top GO terms concentrate on steroid hormone production (testosterone biosynthetic process, glucocorticoid biosynthetic process) and lipid-related metabolism (fatty acid elongation, retinoic acid biosynthesis, sphinganine metabolism, poly-hydroxybutyrate biosynthesis). While some terms (phylloquinone catabolic, acetoin catabolic) are less aligned, the dominant signal is steroid and lipid biosynthesis, suggesting a lipid/hormone metabolic theme for this cluster.","confidence":"Medium","size":23,"edges":8,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0042619","count":10},{"id":"GO:0006666","count":8},{"id":"GO:0008207","count":8},{"id":"GO:0061370","count":8}]},{"hash":"1873391169437948093","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000461","count":1},{"id":"GO:0042255","count":1}]},{"hash":"379143630196287688","title":"Aromatic hydrocarbon catabolism and photosynthesis","description":"The top terms cluster around degradation of aromatic compounds (carbazole, camphor, toluene) indicating aromatic hydrocarbon catabolic metabolism, along with photosynthesis, nonphotochemical quenching, and nitrate assimilation pointing to photosynthetic energy metabolism. A couple of general translation-related terms (methionyl/ leucyl-tRNA aminoacylation) and an outlier (uterus development) may reflect broad housekeeping functions or annotation noise. Overall, the cluster seems to unify energy-related metabolic processes, especially aromatic compound degradation linked with photosynthetic pathways.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046232","count":6},{"id":"GO:0055114","count":4},{"id":"GO:0006431","count":4},{"id":"GO:0006429","count":4},{"id":"GO:0060065","count":4}]},{"hash":"1793264596900082928","title":"Detox and ER-Golgi Transport","description":"This cluster is enriched for detox-related terms (response to toxic substance; cellular oxidant detoxification) and for endoplasmic reticulum to Golgi vesicle-mediated transport, suggesting a group of proteins involved in detox processes and secretory/trafficking pathways. Additional terms (dephosphorylation, transporter regulation) point to membrane-associated regulation, while a few outliers (proprioception, IL-17 signaling) are less connected to the core theme. Overall, the dominant signals support a detox and vesicular transport functional theme.","confidence":"Medium","size":23,"edges":22,"triangles":0,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0019230","count":2}]},{"hash":"1345603901515877698","title":"Mitosis and Cytoskeleton Dynamics","description":"Based on the GO terms, this cluster centers on cytoskeleton-driven processes: regulation and assembly of the mitotic spindle (mitosis) and spindle organization, Rac-mediated signaling, cell migration, and phagocytosis\u2014all of which rely on dynamic cytoskeletal remodeling. Some terms touch plant-specific growth contexts (cytokinin response, stem cell maintenance), but the dominant theme is cytoskeletal regulation during division and movement.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009735","count":1},{"id":"GO:1902455","count":1},{"id":"GO:0060236","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0032837","count":1}]},{"hash":"2112892147904921521","title":"Negative Regulation of Signaling and Synaptic Assembly","description":"It centers on negative control of signaling, including tyrosine dephosphorylation and ERK/PI3K-AKT pathway dampening, and on synaptic organization (postsynaptic density, vesicle clustering). The inclusion of focal adhesion and T cell signaling terms suggests broader regulators that modulate multiple pathways, with a neuronal emphasis.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":17},{"id":"GO:0051895","count":17},{"id":"GO:1903984","count":17},{"id":"GO:2000808","count":17},{"id":"GO:0051898","count":17}]},{"hash":"1553655126321729031","title":"Transmembrane Sugar and Vitamin Transport","description":"The GO terms are dominated by transmembrane transport of sugars (arabinose, galactose, D-xylose, sialic acid), phosphate, organic anions, and vitamins, plus vitamin transmembrane transport and related metabolic activity, suggesting the cluster comprises nutrient transporters. Some osmotic stress response and epithelial maintenance terms may reflect cellular conditions tied to transporter function but do not override the core transport theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":3},{"id":"GO:0006970","count":3},{"id":"GO:0015757","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0015753","count":3}]},{"hash":"1845719330296100406","title":"Plant lipid metabolism and hormone signaling","description":"The terms are dominated by lipid catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine) and lipid-derived signaling (endocannabinoid regulation), plus strigolactone biosynthesis and secondary shoot formation, all pointing to plant hormone\u2013associated metabolic programs. Stilbene catabolism and PHB biosynthesis suggest broader metabolic remodeling related to phenylpropanoids and storage polymers. Overall, the cluster appears to represent lipid metabolism intertwined with plant hormone pathways.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":6},{"id":"GO:2000124","count":6},{"id":"GO:0006660","count":5},{"id":"GO:0052651","count":5},{"id":"GO:0042619","count":5}]},{"hash":"1233420232913040744","title":"Vacuolar protein processing and trafficking","description":"The cluster\u2019s GO terms cluster around vacuolar protein processing, protein storage/vacuole organization, GPI-anchor attachment, and protein localization to the cell surface, suggesting a shared role in the secretory pathway and maturation/trafficking of proteins to vacuoles or membranes (with a few outliers likely due to cross-species annotations).","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003014","count":1},{"id":"GO:0010447","count":1},{"id":"GO:1990019","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0010375","count":1}]},{"hash":"970234712904354434","title":"Immune cell signaling and stress response","description":"The top GO terms show broad signaling roles (intracellular signal transduction, ephrin pathway regulation) plus immune-related processes (myeloid apoptotic process, follicular dendritic cell differentiation) and cytoskeletal/ubiquitination activity, with additional stress-response terms (heat, capsazepine). This points to a cluster of proteins involved in immune signaling modulated by stress and cytoskeletal dynamics, rather than a single specific pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901187","count":4},{"id":"GO:0035556","count":4},{"id":"GO:0009408","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0051017","count":4}]},{"hash":"1011612653676334326","title":"Mitotic cell cycle and DNA repair","description":"This cluster is enriched for DNA repair, kinetochore localization, and spindle assembly checkpoint signaling, plus proteasome/COP9-associated regulation of protein turnover during mitosis, pointing to a theme of genome maintenance and chromosome segregation. A single term about nervous system development appears less central.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0007094","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0000278","count":2}]},{"hash":"586900107224458729","title":"Unknown","description":"The Top Terms span a broad mix of processes (DNA-templated transcription, chemotaxis, placenta development, glucose metabolism, cocaine response, cell size regulation, visual perception, potassium transport, and fat cell differentiation) without a clear common function linking the proteins. The sparse network (low edges, no triangles) further suggests a loose or incidental association rather than a coherent biological module.","confidence":"","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":14},{"id":"GO:0006935","count":13},{"id":"GO:0001890","count":13},{"id":"GO:0006006","count":13},{"id":"GO:0033160","count":13}]},{"hash":"1959447517936351221","title":"Brain development and synaptic signaling","description":"These proteins are enriched in neural-related processes: visual perception, excitatory postsynaptic potential, and long-term synaptic potentiation point to synaptic function and neural processing, while terms like multicellular organism development and heart development suggest broader developmental roles. DNA-templated transcription and mitotic cell cycle indicate active gene regulation and proliferation in developing tissues. Some outliers (defense response to Gram-positive bacterium, abscisic acid\u2013activated signaling) may reflect annotation noise or multifunctionality, but the dominant theme is neural development and synaptic signaling.","confidence":"Medium","size":22,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":12},{"id":"GO:0007275","count":11},{"id":"GO:0050830","count":11},{"id":"GO:0007507","count":11},{"id":"GO:0007601","count":11}]},{"hash":"1338128455615688836","title":"Neural Development and Synaptic Signaling","description":"The cluster shows a clear link between brain development (forebrain radial glial differentiation, radial scaffold formation, substantia nigra development) and synaptic function (excitatory postsynaptic potential, regulation of vesicle exocytosis and endocytosis), suggesting proteins involved in neural development and maturation of synaptic transmission. A few terms about ossification and xenobiotic response appear as weaker, incidental associations rather than core functions of the group.","confidence":"Medium","size":22,"edges":112,"triangles":309,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":5},{"id":"GO:0021762","count":5},{"id":"GO:1900242","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0043931","count":5}]},{"hash":"2206255354485014056","title":"Inflammation and apoptotic signaling","description":"The top GO terms point to inflammatory and cell death pathways (TNF signaling, NF-kappaB regulation, p53-mediated apoptotic signaling, LPS response), suggesting a cluster of proteins involved in stress-induced immune and apoptotic responses. Some plant-specific and metabolic terms appear as noise, but the central theme is immune/stress signaling and apoptosis.","confidence":"Medium","size":22,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042771","count":2},{"id":"GO:0042347","count":2},{"id":"GO:0034051","count":2},{"id":"GO:0033209","count":2}]},{"hash":"1357134089759182721","title":"Endosomal trafficking and MVB sorting","description":"Based on the dominant GO terms, the proteins cluster around endocytosis, various endosome-to-Golgi/vacuole transport steps, and the multivesicular body (MVB) sorting pathway, with actin involvement in endocytic patches. This suggests a cohesive function in vesicular trafficking through endosomal compartments and MVB sorting, despite a couple of unrelated terms that likely reflect noise. ","confidence":"High","size":22,"edges":26,"triangles":7,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":3},{"id":"GO:0006623","count":3},{"id":"GO:0032511","count":3},{"id":"GO:0000147","count":3},{"id":"GO:0006895","count":3}]},{"hash":"2015354740750813863","title":"Golgi-ER Vesicle Transport and Protein Localization","description":"This cluster is dominated by Golgi/ER vesicle trafficking terms, including ER-to-Golgi transport, Golgi-to-plasma membrane transport, and protein localization to the Golgi. Additional terms for lysosomal/vacuolar targeting and vesicle budding reinforce the vesicular transport theme. A few terms (kidney development, EGFR signaling) are tangential, but the dominant signal is Golgi-ER\u2013associated trafficking and localization.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":7},{"id":"GO:0043001","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0000042","count":5}]},{"hash":"77359548990576714","title":"Ubiquitin-Proteasome and Immune Signaling","description":"GO terms point to protein turnover and immune signaling (endopeptidase regulation, deubiquitination, proteasomal degradation, C-type lectin receptor signaling, Fc-epsilon receptor signaling). This suggests a proteostasis\u2013immune signaling module, where proteolysis-related processes intersect immune receptor pathways, with some hints of host-pathogen interaction from viral-process terms. Overall, the cluster appears anchored in ubiquitin-proteasome\u2013mediated proteolysis linked to immune signaling.","confidence":"Medium","size":22,"edges":119,"triangles":315,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0010950","count":4},{"id":"GO:0016579","count":4},{"id":"GO:0016032","count":3},{"id":"GO:0002223","count":3},{"id":"GO:0031145","count":3}]},{"hash":"545591398452577266","title":"Neural development and DNA replication","description":"The cluster is enriched for cell cycle and DNA-related GO terms (mitotic cell cycle, DNA-templated transcription, DNA replication, DNA repair) with neural-development terms (forebrain development, neural tube closure) indicating a group of proteins involved in neural development alongside proliferation and genome maintenance. Less central terms like ER stress\u2013related apoptosis signaling, chemotaxis, and cadmium response reflect broader stress responses but do not dominate the core theme.","confidence":"High","size":22,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":20},{"id":"GO:0006351","count":19},{"id":"GO:0006260","count":19},{"id":"GO:0001843","count":17},{"id":"GO:0007275","count":17}]},{"hash":"2222957118132680450","title":"Ribosome biogenesis and translation","description":"The top GO terms are centered on cytoplasmic translation and ribosome biogenesis, with supporting processes like protein homooligomerization and ER-Golgi trafficking, as well as ubiquitination. This suggests a cluster focused on the core machinery of protein synthesis and maturation, rather than signaling or specialized pathways. While some proliferation-related terms appear, the predominant signal is ribosome assembly and protein production/processing.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0042254","count":2}]},{"hash":"712771170861206455","title":"RNAi Machinery and Gene Silencing","description":"The cluster\u2019s top GO terms are dominated by RNA interference processes\u2014siRNA processing, siRNA-mediated silencing, RNAi antiviral response, and co-transcriptional silencing by RNA interference machinery\u2014suggesting involvement in RNAi machinery and post-transcriptional gene regulation. A few metabolic catabolic terms appear but are less prominent, indicating the primary theme is RNA interference\u2013related functions.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042758","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0070919","count":1},{"id":"GO:0030422","count":1},{"id":"GO:0010495","count":1}]},{"hash":"301404915781403457","title":"Core Metabolism and Protein Synthesis with Cofactor Biosynthesis","description":"This cluster is dominated by central carbon metabolism signals (glycolysis, TCA cycle, 2-oxoglutarate metabolism) alongside translation, and it also includes cofactor biosynthesis pathways (thiamine, malonyl-CoA, fatty acid biosynthesis) and iron-sulfur cluster assembly, with some antibiotic/xenobiotic response. Together these terms point to a core set of cellular processes governing energy production, protein synthesis, and essential cofactors, rather than a single specialized pathway, hence a label centered on core metabolism and protein synthesis with cofactors.","confidence":"Medium","size":22,"edges":224,"triangles":1413,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0006096","count":6},{"id":"GO:0006412","count":4},{"id":"GO:0006103","count":4},{"id":"GO:0046677","count":3}]},{"hash":"508394394118907629","title":"Dopamine signaling and neural development","description":"Dominant terms tie dopamine signaling (cellular response to dopamine, positive regulation of dopamine receptor signaling) with neural development processes (neuron maturation, tangential migration to the olfactory bulb, Wnt signalosome assembly). A few outliers exist, but the core theme is dopamine-related neural development.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903351","count":3},{"id":"GO:2000172","count":2},{"id":"GO:1904887","count":2},{"id":"GO:1903125","count":2},{"id":"GO:0070340","count":2}]},{"hash":"984602729013243777","title":"DNA Damage Response and Translation Control","description":"This cluster centers on translation and transcription regulation in response to DNA damage and UV/gamma radiation. Enrichment for translation (GO:0006412), positive regulation of translation, and ribosomal large subunit biogenesis points to controls of protein synthesis. Simultaneously, GO terms for transcription elongation regulation, transcription antitermination, and p53-mediated DNA damage signaling reflect transcriptional adjustments during stress. Together, these terms suggest a cohesive theme of coordinating gene expression at both transcriptional and translational levels under DNA-damage conditions.","confidence":"High","size":22,"edges":13,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000105","count":3},{"id":"GO:0045727","count":2},{"id":"GO:0032784","count":2},{"id":"GO:1902167","count":2}]},{"hash":"805605559749517383","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":226,"triangles":1443,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":3},{"id":"GO:0031426","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0009793","count":3}]},{"hash":"1194058097966901445","title":"Unknown","description":"The terms are diverse (cell division, innate immune response, various metabolic/biosynthetic processes, and development-related terms) with no clear shared function, and several GO terms are obsolete. The low connectivity (2 edges, max degree 1) suggests a heterogeneous cluster rather than a single pathway, so a reliable, representative label cannot be assigned.","confidence":"","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0045087","count":3}]},{"hash":"56432498193581018","title":"Ribosome biogenesis and translation machinery","description":"The cluster is enriched for translation and ribosome biogenesis terms (translation, cytoplasmic translation, ribosome biogenesis, ribosomal subunit export from nucleus), indicating a core role in protein synthesis. While cell division and cell cycle terms appear, the dominant theme centers on ribosome assembly and translation, justifying a label focused on the protein-synthesis machinery.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000747","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000055","count":2}]},{"hash":"2013525529865875811","title":"Redox Homeostasis and Xenobiotic Metabolism","description":"This cluster is dominated by GO terms for redox balance (cell redox homeostasis, oxidation\u2013reduction processes) and glutathione metabolism, with several xenobiotic-degrading processes (carbazole and camphor catabolic pathways). There is also translation and a response to antibiotic annotation; the translation term may reflect general housekeeping functions or annotation noise. The cohesive theme is redox chemistry coupled with detoxification/biodegradation of xenobiotics.","confidence":"Medium","size":22,"edges":16,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0055114","count":3}]},{"hash":"849297069283088887","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0090617","count":2}]},{"hash":"1003554938337366353","title":"Sterol biosynthesis and lipid metabolism","description":"Proteins in this cluster are strongly linked to sterol and lipid biosynthesis and metabolism: cholesterol via lathosterol, ergosterol biosynthesis, sterol oxidation, ether lipid metabolism, and fatty acid biosynthesis. This lipid-centric signal is compatible with roles in membrane composition and lipid-rich tissues such as myelin and sebaceous glands; a single B cell chemotaxis term is less central but does not negate the overall theme.","confidence":"High","size":22,"edges":37,"triangles":20,"max_degree":16,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0001949","count":11},{"id":"GO:0006675","count":11},{"id":"GO:0032286","count":11},{"id":"GO:0046485","count":7},{"id":"GO:0006633","count":7}]},{"hash":"835251951017784207","title":"APC/C-dependent ubiquitin proteolysis in mitosis","description":"The Top Terms are dominated by mitotic cell cycle, APC/C-dependent catabolic processes, K11-linked and general protein ubiquitination, and meiosis I, pointing to ubiquitin-mediated proteolysis driving cell division via APC/C. A couple of terms (spliceosome maturation and mannitol response) seem ancillary, but the core signal is clear. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":1},{"id":"GO:0070979","count":1},{"id":"GO:0031145","count":1},{"id":"GO:0007127","count":1},{"id":"GO:0042787","count":1}]},{"hash":"683890162147063952","title":"Epithelial development and cell cycle regulation","description":"The cluster is enriched for organ development terms (lung and kidney development) and for control of epithelial proliferation and cell cycle exit (G1 to G0), suggesting a cohesive role in epithelial growth regulation; auxiliary terms like translation regulation and metabolism are present but secondary.","confidence":"Medium","size":22,"edges":226,"triangles":1447,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0017148","count":2},{"id":"GO:1902074","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0006212","count":1}]},{"hash":"631136776914914788","title":"Transcription Regulation and Chromatin Modification","description":"The terms point to regulation of DNA-templated transcription and chromatin modification (including chromatin binding and histone methylation), suggesting a cohesive function in transcriptional control, with some development-related terms as secondary associations.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0021983","count":4},{"id":"GO:0051573","count":4},{"id":"GO:0006351","count":4}]},{"hash":"842029221193312558","title":"Leukocyte receptor signaling cluster","description":"The cluster is enriched for immune signaling GO terms, including stimulatory C-type lectin receptor signaling, Fc-gamma receptor signaling, and complement activation via the lectin pathway, along with ERK cascade involvement. While some terms relate to development or ciliogenesis, the strongest signal comes from leukocyte receptor\u2013mediated signaling pathways, suggesting a coherent immune signaling theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050901","count":2},{"id":"GO:0060271","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1933920063836222270","title":"Proteoglycan and glycosaminoglycan biosynthesis","description":"The cluster is marked by GO terms for proteoglycan and glycosaminoglycan biosynthesis (chondroitin sulfate and heparan sulfate proteoglycans) and UDP-D-xylose metabolism, which provides substrates for GAG chain initiation. The presence of kidney morphogenesis supports an extracellular matrix context, while other carbohydrate biosynthesis terms appear ancillary. This combination best points to proteoglycan/GAG biosynthesis as the core function of the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043951","count":2},{"id":"GO:0005992","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0033319","count":1},{"id":"GO:0060993","count":1}]},{"hash":"286233060369732890","title":"GPCR-driven cAMP/cGMP signaling","description":"This cluster centers on G protein-coupled receptor signaling, including adenylate cyclase activation and cAMP production (and related pathways like adenosine/adrenergic signaling and forskolin response), plus receptor guanylyl cyclase signaling. The presence of blue light signaling and hypoxia detection suggests environmental cue transduction feeding into these second-messenger cascades, with downstream transcriptional regulation. Overall, a coherent GPCR-mediated signaling and second-m messenger theme.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":11},{"id":"GO:0070483","count":10},{"id":"GO:0035556","count":7},{"id":"GO:0071880","count":6},{"id":"GO:0001973","count":6}]},{"hash":"1587235247354344180","title":"Cilium- and sensory signaling","description":"This cluster centers on ciliary and sensory-related functions, with GO terms for cilium assembly, visual perception, and regulation of sensory neuron axon guidance, complemented by signaling-related terms such as pheromone response and regulation of GTPase activity. The mix points to a theme of cilium-associated sensory signaling and related regulatory processes.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":11},{"id":"GO:0043547","count":11},{"id":"GO:0060271","count":10},{"id":"GO:1905490","count":10},{"id":"GO:0035330","count":10}]},{"hash":"1341601711284206907","title":"Developmental signaling and metabolic regulation","description":"This cluster shows a mix of transcriptional regulation (DNA-templated transcription), developmental processes (placenta development), metabolism (glucose metabolic process), and signaling/cytoskeletal regulation (actin binding, peptidyl-threonine phosphorylation) along with transport and chemotaxis. The common thread is broad regulatory coordination of gene expression, signaling, and cytoskeletal/metabolic processes during development and cell movement, rather than a single precise function. ","confidence":"Medium","size":21,"edges":8,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006935","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0033160","count":3}]},{"hash":"1718721545574385474","title":"Fatty acid and secondary metabolite metabolism","description":"These proteins show enrichment in fatty acid pathways (alpha-oxidation, methyl-branched fatty acids) and various secondary metabolite biosynthesis/catabolism (verruculogen, ectoine, stilbene), plus related P450 epoxygenase activity and broader small-molecule metabolism. The mix of primary fatty acid processes with diverse secondary metabolite terms suggests a cluster centered on broad metabolic processing of small molecules rather than a single canonical pathway.","confidence":"Medium","size":21,"edges":26,"triangles":3,"max_degree":5,"top_function":"wound healing","top_go_terms":[{"id":"GO:0006564","count":5},{"id":"GO:0001561","count":5},{"id":"GO:0097089","count":5},{"id":"GO:1902181","count":5},{"id":"GO:0019491","count":5}]},{"hash":"522288721954327274","title":"DNA replication and protein synthesis","description":"The top GO terms point to core gene-expression and genome-duplication processes: translation, ribosome dynamics, mRNA processing/export, and DNA replication/cell division. Other terms like mitochondrial intermembrane space import and chaperone-dependent refolding appear as supporting machinery, with a few viral replication terms as outliers. Taken together, the cluster highlights fundamental cellular machinery for making proteins and duplicating DNA, with some peripheral functions related to protein folding and import. ","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0032790","count":2}]},{"hash":"1346632854391885704","title":"Ubiquitin-Proteasome Regulation in Cell Cycle","description":"The top terms cluster around ubiquitin-dependent protein degradation (proteasomal, ERAD, autoubiquitination, K11/K63 linkages) and cell cycle processes (mitosis, G2/M), with links to DNA repair and development signaling, suggesting a cohesive role in ubiquitin-mediated proteostasis coordinating cell cycle and genome maintenance.","confidence":"High","size":21,"edges":196,"triangles":1103,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":17},{"id":"GO:0000278","count":16},{"id":"GO:0000086","count":16},{"id":"GO:0001701","count":16},{"id":"GO:0030433","count":16}]},{"hash":"1665685272217445659","title":"Cell Cycle and Vesicle Trafficking in Germ Cells","description":"This cluster combines mitosis-related processes (mitotic spindle assembly; spermatid development) with vesicle trafficking and membrane organization (endocytosis; synaptic vesicle budding; mitochondrion-ER tethering), suggesting coordination of cell division and intracellular transport in germ-cell contexts.","confidence":"Medium","size":21,"edges":26,"triangles":8,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":7},{"id":"GO:0007286","count":7},{"id":"GO:1903434","count":6},{"id":"GO:0071851","count":6},{"id":"GO:0071389","count":6}]},{"hash":"1806638471494926854","title":"Developmental transcriptional regulation","description":"The cluster centers on GO terms tied to regulating transcription (regulation of DNA-templated transcription; negative regulation of transcription by RNA polymerase II) across diverse developmental processes (uterus/ovarian development, heart, digestive tract, female genitalia, embryonic skeleton). This suggests proteins that control gene expression during development rather than a single tissue-specific function. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0008585","count":3},{"id":"GO:0048565","count":3},{"id":"GO:0007507","count":3}]},{"hash":"102713225369765875","title":"Phosphorylation and Methylation in Neurotransmission","description":"Top GO terms indicate a strong emphasis on post-translational modifications (phosphorylation, protein methylation, nucleotide phosphorylation) and neurotransmitter handling (dopamine catabolic processes, dopaminergic regulation), with an additional hint of sensory system context (auditory receptor cell development). This suggests a cluster centered on PTMs modulating neural signaling and neurotransmitter metabolism, rather than a single enzymatic pathway. ","confidence":"Medium","size":21,"edges":34,"triangles":4,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:0032259","count":3},{"id":"GO:0046940","count":3},{"id":"GO:0046939","count":3},{"id":"GO:0050668","count":2}]},{"hash":"2073173016929868916","title":"Cannabinoid biosynthesis and xenobiotic response","description":"The top GO terms include cannabinoid biosynthetic process and olivetolic acid biosynthetic process, pointing to Cannabis-type secondary metabolite production. The xenobiotic stimulus and response to cocaine terms suggest a broader foreign compound response accompanying such pathways, while trafficking and protein folding terms reflect cellular logistics supporting specialized metabolism. Overall, the cluster appears centered on cannabinoid biosynthesis with related xenobiotic response.","confidence":"Medium","size":21,"edges":22,"triangles":1,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0006893","count":2},{"id":"GO:1901696","count":1},{"id":"GO:1901697","count":1}]},{"hash":"1042460529616426417","title":"Mitotic Cell Division","description":"The cluster is dominated by GO terms tied to mitosis and cell cycle (cell division and mitotic spindle assembly), suggesting it represents proteins involved in mitotic progression. A few terms about autophagy, RNA processing, and transcription are present but appear ancillary to the core mitotic signal.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0032258","count":3},{"id":"GO:0008584","count":2},{"id":"GO:0007584","count":2}]},{"hash":"25614358142326629","title":"Rac-Mediated Cytoskeletal Remodeling and Adhesion","description":"Top GO terms cluster around Rac/small GTPase signaling driving actin remodeling (filopodium assembly), adhesion processes (substrate adhesion-dependent spreading, tight junctions), and signaling pathways (ephrin, Wnt) linked to synaptic plasticity. This points to a Rac-driven theme coordinating cytoskeletal dynamics with cell\u2013cell adhesion and junction formation, with implications for synaptic remodeling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1900026","count":5},{"id":"GO:0046847","count":5},{"id":"GO:0007264","count":5},{"id":"GO:0070830","count":4},{"id":"GO:0090263","count":4}]},{"hash":"1453270526943852994","title":"Neuronal Actin Dynamics and Axonogenesis","description":"This cluster is dominated by actin cytoskeleton remodeling and Rho/GTPase signaling terms (actin filament organization, regulation of Rho signaling, positive regulation of GTPase activity) and includes neuronal development processes such as axonogenesis and long-term synaptic potentiation, suggesting a module of actin-driven neuronal growth and synaptic remodeling. Additional terms on membrane remodeling (plasma membrane tubulation, regulation of endocytosis) and myelination/heart development components indicate broader but related roles, with the core theme being actin-dependent neuronal dynamics.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0097320","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0007015","count":3},{"id":"GO:0007507","count":2}]},{"hash":"2227520535138737368","title":"Unknown","description":"The terms span diverse processes (translation initiation/reinitiation, transcription, pigmentation, various transports, development, and antibiotic response) with no single shared function or pathway, so a specific, accurate label cannot be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0001731","count":3},{"id":"GO:0043473","count":3},{"id":"GO:0006351","count":3}]},{"hash":"562074385607741781","title":"Ubiquitin-Proteasome Degradation and Innate Antiviral Defense","description":"This cluster centers on ubiquitin-dependent proteolysis (SCF-dependent and ERAD pathways) and autoubiquitination, alongside innate immune signaling (MyD88-dependent TLR) and defense against virus, indicating a coordinated role in protein turnover tied to antiviral innate responses.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":10},{"id":"GO:0042787","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0030433","count":4}]},{"hash":"1224056627531139540","title":"Neural and cartilage development with metal transport","description":"This cluster shows strong representation of metal ion transport (zinc and cadmium, plus potassium import) alongside developmental processes, especially neuron development and cartilage condensation, with related multicellular development and sensory neuron\u2013related terms. The core theme appears to be ion transport linked to neural/skeletal development, despite some noisy terms. ","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071577","count":3},{"id":"GO:0070574","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0009636","count":3}]},{"hash":"1587446221999733699","title":"DNA repair and RNA regulation cluster","description":"The presence of GO terms tied to DNA repair (base-excision repair, DNA recombination) and RNA-based regulation (regulatory ncRNA-mediated gene silencing, nonsense-mediated decay, transcriptional regulation related to nucleic acids) suggests a core function in nucleic acid maintenance and post-transcriptional control. A few terms appear peripheral (striatum development, renal water transport, redox homeostasis), but the dominant theme centers on genome integrity and RNA regulation.","confidence":"Medium","size":21,"edges":43,"triangles":32,"max_degree":14,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0046856","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0000184","count":2},{"id":"GO:0021756","count":2}]},{"hash":"102114783964006938","title":"TORC1-Regulated Growth Signaling","description":"This cluster is dominated by TORC1 signaling and several related phosphorylation/kinase activity terms, with supporting links to GTPase activity, RNA polymerase III\u2013mediated transcription, vesicle transport, and cell division. Collectively these terms point to growth-control and signaling coordination centered on TORC1, making this a coherent label. However, the presence of more general terms (e.g., broad phosphorylation and transport processes) means the connection is strong but not exclusive, so a Medium confidence.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0033674","count":5},{"id":"GO:0038202","count":5},{"id":"GO:0070262","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0051028","count":5}]},{"hash":"1048772649008754006","title":"Vascular and Epithelial Development Signaling","description":"These proteins show GO terms tied to endothelial tube formation, polarized epithelial differentiation, and smooth muscle development, suggesting a theme of vascular and epithelial tissue development. Additional terms for cytokine production, LPS signaling, and Rac-mediated pathways point to associated immune and signaling processes, while apoptosis indicates stress or turnover. Some outliers (antibiotic biosynthetic process, ubiquitination regulation, synaptic vesicle transport) may reflect broader cellular regulation rather than a single cohesive pathway, but the core signal centers on differentiation and signaling in vascular/epithelial contexts.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0097498","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0050663","count":1},{"id":"GO:0048745","count":1}]},{"hash":"540035630472172799","title":"V(D)J Recombination and DNA Repair in Immune Cells","description":"GO terms point to DNA repair (NER, SSB, NHEJ) and lymphocyte receptor rearrangement (TCR and IgV(D)J recombination), plus related processes like DNA replication and translesion synthesis. The immune development term pro-B cell differentiation reinforces the immune-specific context. Together, they describe a functional cluster of proteins involved in DNA rearrangement and repair during lymphocyte development.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006297","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0033153","count":3},{"id":"GO:0042276","count":2},{"id":"GO:0033152","count":2}]},{"hash":"1002600525124144739","title":"Cytoskeletal Dynamics in Development and Migration","description":"The terms cluster around cytoskeletal regulation and movement (positive regulation of GTPase activity; microtubule-based movement; cell migration) and neural development signals (spinal cord development; mRNA transport). TORC1 signaling and serine dephosphorylation imply growth/signaling integration with cytoskeletal processes. Overall, this suggests cytoskeleton-driven development and migration, particularly in neural contexts, with a few outliers such as heart contraction regulation. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007018","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0051028","count":2}]},{"hash":"1002643603303721313","title":"Multicellular Development and Transcription","description":"Based on the top GO terms, the cluster is dominated by developmental processes (male gonad development, skin development, multicellular organism development and growth) tied to a core transcriptional mechanism (DNA-templated transcription). This suggests proteins commonly function in driving developmental programs via gene regulation. While there are peripheral terms related to stress responses, aging, and immune defense, these are less central to the main theme. Therefore, the label reflects the core association with multicellular development and transcriptional control.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008584","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0070059","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0007275","count":6}]},{"hash":"2106180100850981260","title":"Ubiquitin-dependent protein turnover and RNA processing","description":"The term set centers on ubiquitination (K11-linked ubiquitination) and APC-dependent protein degradation, plus box C/D snoRNP assembly, pointing to protein turnover and RNA processing as core themes. Additional terms on translation initiation during ER stress and histone modification support a broader role in gene-expression regulation and cellular homeostasis, especially in the context of the cell cycle. Immune-related terms appear ancillary rather than defining the cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0050689","count":6},{"id":"GO:0000492","count":6},{"id":"GO:1903071","count":6},{"id":"GO:0070979","count":6}]},{"hash":"2102761858918100698","title":"Immune modulation and coagulation regulation","description":"The cluster groups proteins around immune response modulation (negative regulation of chemokine production; neutrophil-mediated killing of fungus) and vascular/tissue remodeling processes (positive regulation of blood coagulation; plasminogen activation; establishment of the endothelial barrier). This points to a coherent theme of coordinating immune activity with coagulation and vascular barrier integrity, despite some outlier terms like midbrain development and transcriptional regulation that may reflect broader annotations or pleiotropy.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0045079","count":2},{"id":"GO:0032078","count":2},{"id":"GO:0030901","count":2},{"id":"GO:0044130","count":2}]},{"hash":"701021906651081145","title":"Diverse metabolite biosynthesis and catabolism","description":"The cluster shows GO terms spanning biosynthesis and catabolism of diverse small molecules (cellulose, lipids, antibiotics, biotin, strigolactones) plus lipid signaling regulation and detoxification; there isn't a single cohesive pathway, suggesting a broad metabolic/metabolite-processing theme. Confidence: High? Actually we concluded Medium. The instruction says to output a confidence score: None, Low, Medium, or High. We'll put Medium.","confidence":"Medium","size":21,"edges":8,"triangles":0,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030245","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0019433","count":5},{"id":"GO:0098869","count":5},{"id":"GO:2000124","count":5}]},{"hash":"1247553515106223802","title":"Cofactor biosynthesis and respiration","description":"The top GO terms cluster around biosynthetic pathways for cofactors (cobalamin, phylloquinone, ubiquinone) and aerobic respiration, with additional links to polyamine biosynthesis and protein methylation. While a couple of terms touch on stress responses or nodulation that are less central, the dominant theme is biosynthesis of cofactors and energy metabolism, representing the core function of this cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0018027","count":1}]},{"hash":"760928308176770","title":"Ubiquitin-Proteasome Regulation in Oocyte Meiosis","description":"The cluster is dominated by GO terms for ubiquitin-dependent proteolysis and SCF-mediated degradation, plus spindle assembly and oocyte maturation, pointing to a coherent theme of ubiquitin-proteasome control of meiosis and oocyte development.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":10},{"id":"GO:0046785","count":8},{"id":"GO:0006516","count":8},{"id":"GO:0021993","count":8},{"id":"GO:0042787","count":8}]},{"hash":"1921880077010087568","title":"Ubiquitin-Driven Proteostasis and Stress Signaling","description":"The top GO terms cluster around ubiquitin-mediated protein turnover and stress responses, including ER-associated degradation, K11-linked ubiquitination, and APC/C-dependent catabolic processes, along with translation initiation upregulation in ER stress. Plant-specific signals (cytokinin signaling, chlorophyll biosynthesis) and organelle organization terms (cilia, photoreceptor outer segments) broaden the context but still fit within proteostasis networks that regulate protein quality control across compartments. Overall, the common theme is proteostasis and stress-responsive regulation of protein turnover and translation, rather than a single defined pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0050689","count":5},{"id":"GO:1903071","count":5},{"id":"GO:0060296","count":5},{"id":"GO:0035845","count":5}]},{"hash":"1218314306795444953","title":"Ribosome biogenesis and translation","description":"The top GO terms point to ribosome biogenesis (including small/large subunit processes) and cytoplasmic translation, as well as tRNA modification, indicating a cluster of proteins involved in ribosome production and protein synthesis. Other terms like cell cycle, cell septum assembly, and conjugation with cellular fusion may reflect coupling to division in yeast but do not overshadow the core theme of ribosome assembly and function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006400","count":2}]},{"hash":"2106349012846950084","title":"Unknown","description":"The terms span diverse, seemingly unrelated biological processes (neural tube development, pollen development, embryo sac development, meiotic recombination, DNA repair, methylation, nucleotide biosynthesis, ion transport, calcium signaling, cardiac action potential), with no clear cohesive theme or shared function. This heterogeneity makes it hard to assign a single, representative label, so Unknown with no confidence is appropriate.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021915","count":2},{"id":"GO:0006231","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0006302","count":1},{"id":"GO:0009555","count":1}]},{"hash":"1119807769060264719","title":"Plant seed lipid and phenylpropanoid metabolism","description":"The terms cluster around lipid metabolism (fatty acid biosynthesis, long-chain fatty acid metabolism, fatty acid import, carnitine metabolism) and phenylpropanoid pathways (phenylpropanoid metabolism, stilbene metabolism) with seed coat development, indicating seed-specific lipid storage coupled with phenylpropanoid-derived defense compounds, possibly regulated at the transcriptional level. A minor outlier term (siderophore biosynthesis) is present but does not dominate the theme.","confidence":"Medium","size":20,"edges":58,"triangles":125,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":4},{"id":"GO:0046272","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009437","count":3},{"id":"GO:0019654","count":3}]},{"hash":"2129533860528892552","title":"NO-Driven Metabolic and Nutrient Responses","description":"This cluster centers on nitric oxide biosynthesis and signaling (NO biosynthetic process, regulation of guanylate cyclase activity) together with diverse metabolic pathways (phenylacetate, carnitine, flavonoid, cysteine) and nutrient-response terms, suggesting a theme of metabolism coordinated with NO signaling and nutrient stress responses.","confidence":"Medium","size":20,"edges":41,"triangles":36,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":10},{"id":"GO:0010124","count":10},{"id":"GO:0009437","count":9},{"id":"GO:1904042","count":9},{"id":"GO:0007584","count":9}]},{"hash":"561701260106345960","title":"MAPK Signaling and mRNA Processing","description":"The cluster is dominated by GO terms for ERK1/ERK2 and p38 MAPK cascades, and cellular responses to PMA and GM-CSF, indicating a MAPK-driven signaling and stimulus-response module. RNA processing terms (splicing and polyadenylation) appear but are less central, suggesting the main theme is signaling with some ancillary RNA processing involvement.","confidence":"Medium","size":20,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0070371","count":2},{"id":"GO:1904628","count":2},{"id":"GO:0038066","count":2},{"id":"GO:0097011","count":2}]},{"hash":"618194550461818797","title":"Actin-based protrusions and cell spreading","description":"This cluster is dominated by GO terms for actin-driven structures and protrusions (lamellipodium, filopodium, microspike, and actin filament bundle assembly) along with positive regulation of adhesion-dependent spreading, pointing to coordinated actin cytoskeleton remodeling and formation of cellular protrusions. While there are additional signaling terms (B cell receptor, insulin receptor, IL-4 production) that appear, they do not override the core actin/protrusion theme. Confidence: High","confidence":"","size":20,"edges":28,"triangles":6,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":7},{"id":"GO:1900026","count":7},{"id":"GO:0046847","count":7},{"id":"GO:0043552","count":6},{"id":"GO:0030035","count":6}]},{"hash":"860028431397142369","title":"DNA replication and cell division","description":"This cluster is dominated by GO terms for DNA replication, replication initiation, and cell division (DNA replication 3, DNA replication initiation 2, cell division 2), indicating a coherent module of replication and cell-cycle machinery. While fatty acid biosynthesis and antibiotic biosynthetic terms appear (2 counts each) these do not define the main theme, which centers on DNA replication and cell cycle processes.","confidence":"High","size":20,"edges":39,"triangles":38,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006270","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0051792","count":2},{"id":"GO:0019367","count":2}]},{"hash":"402684185516031858","title":"TORC1 Growth Signaling and Ribosome Biogenesis","description":"The GO terms strongly point to TORC1 signaling as the core in this cluster, including nutrient response, ribosome biogenesis, and links to translation and cell-cycle processes; related terms like positive regulation of TORC1 and cell division suggest a TORC1-centered growth program.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0038202","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1628043565533497471","title":"Unknown","description":"The term set spans neural signaling (excitatory postsynaptic potential), glial development, and fundamental cell-cycle processes (DNA replication, G1/S transition) as well as morphogenesis, with no single overarching function clearly dominating. This diversity makes it hard to assign a specific, representative label.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0014044","count":2}]},{"hash":"265813154187387280","title":"Unknown","description":"The GO terms are highly heterogeneous: animal development (striatum development, male sex differentiation), signaling and transcription regulation (GPCR signaling regulation, steroid receptor assembly, histone modification/ubiquitination), and even plant-specific processes (cytokinin signaling, chlorophyll biosynthesis). This mix lacks a single cohesive biological function, so a concise, representative cluster name cannot be assigned.","confidence":"","size":20,"edges":5,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021756","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0070979","count":4},{"id":"GO:1902325","count":4},{"id":"GO:0016570","count":4}]},{"hash":"599382717122723719","title":"Nuclear genome maintenance and ribosome biogenesis","description":"The dominant GO terms span nuclear functions: DNA replication and DNA repair, along with RNA processing and ribosome biogenesis (including mRNA surveillance and rRNA maturation). Together they suggest a cluster of nuclear proteins involved in genome integrity and ribosome assembly, with one plant-specific outlier term (embryo sac development) among the annotations.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0071039","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0071028","count":2}]},{"hash":"1998345376807531819","title":"Metabolic Catabolism and Biosynthesis Enzymes","description":"This cluster contains GO terms spanning catabolic processes (triglyceride, diacylglycerol, cellulose catabolism) and multiple biosynthetic pathways (biotin, strigolactone, antibiotic), along with detox-related responses, indicating a broad set of metabolic processing enzymes rather than a single shared pathway. It reflects diverse metabolic functions across contexts, so a label focused on metabolic catabolism and biosynthesis is appropriate.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0019433","count":10},{"id":"GO:0098869","count":10},{"id":"GO:2000124","count":10},{"id":"GO:0030245","count":9},{"id":"GO:0009102","count":9}]},{"hash":"1505881193904125644","title":"Epigenetic Regulation and Ubiquitin-Mediated Proteolysis","description":"The top terms point to histone methylation (H3-K79, H3-K4), DNA-templated transcription, mRNA processing, and ubiquitin-proteasome processes (SCF-dependent degradation, deubiquitination). This suggests a common theme of gene expression control through chromatin modification plus post-translational regulation of proteins, with ubiquitin turnover as a key mechanism. Behavioral annotations may reflect organism-level phenotypes, but the core signal is epigenetic regulation and ubiquitin-mediated proteolysis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034729","count":4},{"id":"GO:0001662","count":4},{"id":"GO:0051568","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0031146","count":3}]},{"hash":"2258676443350273717","title":"TORC1 signaling and fatty acid metabolism","description":"The cluster shows enrichment for TORC1 signaling terms (GO:0038202) and multiple fatty-acyl-CoA related processes (both catabolic and biosynthetic), indicating a core theme of lipid metabolism linked to growth signaling. Developmental terms like spinal cord development appear but are less central to the main function. Thus, the label captures the dominant lipid metabolism theme with a TORC1-growth connection.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":3},{"id":"GO:0035264","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0010124","count":1},{"id":"GO:0036114","count":1}]},{"hash":"762947825954595824","title":"Vision-Related GPCR Signaling and Opsin Regulation","description":"The cluster is dominated by GO terms tied to visual perception (GO:0007601), GPCR internalization (GO:0002031), and regulation of opsin-mediated signaling (GO:0022400), pointing to photoreceptor GPCR signaling. Additional terms like positive regulation of GTPase activity (GO:0043547) support signaling dynamics; a few heart-related terms appear but do not define the core function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0002031","count":3},{"id":"GO:0022400","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0060048","count":3}]},{"hash":"2293089967050844775","title":"Intracellular trafficking and organelle organization","description":"The dominant GO terms point to vesicle transport routes such as Golgi to vacuole, endosome-to-Golgi retrograde transport, and lysosomal transport, along with organelle organization (chloroplast). There is also a cytoskeleton-related term, suggesting broader intracellular transport and structural remodeling; together, these indicate a coherent theme of organelle dynamics and trafficking.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0009644","count":1},{"id":"GO:0009658","count":1},{"id":"GO:0006896","count":1},{"id":"GO:0060052","count":1}]},{"hash":"1988776405192313952","title":"Microtubule organization and spindle dynamics","description":"The terms are dominated by microtubule-related processes: spindle assembly and organization in both mitosis and meiosis, microtubule nucleation, cortical microtubule arrangement, and nuclear migration driven by microtubules. A transport-related term (bicoid mRNA localization) also points to microtubule-dependent movement, supporting a cohesive theme of microtubule-based spindle dynamics rather than unrelated processes. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990734","count":1},{"id":"GO:0030472","count":1},{"id":"GO:0043622","count":1},{"id":"GO:0007058","count":1},{"id":"GO:0051415","count":1}]},{"hash":"379457324552216751","title":"Plant Metabolism and Hormone Biosynthesis","description":"The top GO terms point to plant-specific processes, notably strigolactone biosynthesis and secondary shoot formation, which indicate hormone signaling and developmental control. Additional terms reflect broad metabolic activities (stilbene and other catabolic processes, biotin biosynthesis) common in plants. Although some terms are obsolete or cross-domain, the strongest pattern is plant metabolism linked to hormone biosynthesis, especially strigolactones, justifying this label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0019433","count":5},{"id":"GO:2000124","count":5},{"id":"GO:1901601","count":4}]},{"hash":"2268537969010132400","title":"Unknown","description":"The top GO terms span both neuronal functions (glutamatergic synaptic transmission and dendrite extension) and diverse, seemingly unrelated processes (autophagosome engulfment, ribosomal export, T cell anergy, dolichyl phosphate biosynthesis, and GTPase regulation). There is no single cohesive function or pathway tying all terms together, and the zero edges suggest the proteins do not form a tight functional cluster. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":2},{"id":"GO:1903861","count":2},{"id":"GO:0010794","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0030579","count":2}]},{"hash":"1481255519965348352","title":"Phytochrome signaling and light-regulated transcription","description":"The top GO terms point to light perception (red/far-red phototransduction, detection of visible light), chromophore/tetrapyrrole linkage, and transcriptional regulation, all characteristic of phytochrome receptors coupling light perception to DNA-templated transcription. This cluster likely represents a module of phytochrome-mediated signaling that modulates transcription in response to light.","confidence":"High","size":19,"edges":125,"triangles":439,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":11},{"id":"GO:0018298","count":10},{"id":"GO:0017006","count":10},{"id":"GO:0000160","count":10},{"id":"GO:0009585","count":10}]},{"hash":"1666515488890478381","title":"Kinase signaling and cell cycle checkpoints in development","description":"This cluster centers on phosphorylation and kinase signaling (peptidyl-threonine phosphorylation, collagen-activated RTK signaling, general phosphorylation terms) and connects to cell cycle checkpoint pathways (spindle assembly and intra-S checkpoints), with contributing links to neural development terms (Bergmann glial differentiation, corpus callosum development). The overarching theme appears to be phosphorylation-driven signaling that governs cell division and development, with some immune signaling context. ","confidence":"Medium","size":19,"edges":87,"triangles":140,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007037","count":19},{"id":"GO:1904531","count":19},{"id":"GO:0007094","count":19},{"id":"GO:1902002","count":19},{"id":"GO:0001806","count":19}]},{"hash":"2273866001606543275","title":"Cell migration and cytoskeletal remodeling","description":"This cluster is dominated by GO terms related to cell movement and cytoskeletal dynamics across multiple contexts (T cell, smooth muscle, germ-band extension, cerebral cortex migration) and includes adhesion and signaling components (Rho signaling, myosin II organization). Although a couple terms are unrelated or obsolete, the prevailing theme centers on migration and cytoskeletal regulation during development and tissue remodeling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006012","count":4},{"id":"GO:0035024","count":4},{"id":"GO:0060055","count":4},{"id":"GO:1904901","count":4}]},{"hash":"638087176797796820","title":"Neuronal cytoskeletal dynamics and trafficking","description":"The top GO terms cluster around actin-based protrusions (filopodium assembly and its regulation), small GTPase signaling, cell spreading/adhesion, endocytosis, and protein turnover, with a neuronal signal indicated by GABAergic synaptic transmission. Together, these reflect cytoskeletal remodeling and vesicle trafficking processes central to synapse function and neuronal connectivity.","confidence":"Medium","size":19,"edges":32,"triangles":0,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051489","count":9},{"id":"GO:0046847","count":9},{"id":"GO:0045792","count":9},{"id":"GO:1900026","count":9},{"id":"GO:0051932","count":9}]},{"hash":"748435307355908599","title":"ER-Golgi transport and translation initiation","description":"This cluster is dominated by GO terms for ER-to-Golgi and Golgi-to-ER vesicle transport, with several GTPase regulation terms, indicating a vesicle trafficking theme. It also features multiple terms related to translation initiation, preinitiation complex formation, translation reinitiation, and IRES-dependent translation, suggesting involvement of translation regulation or initiation factors. The co-occurrence of trafficking and translation-related terms points to a multifunctional or overlapping module that connects vesicle trafficking with translational control, potentially including viral translation elements.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0006890","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007584","count":3}]},{"hash":"2173074284292542212","title":"Broad-Substrate Membrane Transporters","description":"This cluster is dominated by GO terms for transmembrane transport of diverse substrates (arabinose, galactose, sialic acid, nitrate, xenobiotics, 4-hydroxyphenylacetate, sodium ions) and includes a vesicular transporter term (neurotransmitter loading into synaptic vesicle). The shared function is membrane transport rather than a single substrate, indicating a group of transporter proteins with broad specificity.","confidence":"High","size":19,"edges":18,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0042128","count":3}]},{"hash":"2184855069150773220","title":"Unknown","description":"The GO terms span immune regulation (negative regulation of neutrophil degranulation and cellular extravasation), development (brain development and blood vessel remodeling), gene expression (DNA-templated transcription), intracellular trafficking (ER-Golgi and Golgi-ER transport), cell division (mitotic spindle assembly), and other varied processes (pigmentation, GTPase activity). This broad, non-overlapping assortment provides no single shared function or pathway to unite the cluster, so a coherent specific label isn\u2019t supported.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043314","count":2},{"id":"GO:0002692","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0006351","count":2}]},{"hash":"704007866560272122","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0072583","count":3},{"id":"GO:0050975","count":3},{"id":"GO:0033138","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0043149","count":3}]},{"hash":"598251034377197531","title":"Amino acid metabolism and energy production","description":"The top GO terms cluster around amino acid catabolism (phenylalanine), serine biosynthesis, and gluconeogenesis, along with mitochondrial ATP synthesis, indicating a cluster focused on metabolism and cellular energy generation; phosphorylation/dephosphorylation and transport further support regulatory and metabolic activity, while a few outliers (embryonic development, cytolysis) do not override the main theme.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0006559","count":3},{"id":"GO:0016310","count":3}]},{"hash":"1970344952853818452","title":"RNA processing and ribosome biogenesis","description":"This cluster centers on RNA metabolism, featuring cytoplasmic translation, mRNA processing and splicing via the spliceosome, mRNA export, and maturation of rRNA species, indicating a cohesive role in RNA processing and ribosome assembly.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0006378","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0000463","count":2}]},{"hash":"2283257475574939733","title":"Bacterial transcriptional regulation and signaling","description":"DNA-templated transcription and its regulation, plus phosphorelay signal transduction and chemotaxis, point to a bacterial regulatory network theme. Some outliers like placenta development or chlorophyll/tetrapyrrole related GO terms do not fit well, but the dominant terms indicate transcriptional control and signaling proteins. Therefore the cluster is best labeled as Bacterial transcriptional regulation and signaling.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030435","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0018298","count":2},{"id":"GO:0006457","count":2}]},{"hash":"930533647125081021","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":151,"triangles":670,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2}]},{"hash":"2215885065398023202","title":"Translation and RNA Regulation","description":"The top GO terms are dominated by translation-related processes (translation, translational initiation, and regulation of translational fidelity), together with RNA-level regulation such as regulatory ncRNA-mediated gene silencing and negative regulation of rRNA processing, indicating a cluster focused on protein synthesis and RNA regulation. Some outliers (DNA repair, isopentenyl diphosphate biosynthesis) likely reflect background housekeeping functions.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006378","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006450","count":2}]},{"hash":"255319277192659535","title":"Chromatin modification and transcription regulation","description":"This cluster is driven by GO terms for nucleosome assembly and histone methylation, along with positive regulation of transcription by RNA polymerase II, indicating epigenetic control of gene expression. The presence of several histone modification terms (H3-K27, H3-K9, H4-K20) reinforces a chromatin-centric function, even though a few terms relate to dexamethasone response or myotube development. Overall, it appears to group proteins involved in chromatin modification and transcriptional regulation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0045944","count":2},{"id":"GO:1904772","count":1},{"id":"GO:0098532","count":1},{"id":"GO:0034771","count":1}]},{"hash":"2280902722684439771","title":"Cytoskeleton remodeling and vesicle trafficking","description":"The top GO terms strongly point to actin dynamics and vesicle trafficking (pointed-end actin filament capping, lamellipodium morphogenesis, COPII vesicle coating regulation, and phagocytic vesicle processing), suggesting a cohesive theme around cytoskeletal remodeling and vesicle transport. Some terms appear peripheral or species-specific (e.g., abscisic acid biosynthesis, nitrite transport), which adds noise but does not override the main cytoskeletal/trafficking signal.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0032435","count":1},{"id":"GO:1903923","count":1},{"id":"GO:0045714","count":1}]},{"hash":"1893710534276747376","title":"Negative regulators of NF-\u03baB signaling and inflammation","description":"This cluster centers on proteins that suppress inflammatory signaling and NF-\u03baB activity, as shown by GO terms for negative regulation of NF-kappaB, chronic inflammatory response, IL-1\u03b2 and IL-8 production, and CD40 signaling. The inclusion of K33- and K29-linked deubiquitination terms points to ubiquitin-editing as a mechanism of control, while muramyl dipeptide response and mucosal immunity terms tie the set to immune sensing/modulation in mucosal tissues. Overall, the proteins appear to form a functional group that dampens immune signaling rather than activates it.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902042","count":2},{"id":"GO:0002677","count":2},{"id":"GO:2000349","count":2},{"id":"GO:0002385","count":2},{"id":"GO:0032691","count":2}]},{"hash":"1019053098018984443","title":"Vesicle trafficking","description":"This cluster is dominated by GO terms tied to intracellular transport within the secretory and endomembrane systems: Golgi to vacuole transport, lysosomal transport, retrograde transport from endosome to Golgi, and dense core granule transport (both positive and negative regulation). The presence of acrosome assembly and neurofilament cytoskeleton organization further supports a theme of vesicle movement along cytoskeletal tracks and secretory pathway involvement. While there are a few broader terms (e.g., transcription regulation, tissue homeostasis), the common thread is vesicle trafficking and secretory transport.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006896","count":1},{"id":"GO:1904810","count":1},{"id":"GO:0060052","count":1},{"id":"GO:1904811","count":1}]},{"hash":"1576934594661799646","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning metabolism (glycerol metabolism, transsulfuration, redox homeostasis, molybdopterin cofactor biosynthesis), RNA modification (tRNA seleno-modification), cell cycle (mitotic M phase), development (spinal cord development), and signaling (peptidyl-tyrosine dephosphorylation). With no apparent shared biological theme and no network connectivity (edges/triangles = 0), there isn\u2019t a coherent function that ties these proteins into a single, interpretable cluster.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032447","count":1},{"id":"GO:0006071","count":1},{"id":"GO:0070329","count":1},{"id":"GO:2000220","count":1},{"id":"GO:0045454","count":1}]},{"hash":"863279279968006552","title":"Ubiquitin-Proteasome-Mediated Degradation","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes (ERAD, SCF-dependent proteasomal degradation) and broader ubiquitin-dependent proteolysis, pointing to proteasome-mediated turnover as the core function. Additional terms on histone ubiquitination and histone modification regulation suggest a linked role in chromatin dynamics and signaling (e.g., NF-kappaB, JNK). Although some terms are obsolete, the overarching theme is ubiquitin-tagged protein degradation with a chromatin regulation angle.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0042787","count":6},{"id":"GO:1903762","count":5},{"id":"GO:0070535","count":5}]},{"hash":"1989610521718708954","title":"Ubiquitin-Proteasome-Mediated Degradation","description":"The cluster is enriched for ubiquitin-dependent protein catabolic processes, SCF-dependent proteasomal ubiquitin-dependent degradation, and protein polyubiquitination, indicating a core theme of ubiquitin-mediated proteolysis. The presence of related terms like regulation of circadian rhythm and mitotic G1 DNA damage checkpoint signaling suggests this degradation system also interfaces with cell cycle control and circadian regulation, supporting a cohesive label focused on ubiquitin-proteasome\u2013driven protein turnover.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0031146","count":10},{"id":"GO:0000209","count":9},{"id":"GO:0030174","count":7},{"id":"GO:0031571","count":7}]},{"hash":"1608478159453197479","title":"Lipid signaling and adipogenesis","description":"This cluster shows enrichment for prostaglandin biosynthesis, responses to fatty acids and retinoic acid, and white fat cell differentiation, plus adiponectin-activated signaling, all pointing to lipid-mediated signaling and adipocyte differentiation. Some terms (brassinosteroid biosynthesis, uterus development) seem less directly related and may reflect annotation noise, but the dominant pattern centers on lipid metabolism and adipogenesis.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":3},{"id":"GO:0016132","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0034653","count":2},{"id":"GO:0032526","count":2}]},{"hash":"244135710496996637","title":"Muscle and Heart Development","description":"The cluster is dominated by GO terms for skeletal muscle fiber development, heart development, and cardiac muscle contraction, suggesting a muscle/heart function signature. Additional signals such as protein phosphorylation and regulation of GTPase activity, plus a hypoxia response, point to signaling and stress-adaptive processes within muscle/heart tissue. A few terms like long-term memory and mitotic cell cycle appear less connected, indicating some noise, but the core theme remains muscle/heart development and function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048741","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0060048","count":4},{"id":"GO:0007616","count":3},{"id":"GO:0007507","count":3}]},{"hash":"458672010933097449","title":"Embryonic Skin Development Signaling","description":"The cluster centers on skin development and embryonic organ development, with strong signals for development-related proliferation and signaling regulation (protein autophosphorylation, GTPase activity, serine/threonine kinase activity). The presence of mitotic cell cycle and hypoxia response terms supports a developmental program coordinating epidermal morphogenesis and growth during embryogenesis.","confidence":"Medium","size":18,"edges":44,"triangles":12,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043588","count":10},{"id":"GO:0031954","count":9},{"id":"GO:0008284","count":9},{"id":"GO:0071456","count":9},{"id":"GO:0000278","count":9}]},{"hash":"439856139518530781","title":"DNA Repair and Recombination","description":"The cluster is enriched for GO terms related to DNA replication, DNA repair, DNA recombination, and the SOS response, including DNA replication (GO:0006260), DNA repair (GO:0006281), DNA recombination (GO:0006310), and SOS response (GO:0009432), plus specific repair pathways like SDSA (GO:0045003) and gamma radiation response (GO:0071480). These together point to a cohesive theme of DNA damage recognition, repair, and maintenance of genome integrity. The translation term (GO:0006412) appears less central to the main theme and may reflect housekeeping or annotation artifacts. ","confidence":"High","size":18,"edges":75,"triangles":227,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0006268","count":5},{"id":"GO:0045003","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0071480","count":5}]},{"hash":"706486987292777844","title":"Neuronal development and synaptic signaling","description":"The top GO terms cluster around neural development, excitatory synaptic transmission, and calcium-dependent neurotransmitter exocytosis, with dopamine response and Wnt signaling pointing to dopaminergic synaptic function and neural maturation. A mitotic cell cycle term may reflect progenitor-related processes or shared components, but overall the group suggests proteins involved in establishing and modulating neural connections and signaling.","confidence":"Medium","size":18,"edges":26,"triangles":14,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":11},{"id":"GO:0045956","count":11},{"id":"GO:0007399","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0050771","count":10}]},{"hash":"68378811455903318","title":"Unknown","description":"The GO terms are highly diverse (amyloid-beta response, mitochondrial DNA repair, PARylation, energy metabolism, stress responses, development), with no clear, single functional theme binding the cluster, suggesting a heterogeneous set of proteins rather than a cohesive pathway.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010990","count":2},{"id":"GO:1904646","count":2},{"id":"GO:0043504","count":2},{"id":"GO:0070212","count":2},{"id":"GO:2001170","count":2}]},{"hash":"949752545478445249","title":"Unknown","description":"The top GO terms are a mix of development (skin and multicellular organism development), cell movement (lamellipodium assembly), neuronal guidance (sensory neuron axon guidance), immune-related phagocytosis, and distinct post-translational modification processes (N-terminal acetylation and its regulation), plus miscellaneous regulatory terms. This diverse set, with no clear, single shared function or pathway, makes it hard to assign a cohesive label to the cluster. There are no reported edges linking members, suggesting the genes may not participate in a common process in this context.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006911","count":1},{"id":"GO:0017196","count":1}]},{"hash":"892640507658105489","title":"DNA-Templated Transcription Regulation","description":"The top GO terms are dominated by DNA-templated transcription and its regulation, indicating the proteins in this cluster are primarily involved in transcriptional control. The other regulatory terms (ER stress response, protein glycosylation, and cardiac signaling) appear as secondary associations, suggesting a broader regulatory role but transcription regulation as the core function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0050913","count":1},{"id":"GO:0050882","count":1},{"id":"GO:0098910","count":1}]},{"hash":"944281740098041418","title":"Biomolecule biosynthesis and modification","description":"These proteins cluster around biosynthetic pathways (cobalamin, biotin, ubiquinone, phosphatidylcholine) and biomolecule maturation/modification (tRNA methylation, N-terminal trimethylation). Outlier terms like nodulation and immobilization response appear incidental, suggesting a general theme of production and processing of biomolecules rather than a single pathway. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":6},{"id":"GO:0035902","count":6},{"id":"GO:0009236","count":6},{"id":"GO:0014075","count":6},{"id":"GO:0006744","count":6}]},{"hash":"766032344431358566","title":"Innate Immune Receptor Signaling and Leukocyte Recruitment","description":"These proteins cluster around innate immune signaling and leukocyte interactions. The top GO terms are dominated by receptors and pathways involved in innate immune recognition (C-type lectin receptor signaling, Fc-gamma receptor signaling) and downstream activation of the complement and leukocyte adhesion processes (lectin pathway, leukocyte tethering/rolling). A few terms related to tissue morphogenesis are present but the strongest, recurring theme is immune receptor signaling and leukocyte recruitment, suggesting the cluster represents innate immune responsiveness rather than a single developmental program.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072287","count":5},{"id":"GO:0002223","count":5},{"id":"GO:0090238","count":5},{"id":"GO:0038094","count":5},{"id":"GO:0050901","count":5}]},{"hash":"1529229301828342008","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA processing and export (splicing, polyadenylation, mRNA transport) and extend to translation initiation and ribosome biogenesis, suggesting a cohesive RNA metabolism and ribosome assembly module.","confidence":"High","size":18,"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":4},{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0048025","count":4}]},{"hash":"1157677160582580298","title":"Developmental Transcription Regulation","description":"The top GO terms cluster around transcription regulation (RNA polymerase II, DNA-templated transcription) and developmental processes (pituitary gland and male gonad development), suggesting a group of proteins involved in controlling gene expression during development; some metabolic/redox terms appear as ancillary signals.","confidence":"High","size":18,"edges":17,"triangles":1,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0051572","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":4}]},{"hash":"989452298139552170","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":97,"triangles":196,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0010019","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0031426","count":2}]},{"hash":"1356362840483155852","title":"Ribosome biogenesis and RNA processing","description":"This cluster is driven by terms related to ribosomal large subunit assembly and export from the nucleus, as well as tRNA and rRNA processing, suggesting a cohesive function in ribosome biogenesis and RNA maturation; some unrelated terms may be noise.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0008033","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0000055","count":2}]},{"hash":"1089489785849331928","title":"GTPase- and GPCR-mediated signaling in heart and brain","description":"The top GO terms point to signaling and cytoskeletal processes, with emphasis on regulation of GTPase activity and GPCR signaling (including acetylcholine receptor signaling and opsin-related pathways), along with neural plasticity markers (long-term potentiation and memory) and visual perception. At the same time, heart development and cardiac muscle contraction terms indicate cardiac function. Together these terms suggest a cohesive cluster of proteins involved in GTPase- and GPCR-driven signaling that modulates both cardiac and neural processes, including cytoskeletal remodeling via actin crosslinking. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007507","count":3},{"id":"GO:0060048","count":3},{"id":"GO:1900271","count":3},{"id":"GO:0007601","count":2}]},{"hash":"67587399687315012","title":"Mitochondrial function and oxidative stress response","description":"The top GO terms point to mitochondrial activity\u2014protein import into the matrix, regulation of mitochondrial membrane permeability, and lipid metabolism (triglyceride biosynthesis)\u2014along with explicit oxidative stress response and detoxification. There are also signals of transcriptional regulation, but the strongest shared theme appears to be mitochondria-centered metabolism and stress handling, suggesting this cluster comprises mitochondrial function-related proteins coordinating metabolism and protective responses.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0010867","count":2},{"id":"GO:1903740","count":2},{"id":"GO:0046902","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0070940","count":2}]},{"hash":"1675065520020535101","title":"Diverse Transmembrane Transporters","description":"Top terms indicate a core function in transmembrane transport across diverse substrates (arabinose, sialic acid, galactose, nitrate, xenobiotics) and vesicular transport, with one outlier term (ascospore formation). This pattern suggests a cluster of membrane transport proteins handling multiple substrates rather than a single, cohesive pathway.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":2},{"id":"GO:0015751","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0015739","count":1},{"id":"GO:0006855","count":1}]},{"hash":"797243741943192854","title":"Vacuolar amino acid transport","description":"The top GO terms show transmembrane transport of several amino acids (lysine, histidine, arginine, proline) into and out of the vacuole, along with a general amino acid transport and a nitrogen starvation response. This coherent theme points to vacuolar amino acid trafficking as the cluster\u2019s function, despite zero edges. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901482","count":1},{"id":"GO:0003333","count":1},{"id":"GO:0090513","count":1},{"id":"GO:0089707","count":1},{"id":"GO:0090518","count":1}]},{"hash":"1508650123616248675","title":"Innate antiviral signaling and ubiquitination","description":"Top GO terms indicate strong enrichment for innate immune processes (innate immune response, defense response to virus, TLR7 signaling) alongside ubiquitin-dependent proteolysis and autoubiquitination, suggesting the cluster reflects antiviral innate immune signaling modulated by ubiquitination. Some other terms related to neural development and extracellular matrix may be incidental. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090141","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0051865","count":2}]},{"hash":"1688564443901691445","title":"DNA Repair and Chromatin Modification","description":"This cluster's terms cluster around DNA metabolism and chromatin state: histone acetylation/methylation regulation and DNA repair/DSB processes, along with replication-related elongation and nuclear envelope attachment. While a few terms touch on cytokinesis and adipose development as secondary signals, the dominant pattern is chromatin remodeling coupled to DNA damage response and replication.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035066","count":2},{"id":"GO:0006271","count":1},{"id":"GO:0070512","count":1},{"id":"GO:0060612","count":1},{"id":"GO:0000910","count":1}]},{"hash":"319341360141173229","title":"Integrin signaling and cell adhesion","description":"Reason: The top GO terms highlight integrin-mediated signaling and downstream ERK/MAPK cascades, coupled with processes like wound healing and regulation of cell survival (anoikis). While there are some broader or peripheral terms (autophagosome maturation, axonal defasciculation), the strongest shared theme centers on integrin-driven adhesion signaling and its role in tissue remodeling and cell survival.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:0097352","count":1},{"id":"GO:0007414","count":1},{"id":"GO:2001237","count":1},{"id":"GO:0070371","count":1}]},{"hash":"1345226927961719623","title":"Plant secondary metabolism and detoxification","description":"Most terms indicate plant metabolism and defense: strigolactone biosynthesis (a plant hormone), chlorophyll catabolism, stilbene catabolism, and 3-phenylpropionate catabolism point to specialized metabolite turnover, while secondary shoot formation reflects development. The presence of detoxification and response to toxic substances reinforces a stress-related metabolic theme. Together these GO terms suggest a plant-specific context rather than a single non-plant pathway.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0009636","count":6},{"id":"GO:0015996","count":6}]},{"hash":"710737554097909751","title":"Golgi\u2013endosome\u2013vacuole vesicle trafficking","description":"This cluster is dominated by GO terms related to vesicle transport within the secretory pathway, including Golgi to vacuole transport, endocytosis, retrograde transport between Golgi and ER, and anterograde synaptic vesicle transport. These terms point to a cohesive role in intracellular trafficking among Golgi, endosome, ER, and vacuole compartments, with a few neuron- or behavior-associated annotations likely reflecting broader tissue contexts rather than core function. High","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0009615","count":2}]},{"hash":"1297390901628102174","title":"Developmental transcription and cell cycle regulation","description":"The top GO terms center on DNA-templated transcription, mRNA processing, and DNA replication, with references to the G1/S transition and multicellular development, suggesting the cluster mainly reflects regulation of gene expression during development and cell proliferation. Immune-related terms are present but less frequent, indicating transcriptional and cell-cycle processes as the dominant theme with some ancillary immune signaling. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0000082","count":2}]},{"hash":"853254046886514703","title":"Heat-stress proteostasis and protein quality control","description":"This cluster centers on cellular stress responses and proteostasis: multiple GO terms point to heat response, ER stress\u2013associated translation regulation, and quality-control pathways such as ubiquitin-proteasome\u2013mediated nuclear quality control, along with redox homeostasis and protein trafficking to membranes/mitochondria. The shared theme is managing protein folding, trafficking, and degradation under stress conditions, with some ancillary links to DNA replication.","confidence":"Medium","size":17,"edges":68,"triangles":116,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0031204","count":5},{"id":"GO:0009408","count":5},{"id":"GO:0006260","count":5},{"id":"GO:1905259","count":5}]},{"hash":"763664019000431742","title":"Multiorgan Development","description":"The top GO terms cluster around development across multiple organs (lung, brain, digestive tract, uterus, female gonad), suggesting the proteins are broadly involved in developmental processes across tissues rather than a single organ. A few terms related to xenobiotic response and stress appear but are secondary; lipid A biosynthesis is likely noise. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0035902","count":3}]},{"hash":"939266490157477837","title":"Ubiquitin-dependent protein turnover and RNA processing","description":"The top GO terms cluster around ubiquitin-mediated protein catabolism (and its regulation) and deubiquitination, pointing to a central theme of ubiquitin-proteasome\u2013related turnover. Additionally, RNA processing and spliceosomal assembly terms suggest concurrent involvement in RNA biogenesis. Some developmental/behavioral terms appear, but they seem less central to the cluster's core function. Overall, the label emphasizes the dominant ubiquitin-driven protein turnover with RNA processing context.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903070","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0008343","count":1}]},{"hash":"294002722860896237","title":"Spliceosome-driven mRNA processing and export","description":"The cluster is dominated by GO terms tied to RNA processing in the nucleus\u2014especially mRNA splicing via the spliceosome, alternative splicing, and positive regulation of splicing, along with mRNA export and regulation of mRNA stability in response to stress. This combination points to a cohesive role in transcriptional mRNA maturation and handling rather than a single-step function, making the spliceosome-centered RNA processing theme a concise and representative label.","confidence":"High","size":17,"edges":132,"triangles":626,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":10},{"id":"GO:0045292","count":8},{"id":"GO:0006378","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0006406","count":6}]},{"hash":"186085733202968417","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":25,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0016554","count":2}]},{"hash":"1565653749521999869","title":"Translation machinery with translational control","description":"This cluster is dominated by GO terms tied to translation and its regulation: translation, translational initiation/termination, ribosomal subunit assembly, cytoplasmic translation, and selenocysteine incorporation, with positive regulation of cytoplasmic translation. The deadenylation-dependent mRNA decay term supports a linked layer of mRNA turnover associated with translation control. A few terms (glial cell proliferation, response to antibiotic) may reflect context rather than core function.","confidence":"High","size":17,"edges":130,"triangles":595,"max_degree":16,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":4},{"id":"GO:0006415","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0002181","count":3}]},{"hash":"1344610304883631618","title":"Embryogenesis and Chromatin Modification","description":"The proteins in this cluster are linked to embryonic development processes (gastrulation, in utero embryonic development, general embryogenesis, and cell proliferation) and to chromatin-level regulation (histone deacetylation, histone H3-K4 demethylation, and regulation of chromatin binding). This combination points to a cohesive role in epigenetic control of gene expression during development, with potential connections to apoptosis as part of developmental regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0007369","count":5},{"id":"GO:0016575","count":5},{"id":"GO:0008283","count":5},{"id":"GO:0007568","count":5}]},{"hash":"315410960984702786","title":"Mitochondrial Respiration and Fe-S Cluster Assembly","description":"This cluster shows enrichment for GO terms tied to the respiratory electron transport chain and redox biology (respiratory chain, oxidative stress response, regulation of cytochrome c release) as well as Fe-S cluster biogenesis (iron incorporation into metallo-sulfur clusters and regulation of Fe-S assembly). The combination points to mitochondrial energy metabolism and metal-sulfur cluster maturation as a unifying theme; other terms (beta-ketoadipate pathway, proprioception) may reflect ancillary associations or annotation noise.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0022904","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0042952","count":1}]},{"hash":"1089772868524581688","title":"Immune Regulation and Deubiquitination","description":"The terms cluster around downregulation of inflammatory signaling (IL-1\u03b2 and IL-8), mucosal immune responses, and suppression of CD40 signaling, along with deubiquitination activities (K33- and K29-linked). The presence of muramyl dipeptide response suggests innate immune sensing. While tRNA processing appears, the dominant theme is immune regulation via ubiquitin-mediated signaling control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:1902042","count":1},{"id":"GO:0002677","count":1},{"id":"GO:2000349","count":1},{"id":"GO:0002385","count":1}]},{"hash":"707820146422803460","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0006310","count":2}]},{"hash":"1663067781259294333","title":"Cardiac development and signaling","description":"This cluster is centered on cardiac-related processes: heart development and secondary heart field specification, plus regulation of heart contraction and catecholamine secretion, all pointing to cardiac differentiation and signaling pathways. While there are broader signaling terms (intracellular signal transduction, GTPase activity) and an outlier fat cell differentiation term, the predominant themes are cardiac development and regulation of cardiac function, suggesting a cohesive cardiac development/signaling module.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":5},{"id":"GO:0045444","count":4},{"id":"GO:0007507","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0009409","count":3}]},{"hash":"729334926701933490","title":"RNA Pol II Transcription Regulation","description":"Most proteins in this cluster are annotated with GO terms centered on DNA-templated transcription and regulation of transcription from RNA polymerase II promoters. The dominant terms are \u201cDNA-templated transcription\u201d and \u201cpositive regulation of transcription from RNA polymerase II promoter\u201d under various conditions, with several obsolete variants, indicating a coherent theme of transcription initiation/control rather than a specific metabolic pathway. A few metabolism-related terms appear, but they are much less represented and do not define the cluster. Overall, the cluster seems to group proteins involved in transcriptional regulation by RNA polymerase II.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0035959","count":3},{"id":"GO:1904741","count":3},{"id":"GO:1900399","count":3},{"id":"GO:0035948","count":3}]},{"hash":"616010527464892957","title":"Unknown","description":"The terms span visual perception, heart development and cardiac contraction, plus various signaling and regulatory processes, with no single theme uniting all terms. This heterogeneity makes it hard to assign a coherent, tissue-specific label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007601","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0022400","count":2},{"id":"GO:0007051","count":2}]},{"hash":"2066783899109534400","title":"Fungal RNA Pol II Transcription Regulation","description":"Top GO terms point to DNA-templated transcription and regulation of transcription from RNA polymerase II promoter, with context in nutrient signals, metabolism, and secondary metabolism (e.g., aflatoxin biosynthesis). This pattern suggests a cluster of fungal transcription regulators modulating RNA Pol II-driven gene expression across primary and secondary metabolic pathways.","confidence":"High","size":16,"edges":64,"triangles":116,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0060303","count":4},{"id":"GO:0035959","count":4},{"id":"GO:1904741","count":4},{"id":"GO:1900399","count":4}]},{"hash":"542996444427389012","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":76,"triangles":177,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0070417","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4}]},{"hash":"2023300332923594239","title":"Cajal body-associated RNA localization and telomere maintenance","description":"The cluster\u2019s top GO terms are centered on scaRNA localization to Cajal bodies, positive regulation of telomerase RNA localization to Cajal bodies, and establishment of protein localization to telomeres, suggesting a theme of nuclear RNA processing and telomere-related localization. While several terms also touch on general protein folding and mitochondrial import, the strongest signal is the Cajal body/telomere axis.","confidence":"Medium","size":16,"edges":102,"triangles":375,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0051085","count":5},{"id":"GO:0045041","count":5},{"id":"GO:0071866","count":5},{"id":"GO:0002931","count":5},{"id":"GO:0090666","count":5}]},{"hash":"894494122540306526","title":"Unknown","description":"The top GO terms span very different biological areas (bone differentiation, angiogenesis, lipid metabolism, oxygen transport, transcription termination, protein repair, mitochondrion targeting, cell adhesion/migration, bacterial motility, proteasome storage granule assembly), with no clear shared function or pathway tying the cluster together. This makes it unlikely to assign a specific, cohesive label beyond Unknown.","confidence":"","size":16,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030091","count":2},{"id":"GO:0015671","count":2},{"id":"GO:1902906","count":1},{"id":"GO:0001649","count":1},{"id":"GO:0006626","count":1}]},{"hash":"2044062552741613925","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000463","count":3}]},{"hash":"645442483845335906","title":"Unknown","description":"The Top Terms are too diverse to define a shared function (toxic-substance response, dephosphorylation, IL-17 signaling regulation, transporter activity regulation, coumarin metabolism, fluoride response, lipoprotein oxidation regulation, protein amidation, miRNA-mediated translation inhibition, binding regulation), and there are no interactions to suggest a cohesive pathway. None","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009636","count":6},{"id":"GO:0016311","count":5},{"id":"GO:1903883","count":5},{"id":"GO:0032411","count":5},{"id":"GO:0046226","count":5}]},{"hash":"1692930904182835801","title":"LPS and lipid A biosynthesis with biofilm formation","description":"Dominant terms cluster around lipopolysaccharide and lipid A biosynthesis and related outer membrane assembly, with biofilm formation supporting a bacterial envelope/community activity theme. Several unrelated/obsolete terms are present, but the core signals point to Gram-negative cell envelope biogenesis and associated biofilm behavior.","confidence":"Medium","size":16,"edges":35,"triangles":42,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045493","count":1},{"id":"GO:0034232","count":1},{"id":"GO:0042244","count":1}]},{"hash":"1471845777108627461","title":"Ubiquitin-Proteasome Proteolysis & Stress Response","description":"The cluster is dominated by ubiquitin-dependent proteolysis and proteasomal degradation terms (SCF-dependent ubiquitin/proteasome pathways and protein polyubiquitination), with supporting signals for DNA damage checkpoints and stress responses (arsenic, cadmium) and some neuronal context (synapse assembly and neuron apoptotic signaling). This points to a cohesive theme of proteostasis\u2014protein turnover via ubiquitin-proteasome systems\u2014across cellular and neuronal stress contexts, with some cell-cycle notes.","confidence":"High","size":16,"edges":25,"triangles":6,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0042787","count":10},{"id":"GO:0031571","count":8},{"id":"GO:1902916","count":7},{"id":"GO:0000209","count":7}]},{"hash":"1000963780362034661","title":"Cell Migration and Cytoskeletal Remodeling","description":"These proteins are enriched for GO terms related to cell movement (T cell migration, ameboid migration, germ-band extension, cortical tangential migration) and cytoskeletal control (Rho signaling, myosin II filament organization, cell-matrix adhesion). Angiogenesis and differentiation in muscle and cardiac contexts further support a theme of migration and remodeling during development and tissue repair. ","confidence":"High","size":16,"edges":87,"triangles":245,"max_degree":15,"top_function":"wound healing","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0035024","count":9},{"id":"GO:0060055","count":9},{"id":"GO:1904901","count":9},{"id":"GO:0072678","count":9}]},{"hash":"1546267438712346733","title":"Neuronal development and dendrite morphogenesis","description":"The cluster is enriched for nervous system development, dendrite morphogenesis, and neural tube closure, with supportive signals for excitatory synaptic activity and dopamine-responsive pathways, suggesting roles in neuronal growth and synapse formation. The presence of translation and ribosome biogenesis terms indicates active protein synthesis underpinning morphogenesis and maturation of neurons, aligning with a coherent theme of neuronal development and synaptic setup.","confidence":"High","size":16,"edges":19,"triangles":14,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0007399","count":3},{"id":"GO:0048813","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001843","count":3}]},{"hash":"1125688221385074551","title":"Transcriptional Regulation Across Tissues","description":"The cluster is driven by transcription-related GO terms (DNA-templated transcription; negative regulation of transcription by RNA polymerase II), with several entries pointing to tissue differentiation (mammary gland and Leydig cell development). This suggests proteins involved in context-specific transcriptional control across different tissues, though a few terms appear unrelated (plant stomatal opening, yeast spindle dynamics), likely reflecting broader or cross-species annotations.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0033327","count":2},{"id":"GO:0033598","count":2},{"id":"GO:2001165","count":2},{"id":"GO:0060749","count":2}]},{"hash":"2197056801977673392","title":"Ribosome Biogenesis, ERAD, and Nutrient Signaling","description":"The top GO terms cluster around ribosome assembly and rRNA maturation, along with protein quality control via ubiquitination/ERAD and growth/nutrient signaling (TORC1, nutrient response). This points to a theme of ribosome production coupled with ER-associated protein homeostasis under nutrient conditions, with a few terms that may be less directly related.","confidence":"Medium","size":16,"edges":20,"triangles":7,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:1904263","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0007338","count":3},{"id":"GO:0030433","count":3}]},{"hash":"1447288373725876676","title":"Ribosome biogenesis and cytoplasmic translation","description":"The cluster is dominated by GO terms related to ribosome assembly and function (ribosome biogenesis, ribosomal subunit export from nucleus, cytoplasmic translation, and tRNA modification), indicating a coherent theme around protein synthesis machinery. Additional terms on the cell cycle and septum assembly likely reflect growth coordination accompanying ribosome production, reinforcing a general \"growth/protein synthesis\" theme. However, the core signal remains ribosome-related processes rather than specific interactions between proteins.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0000747","count":5},{"id":"GO:0000055","count":5},{"id":"GO:1903833","count":5},{"id":"GO:0002181","count":5},{"id":"GO:0007049","count":5}]},{"hash":"2255107929883697825","title":"Diverse stress and metabolism responses","description":"Based on GO terms, the proteins touch multiple stress and metabolic processes: xenobiotic response, redox homeostasis, aluminum ion response, lipopolysaccharide response, abscisic acid biosynthesis, camphor catabolic process, thiamine biosynthetic process, and other scattered processes. There is no clear single pathway or biological process dominating the set; thus the cluster appears heterogeneous, representing a collection of proteins involved in various environmental responses and basic metabolism rather than a cohesive functional module.","confidence":"Low","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":5},{"id":"GO:0042493","count":5},{"id":"GO:0043046","count":5},{"id":"GO:0045454","count":4},{"id":"GO:0007369","count":4}]},{"hash":"492293952230839359","title":"Vitamin and cofactor biosynthesis cluster","description":"The proteins in this cluster are enriched for biosynthetic processes across vitamins (biotin, cobalamin), cofactors (ubiquinone), and lipids (phosphatidylcholine), with additional related modifications like tRNA and N-terminal methylation suggesting coordinated metabolic maturation steps. While there are a few odd terms (nodulation, xenobiotic response), the dominant theme is biosynthesis of essential small molecules and membranes, justifying the label as a Vitamin and cofactor biosynthesis cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":7},{"id":"GO:0030488","count":7},{"id":"GO:0035690","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0009877","count":6}]},{"hash":"309843766357819125","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0031087","count":1},{"id":"GO:0046496","count":1},{"id":"GO:0006744","count":1}]},{"hash":"217656713959928745","title":"Sphingolipid and Phospholipid Metabolism","description":"This cluster is characterized by GO terms tied to lipid processes, notably sphingosine/sphinganine metabolism and phospholipid catabolism/dephosphorylation, plus phosphatidylglycerol biosynthesis, pointing to a theme of sphingolipid and phospholipid metabolism and membrane lipid turnover.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035233","count":1},{"id":"GO:0044329","count":1},{"id":"GO:1902068","count":1},{"id":"GO:0006655","count":1},{"id":"GO:0006668","count":1}]},{"hash":"1988217445325028350","title":"Mitochondrial Metabolite Transport & Insulin Response","description":"The cluster is dominated by GO terms tied to mitochondria and metabolite transport (nucleotide import into mitochondrion, thiamine pyrophosphate and thiosulfate transport, heme transport, magnesium export) plus mitochondrial-related responses and a subset related to insulin signaling and glucose-stimulated insulin regulation, suggesting a coherent theme of mitochondrial transport/metabolism influencing insulin response.","confidence":"Medium","size":16,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":8},{"id":"GO:0000002","count":7},{"id":"GO:0097274","count":7},{"id":"GO:0015886","count":7},{"id":"GO:0030974","count":7}]},{"hash":"175070481725810393","title":"Transmembrane Transport Proteins","description":"The top GO terms are dominated by diverse transmembrane transport activities, covering sugars, vitamins, nitrite/nitrate, xenobiotics, and even neurotransmitter loading into synaptic vesicles. This points to a cluster of membrane transport proteins that mediate uptake/export of varied substrates rather than a single substrate class.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":3},{"id":"GO:0015757","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0015707","count":3}]},{"hash":"220241502915854236","title":"Redox detoxification and glutathione metabolism","description":"This cluster is dominated by GO terms for cellular oxidant detoxification, redox homeostasis, and glutathione derivative biosynthesis, along with xenobiotic and nitrogen compound detoxification and prostaglandin biosynthesis. These common themes point to a cohesive role in antioxidant defenses and detoxification pathways, with some secondary links to immune regulation and development. ","confidence":"High","size":16,"edges":118,"triangles":533,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":14},{"id":"GO:2000255","count":10},{"id":"GO:0045454","count":10},{"id":"GO:2001237","count":9},{"id":"GO:0014003","count":9}]},{"hash":"825890635393979533","title":"Unknown","description":"This cluster shows a mix of plant-specific processes (strigolactone biosynthetic process, secondary shoot formation, stilbene and phenylpropanoid catabolism) and animal/metabolic terms (regulation of cilium beat frequency, fat cell differentiation), plus general metabolism terms (oxidation\u2013reduction, nitrogen utilization, SNARE regulation). The absence of a single coherent function or pathway linking all proteins makes it difficult to assign a shared label, so Unknown with None confidence. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0035544","count":2},{"id":"GO:0060296","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0019433","count":2}]},{"hash":"2156268608094340022","title":"Neural synapse formation and circadian regulation","description":"Enriched neural/synaptic signals: neurexin clustering and spine morphogenesis point to synaptic organization, and circadian regulation hints at neural timing control. Retina-related term aligns with the visual system, while some outliers (osteoblast, cellulose catabolic) likely represent noise.","confidence":"Medium","size":16,"edges":115,"triangles":492,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060041","count":6},{"id":"GO:0002076","count":6},{"id":"GO:0042493","count":6},{"id":"GO:0002087","count":6},{"id":"GO:0097115","count":5}]},{"hash":"458421652229737005","title":"Cellular stress response and signaling regulation","description":"The GO terms show responses to hypoxia and toxic substances, plus negative regulation of extracellular matrix disassembly and receptor recycling, and regulation of lipoprotein pathways, all pointing to cells adjusting to stress while modulating signaling and trafficking pathways. Some terms (sporulation, enkephalin processing) are less immediately aligned but can reflect proteolytic processing active under stress. Overall, the cluster seems to group proteins involved in stress responses and regulatory signaling rather than a single precise pathway.","confidence":"Medium","size":16,"edges":26,"triangles":8,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0010716","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0008284","count":2}]},{"hash":"1674179295008829894","title":"Gene expression and cell cycle regulation","description":"These proteins appear to cluster around gene expression control and cell cycle processes: transcription (DNA-templated transcription), mRNA processing, and chromatin-associated events (histone methylation), along with regulation of protein ubiquitination, which ties to protein turnover; plus mitotic spindle assembly and negative regulation of G0 to G1 transition, indicating coordination of transcriptional activity with cell cycle progression. The platelet activating factor biosynthetic process seems peripheral but does not dominate the cluster\u2019s theme. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0006663","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0031397","count":2}]},{"hash":"1230708159533723314","title":"Cell migration and trafficking regulation","description":"The cluster centers on processes that control cell movement and associated signaling and trafficking, including negative regulation of endothelial cell migration and sprouting angiogenesis, endothelial lumen extension, Rac and PKC signaling regulation, endocytic recycling, and Golgi maintenance, with additional links to broader developmental and cytoskeletal modulation (e.g., dendritic spine remodeling). While the GO terms span diverse contexts, the unifying theme is coordinated regulation of cell movement, signaling pathways, and intracellular trafficking.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090051","count":3},{"id":"GO:0097498","count":3},{"id":"GO:0090038","count":2},{"id":"GO:0090334","count":2},{"id":"GO:0032760","count":2}]},{"hash":"1892224822942290206","title":"Neural development and glutamatergic synaptic regulation","description":"This cluster is enriched for terms about brain and nervous system development, regulation of synaptic vesicle exocytosis, and regulation of glutamatergic transmission, together with neuronal migration and branching. The conjunction of developmental and synaptic regulation terms points to a coherent theme of neural development with specific emphasis on glutamatergic synapses.","confidence":"High","size":15,"edges":4,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":9},{"id":"GO:0010796","count":8},{"id":"GO:0031384","count":8},{"id":"GO:0007420","count":8},{"id":"GO:2000172","count":7}]},{"hash":"2282112575326155622","title":"Chemical stress response and gene regulation","description":"These proteins show multiple GO terms tied to chemical stress responses (response to toxic substance, response to fluoride, coumarin catabolic process) along with broad regulatory functions (dephosphorylation, miRNA-mediated gene silencing, regulation of transporter activity and binding, lipoprotein oxidation regulation). The common theme appears to be cellular handling of chemical challenges coupled with regulatory control of signaling, transport, and gene expression, rather than a single specific pathway.","confidence":"Medium","size":15,"edges":13,"triangles":0,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009636","count":11},{"id":"GO:0016311","count":9},{"id":"GO:1903883","count":9},{"id":"GO:0032411","count":9},{"id":"GO:0046226","count":9}]},{"hash":"180307572067979955","title":"Mitotic Regulation by Ubiquitin-Proteasome","description":"Most prominent terms relate to mitotic cell cycle, spindle assembly, and ubiquitin-dependent proteasomal degradation (SCF- and APC/C-mediated). This points to coordinated control of mitosis via targeted proteolysis, with actin remodeling accompanying cell division. Peripheral terms such as cadmium response and defense/spinal cord development appear less central. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030042","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0031146","count":5},{"id":"GO:0031145","count":5}]},{"hash":"1037186884845233760","title":"Cell Cycle and Development Proteins","description":"The top GO terms are dominated by cell division and mitotic cell cycle, with multiple development-related terms (nervous system development, dendritic spine development, hair follicle placode formation) as well as protein complex localization, suggesting a cluster of proteins coordinating cell proliferation with developmental processes. The presence of innate immune response terms adds some breadth but does not override the central theme of proliferation and development-related functions. ","confidence":"Medium","size":15,"edges":17,"triangles":1,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0000278","count":6},{"id":"GO:0051291","count":6},{"id":"GO:0045087","count":5},{"id":"GO:0007399","count":4}]},{"hash":"1171618702399993508","title":"Neural Development and Transcription Regulation","description":"The cluster centers on transcriptional regulation (DNA-templated transcription and positive regulation of transcription by RNA Pol II) and neural development (brain, forebrain, retina, and multicellular organism development). The presence of aggresome assembly hints at proteostasis processes that can accompany development. While there are a few terms less connected (e.g., male gonad development, fertilization), the dominant signals point to neural development coordinated with transcriptional control, justifying this label.","confidence":"Medium","size":15,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0070842","count":3},{"id":"GO:0008584","count":2}]},{"hash":"1729206686778721836","title":"Actin Dynamics and Myoblast Fusion","description":"The cluster's top terms emphasize actin filament organization and actin cortical patch assembly, along with positive regulation of myoblast fusion. This suggests a cohesive theme of actin cytoskeleton remodeling that drives muscle precursor cell fusion, with translation- and Golgi-related terms likely reflecting broader cellular roles of the included proteins.","confidence":"Medium","size":15,"edges":13,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0034720","count":2},{"id":"GO:0043686","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0031365","count":1},{"id":"GO:1901741","count":1}]},{"hash":"905569126060176644","title":"DNA Repair and PARP-Mediated Chromatin Remodeling","description":"The proteins appear to cluster around DNA damage response and chromatin regulation: single-strand break repair, replication-associated processes, and Poly-ADP-ribosylation (PARP) with links to histone modification pathways. While some terms are flagged obsolete and one term (neuron differentiation) seems unrelated noise, the dominant signal points to DNA repair activities coupled with chromatin remodeling via PARP activity.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006271","count":1},{"id":"GO:0051102","count":1},{"id":"GO:0006288","count":1},{"id":"GO:0070512","count":1},{"id":"GO:0000012","count":1}]},{"hash":"658404816914928975","title":"Ribosome biogenesis and rRNA processing","description":"The cluster is dominated by GO terms centered on maturation of SSU/LSU rRNA from tricistronic transcripts and overall ribosome biogenesis (including 5.8S maturation and large subunit biogenesis). This indicates the proteins mainly participate in ribosome assembly and rRNA processing. A few other terms (e.g., splicing, DNA replication, TORC1 signaling, microtubule movement) appear at much lower counts, likely representing secondary associations or annotation noise, but do not outweigh the ribosome-related signal.","confidence":"High","size":15,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0007018","count":2}]},{"hash":"1042816816770554094","title":"Heart and Eye Development Signaling and Transcription","description":"This cluster centers on developmental processes related to heart development, neural crest formation, and retinal/visual functions (visual perception, retinal bipolar neuron differentiation), together with signaling pathways (phosphatidylinositol-mediated signaling, Wnt calcium modulation) and transcriptional/miRNA regulatory activities. The combination suggests proteins coordinating signaling and transcription during cardiovascular and ocular development.","confidence":"High","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0007223","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010586","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1694703138979959488","title":"Ubiquitin-Dependent Proteolysis and Cell Cycle Control","description":"The top GO terms point to ubiquitin-mediated proteolysis (K11-linked ubiquitination), APC-dependent catabolic processes, and cell division, indicating a core theme of regulating the cell cycle through the ubiquitin-proteasome system. Supporting terms related to ER-associated degradation and translation during ER stress suggest broader proteostasis involvement, with snoRNP assembly and other housekeeping processes providing context for general cellular maintenance. Overall, the cluster appears to group proteins linked to controlled protein turnover and cell cycle progression, with ancillary roles in RNA processing and innate responses. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0050689","count":5},{"id":"GO:0000492","count":5},{"id":"GO:1903071","count":5},{"id":"GO:0070979","count":5}]},{"hash":"267720294588063000","title":"Unknown","description":"The list of top GO terms covers visual perception, chromosome passenger complex localization to the spindle midzone, skeletal muscle fiber development, nervous system development, B cell receptor signaling, germinal center formation, renal sodium ion absorption, circadian rhythm regulation, protein K33-linked ubiquitination, and release from viral latency. This mix indicates no single dominant function or cohesive biological theme linking the proteins, so a concise, specific cluster name cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0035853","count":1},{"id":"GO:0048741","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0050853","count":1}]},{"hash":"1852651077434422740","title":"Unknown","description":"The GO terms are highly diverse, spanning RNA splicing, cell cycle, ciliary motility, feeding behavior, heart contraction, synaptic vesicle exocytosis, and neuronal plasticity, with no single cohesive function uniting them. The lack of edges also suggests no strong functional linkage in this cluster. Therefore, a precise, representative label cannot be determined.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000253","count":1},{"id":"GO:0060296","count":1},{"id":"GO:0018095","count":1},{"id":"GO:0007049","count":1},{"id":"GO:2000825","count":1}]},{"hash":"1251358614412383252","title":"DNA Damage Response & Genome Maintenance","description":"This cluster is dominated by GO terms tied to DNA repair, replication stress, and meiotic recombination (e.g., replication fork arrest, mismatch repair in meiosis, meiotic gene conversion, p53-mediated apoptotic signaling). These point to a shared theme of genome integrity maintenance and DNA damage response, with a couple of terms (oxidative phosphorylation, isotype switching) likely reflecting broader roles or multifunctional proteins within the group.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008340","count":2},{"id":"GO:0043570","count":2},{"id":"GO:0051096","count":2},{"id":"GO:0006119","count":2},{"id":"GO:0042771","count":2}]},{"hash":"1347579522229044219","title":"Unknown","description":"The top GO terms span chloroplast thylakoid membrane import, spindle assembly, telomere/chromosome localization, mechanosensory pain detection, telomeric cohesion regulation, brown fat differentiation, ephrin signaling, intracellular signal transduction, and prostate gland epithelial maturation\u2014contexts that are too disparate to define a single cohesive function. Without a unifying theme, a specific label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045038","count":4},{"id":"GO:0051225","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0070198","count":3},{"id":"GO:0050966","count":3}]},{"hash":"1898849033895717112","title":"Auxin transport and adventitious root development","description":"This cluster is dominated by GO terms related to auxin transport and signaling (polar transport, export across the plasma membrane, transmembrane transport) and specific root development (adventitious root development). These collectively suggest a cohesive function in auxin homeostasis and root formation in plants, with a few unrelated terms like translation appearing as background noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0055085","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0010315","count":1}]},{"hash":"1733456251145370360","title":"Unknown","description":"The terms are spread across maternal development, chromatin organization, and ER/Golgi trafficking with no clear, cohesive shared function or interactions, so there isn\u2019t a single interpretable theme linking these proteins. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046294","count":1},{"id":"GO:0031508","count":1},{"id":"GO:0070863","count":1},{"id":"GO:0007311","count":1},{"id":"GO:0035964","count":1}]},{"hash":"927776913004454408","title":"Pigment Granule Biogenesis and Ubiquitin-Proteasome Regulation","description":"The cluster is enriched in pigmentation-related terms (compound eye pigmentation, pteridine biosynthetic process, endosome to pigment granule transport, endosome to lysosome transport) and in ubiquitin-related protein turnover processes (protein ubiquitination, polyubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process), suggesting a core theme of pigment granule formation/trafficking coordinated with ubiquitin-mediated regulation. Otolith morphogenesis and mechanical-stimulus response appear ancillary and do not define the main function. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032474","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0031146","count":2}]},{"hash":"647673410907685993","title":"Proteasome-Mediated Degradation and NF-\u03baB Signaling","description":"The top GO terms strongly emphasize ubiquitin-dependent proteasomal degradation (GO:0031146) and related regulatory pathways, including NF-\u03baB signaling and transcriptional regulation in the cell cycle. Although some terms are marked obsolete, the core pattern centers on proteasome-driven proteolysis and its signaling connections, particularly NF-\u03baB, with hints of chromatin-associated transcriptional regulation. This suggests a cohesive functional theme around protein turnover and its regulatory consequences.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":6},{"id":"GO:0000083","count":4},{"id":"GO:0042345","count":3},{"id":"GO:0071169","count":3},{"id":"GO:0032088","count":3}]},{"hash":"1680658158185354369","title":"Unknown","description":"The Top Terms span mitochondrial respiration, lipid/receptor trafficking, neuropeptide processing, pheromone maturation, and sporulation, with no unifying function or strong connections among them. The lack of edges and the diversity of processes suggest there is no coherent cluster-wide theme to name beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0001920","count":1},{"id":"GO:0034230","count":1}]},{"hash":"1305980456971312851","title":"Lysosome\u2013Autophagy and Vesicle Trafficking","description":"Proteins in this cluster are enriched for lysosome organization, autophagy (mitochondrial and peroxisomal), endocytosis, vesicle tethering and docking, vesicle fusion, and related trafficking processes. This points to a cohesive theme around lysosome-associated autophagy and general vesicle trafficking, with a few unrelated terms likely due to broad annotations. Confidence reflects a strong, representative connection to lysosome/autophagy and vesicle dynamics.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007040","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0030242","count":2}]},{"hash":"935455072085788587","title":"Transsulfuration and Cysteine Metabolism","description":"The top terms are dominated by sulfur amino acid metabolism: cysteine biosynthesis via cystathionine, transsulfuration, and homocysteine/serine catabolism, suggesting the cluster centers on cysteine and homocysteine metabolic pathways; other terms like protein kinase activation and nuclear import may reflect broader regulatory roles but do not outweigh this core theme.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0019343","count":7},{"id":"GO:0060041","count":7},{"id":"GO:0051289","count":7},{"id":"GO:0032147","count":7},{"id":"GO:1902593","count":7}]},{"hash":"1421202319683951889","title":"Cilia-driven Visual Perception and Sensory Signaling","description":"The cluster's strongest terms point to cilium assembly and visual perception, plus regulation of sensory neuron axon guidance, indicating a core role in ciliary sensory function relevant to vision and neural signaling. Other terms (mitotic cycle, Hippo signaling, tRNA modification, etc.) are more general or less connected, but the predominant theme is ciliary-mediated sensory perception.","confidence":"Medium","size":14,"edges":54,"triangles":90,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":14},{"id":"GO:0000278","count":14},{"id":"GO:0060271","count":12},{"id":"GO:1905490","count":12},{"id":"GO:0035330","count":12}]},{"hash":"150597561645978665","title":"Phytochrome-Driven Light-Responsive Transcription","description":"The cluster is enriched for photoreception and light-response terms (visible light detection; red/far-red phototransduction; very low fluence red light and high-irradiance far-red responses) plus transcriptional regulation. The protein-tetrapyrrole/chromophore linkages and phosphorelay signaling further support a phytochrome-like photoreceptor module that regulates DNA-templated transcription in response to light, yielding a coherent light-sensing transcription cluster.","confidence":"High","size":14,"edges":81,"triangles":263,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0018298","count":7},{"id":"GO:0017006","count":7},{"id":"GO:0000160","count":7},{"id":"GO:0010201","count":7}]},{"hash":"622622452121552466","title":"Nuclear transcription and chromatin remodeling","description":"The GO terms are dominated by nuclear processes: DNA replication, DNA-templated transcription and its regulation, and chromatin dynamics (nucleosome mobilization, histone exchange). These point to gene expression control via chromatin remodeling as the core theme, with a few terms touching stress responses or nuclear fusion that are related but secondary; the sarcomere term appears more as an outlier. Overall, the cluster centers on nuclear transcription and chromatin remodeling.","confidence":"Medium","size":14,"edges":22,"triangles":16,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000742","count":2},{"id":"GO:0030026","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1304767801744192920","title":"Neural and ectodermal development","description":"Based on the top GO terms, the cluster is enriched for nervous system development and dendritic spine development, pointing to neural formation and synapse-related processes. The presence of hair follicle placode formation suggests broader ectodermal/tissue-patterning roles as well, while other terms like gene expression regulation and protein localization fit developmental programs. Taken together, the most representative theme is neural and ectodermal development, though some background terms reflect general cellular processes.","confidence":"Medium","size":14,"edges":29,"triangles":3,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":7},{"id":"GO:0060999","count":7},{"id":"GO:0060789","count":7},{"id":"GO:0071701","count":7},{"id":"GO:0034629","count":7}]},{"hash":"2155191019396921702","title":"Neural Development and Axon Guidance","description":"This cluster centers on neural development and neuron connectivity: retinal ganglion cell axon guidance, optic nerve morphogenesis, corpus callosum development, and dendritic spine morphogenesis. Cilium assembly and substrate adhesion-related spreading support neurite outgrowth and neuronal wiring, while Ran signaling and GTPase regulation relate to intracellular trafficking and cytoskeletal dynamics. A couple of immune-related terms appear but do not define the cluster\u2019s core function.","confidence":"High","size":14,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019236","count":2},{"id":"GO:0001806","count":2},{"id":"GO:0022038","count":2},{"id":"GO:0034446","count":2},{"id":"GO:0031290","count":2}]},{"hash":"98545330455702392","title":"Neuronal signaling and synaptic plasticity","description":"The cluster is dominated by terms tied to neural signaling and synaptic function, including excitatory postsynaptic potentials, regulation of axonogenesis, dopamine response, and cytoskeletal dynamics that underlie neurite outgrowth and synaptic plasticity. While a few terms touch on broader pathways (Wnt, JNK, T cell receptor signaling, cell cycle), the prevailing theme centers on neuronal communication and development.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":10},{"id":"GO:0050771","count":9},{"id":"GO:0060079","count":9},{"id":"GO:1903351","count":9},{"id":"GO:0031532","count":9}]},{"hash":"271345599551020927","title":"Innate Immune Signaling and Ubiquitin\u2013Proteasome Regulation","description":"The cluster is dominated by immune signaling terms (stimulatory C-type lectin receptor signaling, Fc-epsilon receptor signaling) along with processes tied to protein turnover (protein deubiquitination, proteasomal protein catabolism). This suggests a cohesive module where innate immune receptor pathways intersect with ubiquitin-proteasome\u2013mediated regulation of proteins, possibly influencing antiviral responses and antigen processing. Some cell cycle- and signaling pathway terms (anaphase-promoting complex\u2013dependent catabolic process, planar cell polarity via Wnt) may reflect broader regulatory cross-talk, but the core theme remains immune signaling with proteostasis control.","confidence":"High","size":14,"edges":76,"triangles":265,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":10},{"id":"GO:0016032","count":9},{"id":"GO:0002223","count":9},{"id":"GO:0010950","count":9},{"id":"GO:0031145","count":9}]},{"hash":"530652240656855093","title":"Rho GTPase signaling and cell polarity regulation","description":"The top GO terms cluster around Rho GTPase signaling and cell polarity maintenance, including positive regulation of GTPase activity, regulation of Rho signaling, and establishment/maintenance of cell polarity. This points to a coherent theme of cytoskeletal organization and cell shape control, with a few peripheral terms (e.g., protein stabilization, autophagy) present but not central to the main function.","confidence":"High","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0050821","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0031139","count":2},{"id":"GO:2000769","count":2},{"id":"GO:0032005","count":2}]},{"hash":"187749117495126948","title":"ER-stress and trafficking regulators","description":"The terms cluster around ER stress\u2013related apoptotic signaling, regulation of the secretory pathway, intracellular trafficking (endocytosis, endosome localization), and organelle contact (mitochondrion-ER tethering), suggesting a broad role in trafficking and stress-response regulation rather than a single pathway.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":3},{"id":"GO:1903434","count":2},{"id":"GO:0071851","count":2},{"id":"GO:0071389","count":2},{"id":"GO:1990456","count":2}]},{"hash":"1343768887958454688","title":"Neural development and synaptic signaling","description":"The proteins in this cluster are enriched for nervous system development, dendrite morphogenesis, and regulation of synaptic vesicle exocytosis, with Roundabout signaling as an axon guidance-related term. While there are some proliferation-related terms, the dominant pattern points to neural development and synaptic function, suggesting these proteins function together in neural formation and communication.","confidence":"Medium","size":14,"edges":79,"triangles":261,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":7},{"id":"GO:0090307","count":7},{"id":"GO:0035385","count":7},{"id":"GO:0010796","count":7},{"id":"GO:0050852","count":7}]},{"hash":"485375935697833231","title":"Mitochondrial membrane dynamics and signaling","description":"Top terms point to mitochondrial processes (inner mitochondrial membrane organization, regulation of mitochondrial membrane potential, mitochondrion inheritance) as the core theme, suggesting a mitochondria-centric cluster. Secondary signals from PKC, SREBP, proteolysis regulation, and cadherin-mediated adhesion may reflect broader cellular signaling and adhesion context, but mitochondrial dynamics appear primary.","confidence":"High","size":14,"edges":38,"triangles":44,"max_degree":10,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0060355","count":4},{"id":"GO:0001302","count":4},{"id":"GO:0007007","count":3},{"id":"GO:0070528","count":3},{"id":"GO:0010918","count":3}]},{"hash":"478195434841701928","title":"Rho-regulated migration and cytoskeletal remodeling","description":"The GO terms cluster around cell movement and cytoskeletal dynamics: Rho signaling regulation, myosin II filament organization, cell-matrix adhesion, and diverse migratory processes (endothelial, smooth muscle, neuronal) during development and wound healing.","confidence":"High","size":14,"edges":55,"triangles":109,"max_degree":13,"top_function":"wound healing","top_go_terms":[{"id":"GO:0035024","count":14},{"id":"GO:0060055","count":14},{"id":"GO:1904901","count":14},{"id":"GO:0072678","count":14},{"id":"GO:0003366","count":14}]},{"hash":"736269088908093013","title":"Golgi-ER Transport and Growth","description":"The cluster centers on vesicle trafficking between the ER and Golgi (COPII budding, retrograde transport) and links to broader growth and development processes (mitotic cell cycle, cell proliferation, brain development, multicellular growth) as well as ribosome biogenesis, suggesting a coordinated role in growth with intracellular transport.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0042254","count":3}]},{"hash":"1835530795601025504","title":"Intracellular membrane trafficking and organelle dynamics","description":"The top terms cluster around ER-to-Golgi vesicle transport, autophagosome maturation, and Golgi ribbon formation, indicating a cohesive theme of intracellular membrane trafficking and organelle organization. Supporting terms related to mitochondrial import and membrane permeability suggest broader organelle dynamics and metabolic regulation, reinforcing a unified label for this cluster.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0097352","count":2},{"id":"GO:0090161","count":2},{"id":"GO:0010867","count":1},{"id":"GO:1903740","count":1}]},{"hash":"1697213001078632334","title":"Golgi-ER vesicle trafficking and SNARE assembly","description":"The terms are dominated by Golgi- and ER-to-Golgi\u2013related vesicle transport and fusion events (Golgi ribbon formation, ER-to-Golgi, intra-Golgi, Golgi-to-vacuole, retrograde transport) plus SNARE complex assembly, with some related synaptic exocytosis terms, pointing to a cohesive Golgi-centered vesicle trafficking and membrane-fusion function.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0006891","count":3},{"id":"GO:0048280","count":3},{"id":"GO:0006896","count":2}]},{"hash":"579701797224700499","title":"Cardiac Muscle Development and Epigenetic Regulation","description":"The cluster centers on heart and muscle lineage development (heart development, myotube cell development) and is enriched for transcriptional and chromatin-related processes (negative regulation of transcription by RNA polymerase II, histone H3-K36 methylation, nucleosome assembly, peptidyl-lysine dimethylation). The presence of dexamethasone response and hypoxia-regulation terms suggests stress-related signaling that can influence cardiac and muscle gene expression. An outlier term is antibiotic biosynthesis, likely noise. Overall, the theme coherently links cardiac/muscle differentiation with epigenetic control of gene expression.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0014904","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1361937721881355608","title":"Hair Follicle Keratinization and Morphogenesis","description":"The cluster is enriched for keratinization and hair follicle morphogenesis, pointing to a hair follicle/epidermal differentiation program. The presence of mitotic cell cycle terms suggests concurrent proliferation of keratinocytes, while additional GO terms may reflect broader cellular regulatory processes that accompany differentiation.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031424","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0031069","count":3},{"id":"GO:0051291","count":3},{"id":"GO:0000278","count":3}]},{"hash":"223561549777339517","title":"DNA Replication and Transcription in Cell Cycle","description":"The top GO terms are dominated by DNA-templated transcription, DNA replication, and cell division, pointing to nuclear processes linked to the cell cycle. Additional terms for the ER unfolded protein response and ER-to-Golgi transport suggest ancillary roles in protein folding and trafficking, but the major signal in this cluster is DNA metabolism and cell-cycle progression.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0051301","count":4},{"id":"GO:0030968","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0010165","count":3}]},{"hash":"1985100224295460502","title":"Protein deglutamylation","description":"This cluster is driven by GO terms describing deglutamylation of proteins at multiple sites (C-terminal, side chain, and branching point), indicating a shared function in removing glutamyl residues from proteins. Other terms such as heat response or liver-related processes appear less central and could reflect secondary associations. ","confidence":"Medium","size":14,"edges":15,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0035611","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0010757","count":2},{"id":"GO:2000346","count":2}]},{"hash":"1241627919813300259","title":"Mitotic spindle and cell cycle regulation","description":"Based on GO terms, these proteins are enriched for mitosis and cell cycle processes (meiotic spindle disassembly, exit from mitosis, CPC localization to spindle midzone, mitotic actomyosin ring maturation, regulation of CDK activity, and overall cell cycle regulation). A few terms touch on signaling pathways (T cell receptor, VEGF, TRAIL-apoptotic) but do not override the core mitotic theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051229","count":1},{"id":"GO:0050860","count":1},{"id":"GO:1900746","count":1},{"id":"GO:0016239","count":1},{"id":"GO:0031536","count":1}]},{"hash":"239869337085744792","title":"Endosomal sorting via ESCRT/MVB","description":"The top GO terms point to endosome transport, multivesicular body (MVB) assembly, and ubiquitin-dependent protein sorting via the ESCRT machinery, including cytoplasm-to-vacuole targeting and ESCRT-related viral budding. These collectively indicate a core function in endosomal trafficking and MVB formation, with a few peripheral terms likely representing species-specific or broader annotations.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0000742","count":1},{"id":"GO:0043162","count":1},{"id":"GO:0090351","count":1}]},{"hash":"1785591026591303943","title":"RNA processing and translational regulation","description":"Most prominent GO terms center on RNA metabolism and control of protein synthesis: mRNA export from the nucleus, alternative mRNA splicing, regulation of mRNA stability in response to stress, regulation of translational initiation, and IRES-dependent viral translation. Some terms appear obsolete or peripheral (blastocyst formation, histone deubiquitination), but the dominant signal links RNA processing with translation regulation, justifying this label.","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:1902625","count":3},{"id":"GO:1903586","count":3},{"id":"GO:1905663","count":3},{"id":"GO:0001825","count":3}]},{"hash":"1978784655709161842","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0019556","count":2},{"id":"GO:0006147","count":2},{"id":"GO:0044205","count":2}]},{"hash":"526333489397472468","title":"Lignan and phenylpropanoid biosynthesis","description":"The cluster is dominated by GO terms for phenylpropanoid biosynthesis and lignan-specific pathways (lariciresinol, pinoresinol, secoisolariciresinol), along with related anthocyanin-containing compound biosynthesis, pointing to plant secondary metabolite production. A couple of terms appear unrelated or obsolete, but the core signal is cohesive around lignan/phenylpropanoid biosynthesis.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009699","count":5},{"id":"GO:1902125","count":5},{"id":"GO:0001081","count":5},{"id":"GO:1901006","count":5},{"id":"GO:1902131","count":5}]},{"hash":"574721388261864422","title":"Transcriptional Regulation and Growth","description":"Members are enriched for GO terms related to DNA-templated transcription and its regulation, plus processes tied to organismal growth and cell proliferation. The overlap suggests a functional cluster of transcriptional regulators that influence cell growth in multicellular contexts.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008284","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035264","count":2},{"id":"GO:2000616","count":1}]},{"hash":"1718184273683533237","title":"Steroid and lipid hormone biosynthesis and metabolism","description":"The cluster is dominated by GO terms for steroid hormone production (testosterone, androgen, brassinosteroid, ecdysone) and lipid mediator biosynthesis (prostaglandins) along with related oxidation-reduction and xenobiotic metabolism (P450 pathways). This points to a shared theme of steroid and lipid hormone biosynthesis together with detoxification/metabolic processing.","confidence":"Medium","size":14,"edges":14,"triangles":2,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0061370","count":7},{"id":"GO:0008209","count":7},{"id":"GO:0042738","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0010430","count":4}]},{"hash":"1850040497801585783","title":"Amino Acid Catabolism and Heme Biosynthesis","description":"This cluster centers on metabolic processes for breaking down amino acids (alanine, kynurenine/tryptophan, threonine, tyrosine, aspartate, glutamate) and on heme/porphyrin biosynthesis, with fatty acid transport adding a broader metabolic context. Notch signaling appears but is not the dominant theme, so the core label reflects amino-acid metabolism and porphyrin/heme production.","confidence":"Medium","size":14,"edges":60,"triangles":167,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":11},{"id":"GO:0097053","count":10},{"id":"GO:0007219","count":10},{"id":"GO:0006783","count":6},{"id":"GO:0006782","count":6}]},{"hash":"1679052094885930289","title":"Regulation of signaling and cell proliferation","description":"This cluster centers on several regulatory GO terms (e.g., positive regulation of GTPase activity, kinase activity regulation, protein autophosphorylation, and positive regulation of cell proliferation) plus related processes like mRNA transport and hypoxia response. The absence of edges suggests these proteins may participate in diverse regulatory functions rather than a single pathway, so a broad label of signaling and proliferation regulation best captures the shared theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0071456","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0006469","count":4}]},{"hash":"1722436570226941940","title":"Lipid signaling and oxidative stress response","description":"The GO terms point to lipid-related signaling and oxidative stress handling (prostaglandin biosynthesis; cellular response to lipid hydroperoxide; cellular oxidant detoxification) with accompanying inflammatory cues (response to lipopolysaccharide) and broader differentiation contexts (retinoic acid response, Leydig cell differentiation, cornification). The terms are diverse but center around lipid-driven signaling and oxidative stress rather than a single cohesive function, so a cautious, representative label is \u201cLipid signaling and oxidative stress response.\u201d","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0019835","count":2},{"id":"GO:0033327","count":1},{"id":"GO:0001516","count":1},{"id":"GO:0014070","count":1},{"id":"GO:0032496","count":1}]},{"hash":"853722121470742923","title":"RNA Pol II Transcription Regulation","description":"Most prominent GO terms are DNA-templated transcription and regulation of DNA-templated transcription, pointing to a cohesive set of proteins involved in controlling transcription by RNA polymerase II. Additional terms similarly describe positive regulation of transcription from the Pol II promoter under various conditions, reinforcing the transcription-regulation theme. A few sporadic or obsolete terms (e.g., aflatoxin biosynthesis) appear but do not alter the core interpretation. Overall, this cluster likely represents a transcriptional regulation module centered on RNA polymerase II activity.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035959","count":1},{"id":"GO:1904741","count":1},{"id":"GO:1900399","count":1}]},{"hash":"1718767989590342977","title":"Heart Development and Cardiac Muscle Regulation","description":"The top GO terms converge on heart development, regulation of cardiac muscle contraction, and signaling pathways affecting heart function (e.g., negative regulation of protein kinase activity, SMAD phosphorylation, catecholamine secretion). Features like secondary heart field specification and regulation of cardiac hypertrophy further anchor the cluster to cardiac development and cardiac muscle physiology, making this label representative of the shared functions.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0045988","count":1}]},{"hash":"752813839237414945","title":"Cytoskeleton remodeling and cell morphogenesis","description":"The top GO terms cluster around actin cytoskeleton dynamics (lamellipodium/podosome assembly, endocytosis) and morphogenesis across tissues (midbrain, imaginal disc), with GTPase activity regulation linking these processes, indicating a cohesive theme of cytoskeletal remodeling during cell morphogenesis.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:0034260","count":2},{"id":"GO:0000902","count":2},{"id":"GO:1904424","count":2},{"id":"GO:1904693","count":2}]},{"hash":"2025352676691139906","title":"Unknown","description":"The GO terms are highly diverse (chloroplast thylakoid import, telomere localization, pain detection, mitotic cohesion, brown fat differentiation, ephrin signaling, generic signal transduction, heat response, and prostate development) with no single unifying function. Because there is no cohesive theme tying the proteins to one specific process, I cannot assign a representative, specific label.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045038","count":3},{"id":"GO:0070198","count":3},{"id":"GO:0050966","count":3},{"id":"GO:1904908","count":3},{"id":"GO:1903444","count":3}]},{"hash":"1292355862026343802","title":"Epithelial Differentiation and Adhesion Regulation","description":"The top GO terms cluster around epithelial differentiation (skeletal muscle differentiation is an outlier) and keratinocyte proliferation, along with regulation of cell\u2013matrix adhesion via integrins. This points to a cohesive theme of epithelial/surface tissue differentiation and adhesion dynamics, justifying a label focused on epithelial differentiation and adhesion. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035914","count":2},{"id":"GO:0048170","count":1},{"id":"GO:0030859","count":1},{"id":"GO:0043616","count":1},{"id":"GO:0033628","count":1}]},{"hash":"12264189663387495","title":"Developmental morphogenesis and cell adhesion","description":"The top GO terms cluster around developmental processes (root development, renal vesicle formation, embryonic limb joint morphogenesis, superior colliculus development) and tissue organization (adherens junction assembly), with supporting signals in cell cycle regulation and transcription regulation. Although proton transmembrane transport appears among the terms, the dominant theme points to development and morphogenesis with cell\u2013cell adhesion, justifying this label.","confidence":"Medium","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0015991","count":10},{"id":"GO:0007050","count":9},{"id":"GO:0048364","count":9},{"id":"GO:0072033","count":8},{"id":"GO:0010909","count":8}]},{"hash":"897787015055199939","title":"Ribosome biogenesis and ER\u2013Golgi transport","description":"This cluster is driven by strong signals for ribosome biogenesis, including large subunit biogenesis, alongside vesicle trafficking between the ER and Golgi, with additional hints of microtubule dynamics and membrane-related processes that support secretory pathway transport.","confidence":"Medium","size":13,"edges":16,"triangles":6,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0006890","count":2}]},{"hash":"1875264141922561011","title":"Cardiac contraction regulation and heart development","description":"The cluster includes GO terms surrounding regulation of cardiac muscle contraction (positive and negative), heart development (secondary heart field specification, hypertrophy regulation), and catecholamine secretion, indicating a core theme in cardiac function and formation. While there are also general terms like transcription initiation and ribosome biogenesis, the cardiac-related terms appear to be the dominant signal, suggesting these proteins collectively participate in heart muscle regulation and development.","confidence":"Medium","size":13,"edges":17,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0045988","count":1},{"id":"GO:0003108","count":1},{"id":"GO:0060394","count":1}]},{"hash":"889547475141965651","title":"Vesicular Trafficking and Endocytosis","description":"This cluster centers on intracellular membrane transport: endosome-to-lysosome, Golgi-to-endosome, and exocytic vesicle docking, along with endocytosis. The accompanying terms on cell polarity and xenobiotic response can be tied to trafficking and membrane dynamics that support proper neuronal morphology and detox pathways. Overall, the common theme is vesicular transport and membrane trafficking within the endomembrane system.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":3},{"id":"GO:0006904","count":3},{"id":"GO:0006895","count":3},{"id":"GO:0043524","count":3},{"id":"GO:0051291","count":3}]},{"hash":"871588612543518078","title":"ER Stress Response and Protein Folding","description":"Proteins in this cluster are enriched for endoplasmic reticulum\u2013related processes: unfolded protein response, translation initiation during ER stress, and protein folding in the ER, along with COPI-mediated ER-to-Golgi trafficking. Some ancillary terms (egg-laying behavior, aggressive behavior) may reflect annotation artifacts rather than core biology, but the dominant pattern supports ER quality control and export pathways.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0070863","count":1}]},{"hash":"2273320936013623846","title":"Unknown","description":"The proteins are annotated with a mix of RNA-related processes (ribosome biogenesis, pseudouridine synthesis, mRNA splicing) and cytoskeletal/cell-shape dynamics (actin filament formation, ER polarization, bleb regulation, meiosis chromosome movement). With no connecting edges and no dominant shared function, there isn\u2019t a clear single theme to name this cluster beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:1903146","count":1},{"id":"GO:0001522","count":1},{"id":"GO:0045292","count":1},{"id":"GO:1903955","count":1}]},{"hash":"1990944933733318777","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1834933362184110349","title":"Transmembrane transport of amino acids, vitamins, and metals","description":"The Top Terms are dominated by substrate-specific membrane transport activities (cysteine, thiamine, methionine, heme, vitamin transport, molybdate, amino acids) and metal ion import (cadmium), suggesting a cluster of transport proteins mediating uptake of diverse nutrients and metals. A SOS response term appears but is secondary to the transport theme.","confidence":"Medium","size":13,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042883","count":1},{"id":"GO:0015888","count":1},{"id":"GO:0036249","count":1},{"id":"GO:1902943","count":1},{"id":"GO:0003333","count":1}]},{"hash":"308546276668142146","title":"RNA processing and ribosome biogenesis","description":"This cluster is dominated by GO terms related to RNA metabolism, including RNA processing, mRNA splicing via the spliceosome, and rRNA maturation (5.8S, SSU/LSU), as well as nonsense-mediated decay, all aligning with ribosome biogenesis and RNA quality control. The presence of stress granule localization and regulatory ncRNA silencing further supports an RNA-centric function. Some terms like DNA replication and embryonic morphogenesis appear less connected, but the core signals point to RNA processing and ribosome assembly as the main theme.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1903608","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000184","count":3}]},{"hash":"590955800252062789","title":"Ribosome Biogenesis and Translation Regulation","description":"Dominant GO terms center on translation, ribosome biogenesis, and rRNA maturation, with multiple items on regulation of translational initiation, translation reinitiation, and IRES-dependent translation. This pattern points to a cluster of proteins involved in ribosome assembly and the control of protein synthesis, including aspects of viral translation mechanisms.","confidence":"High","size":13,"edges":28,"triangles":40,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0001731","count":2}]},{"hash":"402084369066583734","title":"Cell Wall and Extracellular Polysaccharide Biosynthesis","description":"This cluster is dominated by GO terms for biosynthesis of cell wall components and extracellular polysaccharides (peptidoglycan, slime layer, cell wall mannoproteins, UDP-N-acetylglucosamine), indicating a shared function in building the bacterial envelope rather than cytosolic metabolism. The presence of related biosynthetic processes supports a coherent envelope-related theme, with a possible antibiotic-response signal reflecting cell wall stress. ","confidence":"High","size":13,"edges":35,"triangles":28,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0000902","count":2},{"id":"GO:0006535","count":2},{"id":"GO:0006048","count":2},{"id":"GO:0045228","count":2}]},{"hash":"1145200106214824053","title":"Unknown","description":"The top GO terms are a mix of bacterial membrane targeting (SRP-dependent targeting), flagellum organization, xenobiotic response, cell division, cobalamin biosynthesis, Rho signaling regulation, and cytoskeletal remodeling. This spread suggests no single cohesive function or theme for the cluster, making a confident, specific label unlikely.","confidence":"","size":13,"edges":11,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006614","count":2},{"id":"GO:0044781","count":2},{"id":"GO:0006616","count":2}]},{"hash":"106392334412397684","title":"RNAi and ribosome biogenesis","description":"The top GO terms cluster around RNA interference and siRNA processing (siRNA processing, RNAi-mediated silencing, RNAi-related transcriptional silencing, antiviral RNAi response), indicating a core theme of RNA silencing machinery. A couple of terms point to ribosome biogenesis and rRNA maturation, suggesting a secondary association with RNA processing and ribosomal assembly. Together, this cluster seems to reflect RNA interference pathways with a link to ribosome biogenesis, giving a coherent label that is both specific and representative.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0033615","count":1},{"id":"GO:0070919","count":1},{"id":"GO:0030422","count":1}]},{"hash":"492228631673623100","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000389","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0010087","count":1},{"id":"GO:0030422","count":1}]},{"hash":"1800013056997863047","title":"Phospholipid Biosynthesis","description":"The top GO terms are dominated by lipid biosynthesis: phosphatidylethanolamine biosynthetic process, phosphatidylglycerol biosynthetic process, and phosphatidylserine biosynthetic process, indicating a cluster focused on membrane lipid metabolism. Additional terms like phosphorylation and antibiotic response are present but less represented; overall, the shared function appears to be production of membrane phospholipids.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006646","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0019509","count":2},{"id":"GO:0009088","count":2}]},{"hash":"2205133217731519210","title":"Immune Cytokine Regulation and Epithelial Differentiation","description":"The top GO terms center on regulation of cytokine production (interleukins like IL-5 and IL-10, IL-8) and T-helper 2 differentiation, plus terms related to epithelial development (polarity maintenance and pronephric nephron differentiation) and a general antibiotic response. This suggests a mix of immune signaling components with some roles in epithelial fate, rather than a tight single-pathway module. Therefore, the label aims to capture the combination of immune cytokine regulation and epithelial differentiation signals in the cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045415","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0031139","count":2},{"id":"GO:0016332","count":2}]},{"hash":"2159618595001597035","title":"Cell cycle and ribosome biogenesis","description":"This cluster accumulates proteins linked to cell proliferation (cell division, cell cycle, cell population proliferation) and core gene expression machinery (ribosome biogenesis, ribosomal subunit export, translation initiation and reinitiation, transcription) plus RNA modification (guanine-N7 methylation), indicating a cohesive program for proliferative growth and protein synthesis.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1367257465809996527","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000467","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0048568","count":2}]},{"hash":"875742571646845017","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":25,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":5},{"id":"GO:0006541","count":5},{"id":"GO:0044205","count":4},{"id":"GO:0006207","count":4},{"id":"GO:0006508","count":4}]},{"hash":"1082200684424025244","title":"Unknown","description":"The terms cover diverse areas: several biosynthetic processes (biotin, cobalamin, antibiotic biosynthesis), general cell growth, RNA processing, and various post-translational modifications, plus plant-related and stress-response terms. With no clear shared function linking these proteins (and the cluster having no edges), there isn\u2019t a cohesive theme to name it; thus Unknown with None confidence.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0009877","count":1}]},{"hash":"1363590583554458936","title":"ECM remodeling and morphogenesis","description":"This cluster is driven by collagen and peptide catabolic processes (collagen, bradykinin, neuropeptides) and developmental morphogenesis signals (lung tube branching, intramembranous ossification), indicating a theme of tissue remodeling during organ development. While there are related terms about hormonal response and immune activity, the predominant pattern links extracellular matrix remodeling with morphogenesis.","confidence":"Medium","size":13,"edges":37,"triangles":67,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":11},{"id":"GO:2000179","count":11},{"id":"GO:0097067","count":11},{"id":"GO:0050790","count":11},{"id":"GO:0010815","count":11}]},{"hash":"1768780130722650836","title":"Ubiquitin-Driven Cell Cycle Regulation","description":"The cluster\u2019s top GO terms are dominated by ubiquitination processes (polyubiquitination, ERAD, K11-linked ubiquitination) and APC/mitotic cycle activities (mitotic cell cycle, cell division, APC-dependent catabolic process), pointing to a cohesive theme of regulated protein turnover governing cell cycle progression. The presence of innate immune and antiviral defense terms suggests additional context where ubiquitin signaling intersects with immune responses, but the central thread appears to be ubiquitin-mediated protein degradation linked to cell cycle control.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0070979","count":3},{"id":"GO:0000278","count":3}]},{"hash":"242614546522722565","title":"Plant carbon metabolism and lipid biosynthesis","description":"The top GO terms cluster around carbon handling (carbon dioxide response, carbon utilization) and lipid metabolism (galactolipid and triglyceride biosynthesis, lipid droplet organization) with supporting ER organization and phosphorylation/regulation signals. This combination suggests a plant-focused theme centered on carbon metabolism and lipid biosynthesis/storage, likely involving chloroplast-associated lipids, rather than a single isolated enzymatic process. Medium","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071244","count":2},{"id":"GO:2000122","count":2},{"id":"GO:0015976","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0007078","count":1}]},{"hash":"1423214265490868685","title":"K11-Ubiquitin\u2013Mediated Immune and Cell Cycle Regulation","description":"The Top Terms center on ubiquitin-related processes: K11-linked ubiquitination and APC/C-dependent catabolic activity, which tie to cell-cycle control, alongside innate immune response and defense regulation. This suggests a cohesive theme of ubiquitin-mediated regulation influencing both cell division and immune signaling, despite some peripheral or obsolete terms. Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050689","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0070979","count":1},{"id":"GO:0061179","count":1},{"id":"GO:0032925","count":1}]},{"hash":"526992253931949281","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071037","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0035044","count":1},{"id":"GO:0031664","count":1},{"id":"GO:0043630","count":1}]},{"hash":"1164966768752205005","title":"Rab GTPase Signaling & Trafficking","description":"The top GO terms point to small GTPase\u2013driven processes, especially Rab protein signal transduction, regulation of GTPase activity, and vesicle endocytosis, which together suggest a trafficking- and signaling-focused cluster. Other terms like translation and insulin response appear incidental, but the Rab/GTPase\u2013related terms provide the strongest cohesive thread. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0043087","count":1},{"id":"GO:0045175","count":1},{"id":"GO:0035745","count":1}]},{"hash":"618847619364775863","title":"Oxidative Stress and ROS Production","description":"The GO terms show a clear focus on reactive oxygen species (ROS) generation and stress responses: hydrogen peroxide biosynthesis, respiratory burst, superoxide generation, and cellular stress response to acidic pH. These suggest a cohesive theme around oxidative stress defense and ROS production. Some terms (mechanical sensing, cuticle development, copper import, and cAMP response) are more peripheral and reflect broader cellular processes, but the strongest signal is ROS-related biology.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":2},{"id":"GO:0006590","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0045730","count":1},{"id":"GO:0045726","count":1}]},{"hash":"2243305833520352091","title":"Meiotic recombination and mating-type regulation","description":"The main GO terms point to meiotic processes and mating-type control: joint molecule formation, DNA recombinase assembly in reciprocal meiotic recombination, DNA strand invasion, double-strand break repair via homologous recombination, gene conversion at the mating-type locus, and mating-type switching. Together, these indicate a module dedicated to meiosis-linked recombination and regulation of mating identity, with a few ancillary terms like regulation of nitrogen utilization contributing minimally. This supports a cohesive label focused on meiotic recombination and mating-type control.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006808","count":2},{"id":"GO:0000709","count":1},{"id":"GO:0007533","count":1},{"id":"GO:0010772","count":1},{"id":"GO:0043388","count":1}]},{"hash":"2062126024276491363","title":"Mitotic signaling and cytoskeletal regulation","description":"Based on the top GO terms, this cluster centers on mitotic checkpoint signaling (mitotic spindle assembly checkpoint signaling; mitotic intra-S DNA damage checkpoint signaling) and actin cytoskeletal regulation (positive regulation of actin filament binding), with accompanying phosphorylation signaling pathways. While some terms touch on development and other signaling contexts, the strongest and most coherent theme is how cell cycle control interfaces with cytoskeletal dynamics and phosphorylation signaling.","confidence":"Medium","size":12,"edges":17,"triangles":6,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007037","count":12},{"id":"GO:1904531","count":12},{"id":"GO:0007094","count":12},{"id":"GO:1902002","count":12},{"id":"GO:0001806","count":12}]},{"hash":"1279385805504533244","title":"Neuronal signaling and vesicle trafficking","description":"The terms point to neuronal development and function (substantia nigra development, cochlea morphogenesis) and vesicle-related processes (regulation of synaptic vesicle exocytosis, calcium response) with related autophagy/vesicle trafficking terms. Together, they suggest a cluster of proteins involved in neuronal signaling and vesicle dynamics, though a few terms are less specific to neurons.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000785","count":2},{"id":"GO:0090103","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0032486","count":2}]},{"hash":"1796680998323148865","title":"Vesicle trafficking and exocytosis regulation","description":"This cluster centers on GO terms related to vesicle trafficking and exocytosis across diverse contexts, including synaptic vesicle priming/exocytosis, Golgi-to-plasma membrane transport, and acrosome reaction. The presence of negative regulation terms for vesicle-related processes suggests a theme of modulating vesicle fusion and release, tying together neuronal, reproductive (acrosome), and general membrane-trafficking regulation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043314","count":3},{"id":"GO:0007340","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0002692","count":3},{"id":"GO:0016082","count":3}]},{"hash":"1109990002714045369","title":"Unknown","description":"The terms span mitochondrial protein handling, ribosome RNA processing, nutrient response, and several developmental and cytoskeletal processes, with no clear, single function dominating the cluster. Because there is no cohesive shared theme across the annotated functions, I cannot assign a more specific label beyond Unknown.","confidence":"","size":12,"edges":18,"triangles":2,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0072321","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0007584","count":1},{"id":"GO:0043966","count":1}]},{"hash":"2247331092940868940","title":"Retrotransposon activity and proviral integration","description":"This cluster is dominated by GO terms related to movement and integration of mobile genetic elements, including DNA transposition, retrotransposition, RNA-templated DNA synthesis, DNA replication, and proviral latency/viral entry. The common theme is the mobility and integration of retroelements and associated viral processes, with a few host-symbiont interaction terms that align with these themes. ","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":1},{"id":"GO:1903704","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0046718","count":1}]},{"hash":"1735179181266591842","title":"Actin Remodeling and Cell Migration","description":"The cluster centers on actin cytoskeleton dynamics and migratory responses: ruffle assembly, stress fiber assembly, responses to epidermal growth factor and mechanical stimuli, all pointing to actin-driven remodeling and cell movement. Some terms touch on apoptosis or Golgi localization, but the dominant theme is cytoskeletal rearrangement linked to migration and mechanotransduction.","confidence":"High","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0097178","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0051496","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0008625","count":2}]},{"hash":"1036742024808786421","title":"Nuclear RNA Processing and Export Machinery","description":"These proteins are enriched for RNA processing (tRNA, translation-related) and nucleocytoplasmic transport activities (mRNA and ribosomal subunit export, hnRNP import), pointing to a nucleus-centered RNA maturation and trafficking role. The inclusion of transcription regulation terms suggests a broader involvement in gene expression control within the nucleus.","confidence":"Medium","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0006609","count":3},{"id":"GO:0000122","count":3}]},{"hash":"53853089467561132","title":"Nucleocytoplasmic RNA and ribosome transport","description":"The top GO terms are dominated by mRNA export from the nucleus, ribosomal protein import into the nucleus, NLS-bearing protein import into the nucleus, and ribosomal large subunit export from the nucleus, indicating a clear focus on nucleocytoplasmic trafficking of RNA and ribosomal components. Additional terms related to transcription regulation, centrosome duplication, and broader regulatory processes suggest ancillary cellular regulatory roles associated with nuclear transport contexts. High","confidence":"","size":12,"edges":13,"triangles":6,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":4},{"id":"GO:0006610","count":4},{"id":"GO:0006607","count":4},{"id":"GO:0006609","count":3},{"id":"GO:0000122","count":3}]},{"hash":"188055045667326264","title":"Vesicle trafficking and fusion regulation","description":"The top GO terms cluster around vesicle trafficking and membrane fusion processes, including SNARE complex assembly regulation, vesicle tethering, vesicle docking in exocytosis, and lysosome organization, as well as regulation of vacuole fusion. While a couple of terms touch on development or translation initiation, the dominant signal is vesicle trafficking and organelle membrane dynamics, supporting this label.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0035542","count":1},{"id":"GO:0036205","count":1},{"id":"GO:0099022","count":1}]},{"hash":"2055383985571811728","title":"N-terminal protein acetylation","description":"Dominated by N-terminal acetylation terms across multiple amino acids (serine, methionine, glutamic acid, lysine), indicating a shared function of N-terminal protein acetylation. Other terms are less connected and likely noise, but the core signal supports this label.","confidence":"High","size":12,"edges":47,"triangles":120,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0017198","count":10},{"id":"GO:0018003","count":10},{"id":"GO:0061606","count":10},{"id":"GO:0030187","count":10},{"id":"GO:0001525","count":10}]},{"hash":"1261069212380428096","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0007584","count":2}]},{"hash":"109495760106485228","title":"TLR-Mediated Antiviral Innate Immunity","description":"The top GO terms cluster around innate immune activation, including Toll-like receptor signaling (TLR9 and TLR10), LPS response, dsRNA response, interferon production (IFN-\u03b1/\u03b2), macrophage activation, and defense against viruses, with xenophagy as a pathogen-clearing process. This indicates a cohesive function in sensing pathogens and initiating antiviral and inflammatory responses.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0045359","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0043330","count":4},{"id":"GO:0034162","count":3}]},{"hash":"929705610527002410","title":"Aromatic amino acid metabolism and BH4 biosynthesis","description":"The cluster prominently features L-phenylalanine metabolic process and tetrahydrobiopterin biosynthetic process, connecting aromatic amino acid metabolism with BH4 cofactor production. Additional terms suggest possible roles in protein complex formation (homooligomerization/heterooligomerization) and general transcription, while some entries are obsolete or less coherent with a single theme. Taken together, the core theme is aromatic amino acid metabolism with cofactor biosynthesis, justifying the label with a moderate level of confidence.","confidence":"Medium","size":12,"edges":16,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009409","count":2},{"id":"GO:0006729","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0043496","count":1}]},{"hash":"1926485170573731756","title":"Amino acid\u2013regulated translation under stress","description":"The terms point to translation regulation in response to amino acid availability (amino acid starvation, amino acid stimulus) and to mRNA stability/deadenylation, suggesting a theme of post-transcriptional control of protein synthesis during nutrient stress, with a peripheral nod to related processes like autophagy and chromatin remodeling. ","confidence":"Medium","size":12,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":1},{"id":"GO:0014009","count":1},{"id":"GO:0001514","count":1},{"id":"GO:0034198","count":1},{"id":"GO:2000767","count":1}]},{"hash":"2206014657350787343","title":"Lipid and Small-Molecule Metabolism","description":"The Top Terms largely point to metabolic processing of a variety of organic compounds, especially lipids and related molecules: retinol metabolism, fatty acid omega-oxidation, prostaglandin metabolism, and other small-molecule catabolic processes (xylitol, furaldehyde, pyruvate fermentation). Although there is a single term about response to lipopolysaccharide, the dominant signal is diverse metabolism of lipids and small molecules, with oxidation-reduction processes underpinning these pathways. This suggests a cohesive cluster centered on lipid and small-molecule metabolism, with some incidental immune-associated terms.","confidence":"Medium","size":12,"edges":31,"triangles":31,"max_degree":8,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042572","count":6},{"id":"GO:0042208","count":4},{"id":"GO:0010430","count":4},{"id":"GO:0043458","count":4}]},{"hash":"1172818251158526922","title":"ER-associated protein quality control and membrane trafficking","description":"This cluster is enriched for ERAD/ubiquitin-dependent degradation and ER membrane-associated processes (tail-anchored insertion, protein quality control), with related hints from autophagy (aggrephagy) and receptor trafficking (GPCR internalization, TLR3 signaling regulation), suggesting a core theme of ER-centered protein handling and membrane trafficking rather than a single signaling pathway.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0034140","count":7},{"id":"GO:1903071","count":6},{"id":"GO:0030474","count":6},{"id":"GO:1904021","count":6}]},{"hash":"1333979834793012887","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0010019","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0080156","count":2}]},{"hash":"1955752755852201255","title":"Steroid and lipid mediator biosynthesis","description":"The cluster's GO terms show multiple biosynthetic pathways for steroids (brassinosteroids, ecdysone, testosterone, calcitriol) and lipid mediators (prostaglandin, epoxygenase P450, omega-oxidation), along with cholesterol catabolism and inflammation regulation. This points to a common theme of lipid-derived signaling molecule production and metabolism.","confidence":"High","size":12,"edges":18,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":7},{"id":"GO:0010430","count":6},{"id":"GO:0002677","count":6},{"id":"GO:0016132","count":6},{"id":"GO:0006697","count":6}]},{"hash":"1826647748112787148","title":"Blood coagulation and fibrinolysis regulation","description":"The top GO terms are strongly dominated by blood coagulation, negative regulation of plasminogen activation, and bradykinin catabolic process, pointing to a cohesive coagulation/fibrinolysis theme. Additional terms hint at liver-related roles (liver regeneration, negative regulation of hepatocyte proliferation), suggesting secondary regulatory effects in hepatic contexts. Some terms (insulin processing, Purkinje cell differentiation) appear less connected, likely representing outliers within the cluster. Overall, the cluster centers on coagulation and proteolysis regulation with ancillary hepatic links.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007596","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0035611","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0010757","count":1}]},{"hash":"1238356939610718682","title":"RNA Pol II Transcription Regulation","description":"The top GO terms cluster around DNA-templated transcription and regulation of transcription by RNA polymerase II, including positive regulation under various metabolic conditions and biosynthetic contexts. This points to a group of proteins primarily acting as transcriptional regulators responsive to metabolic cues, rather than a single metabolic pathway.","confidence":"High","size":12,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0035959","count":3},{"id":"GO:1904741","count":3},{"id":"GO:1900399","count":3}]},{"hash":"1461754478632717611","title":"Plant RNA Pol II transcription initiation","description":"This cluster centers on DNA-templated transcription and RNA polymerase II preinitiation complex assembly and transcription initiation, indicating a shared function in transcription initiation. The inclusion of cytokinin-activated signaling pathway suggests a plant context, aligning with plant transcriptional regulation. Obsolete terms like histone H3 acetylation and mitochondrial targeting are outdated annotations that don't change the core theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051123","count":1},{"id":"GO:0006352","count":1},{"id":"GO:0009736","count":1}]},{"hash":"476570490135194372","title":"Vesicle trafficking and exocytosis","description":"The cluster is dominated by GO terms for Golgi-to-plasma membrane transport, exocytosis, vesicle tethering, and vesicle docking, with supporting terms like early endosome to Golgi transport, indicating a coherent secretory/vesicle trafficking function. A few unrelated terms (e.g., chlorophyll biosynthesis regulation, host defense modulation) are present but do not define the overall theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":2},{"id":"GO:0006887","count":2},{"id":"GO:0034498","count":1},{"id":"GO:0090522","count":1},{"id":"GO:0048278","count":1}]},{"hash":"188223519427848504","title":"Lipid metabolism and membrane trafficking","description":"The cluster includes GO terms tied to lipid metabolic processes (sphingosine and sphinganine metabolism, phospholipid turnover and phosphatidylglycerol biosynthesis) and to ER-to-Golgi vesicle transport, suggesting a shared function in lipid remodeling and membrane trafficking. A few terms related to germ cell repulsion and obsolete Wnt signaling appear but are not representative of the dominant lipid- and trafficking-focused themes.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0035233","count":2},{"id":"GO:0044329","count":2},{"id":"GO:1902068","count":2},{"id":"GO:0006655","count":2}]},{"hash":"1366511281376774441","title":"Lipid metabolism and membrane trafficking","description":"This cluster is dominated by GO terms related to lipid handling: sterol biosynthesis, ceramide transport between the ER and Golgi, cholesterol response, and triglyceride storage, all pointing to lipid metabolism and intracellular lipid movement. Additional terms on post-Golgi vesicle transport and maintenance of cell polarity hint at broader membrane trafficking and cellular organization roles. Taken together, the proteins likely function in lipid metabolism coupled with vesicular trafficking, rather than a single specific process. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":1},{"id":"GO:0030011","count":1},{"id":"GO:0016126","count":1},{"id":"GO:0044128","count":1},{"id":"GO:0035621","count":1}]},{"hash":"401911028897542664","title":"Oxidative stress and ribosome biogenesis","description":"This cluster shows enrichment for redox homeostasis and cellular oxidative stress response alongside ribosome biogenesis, rRNA maturation/export, and general transcription/cell cycle terms. The pattern suggests a module linking oxidative stress management with ribosome production and RNA processing, possibly reflecting coordinated growth and stress response.","confidence":"Medium","size":11,"edges":28,"triangles":28,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0034599","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1319942841549522998","title":"Plant transcription and growth signaling","description":"The top GO terms point to nuclear gene regulation (DNA-templated transcription, DNA topological change) and plant-specific development processes (cytokinin signaling, secondary growth, chlorophyll catabolic regulation, chemotaxis, placenta-related term). This suggests a theme of plant gene regulation tied to growth and hormone signaling, rather than a single, tightly connected complex\u2014hence a label centered on plant transcription and growth signaling, despite the diverse terms. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0006265","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0010271","count":3}]},{"hash":"2212590474109720117","title":"Neuronal ion transport and vesicle trafficking","description":"The cluster\u2019s strongest signals are about ion transport (sodium/potassium regulation), neuromuscular control, neurofilament cytoskeleton organization, and retrograde vesicle transport between Golgi and ER, which together point to neuronal signaling, cytoskeletal dynamics, and intracellular trafficking. A few terms (DNA replication, stilbene catabolism, P450 epoxygenase pathway) are less aligned and may reflect broader or multifunctional protein roles. ","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0070389","count":3},{"id":"GO:1990573","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0060052","count":2}]},{"hash":"1070386803316373317","title":"Iron-sulfur cluster assembly and protein maturation","description":"The cluster\u2019s GO terms cluster around iron-sulfur (Fe-S) cluster biology: 2Fe-2S cluster assembly, maturation via Fe-S cluster transfer, protein folding, and linkage to cofactors like tetrapyrroles and chromophores. Although some terms are obsolete or noisy (e.g., placenta development), the core signal points to biogenesis and maturation of Fe-S cluster\u2013-containing proteins and related cofactors. Confidence: High","confidence":"","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051220","count":1},{"id":"GO:0036086","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0044571","count":1},{"id":"GO:1903026","count":1}]},{"hash":"418574996949599315","title":"Neuronal vesicle trafficking and synaptic signaling","description":"This cluster centers on synaptic vesicle exocytosis, small GTPase\u2013mediated signaling, and dendritic spine development, indicating roles in neuronal vesicle transport and synaptic regulation. Membrane transport and phospholipid homeostasis terms further support a focus on membrane trafficking linked to synaptic function, with some obsolete terms not altering the core theme. Overall, the proteins appear coordinated around neuronal communication and vesicle cycling.","confidence":"High","size":11,"edges":37,"triangles":66,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000060","count":8},{"id":"GO:0071806","count":8},{"id":"GO:0060999","count":8},{"id":"GO:0060789","count":8},{"id":"GO:0010796","count":8}]},{"hash":"369014255701029175","title":"Golgi\u2013ER\u2013Endosome Vesicle Transport","description":"This cluster is defined by multiple GO terms describing vesicle transport between the Golgi, endosomes, and the ER, plus related endocytosis and membrane tethering processes. The dominant theme is intracellular vesicular trafficking along the secretory and endocytic pathways, with some related organelle contact-site functions, indicating a cohesive trafficking-focused cluster.","confidence":"Medium","size":11,"edges":14,"triangles":4,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006895","count":5},{"id":"GO:0006890","count":5},{"id":"GO:0035646","count":5},{"id":"GO:1903434","count":4},{"id":"GO:0071851","count":4}]},{"hash":"805882045244836717","title":"Cellular stress response and genome maintenance","description":"The terms cluster around stress-related maintenance of the cell: DNA/RNA repair, translation regulation, and apoptosis control, with others touching on innate immunity and differentiation/oogenesis. Together these suggest proteins involved in preserving genome integrity and modulating cell fate under stress, rather than a single highly specific pathway.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0030154","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0048477","count":1}]},{"hash":"2078664317154470418","title":"Viral entry and replication","description":"The top GO terms cluster around viral infection processes: viral life cycle, fusion of viral and host membranes, entry into the host, occurrence of proviral latency, and RNA-templated DNA synthesis, indicating a coherent viral-host interaction theme; a few unrelated terms are present but do not override the core pattern.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":6},{"id":"GO:0048453","count":5},{"id":"GO:0006457","count":5},{"id":"GO:0075713","count":5},{"id":"GO:0050714","count":5}]},{"hash":"1616742080855800018","title":"Nuclear Import and Nuclear Pore Assembly","description":"The top GO terms center on importing proteins into the nucleus (NLS-bearing import, ribosomal protein import) and nuclear pore complex assembly, with supporting nuclear regulatory processes (desumoylation, Pol III transcription, kinase activity regulation). This points to a cohesive role in nuclear transport and nucleus-associated regulation. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0060188","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0051292","count":5},{"id":"GO:0000060","count":5},{"id":"GO:0043547","count":5}]},{"hash":"1867485745566184060","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000466","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0048701","count":1},{"id":"GO:0000462","count":1}]},{"hash":"677347577201792357","title":"Cell Cycle, Signaling, and DNA Damage Regulation","description":"Proteins in this cluster repeatedly point to regulatory roles across diverse pathways: cell cycle control (meiotic cycle, regulation of DNA damage checkpoint, protein localization related to cytokinesis), signaling cascades (calcineurin-NFAT pathway and its positive regulation), metabolic regulation (glycogen biosynthesis and glucose signaling), and DNA repair/development terms. The common thread is broad regulatory modulation rather than a single enzymatic function, justifying a general, integrative label.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000002","count":2},{"id":"GO:0005979","count":2},{"id":"GO:1901901","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0033173","count":2}]},{"hash":"954623912935300554","title":"Chromatin Remodeling and Transcription Regulation","description":"The cluster is dominated by GO terms for DNA-templated transcription, nucleosome assembly, and chromatin remodeling, with supporting signals from histone modification and chromatin context. This points to a core module governing chromatin structure and transcriptional control. A few terms touch on genome maintenance (telomere and DSB repair) and development, which may reflect pleiotropic roles of chromatin factors. Overall, the functions cohere around chromatin regulation of gene expression and genome integrity.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006334","count":4},{"id":"GO:0043044","count":4},{"id":"GO:0061820","count":3},{"id":"GO:1990414","count":3}]},{"hash":"1302277428787480750","title":"Ubiquitin-Mediated Cell Cycle Control and ER Stress","description":"The top GO terms cluster around mitotic cell cycle and cell division, with K11-linked ubiquitination and APC/C-dependent proteolysis, suggesting regulation of mitosis by ubiquitin-mediated degradation. Additional signals point to unfolded protein response and ER stress, including regulation of translation initiation during ER stress, indicating a proteostasis component linked to cell-cycle control. Some terms are obsolete but the overall theme remains coherent: cell-cycle progression governed by ubiquitin-dependent proteolysis and ER stress\u2013related quality control.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0070979","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0051291","count":3}]},{"hash":"793944452242325302","title":"Unknown","description":"The terms span extracellular matrix metabolism, nuclear processes, development, and stress responses, with little cohesive overlap beyond a few nuclear-related terms. This lack of a single unifying function or pathway suggests no clear theme for the cluster. ","confidence":"","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030212","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0060188","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0035264","count":1}]},{"hash":"1017732120842421411","title":"ER Stress and Proteostasis","description":"The cluster is dominated by GO terms for unfolded protein response, ER stress, and chaperone-assisted protein folding, plus translation changes in response to ER stress and oxidative stress, suggesting a proteostasis/stress-response theme. A few terms touch DNA replication and steroid metabolism, but the core signal points to ER-related protein quality control.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0016233","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0070301","count":2}]},{"hash":"907333534303329840","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms center on ribosome biogenesis (rRNA processing, small/large subunit assembly and export, rRNA methylation) and translation, indicating a ribosome-focused cluster. A few metabolic terms are likely incidental.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0060612","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0097327","count":1}]},{"hash":"1803809642200262221","title":"Unknown","description":"The GO terms span diverse biological themes (DNA repair, cell differentiation, signaling regulation, osmotic stress response) with no clear, shared function across the cluster, and there are no edges linking proteins, suggesting the set is not functionally cohesive. Therefore a concise, representative label cannot be assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042275","count":1},{"id":"GO:0010667","count":1},{"id":"GO:2000587","count":1},{"id":"GO:1990683","count":1},{"id":"GO:0071475","count":1}]},{"hash":"961629304783789878","title":"Mitochondrial Energy Metabolism and Redox Homeostasis","description":"The cluster centers on core energy pathways involving glycolysis, TCA cycle, and mitochondrial complex IV assembly, along with redox homeostasis, suggesting a mitochondria-focused energy production theme. Some developmental and immune-related terms appear as outliers rather than core features.","confidence":"Medium","size":11,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0033617","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0051573","count":1}]},{"hash":"1526230333727556632","title":"Redox balance and calcium signaling","description":"Top GO terms cluster around cellular redox homeostasis and oxidant detoxification, with supporting links to mitochondria (membrane potential regulation) and calcium release control (ryanodine receptor activity). Metabolic terms for L-ascorbic acid and homogentisate catabolism, plus a response to arsenic, reinforce a broader oxidative stress and mitochondrial/metabolic context. Platelet aggregation and osteoblast differentiation terms suggest downstream cellular responses but the core signal appears to be redox balance intertwined with calcium signaling and mitochondrial function.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":9},{"id":"GO:0098869","count":9},{"id":"GO:0060316","count":8},{"id":"GO:0019852","count":8},{"id":"GO:0060315","count":8}]},{"hash":"572782713270704450","title":"Unknown","description":"The terms are highly diverse (APP biosynthesis, heme/iron metabolism, plant tropisms, muscle and immune functions) with only single annotations and no interactions, giving no coherent functional theme to name a specific cluster function.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042984","count":1},{"id":"GO:0042167","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0033212","count":1},{"id":"GO:0045497","count":1}]},{"hash":"1949089998697901221","title":"Ubiquitin-Proteasome-Mediated Spindle and Development","description":"This cluster is dominated by ubiquitin-dependent protein catabolism, including SCF-proteasomal degradation, and involves microtubule-related activities such as polymerization and spindle assembly in meiosis, with support from oocyte maturation and broader developmental processes (neural tube and ventricle development). The shared theme links proteostasis and microtubule dynamics in cell division and development.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0006516","count":3},{"id":"GO:0046785","count":3},{"id":"GO:0051436","count":3}]},{"hash":"1366046029160444446","title":"Exosome-dependent RNA processing and rRNA maturation","description":"Most terms point to ribosomal RNA processing and RNA quality control (snoRNA processing, ITS2 cleavage, exosome-dependent transcription termination, nonfunctional rRNA decay, and general rRNA maturation). A few outlying terms exist but do not define the cluster\u2019s core function. Confidence: High","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000009","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0071035","count":1},{"id":"GO:0043144","count":1}]},{"hash":"1578376707033783950","title":"Golgi\u2013ER vesicle trafficking and SNARE-mediated secretion","description":"This set centers on vesicle transport within the secretory pathway, with terms for retrograde Golgi-to-ER and intra-Golgi transport, ERGIC fusion, SNARE complex assembly, and general protein transport. The presence of eosinophil degranulation and histamine secretion hints at secretory granule exocytosis, supporting a theme of vesicle trafficking and secretion. Overall, it points to Golgi\u2013ER trafficking machinery and SNARE-mediated secretion.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900483","count":1},{"id":"GO:0034197","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0043308","count":1},{"id":"GO:0006891","count":1}]},{"hash":"2076961352520126263","title":"Neural crest and heart development regulators","description":"This cluster centers on heart development and neural crest cell development (GO:0007507, GO:0014032), with entries involving regulation of heart contraction and transcriptional regulation (GO:0008016, GO:0045944, GO:0000122) as well as broader signaling and neural activity (regulation of synaptic processes, cAMP response). The mix suggests a regulatory module coordinating neural crest\u2013derived tissue development and cardiac function, with shared signaling and transcriptional control mechanisms. Confidence: Medium","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0014032","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0000122","count":2}]},{"hash":"1817990408274771369","title":"NOD2-driven antiviral innate immunity","description":"The cluster is dominated by innate immune and antiviral terms (innate immune response, defense response to virus) and a clear link to NOD2 signaling, with additional involvement of ubiquitin-proteasome\u2013related degradation processes, suggesting regulation of antiviral signaling. Some neuronal terms appear incidental, but the main signal centers on innate antiviral defense mediated by NOD2 and protein turnover. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0031146","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0070431","count":3}]},{"hash":"2105378164943030645","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033358","count":2},{"id":"GO:1902653","count":2},{"id":"GO:0009699","count":2},{"id":"GO:0019673","count":2},{"id":"GO:0001081","count":2}]},{"hash":"1857205860292748906","title":"Cell signaling and cytoskeletal remodeling","description":"This cluster pulls together diverse signaling pathways (Wnt, ephrin receptor, T cell receptor) and cytoskeletal processes (filopodium assembly, cell spreading, small GTPase signaling) with endocytosis, suggesting proteins that transduce external cues into adhesion, migration, and membrane trafficking changes.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":6},{"id":"GO:0090263","count":6},{"id":"GO:0050852","count":6},{"id":"GO:0046847","count":6},{"id":"GO:0007264","count":6}]},{"hash":"2005018172356913550","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":13,"triangles":7,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070417","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0000467","count":4},{"id":"GO:0090394","count":4}]},{"hash":"413459386857333182","title":"GPCR-mediated cAMP/cGMP signaling","description":"The terms point to a module of G protein-coupled receptor signaling with downstream cyclic nucleotide production, including cAMP and cGMP biosynthesis (adenylate cyclase- and guanylyl cyclase\u2013related pathways), and related responses (forskolin response, blue light signaling). This pattern also aligns with oocyte maturation regulation and other GPCR-driven cellular responses, suggesting a cohesive GPCR-coupled second messenger signaling cluster.","confidence":"High","size":10,"edges":11,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0071880","count":1},{"id":"GO:0001973","count":1},{"id":"GO:0007168","count":1},{"id":"GO:0009785","count":1}]},{"hash":"792032949535420281","title":"Proteostasis under mitochondrial and ER stress","description":"The GO terms point to mitochondrial function (oxidative phosphorylation, complex III assembly) and ER proteostasis (unfolded protein response, protein processing/assembly, turnover). Together with protein maturation/turnover processes and general stress-related transcription regulation, the cluster centers on protein quality control and stress responses across organelles. Confidence: Medium","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031117","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0016485","count":2},{"id":"GO:1903862","count":2},{"id":"GO:0070987","count":2}]},{"hash":"2162940854767694139","title":"DNA replication and repair proteins","description":"Based on the GO terms, the cluster centers on DNA synthesis and genome maintenance, including mitotic leading/lagging strand elongation, general DNA replication, nucleotide-excision repair, UV-damage repair, and homologous recombination repair. A few non-replication terms appear, but the dominant theme reflects replication and DNA repair machinery. This suggests the proteins collectively participate in DNA synthesis and repair processes rather than a single non-related function.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903460","count":1},{"id":"GO:0043150","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006297","count":1},{"id":"GO:1903459","count":1}]},{"hash":"1955022441422580564","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"The top GO terms cluster around actin cytoskeleton organization, lamellipodium assembly, Rac/Rho signal regulation, and cell migration/adherence-dependent spreading, pointing to coordinated actin remodeling driving movement. While heart development and insulin signaling terms appear, the dominant theme is cytoskeleton-driven migration and protrusion; hence this label best represents the cluster\u2019s function.","confidence":"High","size":10,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0032633","count":3},{"id":"GO:0035020","count":3},{"id":"GO:0035023","count":3}]},{"hash":"222021358873661778","title":"Rho/Rac signaling drives actin remodeling and migration","description":"The cluster centers on Rho/Rac-regulated actin dynamics, lamellipodium assembly, and cell migration/adherence, pointing to coordinated cytoskeletal remodeling as a core function; the presence of terms like heart development, insulin signaling, IL-4 production, and B cell maturation likely reflect broader developmental and immune-context roles rather than a separate function.","confidence":"High","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0008286","count":5},{"id":"GO:0032633","count":5},{"id":"GO:0035020","count":5}]},{"hash":"1850109168718052417","title":"Methylation and Cofactor Biosynthesis","description":"The cluster centers on protein methylation events (N-terminal peptidyl-glycine methylation; peptidyl-lysine dimethylation) and biosynthetic pathways for cofactors and related metabolites (cobalamin, ubiquinone, polyamines, carnosine). This suggests a combined theme of post-translational modification and metabolic cofactor production common in microbial cellular processes, with some ancillary stress-related terms. Overall, these terms point to methylation-related regulation coupled with cofactor biosynthesis rather than a single signaling or structural function.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":1},{"id":"GO:0010038","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1765780829214821367","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0048568","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000472","count":2}]},{"hash":"1470733357576688972","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":5,"triangles":0,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0000467","count":4},{"id":"GO:0034475","count":4},{"id":"GO:0034476","count":4}]},{"hash":"1382556588899290357","title":"Nuclear RNA processing and genome maintenance","description":"This cluster is enriched for rRNA maturation (5.8S and LSU/SSU), DNA replication, chromatin remodeling, telomere protection, and subtelomeric heterochromatin formation, pointing to nuclear RNA processing and genome integrity roles; additional terms like G-quadruplex DNA and tRNA wobble modification support DNA/RNA metabolism, while a few entries (antibiotic biosynthetic process, embryonic cranial skeleton morphogenesis) are less connected.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0002098","count":2}]},{"hash":"1008868231468671833","title":"DNA methylation driven gene silencing","description":"The terms point to epigenetic regulation through DNA methylation and chromatin-based control of gene expression, including DNA methylation\u2013dependent heterochromatin formation and siRNA-directed methylation, i.e., methylation-mediated gene silencing. A few terms about translation or ubiquitination appear but are not central to the cluster\u2019s theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0090308","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0010424","count":1},{"id":"GO:0071158","count":1}]},{"hash":"537647263962845762","title":"Unknown","description":"The GO terms span immune recombination, signaling, transcription, apoptosis, viral processes, meiosis, desumoylation, and metabolic responses, with no single shared function linking them and no edges among the proteins (Edges: 0, Triangles: 0, Max Degree: 0). This lack of coherence supports labeling the cluster Unknown with None confidence.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033153","count":2},{"id":"GO:0033674","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0045945","count":1},{"id":"GO:0042518","count":1}]},{"hash":"486488873804737455","title":"DNA Damage Response and Translational Regulation","description":"This cluster includes translation and ribosome biogenesis terms alongside transcription regulation and DNA damage\u2013response terms tied to p53 signaling, gamma radiation, and UV exposure. Together they suggest a stress-responsive program that links transcriptional control with translational regulation in response to DNA damage.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045727","count":1},{"id":"GO:0032784","count":1},{"id":"GO:1902167","count":1},{"id":"GO:0071480","count":1}]},{"hash":"485772710548609298","title":"Steroid hormone biosynthesis and lipid metabolism","description":"The top GO terms are dominated by steroid biosynthesis (testosterone, glucocorticoids, retinoic acid) and related lipid metabolic processes (fatty acid elongation, sphinganine metabolism, phylloquinone and other lipid-derived pathways). This points to a coherent theme around steroid hormone production and lipid metabolism, with a secondary signal of transcription regulation that may reflect regulatory roles. Overall, a steroidogenesis/lipid metabolism cluster best fits the data.","confidence":"High","size":10,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006666","count":4},{"id":"GO:0008207","count":4},{"id":"GO:0061370","count":4}]},{"hash":"299243610684483808","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009699","count":4},{"id":"GO:0019673","count":4},{"id":"GO:0009243","count":4},{"id":"GO:0042351","count":4}]},{"hash":"1095962554120531403","title":"Magnesium and cobalt ion transport","description":"The top GO terms point to transmembrane transport of metal ions, especially Mg2+ transport in mitochondria and cobalt ion transport. This suggests a cohesive module of proteins involved in metal ion homeostasis across membranes, potentially including mitochondrial Mg2+ transporters. The network metrics (small cluster, limited triangles, and ReCIPE re-additions) further support a focused ion-transport function.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045016","count":1},{"id":"GO:1903830","count":1},{"id":"GO:0006824","count":1}]},{"hash":"85222248200260555","title":"Steroid and lipid metabolism","description":"The top GO terms cluster around lipid and steroid biosynthesis and processing (3-keto-sphinganine metabolism, C21-steroid hormone metabolism, testosterone and glucocorticoid biosynthesis, and fatty acid elongation), with additional lipid-related metabolite terms (retinoic acid and phylloquinone) that support a broader lipid/metabolite theme. Despite a few peripheral terms, the dominant pattern is steroid and lipid metabolism.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006666","count":3},{"id":"GO:0008207","count":3},{"id":"GO:0061370","count":3},{"id":"GO:0006704","count":3},{"id":"GO:0030497","count":3}]},{"hash":"513028544716388773","title":"Amino acid and small-molecule metabolism","description":"This cluster shows enrichment across amino-acid catabolic pathways (serine/threonine/cysteine, transsulfuration), hydrogen sulfide production, and broader small-molecule metabolism (fatty acid omega-oxidation, pyruvate fermentation to ethanol, xylitol and furaldehyde metabolism, prostaglandin metabolism). The shared theme is general metabolic processing of diverse small molecules rather than a single cohesive pathway, so the label reflects a broad metabolic function without overfitting to one process.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0019518","count":5},{"id":"GO:0006565","count":4},{"id":"GO:0019343","count":4},{"id":"GO:0019346","count":4},{"id":"GO:0070814","count":4}]},{"hash":"132627784819892667","title":"Central Metabolism with Xenobiotic Response","description":"Contains glycolysis, TCA cycle, and 2-oxoglutarate metabolism, indicating core energy metabolism. It also includes retinol metabolism, thymidine catabolism, and responses to xenobiotic stimulus and lipopolysaccharide, suggesting metabolic regulation linked to detox/immune-like stress pathways. Overall, the cluster centers on central metabolism with accompanying xenobiotic response features.","confidence":"Medium","size":10,"edges":20,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042493","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0042208","count":3},{"id":"GO:0032496","count":3}]},{"hash":"754719055689141243","title":"Calcium\u2013Calcineurin\u2013NFAT Neuronal Signaling","description":"This cluster centers on calcium-activated signaling and NFAT regulation, with links to synaptic vesicle exocytosis, long-term memory, and kinase/GTPase regulation, indicating calcium-driven neuronal signaling and plasticity; Schwann cell development hints peripheral glial context but does not outweigh the neuronal signaling theme.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071902","count":3},{"id":"GO:2000300","count":2}]},{"hash":"1393957061448772208","title":"Chromatin remodeling and assembly","description":"This cluster centers on chromatin organization and remodeling, with terms for heterochromatin formation, transcription-coupled remodeling, nucleosome and CENP-A assembly, and general chromatin remodeling/histone modification, suggesting a cohesive function in chromatin structure maintenance and transcription regulation.","confidence":"High","size":10,"edges":17,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":6},{"id":"GO:0045815","count":5},{"id":"GO:0006335","count":4},{"id":"GO:0051290","count":4},{"id":"GO:0000122","count":4}]},{"hash":"1258248388199256403","title":"Steroid and lipid metabolism","description":"The top GO terms cluster around biosynthesis and metabolism of steroids and lipid-derived molecules (testosterone, glucocorticoids, fatty acid elongation, retinoic acid, 3-keto-sphinganine, phylloquinone), suggesting a cohesive theme of lipid/steroid biosynthesis and processing. A few terms like antibiotic response are outliers, but the dominant signal points to steroid and lipid metabolism. ","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006666","count":2},{"id":"GO:0008207","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0006704","count":2},{"id":"GO:0030497","count":2}]},{"hash":"1040082411569213481","title":"Unknown","description":"The top terms span a very wide range of functions (DNA repair, redox homeostasis, signaling via cAMP and phosphoinositides, corneocyte development, renal water transport) with several terms marked obsolete and no clear shared pathway. This makes it hard to assign a cohesive, specific function to the cluster, so Unknown is the best representation of a lack of a single unifying theme.","confidence":"","size":10,"edges":13,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:2001153","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0044179","count":1},{"id":"GO:0046856","count":1},{"id":"GO:0006284","count":1}]},{"hash":"1987345668020000505","title":"Ciliary sensory perception and signaling","description":"The top terms strongly point to ciliary function and sensory biology, with cilium assembly and visual perception as core themes, complemented by sensory neuron guidance and pheromone response. A couple of terms relate to more general cellular processes, but the dominant pattern supports a ciliary/sensory signaling theme.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060271","count":8},{"id":"GO:1905490","count":8},{"id":"GO:0035330","count":8},{"id":"GO:0006547","count":8},{"id":"GO:0007117","count":8}]},{"hash":"727999864869518554","title":"Mitotic cell division and Golgi-ER trafficking proteins","description":"The top GO terms point to mitotic cell cycle, cell division, mitotic spindle assembly, and growth, indicating involvement in mitosis and proliferation. Simultaneously, COPII vesicle budding and retrograde Golgi-to-ER transport suggest a role in secretory pathway trafficking. Together, these terms imply a cluster of proteins linked to mitotic machinery and secretory trafficking, potentially coordinating cell division with intracellular transport during development.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0090114","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0051260","count":3}]},{"hash":"2284788203268953768","title":"Developmental morphogenesis and EMT signaling","description":"This cluster centers on developmental processes (ectoderm, cranial skeletal system, renal vesicle formation), with themes of cell migration, adhesion, and signaling (GTPase activity, calcium signaling, Wnt/EMT). The combination suggests roles in tissue morphogenesis and epithelial-to-mesenchymal transition during organ development.","confidence":"High","size":9,"edges":26,"triangles":39,"max_degree":8,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0016477","count":7},{"id":"GO:0048364","count":7},{"id":"GO:1904888","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0006974","count":6}]},{"hash":"1545986127955309958","title":"Neuronal signaling and synaptic plasticity","description":"The cluster is dominated by neural signaling and plasticity terms, including excitatory postsynaptic potential and long-term synaptic potentiation, plus development-related terms (Bergmann glial differentiation, multicellular development) and signaling pathways (insulin receptor signaling, GTPase activity regulation, phosphorylation). Some terms like visual perception and abscisic acid signaling are less clearly connected, but the core pattern points to neurons, synaptic function, and brain development.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0010800","count":2},{"id":"GO:0060020","count":2}]},{"hash":"1253909383917654402","title":"Cell Cycle and Mitosis","description":"This cluster's top GO terms include multiple entries for cell cycle (GO:0007049), cell division, and mitotic spindle assembly, indicating a shared involvement in mitosis and cell-cycle control. While there are some unrelated signaling terms, the preponderance of mitosis-related functions best captures the cluster's core theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0090307","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0071353","count":3}]},{"hash":"872256212933452739","title":"DNA-Templated Transcription Regulation","description":"The cluster is named for the strongest signal in the GO terms: regulation of DNA-templated transcription and DNA-templated transcription themselves, suggesting a core link to gene expression control. While other terms (metabolic, biosynthetic, transport, and microtubule-related processes) appear, they are less dominant and may reflect annotation breadth or multifunctionality of the proteins. Overall, the transcription regulation theme best captures the shared function.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0008209","count":3},{"id":"GO:0061370","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2287672776665154274","title":"Vertebrate Neural Tube Development","description":"Most of the top GO terms point to vertebrate development with a focus on neural formation, including neural tube closure and forebrain development, alongside broader embryonic/multicellular development and skeletal system development. While there are some stress-related terms, the central pattern is developmental processes in vertebrates, especially neural development. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0071276","count":3}]},{"hash":"338107013505898992","title":"Cell Cycle and Development","description":"The top GO terms strongly emphasize mitotic processes (G1/S and G2/M transitions, mitotic cell cycle, sister chromatid movement) with additional development-related terms (hemopoiesis, nervous system development, axon extension, cotyledon development). This pattern suggests a protein set involved in core cell cycle regulation alongside broader developmental programs. However, the mix of diverse, cross-context terms and lack of direct interaction data makes the theme broad rather than a single cohesive pathway, so the label reflects a general cell-cycle\u2013developmental theme rather than a tightly connected function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030097","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0045773","count":3}]},{"hash":"389934856330612928","title":"Mitochondrial Redox and Iron Homeostasis","description":"The cluster centers on oxidative stress response and redox processes, with supporting hints from mitochondrial intermembrane space protein import and iron ion homeostasis, suggesting a mitochondrial stress-response and metal homeostasis theme; some terms appear less related, but the core signal is mitochondrial redox/iron balance.","confidence":"Medium","size":9,"edges":29,"triangles":41,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045041","count":1},{"id":"GO:0006879","count":1}]},{"hash":"1314325402921024435","title":"Nuclear chromatin remodeling and ribosome biogenesis","description":"This cluster is driven by chromatin-related processes (rDNA heterochromatin formation, chromatin remodeling) and ribosome biogenesis (ribosomal large subunit biogenesis), pointing to a nuclear/nucleolar functional theme. The other biosynthesis terms are diverse and lower in frequency, so they do not define a single cohesive function for the cluster.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0009877","count":1},{"id":"GO:0009236","count":1}]},{"hash":"228731379366431548","title":"N-terminal protein acetylation","description":"The dominant GO terms are all about N-terminal acetylation of various amino acids, indicating the cluster is centered on N-terminal acetylation activity (likely N-terminal acetyltransferases or substrates). A few other terms appear but do not define the core function.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":5},{"id":"GO:0017198","count":4},{"id":"GO:0061606","count":4},{"id":"GO:0030187","count":4},{"id":"GO:0018002","count":4}]},{"hash":"695419490406864465","title":"Dopaminergic Signaling and Nuclear Regulation","description":"The cluster shows enrichment for dopaminergic synaptic transmission, signaling pathways (including PI3K/AKT and NF-kappaB related regulation), transcriptional activity (DNA-templated transcription), and nuclear-cytoplasmic regulation (proteasomal degradation control and nuclear export). This combination suggests a module combining neuronal signaling with transcriptional regulation and stress-responsive processes in dopaminergic neurons. However, the connections are somewhat broad and some terms are obsolete, so the cohesion is not perfect.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033138","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0032435","count":2}]},{"hash":"564782354151764247","title":"DNA Damage Response and DSB Repair Regulation","description":"This cluster is dominated by GO terms tied to DNA damage response and regulation of double-strand break repair, including responses to ionizing radiation, regulation of homologous recombination and nonhomologous end joining, and mitotic G2 DNA damage checkpoint signaling, plus chromatin localization. While a few unrelated terms appear, the core signal points to DDR and chromatin-associated repair functions.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032781","count":2},{"id":"GO:1905168","count":1},{"id":"GO:2001032","count":1},{"id":"GO:0010212","count":1},{"id":"GO:0071168","count":1}]},{"hash":"796459974605817613","title":"Neuronal Exocytosis and Dendrite Development","description":"Top terms cluster around synaptic vesicle and dense core granule exocytosis, glutamatergic transmission, and promotion of dendrite extension, pointing to a cohesive theme of neuronal synapse function and neurite outgrowth. A few terms relate to transcription or non-neuronal processes, which are likely less central to the main theme. Overall, the cluster appears to reflect neuronal exocytosis and dendrite development.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":2},{"id":"GO:0045945","count":1},{"id":"GO:2000300","count":1},{"id":"GO:0001324","count":1},{"id":"GO:1905415","count":1}]},{"hash":"1170180177152904729","title":"Ubiquitin-Mediated Regulation of Cell Cycle and Death","description":"The GO terms show a clear emphasis on ubiquitination processes (polyubiquitination, K6-linked ubiquitination, ERAD) and downstream regulation of cell fate (apoptosis, necroptosis) and cell cycle, with additional notes on ribosome biogenesis and histone-related processes that can be tied to ubiquitin signaling and proteostasis. Together, these suggest a cluster centered on ubiquitin-dependent control of protein turnover and cellular fate decisions, with some chromatin and ribosome biogenesis context. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0043981","count":2},{"id":"GO:0036205","count":2}]},{"hash":"694986545538217038","title":"Actin cytoskeleton remodeling and endocytosis","description":"This cluster centers on actin dynamics (fragmentation, lamellipodium/ruffle assembly, depolymerization and bundle regulation) together with receptor-mediated endocytosis and spine morphogenesis, suggesting a cohesive role in actin-driven membrane remodeling and related cellular morphogenesis.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006898","count":2},{"id":"GO:0030043","count":1},{"id":"GO:0097178","count":1},{"id":"GO:0010593","count":1},{"id":"GO:0030307","count":1}]},{"hash":"677006051174627257","title":"Gene expression regulation and ribosome biogenesis","description":"This cluster centers on transcription (DNA-templated transcription) and multiple translation-related processes (translation preinitiation complex formation, translation reinitiation), plus ribosome biogenesis and mRNA transport, indicating coordinated control of gene expression at transcriptional and translational levels. The presence of mitotic cell cycle and cellular response to hypoxia suggests links to proliferative and stress-adaptive contexts where protein synthesis machinery is upregulated. Overall, it reflects a cohesive theme of gene expression regulation and ribosome assembly under growth/hypoxic conditions.","confidence":"Medium","size":9,"edges":25,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0008284","count":2}]},{"hash":"1641601579869773668","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070534","count":2}]},{"hash":"1936155336467367103","title":"Lipid metabolism and steroid biosynthesis","description":"The top GO terms cluster around lipid-derived metabolite production and processing, including fatty acid omega-oxidation, prostaglandin and cholesterol catabolism, and biosynthesis of hormones such as testosterone, calcitriol, ecdysone, and brassinosteroids, as well as epoxygenase P450 pathways. This points to a cohesive theme of lipid metabolism and steroid/hormone biosynthesis across species.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010430","count":3},{"id":"GO:0002677","count":3},{"id":"GO:0016132","count":3},{"id":"GO:0006697","count":3},{"id":"GO:0061370","count":3}]},{"hash":"1078478248881514132","title":"Immune activation and tissue remodeling signals","description":"The top GO terms cluster around immune activity (T cell activation) and adhesion/ECM remodeling (regulation of integrin-mediated cell-cell adhesion, negative regulation of ECM disassembly), with supporting stress and metabolic signals (hypoxia response, oxidative detoxification, insulin secretion regulation) and some behavioral associations. This pattern suggests a broader theme of immune-related tissue remodeling and stress signaling rather than a single specific function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0033632","count":5},{"id":"GO:0036343","count":5},{"id":"GO:0042110","count":5},{"id":"GO:0010716","count":5},{"id":"GO:0001666","count":5}]},{"hash":"2281959844363252005","title":"Gene Expression Regulation and Chromatin Modification","description":"Top GO terms emphasize transcriptional regulation by RNA polymerase II and histone acetylation, indicating a cluster tied to controlling gene expression via chromatin state. Some terms also touch on translation and microtubule assembly, which may reflect broader cellular processes or annotation overlap.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046898","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0046785","count":1},{"id":"GO:0001578","count":1}]},{"hash":"966048890418711879","title":"Brassinosteroid biosynthesis and plant development","description":"The dominant terms are brassinosteroid biosynthetic process and brassinosteroid homeostasis, plus trichome branching, pointing to a plant hormone biosynthesis and developmental theme. Dolichol/polyprenol-related terms accompany this lipid/metabolic context, further supporting a link to isoprenoid-derived hormone pathways. A few outlier terms (ectodermal fate, genitalia development, circadian sleep) likely reflect cross-species or broad annotations rather than the cluster\u2019s core function. There are no edges, so the label reflects shared functional themes rather than direct interactions.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001713","count":1},{"id":"GO:0030539","count":1},{"id":"GO:0042747","count":1},{"id":"GO:0010268","count":1},{"id":"GO:0006702","count":1}]},{"hash":"233769269906663143","title":"Unknown","description":"This cluster's top GO terms span lipid biosynthesis regulation, mitochondrial function, transcription regulation and processing, protein handling, microtubule dynamics, and cell cycle control, with no clear unifying function. The diverse annotations and lack of a shared pathway make a cohesive label difficult.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010867","count":1},{"id":"GO:1903740","count":1},{"id":"GO:0046902","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1}]},{"hash":"803583277820366798","title":"Ribosome Biogenesis and rRNA Maturation","description":"The prominent GO terms are all about maturation of SSU/LSU/5.8S rRNA and ribosome biogenesis, indicating a theme of ribosome assembly and rRNA processing. Additional terms related to translation initiation/reinitiation and transcription are present but secondary, supporting the core ribosome-focused function of this cluster.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0007369","count":2}]},{"hash":"1006074848945252075","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms cluster around ribosome production: formation of translation preinitiation complex, translation reinitiation, maturation of 5.8S and LSU rRNA from tricistronic transcripts, ITS1 cleavage to separate rRNA components, RNA guanine-N7 methylation, and associated transcription/export processes. Together these indicate a module focused on ribosome assembly and the early stages of translation. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0036265","count":2}]},{"hash":"902404458525985475","title":"Unknown","description":"The top GO terms span diverse areas (cardiac muscle differentiation, receptor internalization, nucleotide/uracil salvage, antibiotic response, Rho signaling regulation, and angiogenesis in wound healing) with no clear, single shared function. This suggests the proteins may be functionally heterogeneous or the cluster may be an assembly without a unified biology.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055007","count":2},{"id":"GO:0031623","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0046677","count":2}]},{"hash":"253710300436133319","title":"Ribosome Large Subunit Biogenesis and rRNA Maturation","description":"The cluster is dominated by GO terms for maturation of 5.8S rRNA, large subunit ribosome assembly, preribosome assembly, and export from the nucleus, all pointing to ribosome biogenesis. A few terms (chromatin assembly and membrane-related processes) appear less connected and may reflect broader cellular roles, but the core signal centers on large subunit formation and rRNA processing.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":2},{"id":"GO:0010163","count":1},{"id":"GO:0090333","count":1},{"id":"GO:0042391","count":1},{"id":"GO:0051260","count":1}]},{"hash":"536640701028193773","title":"Unknown","description":"The terms are scattered across translation machinery (rRNA maturation, translation initiation), ubiquitination, chromatin modification, actin regulation, development, immune signaling, and nutrient response, with only single-term hits; there is no clear shared function tying these proteins together, so no coherent label can be assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":1},{"id":"GO:0070979","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0000462","count":1},{"id":"GO:2000011","count":1}]},{"hash":"334751670989241050","title":"Nucleotide Salvage Pathways","description":"Top GO terms cluster around salvage and interconversion of nucleosides and nucleotides (guanosine/inosine/cytidine/uridine salvage, purine nucleoside catabolic, nicotinate nucleotide/NAD salvage), indicating a cohesive theme of nucleotide salvage metabolism. The lack of edges suggests these proteins participate in related salvage processes rather than a single, tightly connected complex.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006206","count":2},{"id":"GO:0034356","count":2},{"id":"GO:0006179","count":2},{"id":"GO:0006216","count":2},{"id":"GO:0006190","count":2}]},{"hash":"1507424560890521940","title":"DNA replication, transcription, and genome mobility","description":"Top GO terms indicate core DNA metabolism (replication, transcription, DNA integration) and genome dynamics (transposition, RNA-templated DNA synthesis). A few terms about SRP-dependent cotranslational targeting to membranes appear, but they are less represented, so the dominant theme is DNA-related processes and genome mobility.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0006617","count":1},{"id":"GO:0006355","count":1}]},{"hash":"966410938001312774","title":"Bacterial transcription and cofactor biosynthesis","description":"This cluster is dominated by GO terms for DNA-templated transcription and DNA replication, indicating core gene expression and genome maintenance. It also includes multiple biosynthetic processes for cofactors (bacteriochlorophyll, cobalamin) and iron-sulfur cluster assembly, along with metal ion response, pointing to a bacterial grouping focused on biosynthesis of essential cofactors and metal handling. A conjugation-related term may reflect mobile elements but does not override the central theme. Therefore, the label Bacterial transcription and cofactor biosynthesis is appropriate.","confidence":"High","size":9,"edges":14,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006261","count":2},{"id":"GO:0006890","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0010038","count":1}]},{"hash":"1953459078079637207","title":"Transmembrane Transporters for Sugars and Neurotransmitters","description":"These proteins collectively map to various transmembrane transport processes across multiple substrates\u2014sugars (arabinose, galactose), sialic acid, nitrates, xenobiotics, and sodium ions\u2014as well as neurotransmitter loading into synaptic vesicles. The shared feature is membrane transport activity with diverse substrates, including a neurotransmitter packaging role, which supports a concise label for a transporter-focused cluster.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0042128","count":2}]},{"hash":"1854570202883607842","title":"ECM-Driven Signaling in Cardiovascular and Neural Systems","description":"The cluster centers on extracellular matrix organization and signaling pathways that influence vascular/heart function and neural activity, as evidenced by ECM-related GO terms, regulation of VEGF signaling, heart contraction, axonogenesis, and synaptic vesicle exocytosis, with accompanying kinase signaling modulation.","confidence":"Medium","size":9,"edges":34,"triangles":70,"max_degree":8,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0030948","count":5},{"id":"GO:0030198","count":5},{"id":"GO:0042267","count":5},{"id":"GO:0006470","count":4},{"id":"GO:0007409","count":4}]},{"hash":"1681830562041410277","title":"Methylation-driven chromatin and RNA modification","description":"Ribosomal RNA and histone methylation with transcriptional regulation (epigenetic chromatin function).","confidence":"High","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":5},{"id":"GO:0018027","count":4},{"id":"GO:0018013","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0000183","count":3}]},{"hash":"1857775946339258942","title":"Unknown","description":"The Top Terms cover amino acid catabolism/biosynthesis (alanine, tyrosine, aspartate, kynurenine), Notch signaling, fatty acid transport, fruit ripening, and cobalamin biosynthesis, indicating a highly heterogeneous set of functions with no single cohesive theme. Thus a reliable single-label name is not apparent.","confidence":"","size":9,"edges":34,"triangles":70,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":4},{"id":"GO:0007219","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006571","count":3}]},{"hash":"412777646054699643","title":"ER-Golgi trafficking and ER stress response","description":"GO terms highlight ER-to-Golgi vesicle transport and COPII budding, indicating a secretory pathway core. The presence of ER stress\u2013related apoptosis and developmental terms further ties these proteins to ER-associated trafficking and stress signaling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0070059","count":3}]},{"hash":"1145250849162990350","title":"Unknown","description":"The terms are highly diverse (cell division, muscle and nervous system development, B cell signaling, germinal center formation, kidney function, circadian rhythm, and ubiquitin-related processes) with no single cohesive function. Only two items touch on ubiquitination, which is insufficient to define a clear theme for the cluster.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035853","count":1},{"id":"GO:0048741","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0050853","count":1},{"id":"GO:0002467","count":1}]},{"hash":"2266051289728227617","title":"Unknown","description":"The top terms span RNA processing, translation initiation, transcription regulation, several developmental processes (gastrulation, male gonad development, patterning), cytoskeletal regulation, nutrient response, histone modification, and inflammatory cytokine production. This broad mix shows no single cohesive function or pathway tying all proteins together, so a concise, unified label isn\u2019t supported.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0007584","count":1},{"id":"GO:0043966","count":1},{"id":"GO:2000011","count":1},{"id":"GO:0007369","count":1}]},{"hash":"1822399668530139098","title":"Steroid and Lipid Hormone Biosynthesis","description":"The top GO terms cluster around production and breakdown of lipid-derived hormones and steroids, including brassinosteroids, ecdysone, testosterone, prostaglandins, cholesterol catabolism, fatty acid omega-oxidation, and epoxygenase P450 pathways. The recurrence of P450-mediated oxidation supports a lipid metabolism theme, tying hormone biosynthesis to lipid processing; the inflammation term can be linked via prostaglandin signaling. Overall, this cluster represents steroid and lipid hormone biosynthesis and metabolism.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010430","count":8},{"id":"GO:0002677","count":8},{"id":"GO:0016132","count":8},{"id":"GO:0006697","count":8},{"id":"GO:0061370","count":8}]},{"hash":"805665409899460561","title":"Bacterial transcriptional regulation and motility","description":"The top GO terms cluster around DNA-templated transcription and its regulation, two-component phosphorelay signaling, and motility-related processes (chemotaxis and flagellum-dependent movement), along with sporulation regulation. This combination indicates a group of proteins involved in environmental sensing and transcriptional control that governs bacterial movement and developmental responses, rather than metabolic pathways. The plant hormone-related term may be an annotation artifact in this context.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006935","count":3},{"id":"GO:0000160","count":3},{"id":"GO:0071973","count":3}]},{"hash":"1801562616909968182","title":"Chromatin modification and developmental transcription","description":"Dominant GO terms point to chromatin-level control of gene expression (histone H3K4 and H3K79 methylation) and DNA-templated transcription, accompanied by developmental processes (skin and smooth muscle development). Although several terms are obsolete and there are no network edges, the recurring theme is transcription regulation via chromatin modification during development, with hints of signaling crosstalk (ERK cascade).","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1849157159168928043","title":"Developmental growth signaling and proliferation","description":"The top GO terms point to positive regulation of kinase activity (autophosphorylation, serine/threonine kinase activity) and GTPase signaling, together with processes tied to cell proliferation and multicellular development (including skin development). This pattern suggests a broad theme of signaling pathways that promote growth and developmental programs in multicellular contexts, with some ancillary links to mRNA transport and hypoxic response. The lack of direct interaction data means the label captures a general functional theme rather than a specific pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043588","count":2}]},{"hash":"1759123740500712972","title":"Germline Autophagy and Development","description":"This cluster is characterized by autophagy-related terms (autophagy; negative regulation of autophagy) along with several germline and developmental terms (spermatid differentiation; male germ-line cyst formation; meiotic chromosome condensation), suggesting a theme around autophagy\u2019s role in germline development and maturation. Additional terms related to translation initiation and dexamethasone response imply broader stress/translation regulation, but the strongest shared signal links autophagy with germline development.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006914","count":2},{"id":"GO:0048515","count":1},{"id":"GO:0048136","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0010507","count":1}]},{"hash":"513271076816848268","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to ribosome biogenesis, translation, and maturation of rRNA, with translational initiation also represented, indicating proteins involved in assembling and initiating protein synthesis. The viral genome replication and DNA replication terms appear as smaller outliers and do not define the main function. Overall, the core theme is ribosome assembly and protein synthesis.","confidence":"High","size":8,"edges":12,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019079","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006260","count":2}]},{"hash":"268955764714022488","title":"Signaling and Cytoskeletal Dynamics","description":"This cluster centers on receptor-mediated signaling pathways (Wnt, T cell receptor, ephrin) and cytoskeletal-related processes (mitotic spindle assembly, actin reorganization, endocytosis), with synaptic and dopamine-related signaling also represented. The common theme appears to be signaling coupled to cytoskeletal remodeling across diverse contexts, suggesting a general signaling-cytoskeleton module rather than a single, narrow pathway.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0043552","count":5},{"id":"GO:0048013","count":5}]},{"hash":"1750864434062061501","title":"TGF-beta/BMP Signaling Regulation","description":"The cluster is enriched in GO terms related to negative regulation of TGF-beta receptor signaling, BMP signaling, SMAD complex assembly, and cellular response to TGF-beta stimulus, suggesting the proteins collectively modulate TGF-beta/BMP pathways. Some terms reference unrelated processes like photosystem stoichiometry adjustment and meristem maintenance, which may reflect cross-species annotations, but the dominant theme is signaling pathway regulation in development.","confidence":"Medium","size":8,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0080005","count":2},{"id":"GO:0042006","count":2},{"id":"GO:0030512","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0071560","count":2}]},{"hash":"295614260949482129","title":"Developmental transcription and neural development","description":"The cluster centers on DNA-templated transcription and neural development terms (forebrain development, neural tube closure, multicellular organism development) with overlap to cell cycle regulation, suggesting a core role in developmental gene regulation and neural patterning. The presence of stress-related terms (ER stress\u2013induced apoptosis, cadmium response, defense to bacteria) indicates additional contextual responses but does not override the main developmental theme.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000278","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0007275","count":4}]},{"hash":"1504460668810048495","title":"Regulated neuronal synaptic vesicle cycling","description":"This cluster is dominated by GO terms tied to synaptic function: excitatory postsynaptic potential and the regulation of both synaptic vesicle endocytosis and exocytosis, pointing to controlled vesicle trafficking at the synapse. The presence of substantia nigra development suggests a neural context, while other terms like xenobiotic response or mitotic processes are broader or less central, but do not override the synaptic theme. Overall, the common thread appears to be regulation of vesicle cycling in neurons. ","confidence":"Medium","size":8,"edges":12,"triangles":3,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0021762","count":3},{"id":"GO:1900242","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0043931","count":3}]},{"hash":"1729093422140019126","title":"Melanosome biogenesis and lysosome trafficking","description":"Top GO terms point to melanosomes and lysosome-related organelles, including endosome-to-melanosome transport, eye pigment granule organization, melanocyte differentiation, lysosome localization and lumen acidification, autophagosome maturation, and vesicle transport. This pattern indicates a cohesive role in pigment cell biology, specifically pigment granule biogenesis and trafficking within lysosome-related organelles, with supplementary vesicular transport processes.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033299","count":1},{"id":"GO:0035646","count":1},{"id":"GO:0008057","count":1},{"id":"GO:0031629","count":1},{"id":"GO:0050942","count":1}]},{"hash":"2155598687877567045","title":"Neuronal development and chromatin regulation","description":"The top GO terms highlight neuron projection extension and multicellular development, pointing to a neurodevelopmental theme. Concurrently, positive regulation of chromatin binding and histone H3-K9 methylation regulation suggest epigenetic control mechanisms modulating development. While there are stress-related terms (xenobiotic/toxic response, apoptosis), the dominant signal ties neuronal development to chromatin regulation. Confidence: Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0035563","count":3},{"id":"GO:1990138","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0006915","count":2}]},{"hash":"807638930778669559","title":"Unknown","description":"The top GO terms are highly diverse, spanning spindle pole body duplication, nuclear membrane reassembly, hippo signaling, inner cell mass fate, GPCR internalization regulation, store-operated calcium channel activity, ubiquitin-mediated degradation, and general protein phosphorylation. There is no single coherent biological function or pathway linking these terms, suggesting the cluster does not reflect a unified process.","confidence":"","size":8,"edges":10,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":1},{"id":"GO:0002814","count":1},{"id":"GO:0030474","count":1},{"id":"GO:0031468","count":1},{"id":"GO:1904021","count":1}]},{"hash":"235130427682002160","title":"Cell cycle and embryonic development regulators","description":"Top GO terms point to mitotic and chromosomal regulation (mitotic spindle assembly, centromeric cohesion), along with broader regulatory processes (GTPase activity, K11-linked ubiquitination, histone H3 acetylation). Developmental terms (gastrulation, pattern formation, male gonad development) suggest involvement in embryonic patterning alongside cell-cycle control. The cluster thus seems to combine regulators of cell division with developmental signaling pathways rather than a single, narrowly defined function.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0090307","count":2},{"id":"GO:0070602","count":2},{"id":"GO:0007584","count":1},{"id":"GO:0070979","count":1}]},{"hash":"1630837748450643919","title":"Transcription regulation and metabolic biosynthesis","description":"The cluster combines transcription-related GO terms (DNA-templated transcription and negative regulation of transcription by RNA polymerase II) with several biosynthetic pathways (cobalamin, ubiquinone, biotin, polyamine, phosphatidylcholine) and growth-related processes, suggesting a group of proteins tied to both gene expression control and broad metabolism. Some terms (nodulation, N-terminal peptidyl-alanine trimethylation) are less central, but overall the theme points to transcription regulation linked to metabolic biosynthesis. ","confidence":"Medium","size":8,"edges":19,"triangles":20,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0009877","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0006744","count":2}]},{"hash":"21789651977687296","title":"Multisystem Embryonic Development","description":"The proteins in this cluster are linked to developmental processes across multiple organ systems (gonads, kidney/urogenital tract, heart valves, forebrain) and include differentiation and regulatory pathways (e.g., TGF-beta and cytokine regulation). This suggests a broad role in embryonic organogenesis rather than a single, cohesive pathway.","confidence":"Medium","size":8,"edges":18,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0061290","count":3},{"id":"GO:0003180","count":3},{"id":"GO:2000977","count":3}]},{"hash":"2005521822205889537","title":"Calcium-dependent signaling and cell-cycle control","description":"This cluster centers on calcineurin-NFAT signaling (calcium-dependent) and its positive regulation, with supporting terms for meiotic cell cycle, DNA damage checkpoint regulation, cytokinesis localization, and mitochondrial double-strand break repair. Together these suggest a theme where calcium-mediated signaling intersects with cell-cycle regulation and genome maintenance, with peripheral metabolic and developmental terms.","confidence":"Medium","size":8,"edges":18,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:2000002","count":2},{"id":"GO:0005979","count":2},{"id":"GO:1901901","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0033173","count":2}]},{"hash":"2014211304678072718","title":"Gene Expression Regulation and RNA Metabolism","description":"The terms cluster around transcription regulation (DNA-templated transcription and its regulation), mRNA stability, miRNA turnover, and translation, suggesting a core theme of gene expression control at both transcriptional and post-transcriptional levels. Some virus-related terms hint at host-RNA interactions, but overall the group reflects RNA processing, regulation, and protein synthesis pathways that coordinate expression of genes.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0010323","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2}]},{"hash":"63416217554655891","title":"N-terminal acetylation and melatonin biosynthesis","description":"Strong representation of N-terminal peptidyl acetylation terms indicates NAT activity, with melatonin biosynthesis as a connected pathway, implying acetyltransferases that act on N-termini and potentially melatonin-related regulation.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":4},{"id":"GO:0017198","count":3},{"id":"GO:0018003","count":3},{"id":"GO:0061606","count":3},{"id":"GO:0018002","count":3}]},{"hash":"239713801833297088","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":23,"triangles":36,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0071035","count":4},{"id":"GO:0034476","count":4}]},{"hash":"300672565551987981","title":"Photorespiration and related carbon metabolism","description":"The cluster shows strong enrichment for photorespiration-related processes (glycolate catabolic process, photorespiration, L-glutamate biosynthetic process, glycine hydroxymethyltransferase activity) and related carbon metabolism, with translation terms present but less representative. Together they point to plant photorespiration and associated amino acid metabolism as the core function of this protein group.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0009854","count":1},{"id":"GO:0001561","count":1},{"id":"GO:0018924","count":1},{"id":"GO:0019516","count":1}]},{"hash":"1865792311666419193","title":"Kinetochore Assembly and Spindle Organization","description":"Most top GO terms cluster around kinetochore components, kinetochore assembly, spindle organization, and spindle attachment to kinetochores during mitosis/meiosis, indicating a primary theme of kinetochore\u2013spindle function. The other terms (catabolic and biosynthetic processes) appear only once and are likely incidental. Therefore, the cluster is best described by a kinetochore/spindle organization theme.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000256","count":1},{"id":"GO:0051315","count":1},{"id":"GO:0010136","count":1},{"id":"GO:0030472","count":1},{"id":"GO:1903394","count":1}]},{"hash":"260487418663982221","title":"Post-transcriptional gene regulation","description":"This cluster shows strong enrichment for RNA processing and regulation of gene expression after transcription, including mRNA export from the nucleus, alternative splicing, stress-related mRNA stability control, and initiation of translation (including IRES-dependent initiation). The common theme is post-transcriptional regulation of mRNA fate and protein synthesis.","confidence":"High","size":8,"edges":12,"triangles":8,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006406","count":7},{"id":"GO:1902625","count":7},{"id":"GO:1905663","count":7},{"id":"GO:0001825","count":7},{"id":"GO:1903586","count":7}]},{"hash":"1527991688371946624","title":"Transcription Machinery and Ribosome Biogenesis","description":"The terms cluster around RNA polymerase I/II/III\u2013mediated transcription, transcription elongation, and ribosome biogenesis, indicating a combined focus on transcriptional machinery and ribosome production. A few outlier terms (sporulation, chitin response) exist but do not redefine the main theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006360","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0006366","count":1}]},{"hash":"1350774879705327514","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002031","count":3},{"id":"GO:0006295","count":2},{"id":"GO:0015995","count":2},{"id":"GO:0006363","count":2},{"id":"GO:0070911","count":2}]},{"hash":"1426575993046051787","title":"Endosomal Trafficking","description":"The top GO terms point to vesicle transport within the endomembrane system\u2014early/late endosome trafficking to late endosome, lysosome, Golgi, and CvT pathway delivery to the vacuole\u2014indicating a cluster centered on endosomal transport processes. A few unrelated metabolic or aging terms appear but are not representative of the core function.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045022","count":2},{"id":"GO:0008333","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0034498","count":2}]},{"hash":"1657459359607380279","title":"Renal development and water transport","description":"The top GO terms point to metanephric kidney development (descendant tubule and glomerulus vasculature), alongside transport processes for water and urea and overall water homeostasis, suggesting a coherent renal and fluid-handling theme. A few terms related to other organs appear, but the dominant signal is kidney development and renal fluid transport.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080029","count":1},{"id":"GO:0009992","count":1},{"id":"GO:0072220","count":1},{"id":"GO:0015840","count":1},{"id":"GO:0072239","count":1}]},{"hash":"2256982017226197866","title":"Neural adhesion and axon guidance regulators","description":"The top GO terms point to neural development and connectivity, including corpus callosum development and fasciculation of motor neuron axons, along with integrin-mediated cell adhesion and regulation of key signaling pathways (Rho, JNK, MAPK). While some terms touch broader processes like transcription or immune activity, the strongest theme is neuronal adhesion and axon pathfinding regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033628","count":2},{"id":"GO:0035024","count":2},{"id":"GO:0001806","count":2},{"id":"GO:0022038","count":2},{"id":"GO:0046329","count":2}]},{"hash":"1444644927111010337","title":"Actin Cytoskeleton Organization and Cell Polarity","description":"This cluster is driven by actin-related processes (actin filament network formation, formin-nucleated actin cable assembly) and cell-shape regulation, with supporting signals for ER polarization and centrosome localization, indicating a core theme of cytoskeletal remodeling and polarity during division and development; additional terms reflect related morphogenetic and meiotic contexts.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":2},{"id":"GO:0061164","count":2},{"id":"GO:0051758","count":2},{"id":"GO:0008360","count":2},{"id":"GO:1904171","count":2}]},{"hash":"947303149405571963","title":"Unknown","description":"The top GO terms are highly diverse, spanning ubiquitination, chlorophyll biosynthesis regulation, histone modification (obsolete), protein secretion, transcriptional regulation, cytokinin signaling, steroid receptor assembly, male differentiation, GPCR signaling, and cell cycle. There is no clear, cohesive biological theme linking these terms into a single functional cluster, and the lack of edges suggests these proteins do not share a common interaction network in this dataset. Therefore, a concise, unified label is not justifiable.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":2},{"id":"GO:1902325","count":2},{"id":"GO:0016570","count":2},{"id":"GO:0050714","count":2},{"id":"GO:2000531","count":2}]},{"hash":"1546382041504306145","title":"Unknown","description":"With zero edges/triangles and no shared GO terms, there is no discernible functional theme connecting these proteins. The lack of annotation overlap means I cannot assign a meaningful label beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2158460255177797903","title":"Fatty acid and xenobiotic metabolism","description":"This cluster centers on oxidation-related processing of lipids and small molecules: fatty acid omega-oxidation, prostaglandin metabolism, plus metabolism of aldehydes and sugars (furaldehyde, xylitol) and ethanol-related pathways. While immune-related responses (to LPS and antineoplastic agents) appear, the dominant theme is lipid/small-molecule metabolism and detoxification, making this label representative of the cluster\u2019s functions.","confidence":"Medium","size":8,"edges":8,"triangles":2,"max_degree":4,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0010430","count":4},{"id":"GO:0043458","count":4},{"id":"GO:0006693","count":4},{"id":"GO:0033859","count":4}]},{"hash":"1062804484525578889","title":"DNA Damage Response and Repair","description":"Most GO terms indicate DNA damage response and repair, including direct DNA repair, replication fork arrest, helicase regulation, and p53-mediated apoptosis in DNA damage. Additional terms reflect meiotic mismatch repair and maintenance of repeats, with marginal signals for immune isotype switching and energy metabolism. The dominant theme is DNA damage response/repair.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0008340","count":1},{"id":"GO:0043570","count":1},{"id":"GO:0051096","count":1},{"id":"GO:0006119","count":1}]},{"hash":"1836614050449613668","title":"Developmental Regulation and Proteostasis","description":"The terms cluster around embryonic and neural development (in utero embryonic development, midbrain morphogenesis, osteoblast differentiation) and proteolysis/regulation of transcription (ubiquitin-dependent proteasomal catabolism and negative regulation of transcription by RNA Pol II), implying a group of proteins coordinating development with proteostasis.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0007296","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0032436","count":2}]},{"hash":"277249422072894814","title":"Nucleotide and Vitamin Metabolism","description":"The top GO terms cluster around metabolic processes related to nucleotides and vitamins (uracil catabolism, nicotinamide metabolic process, nicotinate nucleotide salvage), plus RNA methylation and general nutrient response/utilization, with a few additional bacterial catabolic pathways (creatinine, phenazine). This points to a broad metabolic cluster focused on nucleotide/vitamin processing and nutrient handling rather than a single highly specific function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":3},{"id":"GO:0006769","count":3},{"id":"GO:0002047","count":3},{"id":"GO:0001302","count":3},{"id":"GO:1904524","count":3}]},{"hash":"1666790409948671387","title":"Proteolysis and Tissue Remodeling","description":"The top GO terms point to proteolytic processes (collagen catabolic, bradykinin catabolic, neuropeptide catabolic, and general proteolysis) and developmental morphogenesis (lung branching, intramembranous ossification, neural precursor proliferation). This pattern suggests the cluster centers on extracellular matrix remodeling and tissue development, with auxiliary signals like thyroid hormone response and occasional immune-related activity (T cell cytotoxicity). Overall, a cohesive theme of proteolysis-driven remodeling and organogenesis.","confidence":"High","size":8,"edges":25,"triangles":40,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":8},{"id":"GO:2000179","count":8},{"id":"GO:0097067","count":8},{"id":"GO:0050790","count":8},{"id":"GO:0010815","count":8}]},{"hash":"764748965747549987","title":"Glycosylation and cell wall biosynthesis","description":"The cluster centers on protein O-linked glycosylation (via N-acetyl-galactosamine and via serine/threonine) and cell envelope formation (cell wall organization, mycolate layer assembly), with UDP-glucose metabolism supplying sugar donors and hyaluronan biosynthesis as related glycan production. Some terms like steroid biosynthesis and immunoglobulin production are less connected and likely noise, but the dominant theme points to glycosylation-linked cell wall biosynthesis.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006694","count":1},{"id":"GO:0002378","count":1},{"id":"GO:0016266","count":1},{"id":"GO:0006011","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1366600258159652057","title":"Glial Stress Response and Detoxification Signaling","description":"The terms cluster around anti-apoptotic regulation, detoxification of xenobiotics, glutathione biosynthesis, prostaglandin signaling, and growth-factor responses, with one term for oligodendrocyte development, suggesting a glial context where survival, detoxification, and signaling converge.","confidence":"Medium","size":8,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2001237","count":7},{"id":"GO:0014003","count":7},{"id":"GO:1901687","count":7},{"id":"GO:2000255","count":7},{"id":"GO:0070458","count":7}]},{"hash":"2032787575444123907","title":"Mitochondrial Dynamics and Membrane Trafficking","description":"The top terms emphasize mitochondrial fusion, intracellular distribution of mitochondria, and establishment of mitochondrial localization, pointing to mitochondrial dynamics as the core theme. Additional terms related to trafficking processes (clathrin-mediated endocytosis, postsynaptic receptor internalization, Golgi organization) suggest a broader link to intracellular membrane trafficking that interfaces with mitochondria. Overall, the cluster seems best described by coordinated mitochondrial dynamics with membrane trafficking roles.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0034643","count":3},{"id":"GO:0000002","count":3},{"id":"GO:0007605","count":3},{"id":"GO:1901741","count":3}]},{"hash":"643063807233799370","title":"Plant phenylpropanoid and phytohormone metabolism","description":"The top GO terms point to plant-specific secondary metabolism, including phenylpropanoid catabolism (3-phenylpropionate), stilbene catabolism, and strigolactone biosynthesis, along with xenobiotic response, suggesting a cluster of plant metabolic pathways and hormone biosynthesis rather than basic cellular processes.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0043488","count":2}]},{"hash":"1574478857308956015","title":"Chromatin Regulation & Genome Integrity","description":"This cluster shows enrichment for chromatin organization and transcription-related terms, including K11-linked ubiquitination and telomere maintenance, as well as DNA repair processes like translesion synthesis. The mix of chromatin modification, transcription regulation, and genome stability functions suggests a cohesive theme around epigenetic control and genome integrity, despite some obsolete GO entries.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010620","count":8},{"id":"GO:0070979","count":8},{"id":"GO:0090089","count":8},{"id":"GO:0006344","count":8},{"id":"GO:0033128","count":8}]},{"hash":"1636178288224109120","title":"Plant RNA Processing and Decay","description":"Top GO terms indicate chloroplast mRNA processing, nuclear RNA catabolic processes (snRNA and rRNA), and polycistronic mRNA processing, plus protein localization to the nucleoplasm. These collectively point to RNA maturation and turnover in plant cells (both chloroplasts and nucleus) as the core theme of the cluster, with other terms related to growth and metabolism serving as secondary context.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":1},{"id":"GO:0031426","count":1},{"id":"GO:0080163","count":1},{"id":"GO:0048507","count":1},{"id":"GO:0043086","count":1}]},{"hash":"318001281311391518","title":"Tissue Remodeling and Morphogenesis","description":"The cluster's GO terms cluster around catabolic processes that degrade extracellular matrix components (collagen, bradykinin, neuropeptides) and developmental morphogenesis events (intramembranous ossification, epithelial tube branching in lung morphogenesis), with supporting signaling cues such as thyroid hormone response and neural precursor proliferation. An immune term (T cell\u2013mediated cytotoxicity) is present but does not dominate, so the core theme is remodeling of tissue structure coupled with morphogenetic development.","confidence":"Medium","size":7,"edges":11,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":3},{"id":"GO:2000179","count":3},{"id":"GO:0097067","count":3},{"id":"GO:0050790","count":3},{"id":"GO:0010815","count":3}]},{"hash":"2156991366164677329","title":"Mitotic spindle dynamics and cytokinesis","description":"The top GO terms center on cell division and microtubule regulation\u2014mitotic spindle elongation, plus-end microtubule dynamics, centrosome separation, and actomyosin contractile ring assembly for cytokinesis\u2014indicating a cohesive role in mitosis and cytokinesis. Some terms like root development or stress granule disassembly are less central but do not override the prevailing theme of spindle and division-related processes.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0000022","count":3},{"id":"GO:0000915","count":3},{"id":"GO:0048364","count":3},{"id":"GO:0033624","count":3}]},{"hash":"1257850980889180144","title":"Mitotic spindle and microtubule dynamics","description":"The top GO terms cluster around microtubule-based processes (spindle elongation, centrosome separation, plus-end depolymerization/sliding, and axonemal microtubule changes), suggesting a shared theme of dynamic cytoskeletal regulation in cell division and intracellular transport. Some terms (root development, stress granule disassembly, integrin regulation) are less central but may reflect broader cytoskeletal and regulatory connections.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":4},{"id":"GO:0000915","count":4},{"id":"GO:0048364","count":4},{"id":"GO:0033624","count":4},{"id":"GO:0060404","count":4}]},{"hash":"26235101525176119","title":"Metabolic catabolism, redox homeostasis, and insulin signaling","description":"This cluster shows enrichment for several catabolic pathways (valine, phenylacetate, carnitine, phylloquinone), plus cell redox homeostasis and responses related to insulin, including negative regulation of insulin secretion. These terms together suggest a metabolism- and redox-centric module with links to insulin signaling, rather than a tightly cohesive single pathway. The connections are plausible but not uniformly strong across all terms, so a medium confidence is appropriate.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006574","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0014823","count":1},{"id":"GO:0042372","count":1},{"id":"GO:0010124","count":1}]},{"hash":"323441932455698369","title":"GPCR Signaling and Endocytosis","description":"Top GO terms point to receptor-mediated signaling (GPCR pathways, adrenergic signaling, TGF-beta signaling) and vesicle trafficking/endocytosis (clathrin-mediated endocytosis, endosomal transport), with additional notes on cell adhesion (integrin activation) and heart-related signaling, and a GM-CSF immune response context. This combination suggests a theme around coordinated signal transduction via receptors and vesicle trafficking that can influence heart and immune cell functions.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:0000902","count":1},{"id":"GO:0016197","count":1},{"id":"GO:0003108","count":1},{"id":"GO:0030845","count":1}]},{"hash":"1991196237902788319","title":"DNA Replication and Repair Cluster","description":"This cluster is dominated by GO terms for DNA-templated transcription, DNA replication, DNA repair, and mitotic cell cycle, indicating proteins mainly involved in genome maintenance and cell cycle regulation. Peripheral terms like viral process and nervous system development likely reflect multifunctional proteins or annotation spillover, but the core signal points to DNA replication/repair machinery.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006281","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0016032","count":4}]},{"hash":"404492074717630702","title":"Developmental morphogenesis and growth regulation","description":"This cluster features GO terms tied to development and morphogenesis (multicellular development, budding/pseudohyphal growth, dendritic spine morphogenesis) and regulation of growth/signaling (apoptotic regulation, inhibition of Wnt signaling, inhibition of proliferation), suggesting a unifying theme of morphogenesis governed by growth and developmental signaling across cell types.","confidence":"Medium","size":7,"edges":9,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0007121","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0007118","count":2}]},{"hash":"1463792340660849893","title":"Chromatin regulation in neural development","description":"The cluster combines neural development signals (substantia nigra development) with chromatin-related processes (histone deacetylation, nucleosome density regulation, heterochromatin formation) and synaptic activity terms (excitatory postsynaptic potential), plus related cellular processes like DNA replication and ER-Golgi transport. The common thread appears to be chromatin remodeling and genome maintenance in neural development, with accompanying synaptic signaling components, making this label representative of the core function of the cluster.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":3},{"id":"GO:0090394","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1716700085343584677","title":"Neural development and axon guidance","description":"The dominant GO terms describe neural development and axon pathfinding, including corpus callosum development, optic nerve morphogenesis, retinal ganglion cell axon guidance, fasciculation of motor neuron axons, and dendritic spine morphogenesis. Hyaluronan metabolism ties into extracellular matrix remodeling during neural development, while DNA-templated transcription and telomere maintenance are less central to this cluster. Overall, the set coherently points to nervous system development and axon guidance.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001806","count":2},{"id":"GO:0022038","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0030212","count":2}]},{"hash":"678484305035489026","title":"Quinone Biosynthesis with Fatty and Amino Acid Metabolism","description":"The top GO terms show strong signals for phylloquinone and menaquinone biosynthesis, along with several amino acid catabolic/biosynthetic and fatty acid beta-oxidation/transport processes. This suggests a cluster centered on quinone-related biosynthesis and broader metabolic pathways, though some terms are more peripheral. Overall, a cohesive, specific label is quinone biosynthesis with fatty and amino acid metabolism.","confidence":"Medium","size":7,"edges":8,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0006574","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0006635","count":3}]},{"hash":"2052950730046719686","title":"Ribosome biogenesis and vesicle trafficking","description":"The top GO terms point to ribosome processing and export (rRNA processing; ribosomal large subunit export from nucleus) alongside trafficking-related processes (protein targeting to vacuole in autophagy; positive regulation of receptor-mediated endocytosis) and ubiquitin-dependent protein turnover. This suggests a cluster centered on intracellular trafficking and ribosome biogenesis/assembly, though some terms are obsolete artifacts that add noise. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071211","count":1},{"id":"GO:2000650","count":1},{"id":"GO:2000058","count":1},{"id":"GO:2000232","count":1},{"id":"GO:0048260","count":1}]},{"hash":"325773998562367506","title":"Unknown","description":"The GO terms are highly diverse, ranging from antibiotic biosynthesis and response to antibiotic (bacteria-focused) to eukaryotic RNA processing (mRNA export, splicing, stability) and development signals (blastocyst formation) including a TGF-beta response. There is no clear, unified biological function linking these terms, so a cohesive cluster label cannot be confidently assigned.","confidence":"","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0017000","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006406","count":1},{"id":"GO:1902625","count":1}]},{"hash":"1542521532354224223","title":"Translation Fidelity and tRNA Metabolism","description":"The cluster centers on terms related to regulating translational fidelity and tRNA metabolic processes, pointing to a function in translation accuracy and tRNA handling. The obsolete D-leucine and D-tyrosine catabolic terms likely reflect outdated annotations rather than a true core function. Overall, the common theme is translation quality control and tRNA metabolism, with a cohesive but modestly connected network.","confidence":"Medium","size":7,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":1},{"id":"GO:0006399","count":1},{"id":"GO:1900832","count":1},{"id":"GO:1900829","count":1}]},{"hash":"854507129048015140","title":"Neural development and photoreceptor differentiation","description":"The GO terms show a strong emphasis on nervous system development, photoreceptor cell development, and action potential, suggesting a neural/photoreceptor differentiation theme. While there are outlier terms related to morphogenesis, cell adhesion, and autophagy, the core signals point to neural development, hence a medium confidence. ","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006878","count":1},{"id":"GO:0070830","count":1},{"id":"GO:0042461","count":1},{"id":"GO:0001508","count":1},{"id":"GO:0040032","count":1}]},{"hash":"387635847511260885","title":"Endomembrane trafficking and signaling regulation","description":"The top GO terms point to intracellular transport and membrane-associated processes (endocytosis, endosome localization, secretory pathway regulation, and organelle contact like mitochondrion-ER tethering). Additional terms about ribosome export and neuronal connectivity (axonogenesis, synaptic structure) support a broader role in vesicle trafficking and signaling coordination within cells, especially in neurons. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903434","count":2},{"id":"GO:0071851","count":2},{"id":"GO:0071389","count":2},{"id":"GO:1990456","count":2},{"id":"GO:0043124","count":2}]},{"hash":"388644376725581789","title":"Telomere maintenance and genome stability","description":"This cluster centers on telomere biology and DNA integrity, with terms for telomere lengthening, subtelomeric heterochromatin, and protection from NHEJ at telomeres, as well as DNA replication elongation and nucleotide-excision repair, pointing to a shared theme of preserving genome integrity at chromosome ends and during replication.","confidence":"High","size":7,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006271","count":1},{"id":"GO:0070512","count":1},{"id":"GO:0010833","count":1},{"id":"GO:0033152","count":1},{"id":"GO:0000910","count":1}]},{"hash":"1442818874951432742","title":"Actin Cytoskeleton Dynamics and Cell Polarity","description":"The top GO terms cluster around actin filament network formation, formin-nucleated actin cable assembly, and regulation of cell shape, plus centrosome localization and ER/polarity-related processes, pointing to a cohesive theme of actin-driven cytoskeletal remodeling and cellular polarity. Some terms touch development and meiosis, but these still relate to cytoskeletal dynamics.","confidence":"High","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":4},{"id":"GO:0061164","count":4},{"id":"GO:0051758","count":4},{"id":"GO:0008360","count":4},{"id":"GO:1904171","count":4}]},{"hash":"112692557255792728","title":"N-terminal methylation and mRNA capping enzymes","description":"Based on the top GO terms, the cluster is enriched for N-terminal peptidyl methylation (glycine, alanine, serine) and 7-methylguanosine mRNA capping, indicating methyltransferase activities as the core function. Other terms, such as nodulation, stress response, and biosynthetic processes (ubiquinone, cobalamin), appear but are less central to the cluster\u2019s main theme. Overall, the strongest theme is methyltransferase activity affecting both protein N-termini and RNA capping.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":5},{"id":"GO:0018012","count":5},{"id":"GO:0035572","count":5},{"id":"GO:0006370","count":5},{"id":"GO:0035573","count":5}]},{"hash":"1133533108534756237","title":"Unknown","description":"The top terms span stress granule dynamics, mRNA export, transcription elongation, mitochondrial import, DNA/viral replication, and protein processing, with no single coherent biological function linking the proteins. The graph is edgeless (no edges, no triangles), indicating little connectivity within the cluster. Given the lack of a common theme, the appropriate label is Unknown, with confidence None.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":2},{"id":"GO:0045041","count":1},{"id":"GO:0006271","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0006406","count":1}]},{"hash":"1963949105483870642","title":"Cell polarity and actin cytoskeleton regulation","description":"This cluster centers on establishment and maintenance of cell polarity and the regulation of the actin cytoskeleton, including phosphorylation events that modulate cytoskeletal dynamics, myosin II assembly, and signaling pathways such as TORC2 and PI3K/AKT. The GO terms point to a cohesive theme of polarity control linked to cytoskeletal organization and associated signaling, even though the proteins aren\u2019t connected by edges in the graph.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033135","count":1},{"id":"GO:0030950","count":1},{"id":"GO:0030010","count":1},{"id":"GO:0031532","count":1},{"id":"GO:0043520","count":1}]},{"hash":"972294692956844084","title":"Viral Entry and Replication","description":"The set is dominated by virus-related terms: viral life cycle, fusion of viral membrane with host, symbiont entry into host, and RNA-templated DNA synthesis (reverse transcription), plus proviral latency. These point to viral infection and replication processes. A plant development term and some obsolete terms appear as noise, but the core signal reflects virus\u2013host interactions.","confidence":"High","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":"protein folding","top_go_terms":[{"id":"GO:0048453","count":3},{"id":"GO:0006457","count":3},{"id":"GO:0075713","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0050714","count":3}]},{"hash":"546033135181535519","title":"Unknown","description":"The top GO terms cover reproductive development (sporulation, male sex differentiation, prostate gland development) and hormone signaling (steroid receptor complex assembly) but also unrelated metabolic/quality-control terms (serine biosynthesis, oxidation-reduction, ERAD). With no edges connecting the proteins, there isn't a single coherent function uniting all terms, so the cluster cannot be confidently named.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0009854","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0030433","count":2}]},{"hash":"978923520183942338","title":"Translation initiation and ribosome biogenesis","description":"The top GO terms cluster around formation of translation preinitiation complex, regulation and reinitiation of translation, IRES-dependent viral translation initiation, and ribosome biogenesis, indicating proteins involved in assembling and starting translation and ribosome production. A few peripheral terms (nutrient response, ubiquitination, histone acetylation, rRNA maturation) are less central.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0042254","count":3}]},{"hash":"97555996527392843","title":"Excitatory Synapse Assembly and Neurotransmission","description":"This cluster shows multiple GO terms tied to synaptic function (excitatory synapse assembly, negative regulation of EPSP, acetylcholine catabolic process in the synaptic cleft, and synaptic vesicle clustering) and learning-related plasticity, suggesting a cohesive role in excitatory neurotransmission and synapse formation. A few terms (transcription/DNA-templated processes and circadian regulation) are peripheral but do not override the dominant synaptic theme.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046294","count":2},{"id":"GO:0010841","count":2},{"id":"GO:0042136","count":2},{"id":"GO:2000809","count":2}]},{"hash":"762699307205921635","title":"Unknown","description":"The terms are heterogeneous: vesicle transport along microtubules and microtubule cytoskeleton organization hint at cytoskeletal/trafficking roles, but other terms point to unrelated developmental processes (rhabdomere and eggshell pattern formation, osteoclast development) or general transcription by RNA polymerase II. There is no single cohesive function uniting these proteins, so no accurate cluster label can be assigned beyond Unknown.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0047496","count":1},{"id":"GO:0051081","count":1},{"id":"GO:2000574","count":1},{"id":"GO:0006366","count":1},{"id":"GO:1900524","count":1}]},{"hash":"560495869824501012","title":"DNA Damage Checkpoints and Calcineurin-NFAT Signaling","description":"The top terms show a clear focus on DNA damage checkpoints (mitotic intra-S checkpoint signaling, regulation of DNA damage checkpoint) alongside regulation of the calcineurin-NFAT pathway (regulation and positive regulation), suggesting a coordinated theme of DNA damage response intertwined with calcium-NFAT signaling. Additional terms related to cell cycle and Schwann cell development support a broader signaling context, though they are less central.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031573","count":3},{"id":"GO:0051531","count":3},{"id":"GO:2000002","count":2},{"id":"GO:0005979","count":2},{"id":"GO:1901901","count":2}]},{"hash":"131636148462197021","title":"Cell growth and mitosis machinery","description":"These proteins cluster around key growth and division processes: mitotic cell cycle and spindle assembly, cell population proliferation, and multicellular growth; and they also involve protein biosynthesis and secretory/trafficking pathways (ribosome biogenesis; COPII vesicle budding; Golgi-ER retrograde transport). The combination suggests a cohesive theme of growth-related cytoskeletal/division machinery coupled with the secretory pathway that supports cell proliferation. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0042254","count":3}]},{"hash":"556857731719444879","title":"Unknown","description":"The Top Terms are very diverse, spanning mitochondrial import, viral genome replication, mRNA export, microtubule regulation, ER-associated degradation, transcription elongation, protein processing, vesicle formation, oxidative phosphorylation, and stress granule disassembly. There\u2019s no unifying biological theme or common pathway that ties these terms together for this cluster, so a coherent, specific label isn\u2019t apparent.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0031117","count":1},{"id":"GO:0071712","count":1}]},{"hash":"366875669995686900","title":"Broad negative regulation of cellular processes","description":"The terms show a consistent emphasis on negative regulation across several cellular processes (gene expression via methylation, neurotransmitter secretion, endocytosis, autophagosome maturation, glucokinase activity, store-operated calcium channel activity) and regulation by sumoylation and translation. Some terms also point to membrane targeting (tail-anchored ER insertion). While not a single shared pathway, the common theme is proteins acting as regulators that constrain multiple cellular processes.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":6},{"id":"GO:0010216","count":4},{"id":"GO:1904049","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0097237","count":4}]},{"hash":"1986179998159791082","title":"Ubiquitin-mediated degradation and chromatin modification","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes and protein polyubiquitination, along with histone ubiquitination and histone catabolic/dosage compensation-related chromatin regulation terms. The pattern suggests a cohesive module centered on ubiquitin signaling driving protein turnover and chromatin modifications, with a minor tie to X-chromosome inactivation/dosage compensation. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0000209","count":2},{"id":"GO:1903762","count":2},{"id":"GO:0070535","count":2},{"id":"GO:0070512","count":2}]},{"hash":"351241053466528660","title":"ER-Golgi vesicle trafficking","description":"This cluster is dominated by GO terms related to ER-to-Golgi and Golgi-to-ER transport, Golgi organization, and COPII vesicle coating regulation, plus intracellular protein transport. The convergence on ER\u2013Golgi trafficking and Golgi maintenance suggests a coherent functional theme around vesicle transport and Golgi structure.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0007030","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0003400","count":2},{"id":"GO:0006890","count":2}]},{"hash":"1480104581490078783","title":"Unknown","description":"The top GO terms cover a mix of disparate processes (endosome transport, axon guidance and regeneration, glial differentiation, insulin signaling, T cell signaling, kinetochore localization, and kinase regulation). There isn\u2019t a single cohesive function or pathway linking the proteins, so a clear, specific label isn\u2019t justifiable.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":2},{"id":"GO:0008045","count":2},{"id":"GO:0060020","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0008285","count":2}]},{"hash":"884519052546022292","title":"Muscle energy metabolism and regeneration","description":"This cluster prominently features glycolysis and gluconeogenesis signals, along with skeletal muscle tissue regeneration, suggesting a theme of energy handling in muscle and its capacity to repair. Additional terms about nutrient/fatty acid response and hypoxia-related survival support a broader muscle metabolic/adaptive context. Obsolete GO terms are ignored for interpretation. ","confidence":"Medium","size":7,"edges":10,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":3},{"id":"GO:0019878","count":2},{"id":"GO:0019518","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0032889","count":2}]},{"hash":"582746856007661042","title":"NF-\u03baB signaling and ubiquitin regulation in immunity","description":"These proteins cluster around NF-\u03baB pathway activation (positive regulation of canonical NF-\u03baB signaling) and ubiquitin-dependent protein turnover, with immune-context terms like spleen development and T follicular helper cell differentiation, plus related transcriptional regulation (positive regulation of DNA binding). The mix suggests a theme of immune signaling coordinated with protein ubiquitination and transcriptional control, though the links are broad. Confidence: Medium","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043388","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0016032","count":3},{"id":"GO:1903762","count":2}]},{"hash":"347209338436856760","title":"Redox-Linked Metabolism and Chromatin Regulation","description":"This cluster centers on redox biology and metabolism (oxidation-reduction, oxidant detoxification, selenium response, 2-oxoglutarate metabolism), with hints toward chromatin regulation (chromatin binding, histone methylation) via 2-OG\u2013dependent processes. The combination suggests proteins involved in redox/metabolic control that may also influence epigenetic regulation and related cellular outcomes (e.g., neural precursor proliferation). Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0010269","count":2},{"id":"GO:0046886","count":2},{"id":"GO:0035563","count":2}]},{"hash":"2266546464115334040","title":"Unknown","description":"Seven proteins in this cluster show no connections (no edges or triangles) and there are no GO terms reported (Top Terms is empty), so there is no coherent functional signal to define a theme. Without shared terms or interactions, I cannot assign a meaningful label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"889392046204110449","title":"Developmental signaling and cytoskeletal regulation","description":"The terms point to broad development and morphogenesis across multiple tissues (nervous, skeletal, heart) and include signaling pathways (Rho, GTPase) and calcium-dependent exocytosis, suggesting a general development/morphogenesis theme rather than a single tissue-specific function.","confidence":"Medium","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0007124","count":3}]},{"hash":"950937941062279301","title":"Unknown","description":"The terms span nuclear cell cycle regulation and transcription alongside centrosome dynamics, but also brain and placenta development and immune responses, giving no single cohesive function for the cluster. This mixture of cellular, developmental, and immune themes makes a unified label unlikely. ","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010571","count":4},{"id":"GO:0007098","count":4},{"id":"GO:0022038","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0046827","count":4}]},{"hash":"514772386260606750","title":"Ion transport and metal homeostasis","description":"The top GO terms cluster around ion transport and homeostasis across membranes, especially potassium, sodium, and zinc transport. Despite a few outliers (serine biosynthesis, otolith mineralization, pheromone response), the dominant pattern is regulation of ion flux, suggesting these proteins function in maintaining ionic balance and metal ion transport.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"establishment or maintenance of cell polarity","top_go_terms":[{"id":"GO:1990573","count":4},{"id":"GO:0006564","count":4},{"id":"GO:0045299","count":4},{"id":"GO:0002028","count":4},{"id":"GO:0046272","count":4}]},{"hash":"667874924148989978","title":"Cardiac Contraction Regulation & Heart Development","description":"The terms are dominated by regulation of cardiac muscle contraction (both positive and negative), heart development (heart rudiment and secondary heart field specification), and modulation of catecholamine secretion, pointing to a cluster of proteins involved in heart function and formation. Some unrelated terms (centromeric cohesion, Wnt forebrain signaling) appear as noise, so the connection is strong but not perfect.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045988","count":2},{"id":"GO:0003108","count":2},{"id":"GO:0060394","count":2},{"id":"GO:0003139","count":2},{"id":"GO:0033605","count":2}]},{"hash":"929627238059560813","title":"Unknown","description":"GO terms span transcription and a wide array of disparate metabolic and biosynthetic processes, with little overlap among the six proteins. Because there isn't a clear shared function or pathway linking these terms, a concise, representative label cannot be defined.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009103","count":2},{"id":"GO:0006571","count":2},{"id":"GO:0006533","count":2},{"id":"GO:0019551","count":2}]},{"hash":"1543738568791036515","title":"Neuronal development and synaptic plasticity","description":"The top GO terms are dominated by neural-related functions: neuron development, axonogenesis, visual perception, EPSP, and long-term potentiation, all pointing to roles in neural differentiation and synaptic signaling/plasticity. While a couple terms touch on non-neural processes (e.g., ABA signaling, heart development), the prevalent theme centers on neuronal maturation and synaptic function.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0009738","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0014044","count":4}]},{"hash":"1154382500459000453","title":"Cell Division and Cytokinesis","description":"The top GO terms center on mitotic spindle assembly, microtubule nucleation, and various aspects of cytokinesis and cell division (including FtsZ-dependent cytokinesis and division site positioning), spanning both eukaryotic and bacterial systems. This suggests a cohesive cluster of proteins involved in the machinery that drives cell division across organisms.","confidence":"High","size":6,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903087","count":5},{"id":"GO:0007020","count":5},{"id":"GO:0043093","count":4},{"id":"GO:0051256","count":4},{"id":"GO:2000767","count":4}]},{"hash":"775879859217739373","title":"Cell cycle checkpoints and DNA replication","description":"The most represented GO terms are mitotic spindle assembly checkpoint signaling, mitotic intra-S DNA damage checkpoint signaling, and DNA replication, all pointing to regulation of cell cycle progression. Other terms like parathyroid hormone response, mesoderm formation, and actin binding appear less central but may reflect broader cellular signaling and cytoskeletal roles. Overall, the cluster seems to reflect proteins involved in ensuring proper replication and chromosome segregation during cell division.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001707","count":3},{"id":"GO:0071374","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0007037","count":2}]},{"hash":"261075140716883963","title":"Xenobiotic Metabolism and Catabolic Pathways","description":"The Top Terms include multiple catabolic processes (allantoin, ureide, purine base, carnitine) and xenobiotic/ detoxification-related terms (response to xenobiotic stimulus, antibiotic biosynthetic process, redox homeostasis). This points to a cluster of proteins involved in breaking down xenobiotics and nitrogenous compounds and maintaining redox balance, rather than a single, narrow function. The antibiotic biosynthetic process likely reflects broader secondary metabolism rather than a shared role across all proteins. ","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0000256","count":3},{"id":"GO:0010136","count":3},{"id":"GO:1901766","count":3},{"id":"GO:0006145","count":3}]},{"hash":"525236362757532892","title":"Unknown","description":"The terms are highly diverse, spanning brain development (substantia nigra), bone maturation, xenobiotic response, mitosis and cell cycle control, trafficking and secretory pathway regulation, hormone response, and mitochondria\u2013ER tethering, with no obvious shared function or pathway tying them together. This suggests the proteins in this cluster do not reflect a single coherent biological process, so a simple, specific label is not supported by the GO signals.","confidence":"","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":5},{"id":"GO:0032456","count":5},{"id":"GO:0043931","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0000278","count":5}]},{"hash":"1592916531582120279","title":"Neural development and brain region patterning","description":"The cluster\u2019s top GO terms strongly center on brain and facial region development (forebrain, nucleus accumbens, nose development) and anterior/posterior pattern specification, with retinoic acid receptor signaling reinforcing neural differentiation and regional identity. Supporting signals include response to cAMP and nutrient cues, suggesting developmental signaling contexts. Some terms (folate catabolism, hypoxia response) appear noisy but do not override the dominant neural development theme.","confidence":"High","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":5},{"id":"GO:0051591","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0021768","count":5},{"id":"GO:0048384","count":5}]},{"hash":"54249870846334187","title":"Dendritic Spine Morphogenesis and Actin Remodeling","description":"The cluster centers on neuronal spine development and cytoskeletal remodeling: positive regulation of dendritic spine development and morphogenesis, Rac signaling, and actin-driven processes such as lamellipodium and ruffle assembly, all indicative of actin dynamics governing dendritic spine formation (with hippocampus development as a supporting neuronal-context term). Some trafficking and mRNA decay terms are present but secondary to the spine/actin theme.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060999","count":2},{"id":"GO:0045792","count":2},{"id":"GO:0043001","count":2},{"id":"GO:0097178","count":2},{"id":"GO:0061001","count":2}]},{"hash":"394345987093721064","title":"Fungal sterol and sphingolipid metabolism","description":"This cluster is dominated by terms tied to fungal lipid biosynthesis and membrane composition: ergosterol biosynthesis regulation, unsaturated fatty acid biosynthetic process, and mannosyl-inositol phosphorylceramide metabolic process point to sterol and sphingolipid pathways common in fungi. Nitrate assimilation and arabinose transport also appear in fungal metabolism, while osmotic stress response aligns with membrane/transport stress. Some terms (sebaceous gland differentiation, CNS myelin maintenance) are outliers likely from unrelated annotations, but the strongest signal centers on fungal lipid metabolism and membrane biogenesis.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0032443","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0000001","count":2}]},{"hash":"192613349925745734","title":"Neurodevelopment and synaptic signaling","description":"The cluster is enriched for nervous system development, neurogenesis, and axon guidance pathways (ROBO, SHH) suggesting a neurodevelopmental focus. Actin dynamics and regulation of synaptic vesicle exocytosis align with neurite outgrowth and synapse formation, reinforcing the neural theme, while other terms like kidney development and apoptosis appear as broader regulatory contexts rather than core functions. ","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0035385","count":2},{"id":"GO:0022008","count":2},{"id":"GO:0001822","count":2},{"id":"GO:0006915","count":2}]},{"hash":"288250899966872645","title":"Histone acetylation and chromatin regulation","description":"Top terms point to histone H4 acetylation at multiple lysines (K16, K8, K5), indicating chromatin modification as a unifying theme. Other signals include transcription regulation by RNA polymerase III and DNA damage response, which are commonly linked to chromatin state; nucleolus localization further supports chromatin organization context. Some terms are outliers and contribute little to the core theme, but the histone acetylation signals are strong enough to anchor the cluster\u2019s identity.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043984","count":1},{"id":"GO:1904751","count":1},{"id":"GO:0043982","count":1},{"id":"GO:0051974","count":1},{"id":"GO:0043981","count":1}]},{"hash":"1984648962282662344","title":"Actin Cytoskeleton Remodeling and Signaling","description":"The cluster centers on actin dynamics, with GO terms for actin polymerization/branching, filopodium formation, and dendritic spine development, plus small GTPase\u2013mediated signaling. It also connects to endocytosis and multiple signaling pathways (EGFR, Wnt, T cell receptor), indicating proteins that coordinate cytoskeletal remodeling with diverse signal transduction.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0007173","count":2},{"id":"GO:0030838","count":2},{"id":"GO:0090263","count":2}]},{"hash":"668518809391005491","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"Based on the top GO terms, the cluster centers on actin filament organization and cytoskeletal remodeling (actin organization, actin cytoskeleton reorganization, dendrite extension, spine modification) and associated cell movement (myoblast migration, dendritic changes). The presence of terms for Rac signaling regulation and contractile structures corroborates actin dynamics governing cell shape and motility, outweighing peripheral terms like osmotic stress. Thus, the label captures the core function of actin-driven remodeling and movement in diverse cell types.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097484","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0014839","count":1},{"id":"GO:0035021","count":1},{"id":"GO:0007015","count":1}]},{"hash":"563172181284681790","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"The top GO terms cluster around actin-related processes (actin cortical patch assembly/localization, mitotic actomyosin contractile ring assembly, cell polarity and shape maintenance) and cell movement (mesenchyme migration) as well as cytokinesis, with calcium signaling and gene expression regulation providing modulatory context. This points to a cohesive theme of actin-driven cytoskeletal dynamics governing division and migration.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010628","count":6},{"id":"GO:0021762","count":6},{"id":"GO:0000281","count":6},{"id":"GO:0051592","count":6},{"id":"GO:0016344","count":6}]},{"hash":"2291814966162205290","title":"Vesicle trafficking and epithelial polarity","description":"The terms point to secretory and trafficking processes (synaptic vesicle budding, exocytosis), lysosome/autophagy pathways (lysosomal membrane organization, phagophore assembly), and epithelial cell organization (apical/basal polarity, apical protein localization) with supporting cytoskeletal dynamics (tubulin complex assembly) and signaling (EGFR). This suggests a cohesive theme of vesicle trafficking and polarity in epithelial contexts, with autophagy-related processes contributing to membrane/Vesicle dynamics.","confidence":"High","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070142","count":6},{"id":"GO:0097212","count":6},{"id":"GO:0001822","count":6},{"id":"GO:0007173","count":6},{"id":"GO:0034976","count":6}]},{"hash":"722717392017166506","title":"Chromatin methylation and transcription regulation","description":"This cluster is dominated by methylation-related GO terms (peptidyl-glutamine, rRNA, histone H4-R3, and arginine methylation) and a link to transcription control (negative regulation of transcription by RNA Pol II) along with cell-cycle signals (mitotic spindle assembly, cellular senescence, cell growth). Together, these point to epigenetic chromatin modification and coordination with cell-cycle processes rather than a single specialized pathway, making a label centered on chromatin methylation and transcription regulation appropriate.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0018364","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0043985","count":2}]},{"hash":"85951190585085495","title":"Cajal body RNA localization and telomere trafficking","description":"Top GO terms predominantly point to localization of RNA and proteins to Cajal bodies and telomeres (scaRNA localization to Cajal body; positive regulation of telomerase RNA localization to Cajal body; positive regulation of establishment of protein localization to telomere), suggesting a cohesive theme of nuclear body\u2013 and telomere-related trafficking. Some terms about mitochondrial import and stress responses appear as less central outliers but do not strongly redefine the main pattern.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051085","count":6},{"id":"GO:0045041","count":6},{"id":"GO:0071866","count":6},{"id":"GO:0002931","count":6},{"id":"GO:0090666","count":6}]},{"hash":"471014572478488884","title":"Brain development and synaptic signaling","description":"The top GO terms center on brain development (substantia nigra development; brain development) and excitatory postsynaptic potential, indicating neuronal development and synaptic activity. Supporting terms reflect general neuronal cellular processes (ER to Golgi transport; dephosphorylation) that commonly occur in neurons, while a couple of outliers (meiotic cell cycle) are less connected. Overall, the cluster seems best represented by neuronal development and synaptic signaling functions.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0016311","count":3}]},{"hash":"94540191843855264","title":"Neural development and photoreceptor differentiation","description":"The cluster shows strong signals for nervous system development, photoreceptor development, and action potential, pointing to neural differentiation and function as the core theme. Some terms touch on cell adhesion, cytoskeleton polarization, and morphogenesis that can be relevant to neural tissue organization; a couple terms like copper homeostasis or phagophore localization appear peripheral. Thus the label reflects the main pattern with moderate confidence.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006878","count":1},{"id":"GO:0070830","count":1},{"id":"GO:0042461","count":1},{"id":"GO:0001508","count":1},{"id":"GO:0040032","count":1}]},{"hash":"1982250978709071957","title":"Gene Expression and Translation Initiation","description":"The top GO terms center on transcription (DNA-templated transcription) and components of the translation initiation machinery (formation of translation preinitiation complex / translation initiation), with references to RNA processing (rRNA maturation). This suggests a core theme around gene expression regulation at both transcriptional and translational levels, though several developmental terms appear that may reflect annotation breadth rather than a cohesive functional module. Therefore the name captures the primary signals but is tentative due to heterogeneity.","confidence":"Low","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1627127443127240851","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to translation and ribosome assembly, including translation, ribosome biogenesis, ribosomal large subunit assembly, and mitochondrial translation, plus supporting terms like translation termination and rRNA modification. The shared focus on protein synthesis machinery suggests these proteins work together in ribosome construction, translation execution, and related quality-control steps; occasional stress-response terms appear ancillary. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0006415","count":1}]},{"hash":"1115470031493203002","title":"RNA Processing and Translation Regulation","description":"The cluster is dominated by GO terms related to mRNA processing and post-transcriptional control\u2014nuclear mRNA export, alternative splicing, mRNA stability in response to stress, and regulation of translational initiation (including IRES-dependent initiation). This suggests a cohesive role in RNA metabolism and translation control rather than a single enzymatic pathway.","confidence":"High","size":6,"edges":7,"triangles":1,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:1902625","count":3},{"id":"GO:1903586","count":3},{"id":"GO:1905663","count":3},{"id":"GO:0001825","count":3}]},{"hash":"429469002085732759","title":"Post-transcriptional RNA processing and translation control","description":"These proteins cluster around post-transcriptional gene regulation: mRNA export, alternative splicing, mRNA stability under stress, and control of translation initiation (including IRES-dependent viral translation). Although some terms are obsolete, the central theme is RNA processing and the regulation of translation, indicating a cohesive post-transcriptional regulatory function for the cluster.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:1902625","count":2},{"id":"GO:1903586","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0001825","count":2}]},{"hash":"1000707699058010475","title":"Nuclear transport and cell cycle regulation","description":"The Top GO terms point to nuclear-cytoplasmic processes (NLS-bearing protein import into nucleus, mRNA transport) alongside regulators of growth and division (positive regulation of cell proliferation, mitotic cell cycle) and signaling (GTPase activity, kinase activity) as well as apoptosis. This suggests a broad theme around coordinating transport with cell cycle and signaling regulation rather than a single, cohesive pathway, so the label focuses on the shared emphasis on transport and cycle signaling.","confidence":"Low","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006607","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0008284","count":3},{"id":"GO:0042144","count":3}]},{"hash":"1477158301132548241","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0048701","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0000467","count":1},{"id":"GO:0090394","count":1}]},{"hash":"378946350820349275","title":"Transmembrane Transporters for Sugars, Ions, and Xenobiotics","description":"The top GO terms collectively point to membrane transport activities across diverse substrates (arabinose, galactose, sialic acid, nitrate, sodium ions, 4-hydroxyphenylacetate, xenobiotics) and related processes like neurotransmitter loading into vesicles, suggesting this cluster comprises broad-substrate membrane transporter proteins rather than a single pathway.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0042128","count":2}]},{"hash":"1064470478414097433","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1794126666290185474","title":"Ribosome Biogenesis and Nucleolar Transcription","description":"This cluster is dominated by terms related to ribosome biogenesis, translation, nucleolus organization, and transcription by RNA polymerases I, II, and III, indicating a group of proteins involved in ribosome production and nucleolar transcriptional activity; a few development terms seem incidental.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0045572","count":1},{"id":"GO:0035214","count":1},{"id":"GO:0007000","count":1}]},{"hash":"2190778986915955579","title":"Cell Cycle Control and DNA Repair","description":"The top GO terms cluster around regulation of the G1/S transition, ubiquitin-dependent protein degradation, and DNA repair processes, suggesting a module focused on cell-cycle control via proteolysis and genome maintenance. While redox homeostasis and phosphoinositide signaling can intersect with cell-cycle signaling, and a couple terms (renal water transport, hemolysis) may reflect broader context or noise, the core theme centers on cell-cycle progression and DNA integrity. ","confidence":"Medium","size":6,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1900087","count":3},{"id":"GO:0042787","count":2},{"id":"GO:2001153","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0044179","count":2}]},{"hash":"1104441150976740403","title":"Unknown","description":"The Top Terms are a scattered mix across protein processing (ER targeting, signal peptide processing), differentiation (Leydig cells), lipid signaling (prostaglandin biosynthesis, lipid hydroperoxide response, retinoic acid response), immune/oxidative stress (LPS response, oxidant detoxification), and skin cornification. There is no unifying function or pathway across the proteins, and there are no edges connecting them, so a coherent cluster label cannot be established.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1},{"id":"GO:0033327","count":1},{"id":"GO:0001516","count":1},{"id":"GO:0014070","count":1}]},{"hash":"2281516546977361526","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, autoubiquitination, K48-linked ubiquitination) and ERAD, suggesting targeted protein turnover. Some terms describe degradation of receptors (Wnt receptor catabolic process) and growth regulation, which align with ubiquitin-mediated proteostasis impacting signaling and cell-cycle checkpoints. Overall, the cluster appears to group proteins involved in tagging and degrading substrates via the ubiquitin-proteasome system.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0051865","count":2},{"id":"GO:0060816","count":2},{"id":"GO:1900095","count":2},{"id":"GO:0038018","count":2}]},{"hash":"1773902640114043967","title":"Neuromuscular development and movement","description":"This cluster shows strong representation of GO terms for spinal cord motor neuron differentiation, neuromuscular processes controlling balance, and musculoskeletal movement, indicating a core neuromuscular development/function theme. Other terms like IGF receptor signaling, cell-cycle checkpoint signaling, and mRNA regulation appear but do not shift the focus from neuromuscular function. Therefore, a neuromuscular development and movement label fits best.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021522","count":1},{"id":"GO:0031571","count":1},{"id":"GO:0048873","count":1},{"id":"GO:0048009","count":1},{"id":"GO:0016441","count":1}]},{"hash":"2109822939567335644","title":"RNA processing and translation regulation","description":"Most terms point to RNA metabolism and protein synthesis, including spliceosome dynamics, mRNA decay, translation initiation and elongation, cytoplasmic translation, and selenocysteine incorporation. A couple of terms relate to DNA damage response and neurotrophic signaling, which are less central but may reflect broader stress or signaling cross-talk. Overall, the dominant theme is RNA processing and control of translation.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0000388","count":2},{"id":"GO:0009432","count":2},{"id":"GO:1990416","count":2},{"id":"GO:0006289","count":2}]},{"hash":"20038792629124521","title":"Tyrosine phosphatase signaling in development","description":"Enriched for peptidyl-tyrosine dephosphorylation, this cluster likely contains proteins involved in tyrosine phosphatase\u2013mediated signaling. The presence of developmental terms (multicellular organism development, neuron development, sensory perception of pain) alongside cell-cycle and kinetochore-related terms suggests a role in signaling that coordinates development with cell division and proteostasis.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0045736","count":2}]},{"hash":"344743403269694299","title":"DNA Damage Repair and Stress Response","description":"GO terms center on DNA repair (base-excision repair; regulation of double-strand break repair via SSA) and damage events (depurination). Additional terms show responses to light and to xenobiotics/ethanol, indicating a broader chemical-stress context. Together, these proteins likely participate in sensing or repairing DNA damage and mounting a stress response.","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0072421","count":4},{"id":"GO:0009416","count":4},{"id":"GO:1901291","count":4},{"id":"GO:0006284","count":4},{"id":"GO:0007568","count":4}]},{"hash":"915322275282782989","title":"Mitotic cell cycle and ER-Golgi trafficking","description":"The cluster is dominated by mitosis-related terms (mitotic spindle assembly, mitotic cell cycle, cell division, cell population proliferation) together with vesicle trafficking terms linking the ER and Golgi (ER-to-Golgi transport, COPII-coated vesicle budding, retrograde Golgi\u2013ER transport). This suggests a functional group involved in cell cycle progression coordinated with secretory pathway dynamics. Additional terms like ribosome biogenesis and brain development are present but less central, indicating a core theme of dividing cells coordinating membrane trafficking.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0090114","count":5}]},{"hash":"26218990357054252","title":"Developmental Morphogenesis and Differentiation","description":"Although terms span several tissues, they center on embryonic development and tissue morphogenesis (neural tube, heart, kidney) and cell differentiation (neurons, macrophages) with some apoptosis regulation. The cluster thus likely reflects broad developmental programs rather than a single pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001237","count":1},{"id":"GO:0001935","count":1},{"id":"GO:0071866","count":1},{"id":"GO:0003203","count":1},{"id":"GO:0044334","count":1}]},{"hash":"626361083010721036","title":"Unknown","description":"The Top Terms are very diverse, including obsolete oxidation-reduction and RNA exonuclease functions, poly-hydroxybutyrate biosynthesis, DNA catabolic process, IRE1-mediated unfolded protein response, SRP-dependent cotranslational targeting to membrane, flagellum organization, cell division, and sphinganine metabolism. There is no single unifying function or pathway that ties these terms together, and the cluster shows no edges or interactions, suggesting the proteins do not share a cohesive role. Therefore, I cannot assign a meaningful specific label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":2},{"id":"GO:0090503","count":1},{"id":"GO:0006308","count":1},{"id":"GO:0036498","count":1}]},{"hash":"1461230616654402498","title":"Iron-Sulfur Cluster Biogenesis and Cofactor Metabolism","description":"The terms center on iron-sulfur cluster assembly and iron homeostasis, indicating a core role in metal cofactor handling. Additional terms point to biosynthesis of quinones (phylloquinone, menaquinone) and various carbon metabolism pathways, typical of bacterial metabolic networks that rely on cofactors for energy and redox processes. Together, they suggest a cohesive theme around cofactor biosynthesis and metal-dependent metabolism rather than a single, narrow function.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0016226","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0006879","count":1},{"id":"GO:0009399","count":1}]},{"hash":"1556705766237690752","title":"Unknown","description":"The top terms cover a broad mix of cellular trafficking (ER-Golgi transport, ERAD, protein import into mitochondria, protein processing), gene expression processes (mRNA export, transcription elongation), replication (DNA and viral genome replication), development (lung development), and cytoskeletal regulation, with no single unifying function evident. Given this heterogeneity and lack of a cohesive theme, there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0045041","count":1},{"id":"GO:0019079","count":1}]},{"hash":"2050514976686005123","title":"ER Stress and Redox-Driven Protein Processing","description":"These GO terms cluster around stress-responsive protein maturation and trafficking: endoplasmic reticulum stress response, oxidative/redox homeostasis, protein processing, and Golgi localization, with deglutathionylation implying redox regulation of proteins. Transcriptional regulation terms are present but appear less central, suggesting the core theme is how cells handle protein folding/processing under oxidative and ER stress. Overall, the cluster points to redox-modulated protein processing under ER stress.","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":1},{"id":"GO:0016485","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0043388","count":1}]},{"hash":"1767566564627354375","title":"Golgi\u2013Endosome\u2013Vacuole Vesicle Trafficking","description":"The cluster shows strong enrichment for GO terms related to vesicle transport across the secretory pathway (Golgi to vacuole, endocytosis, retrograde and anterograde transport between Golgi, ER, and endosomes, etc.), indicating a cohesive function in intracellular vesicle trafficking and protein targeting. Some neuron-related terms appear less consistent with this core theme and may reflect broader or organism-specific annotations, but the vesicle trafficking signal is dominant.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0009615","count":2}]},{"hash":"1015480013077955365","title":"Plant polysaccharide degradation and host symbiosis","description":"The proteins are linked to arabinose, arabinan, xylan, and xylitol catabolic/metabolic processes, pointing to degradation of plant polysaccharides. The inclusion of a symbiotic process benefiting the host supports a host-associated microbial role, while additional terms like fatty acid omega-oxidation, ethanol fermentation, and LPS response suggest broader microbial metabolism and host interaction within this cluster. Overall, the cluster appears to represent plant polysaccharide utilization in a symbiotic context with associated metabolic activities.","confidence":"Medium","size":6,"edges":9,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046373","count":2},{"id":"GO:0031222","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0085030","count":2},{"id":"GO:0010430","count":1}]},{"hash":"1798941117520658055","title":"Unknown","description":"The Term set spans ER-to-Golgi transport, DNA replication, lipid and glucose metabolic regulation, dephosphorylation, kinase activity regulation, immune signaling, transporter regulation, and GTPase regulation, with no clear, single cohesive function tying all proteins together. This diversity suggests no specific, interpretable cluster function can be assigned.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0010867","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0006469","count":1}]},{"hash":"322052172197958196","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0002107","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0010606","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1639342553470859275","title":"Unknown","description":"The GO terms for this cluster are mixed and do not point to a single cohesive function: neuronal signaling terms (synaptic vesicle transport and sodium channel regulation) appear alongside chromatin processes, immune signaling, and development terms, suggesting no clear shared theme across the proteins.","confidence":"","size":6,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048536","count":2},{"id":"GO:1900095","count":2},{"id":"GO:1905150","count":2},{"id":"GO:0048490","count":2},{"id":"GO:0090282","count":2}]},{"hash":"826141574162710358","title":"Ciliary Function and Sensory Signaling","description":"The cluster shows several GO terms tied to cilia and sensory perception (cilium assembly, visual perception, sensory neuron axon guidance), suggesting a set of proteins involved in ciliary structure and sensory signal transduction. Some terms (GTPase regulation, protein secretion, tRNA modification) may reflect broader cellular roles or incidental annotations, but the core theme appears to be ciliary biology and sensory signaling.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0060271","count":1},{"id":"GO:1905490","count":1},{"id":"GO:0035330","count":1}]},{"hash":"1443237301876726230","title":"Unknown","description":"The terms span transcription, chemotaxis, placenta development, metabolism, transport, signaling, and cell-cycle processes with no single shared function tying the proteins together; there are no edges or clusters indicating a cohesive interaction, so a unified functional label cannot be inferred.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006935","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0033160","count":4}]},{"hash":"534703001156800064","title":"Plant Development and Abiotic Response","description":"This cluster\u2019s terms center on plant growth and tissue formation (phloem/xylem histogenesis, meristem regulation, seed germination, leaf senescence) and responses to abiotic cues (sucrose, abscisic acid, cold). While a few terms are less related (sorocarp stalk development, obsolete sulfate transport), the dominant pattern reflects plant development plus environmental/stress signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010087","count":1},{"id":"GO:0010150","count":1},{"id":"GO:0071329","count":1},{"id":"GO:0071215","count":1},{"id":"GO:0010029","count":1}]},{"hash":"1404278609804397029","title":"Mitotic Checkpoint Signaling","description":"The top GO terms highlight mitotic checkpoint processes (mitotic spindle assembly checkpoint signaling and mitotic intra-S DNA damage checkpoint signaling) and regulation of phosphorylation, which together point to cell-cycle control in mitosis as the central theme. While there are also terms related to signaling and development, the strongest, recurring signals relate to checkpoint regulation during cell division, justifying this label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007037","count":3},{"id":"GO:1904531","count":3},{"id":"GO:0007094","count":3},{"id":"GO:1902002","count":3},{"id":"GO:0001806","count":3}]},{"hash":"1339045805561268696","title":"Signaling Regulation and Protein Quality Control","description":"The top GO terms cluster around regulation of TGF-beta signaling (including SMAD-related processes) and related signaling control, plus protein quality control processes such as sumoylation and ERAD. This suggests a common theme of modulating signaling pathways via post-translational modification and protein homeostasis, even though a few terms relate to development and photosystem context that are less directly connected. Overall, the proteins appear linked by regulatory influence on signaling and protein stability rather than a single, narrow function.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:1904378","count":2},{"id":"GO:0080005","count":1},{"id":"GO:0042006","count":1},{"id":"GO:0030512","count":1}]},{"hash":"2152239351497618073","title":"Neural development and GABAergic signaling","description":"The strongest GO signals point to nervous system development (including substantia nigra development) and GABAergic synaptic transmission, suggesting a neuronal development role with inhibitory synaptic function. Filopodium assembly and neurite-related processes further support neural connectivity; some terms like cell cycle/DNA replication may be noise, but the core theme is brain development and GABAergic signaling.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045740","count":2},{"id":"GO:0039694","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0051489","count":2}]},{"hash":"967981296949031882","title":"Plant development and abiotic stress responses","description":"The top GO terms cluster around vascular tissue development (phloem/xylem histogenesis), meristem regulation, seed germination control, leaf senescence, and abiotic/metabolic signaling (ABA, cold, sucrose). This suggests proteins involved in plant growth, tissue formation, and stress response, with a few outliers (sorocarp stalk development, obsolete sulfate transport) that may reflect annotation noise. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010087","count":2},{"id":"GO:0010150","count":2},{"id":"GO:0071329","count":2},{"id":"GO:0071215","count":2},{"id":"GO:0010029","count":2}]},{"hash":"1896434305990657169","title":"Microtubule dynamics and intracellular transport","description":"The terms are dominated by microtubule-related processes: spindle elongation, centrosome separation, plus-end depolymerization/sliding, and axonemal/dendritic transport along microtubules. While there are some outliers (root development, stress granule disassembly, integrin regulation), the overarching pattern ties to microtubule dynamics and motor-driven transport across mitotic and neuronal contexts.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":4},{"id":"GO:0000915","count":4},{"id":"GO:0048364","count":4},{"id":"GO:0033624","count":4},{"id":"GO:0060404","count":4}]},{"hash":"471717282249431310","title":"Wnt signaling in neuronal development","description":"These proteins show a cohesive theme around Wnt pathway regulation and neural development, including positive regulation of canonical Wnt signaling, dendritic spine development, and nerve branching morphogenesis, with additional links to neuronal apoptosis regulation and small GTPase\u2013mediated signaling that likely drive cytoskeletal and synaptic changes. While one term about mating projection growth is less relevant, the dominant signals point to Wnt-driven neural development and maturation.","confidence":"High","size":5,"edges":6,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":4},{"id":"GO:0043525","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0043524","count":4},{"id":"GO:0031384","count":4}]},{"hash":"722495650747661914","title":"Neuromuscular and Neural Development Signaling","description":"This cluster shows strong representation of developmental and synaptic terms: excitatory postsynaptic potential and long-term potentiation point to synaptic function, while myoblast fusion, Schwann cell development, heart development, and multicellular organism development indicate broader neuromuscular and neural tissue growth. The shared theme is the development and signaling of nervous and muscular systems, with some signaling pathway activity like threonine phosphorylation. The abscisic acid term is likely an annotation artifact and does not redefine the main theme. ","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0009738","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0007275","count":4}]},{"hash":"1032807324019489047","title":"Developmental and Brain Formation","description":"The cluster\u2019s top GO terms are dominated by development-related processes\u2014multicellular organism development, brain development, neural tube closure, and skeletal system development\u2014pointing to a developmental/neuronal formation theme. Additional terms such as mitotic cell cycle and DNA-templated transcription reflect general growth readiness, supporting a broad developmental context rather than a single specific pathway.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0070059","count":4}]},{"hash":"1693691445510146376","title":"Unknown","description":"The top GO terms are highly heterogeneous, including metabolic pathways (glycolate catabolic process, fatty acid alpha-oxidation, L-glutamate biosynthetic process), development (retina development in camera-type eye), protein-protein interaction (protein homotetramerization), and immune-related activity (lymphocyte proliferation), with several items marked obsolete. This lack of a coherent, single function or pathway makes it difficult to assign a specific, representative label, so I categorize the cluster as Unknown.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009854","count":1},{"id":"GO:0019516","count":1},{"id":"GO:0080114","count":1},{"id":"GO:0060041","count":1},{"id":"GO:0051289","count":1}]},{"hash":"856351334390059002","title":"Stress-Responsive Signaling and Trafficking","description":"These proteins touch on several related themes: stress responses (osmotic stress, immune signaling modulation), signaling pathway regulation (PI3K/AKT inhibition), cytoskeletal dynamics (lamellipodium morphogenesis), cell cycle control (exit from mitosis), and vesicle trafficking (COPII cargo loading). The terms point to a broad, but not tight, coupling between stress signaling, trafficking, and dynamic cellular processes, with some tissue-specific connections (lung morphogenesis, muscle atrophy). Therefore, the label captures a general theme rather than a precise, single function.","confidence":"Low","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000394","count":1},{"id":"GO:1902174","count":1},{"id":"GO:0031536","count":1},{"id":"GO:0090110","count":1},{"id":"GO:0071470","count":1}]},{"hash":"30836655484753779","title":"Unknown","description":"The GO terms are highly diverse (DNA-templated transcription, kinetochore localization, cytoskeleton and actin regulation, neuronal learning, cholesterol biosynthesis, and various signaling/processes), with no clear, common function linking the proteins. Therefore, there isn\u2019t a coherent theme to name a specific cluster function.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0008542","count":2},{"id":"GO:0006695","count":2}]},{"hash":"529319861158170990","title":"Mitotic cell cycle proteins","description":"This cluster is characterized mainly by GO terms linked to mitosis and cell division (mitotic cell cycle and cell division both with counts of 2), suggesting core involvement in chromosome segregation and mitotic progression. Additional terms like protein heterooligomerization and positive regulation of TORC2 signaling hint at protein complex assembly and growth/cytoskeletal regulation that can influence the cell cycle, while a few outliers (defense response to protozoan, transcriptional regulation) are less central. Overall, the dominant theme appears to be mitotic control and division machinery.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043524","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0010628","count":1}]},{"hash":"1280844646611581559","title":"Rho GTPase\u2013regulated axonogenesis and synaptic signaling","description":"This cluster is dominated by GO terms for regulation of GTPase activity and Rho signaling, which points to cytoskeletal dynamics guiding axon growth. The presence of terms related to axonogenesis, synaptic vesicle exocytosis, and glutamatergic transmission supports a neuronal function theme centered on Rho-mediated neuronal development and synaptic communication.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0050772","count":2},{"id":"GO:0045945","count":1},{"id":"GO:2000300","count":1}]},{"hash":"926908884530463300","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042256","count":2},{"id":"GO:0071035","count":1},{"id":"GO:0006271","count":1},{"id":"GO:0070535","count":1},{"id":"GO:0070512","count":1}]},{"hash":"745220426503955529","title":"Amino acid metabolism and pigment biosynthesis","description":"This cluster shows a strong focus on biosynthesis and catabolism of amino acids (lysine, ornithine/arginine, beta-alanine, biotin) and on pigment-related biosynthetic pathways (chlorophyll and protoporphyrinogen IX), with GABA and putrescine catabolism tying into amino-acid\u2013derived metabolism. An outlier term about cocaine response is present but does not derail the main metabolic theme.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":4},{"id":"GO:0006782","count":3},{"id":"GO:0009450","count":3},{"id":"GO:0015995","count":3},{"id":"GO:0009447","count":3}]},{"hash":"2201234204912002911","title":"Transcription-Translation and rRNA Maturation","description":"The terms point to both transcription-related activities (DNA-templated transcription, transcription regulation, antitermination) and translation, plus maturation of SSU rRNA, indicating a cluster of proteins involved in RNA biogenesis and ribosome assembly rather than a single pathway.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0031564","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1811537293605631342","title":"Copper transport and homeostasis","description":"This cluster is dominated by GO terms about copper ion transport across membranes, intracellular copper homeostasis, and copper import, with an additional note on xenobiotic transport and cisplatin response, all pointing to a cohesive theme of copper handling and detoxification across the membrane. Other terms appear peripheral or ancillary to this core function. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902311","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0098705","count":2},{"id":"GO:0072719","count":2}]},{"hash":"284650901231096836","title":"DNA Damage Response and RNA Processing","description":"The top terms point to DNA damage response and repair (nucleotide-excision repair, UV-damage excision repair, intra-S DNA damage checkpoint signaling, response to UV-B) and related cell-cycle regulation (positive regulation of cell cycle, mitotic recombination). There is a secondary signal for RNA processing (mRNA splicing via spliceosome), suggesting these proteins may also participate in RNA processing. Overall, the dominant theme is DNA damage response and repair with a potential co-occurring RNA-processing role.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0031573","count":1},{"id":"GO:0070914","count":1},{"id":"GO:0006289","count":1}]},{"hash":"89120509667980641","title":"Translesion DNA Synthesis (TLS) Cluster","description":"Dominant GO terms are two translesion synthesis processes (error-prone and error-free), pointing to a TLS-mediated DNA damage tolerance cluster; the remaining terms reflect diverse metabolic processes and stress responses that are less central.","confidence":"High","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042276","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0018189","count":1},{"id":"GO:0019243","count":1},{"id":"GO:0035900","count":1}]},{"hash":"1620255235267860094","title":"Unknown","description":"The top GO terms span RNA modification (pseudouridine synthesis), translation regulation, DNA mobility (integration, transposition, proviral latency), and cell cycle processes. This mix lacks a single coherent function tying all proteins together, making a unified cluster label inappropriate. Therefore, the label is Unknown with no confidence in a representative function.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000455","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0007049","count":1}]},{"hash":"118188179704476061","title":"Nuclear DNA Replication and Transcription Control","description":"This cluster centers on nuclear processes: DNA topology changes and replication elongation, chromatin formation, mitotic chromosome condensation, transcription elongation and regulation by RNA polymerase II, and circadian regulation of gene expression, plus related cell-cycle events like embryonic cleavage and nuclear migration. The shared theme is nuclear DNA metabolism and transcription regulation during the cell cycle, making this label appropriate.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006265","count":1},{"id":"GO:0006271","count":1},{"id":"GO:0000183","count":1},{"id":"GO:0007076","count":1},{"id":"GO:0006368","count":1}]},{"hash":"633980169999649117","title":"Ribosome Biogenesis and Translation","description":"The GO terms are dominated by ribosome biogenesis (including small/large subunit biogenesis and export) and cytoplasmic translation, with supporting tRNA modification, pointing to core ribosome assembly and protein synthesis functions; a few cell division terms are present but secondary. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0042274","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0042254","count":1}]},{"hash":"836434665377680195","title":"Unknown","description":"The top GO terms are broad and span animal development (brain development, gastrulation, male gonad development) and plant patterning, plus unrelated cellular processes (translation initiation, rRNA maturation, Arp2/3 regulation). With no edges connecting the proteins and no cohesive functional theme, there\u2019s no clear common function to label this cluster, so it\u2019s Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0000462","count":2}]},{"hash":"772217118085577863","title":"Transcription and RNA Processing Regulation","description":"The cluster\u2019s GO terms point to multiple layers of gene expression control, including transcriptional regulation by RNA Pol II, mRNA export, alternative splicing, mRNA stability during stress, and translational initiation. These together suggest a coherent module of transcriptional and post-transcriptional regulators, despite a few obsolete terms that may reflect historical annotations. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0006406","count":1},{"id":"GO:1902625","count":1},{"id":"GO:1903586","count":1},{"id":"GO:1905663","count":1}]},{"hash":"588213822839092459","title":"Cerebellar Purkinje Cell Signaling and LTD","description":"The top GO terms strongly point to cerebellar function and Purkinje cell activity: cerebellar molecular layer development, GABA secretion (inhibitory signaling), and positive regulation of long-term synaptic depression at Purkinje cell synapses, along with membrane depolarization in Purkinje cells. These together suggest a cohesive theme of Purkinje cell signaling and cerebellar LTD, despite some heart-related terms appearing in the list. ","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":3},{"id":"GO:1990573","count":2},{"id":"GO:0051592","count":2},{"id":"GO:0098910","count":2},{"id":"GO:1900454","count":2}]},{"hash":"1038277081235820615","title":"Global Regulators of Cellular Processes","description":"This cluster\u2019s GO terms are all regulatory in nature, spanning cell cycle control, apoptosis and necroptosis regulation, transcriptional control, ubiquitination, ribosome biogenesis, and TLR signaling regulation. The common thread is broad regulation of diverse cellular processes rather than a single pathway, suggesting these proteins act as general regulators of cell fate and homeostasis.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060544","count":1}]},{"hash":"1145983964386303205","title":"Diverse membrane transporters (amino acids, vitamins, metals)","description":"The top GO terms are dominated by various transporter activities across membranes, covering amino acid (methionine, cysteine), vitamin/thiamine, and metal ion transport (molybdate, heme, mercury). A few stress-response terms are present, but the core signal is transport across membranes for multiple substrates, suggesting a cluster of diverse membrane transport proteins.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0042883","count":1},{"id":"GO:0015888","count":1},{"id":"GO:0003333","count":1},{"id":"GO:0015689","count":1}]},{"hash":"993279751161123295","title":"Proteolysis and ECM remodeling","description":"This cluster is dominated by GO terms describing proteolytic and catabolic processes affecting extracellular components and signaling peptides (e.g., collagen catabolic, bradykinin catabolic, neuropeptide catabolic), plus related regulation of catalytic activity. The presence of development-related remodeling terms (lung morphogenesis, intramembranous ossification) further supports a theme of extracellular matrix remodeling and peptide turnover driven by proteases. Overall, a proteolysis/ECM remodeling theme best captures the shared functions of the proteins in this group.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":2},{"id":"GO:2000179","count":2},{"id":"GO:0097067","count":2},{"id":"GO:0050790","count":2},{"id":"GO:0010815","count":2}]},{"hash":"1082043577390883386","title":"Mitochondrial apoptosis signaling","description":"The GO terms cluster around mitochondrial outer membrane processes (protein insertion, cytochrome c release), oxidative stress\u2013driven programmed cell death (H2O2-mediated PCD), and cellular responses to TGF-beta, all pointing to mitochondrial stress signaling that culminates in apoptosis. Despite the small size and lack of edges, the dominant theme is mitochondrial apoptotic regulation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903638","count":1},{"id":"GO:1903645","count":1},{"id":"GO:0010421","count":1},{"id":"GO:0090200","count":1},{"id":"GO:0071560","count":1}]},{"hash":"1982981160878653771","title":"Mitotic cell cycle regulation","description":"The dominant GO terms point to cell cycle transitions (G1/S and G2/M), mitotic events such as spindle pole separation and re-entry into mitosis, and transcriptional regulation related to mitosis, suggesting a cohesive theme of mitotic control. A few terms are more tissue- or context-specific (mammary epithelial proliferation, response to toxic substances, insulin signaling) but do not outweigh the core signal of cell cycle regulation. Confidence: Medium","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0033598","count":2},{"id":"GO:0010696","count":2},{"id":"GO:0000320","count":2},{"id":"GO:0000082","count":2}]},{"hash":"1765989417329453510","title":"ER Stress and Protein Quality Control","description":"The set is dominated by GO terms linked to the endoplasmic reticulum stress response, unfolded protein response, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, with related terms about translation initiation during ER stress and membrane targeting. This points to a cohesive module handling misfolded proteins in the ER and coordinating degradation and translation responses.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0036494","count":2}]},{"hash":"1969688051278322825","title":"Adipose mitochondrial apoptosis and lipid metabolism","description":"The top GO terms point to mitochondrial membrane permeabilization and apoptotic signaling, indicating a role in mitochondrial control of cell death. The accompanying terms on adipose tissue development, hormone response, and lipid metabolic processes (fatty acid beta-oxidation, acetyl-CoA pathways, cholesterol transport) suggest these proteins coordinate adipocyte lipid metabolism with mitochondrial regulation.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1902109","count":4},{"id":"GO:0060612","count":4},{"id":"GO:0009725","count":4},{"id":"GO:1901029","count":4},{"id":"GO:0014070","count":4}]},{"hash":"2176619675318167348","title":"Plant Cell Wall and Pollen Wall Biosynthesis","description":"The dominant GO signals point to plant-specific wall-building processes: plant-type secondary cell wall biogenesis, cell wall organization, and pollen exine formation, suggesting a coherent theme around plant cell wall and pollen wall synthesis. Some proteoglycan biosynthesis terms appear but do not override the plant-centric pattern.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900087","count":2},{"id":"GO:0050650","count":1},{"id":"GO:0010584","count":1},{"id":"GO:0009834","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1922358834732627233","title":"Paraxial and Axial Mesoderm Somitogenesis","description":"The cluster is dominated by mesoderm-related development terms: paraxial mesoderm development, axial mesoderm development, and somitogenesis, with a Notch signaling regulation term that often modulates segmentation. While glycosphingolipid biosynthesis terms are present, the core theme ties to mesoderm patterning and somite formation.","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":1},{"id":"GO:0051999","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0072358","count":1}]},{"hash":"384239456853514527","title":"Unknown","description":"The top terms are scattered across transcription, chromatin modification, ribosome biogenesis, protein turnover, nutrient response, and development, with no single shared function or interaction pattern; the cluster has no edges (Edges: 0, Max Degree: 0), so there is no cohesive theme to label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0043966","count":2}]},{"hash":"1992021711073805691","title":"Redox Homeostasis and Detoxification","description":"This cluster is defined by GO terms for redox balance and detoxification, including cell redox homeostasis, cellular oxidant detoxification, glutathione derivative biosynthetic process, and xenobiotic catabolic process. Additional terms on apoptotic signaling regulation and neural/immune development suggest broader regulatory roles, but the common thread remains antioxidant defense and detox pathways.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000255","count":5},{"id":"GO:0045454","count":5},{"id":"GO:0098869","count":5},{"id":"GO:2001237","count":4},{"id":"GO:1901687","count":4}]},{"hash":"742411909822871806","title":"Unknown","description":"The listed GO terms are highly heterogeneous, spanning sporulation, multiple developmental processes (lung morphogenesis, ossification, bone resorption), neural precursor proliferation, thyroid hormone response, neuropeptide catabolism, and immune activity (T cell cytotoxicity). There is no single cohesive biological theme that ties these terms together, so a meaningful, specific label cannot be assigned. None","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0030435","count":3},{"id":"GO:2000179","count":2},{"id":"GO:0097067","count":2},{"id":"GO:0010813","count":2}]},{"hash":"1640177218073546321","title":"Unknown","description":"The top GO terms show a highly diverse mix, including lipid metabolism (triglyceride catabolic process; regulation of endocannabinoid signaling), structural/cell wall processes (peptidoglycan biosynthetic process; cell wall organization; regulation of cell shape), metabolism (amino acid metabolic process), DNA repair, and growth factor\u2013related responses (endothelial proliferation; cellular response to hepatocyte growth factor). With only a single edge and no clear unifying function across these terms, there isn\u2019t a coherent shared biological theme tying the proteins together. Therefore, the cluster cannot be assigned a meaningful specific function name beyond Unknown.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0009252","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0008360","count":1}]},{"hash":"1843452976138135283","title":"Cell signaling and stimulus response","description":"Based on the GO terms, the cluster centers on cellular responses to various stimuli (xenobiotic, mineralocorticoid), defense responses, and signaling pathways (TORC2) that regulate gene expression and cellular behavior, with a peripheral note of development processes like dendrite formation. This suggests a coherent theme around signal transduction and stimulus-induced responses, though some terms are unrelated or obsolete.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010796","count":2},{"id":"GO:0031384","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0010628","count":1},{"id":"GO:0042832","count":1}]},{"hash":"383562372344488958","title":"Chromatin and Telomere Maintenance","description":"The key terms concentrate on chromatin organization and telomere biology (nucleosome assembly, subtelomeric heterochromatin formation, and protection from non-homologous end joining at telomeres), suggesting a core theme around chromosome structure and genome stability. Some terms point to plant-specific processes (chloroplast organization, cell wall biogenesis) and other stress responses that appear less connected, so the strongest, cohesive signal is chromatin/telomere-related. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009644","count":1},{"id":"GO:0009658","count":1},{"id":"GO:0006970","count":1},{"id":"GO:1901348","count":1},{"id":"GO:1901347","count":1}]},{"hash":"801325873943359352","title":"Unknown","description":"No GO terms or shared functional signal are present; there are no edges or enrichment terms to define a common function among the five proteins, and ReCIPE re-adding offers no context. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1992913200044122226","title":"Dopamine and Serotonin Regulation","description":"Top GO terms center on dopamine metabolic process (positive regulation) and dopamine catabolic process, along with negative regulation of serotonin secretion, pointing to a core theme of neurotransmitter regulation. Additional terms about responses to corticosterone, xenobiotic stimuli, lipopolysaccharide, and various chemicals suggest the cluster captures neuronal responses to chemical stressors as a broader context. The absence of molecular edges indicates this may reflect co-regulated or functionally related proteins rather than direct interactions, but the strongest signal is neurotransmitter regulation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010269","count":2},{"id":"GO:0042135","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0045964","count":2},{"id":"GO:0051412","count":2}]},{"hash":"25952416275137075","title":"Cholesterol and Lipid Metabolism","description":"The top GO terms cluster around cholesterol handling and broader lipid metabolism, including cholesterol homeostasis, reverse cholesterol transport, HDL particle remodeling, and lipid storage, suggesting a module focused on cholesterol transport and lipid management; the terms collectively point to a cohesive lipid/membrane lipid metabolism theme despite no detected interactions.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046338","count":1},{"id":"GO:0043691","count":1},{"id":"GO:0042632","count":1},{"id":"GO:0019915","count":1},{"id":"GO:0006672","count":1}]},{"hash":"1452720949981901841","title":"Ciliary and sensory signaling","description":"This cluster is dominated by GO terms related to cilium assembly, visual perception, and sensory neuron signaling (cilium-related processes and sensory perception), suggesting a shared role in ciliary/visual sensory pathways. Some other terms (Hippo signaling regulation, kinetochore localization, tRNA modification, protein secretion) are more peripheral, so the core theme is ciliary and sensory signaling with moderate confidence. ","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060271","count":4},{"id":"GO:1905490","count":4},{"id":"GO:0035330","count":4},{"id":"GO:0006547","count":4},{"id":"GO:0007117","count":4}]},{"hash":"1117427831853799446","title":"Quinone biosynthesis and fatty acid metabolism","description":"This cluster is dominated by GO terms for quinone biosynthesis (phylloquinone and menaquinone) and shows additional enrichment for fatty acid beta-oxidation and other central carbon metabolic processes (TCA cycle, valine and phenylacetate catabolism). The common theme is quinone-related biosynthesis linked to energy metabolism in bacteria, justifying a label centered on quinone biosynthesis with fatty acid metabolism.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0006574","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0006635","count":3}]},{"hash":"698701829543563029","title":"Kinetochore and Mitotic Checkpoint Signaling","description":"This cluster is dominated by terms about kinetochore localization, mitotic spindle assembly checkpoint signaling, and regulation of CDK activity and phosphorylation, pointing to a coherent theme of mitotic control and kinetochore-associated signaling. A few terms (vacuolar transport, immune and neural differentiation) appear peripheral, likely annotation noise, but the core signals support the mitosis-related interpretation.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":4},{"id":"GO:0045736","count":4},{"id":"GO:0007037","count":3},{"id":"GO:1904531","count":3},{"id":"GO:0007094","count":3}]},{"hash":"1347568138174645776","title":"Unknown","description":"The top GO terms span very different biological areas (oxidation-reduction, mating/conjugation, plant hormone biosynthesis and development, cell division structures, and various catabolic or regulatory processes). There isn't a single cohesive function tying these four proteins, so a meaningful concise label is not evident.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0019433","count":1},{"id":"GO:1901601","count":1},{"id":"GO:0000022","count":1}]},{"hash":"1288196798028071135","title":"Unknown","description":"The top GO terms span ribosome biogenesis and translation initiation, plant/developmental processes, actin cytoskeleton regulation, histone acetylation, and inflammatory cytokine production. The terms do not converge on a single cohesive function for the cluster, with ribosome/translation hints contradicted by diverse developmental and cytoskeletal terms, so no clear unifying theme emerges.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0000462","count":2},{"id":"GO:2000011","count":2}]},{"hash":"2037057901745765145","title":"Developmental Morphogenesis Across Tissues","description":"The top GO terms point to morphogenesis and organ development across several tissues (cranial skeleton, cerebellum, spinal cord, middle ear, prostate, spleen), indicating a general developmental/morphogenetic role rather than a single tissue-specific function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":1},{"id":"GO:0045686","count":1},{"id":"GO:0060527","count":1},{"id":"GO:0048536","count":1},{"id":"GO:0009722","count":1}]},{"hash":"1302881770948197257","title":"miRNA Regulation and Silencing","description":"Dominant GO terms in the cluster are centered on miRNA pathways: miRNA-mediated gene silencing, miRNA metabolic process, and positive regulation of miRNA-mediated gene silencing, suggesting the proteins collectively relate to RNA interference regulation. Other terms (peptide amidation, actin ubiquitination, cytokine signaling, stem cell proliferation) appear less consistently and may be incidental noise. Overall, the strongest theme is miRNA regulation.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903883","count":3},{"id":"GO:0018032","count":3},{"id":"GO:0035278","count":3},{"id":"GO:0001519","count":3},{"id":"GO:0007014","count":3}]},{"hash":"1990126802346716521","title":"Mitotic Cell Division and Golgi-ER Trafficking","description":"Top GO terms indicate strong involvement in mitosis and cell proliferation (mitotic cell cycle, cell division, mitotic spindle assembly, multicellular organism growth) along with secretory pathway activity (COPII-coated vesicle budding, retrograde vesicle transport from Golgi to ER) and protein oligomerization. Together, these suggest a cluster centered on mitotic progression complemented by Golgi-ER trafficking processes. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0090114","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1103365127017230897","title":"Retinoic acid signaling and neural development","description":"The top GO terms cluster around retinol/retinoic acid metabolism and signaling (retinol metabolic process, retinoic acid receptor signaling pathway) together with neural development (forebrain development, nucleus accumbens development, anterior/posterior pattern specification), suggesting a program of retinoid-driven brain patterning and development. Confidence: High","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006069","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0006068","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0051591","count":2}]},{"hash":"112471188462880291","title":"Transcription elongation and chromatin regulation","description":"The listed GO terms cluster around regulation and elongation of transcription by RNA polymerases I and II, plus chromatin-related processes such as heterochromatin boundary formation and histone modification. Although there are a few differentiation-focused terms, the dominant signal points to transcriptional control and chromatin state as the shared function of this protein set.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001209","count":1},{"id":"GO:0010048","count":1},{"id":"GO:0045638","count":1},{"id":"GO:0033696","count":1},{"id":"GO:0021529","count":1}]},{"hash":"2197256136003352268","title":"Unknown","description":"The GO terms are highly diverse (glycosylation, pollen tube guidance, growth regulation, RNA processing, translation, energy homeostasis, meiosis) and there are no edges or clear connections among the proteins, so there is no cohesive theme to assign a specific function to the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0010183","count":1},{"id":"GO:0030307","count":1},{"id":"GO:0006406","count":1}]},{"hash":"2056457382406312242","title":"Viral assembly and release","description":"The GO terms show clear enrichment for viral particle formation and exit (virion/capsid assembly, viral assembly, viral release from host cell), which dominates the cluster signal. Other terms (cell cycle, unfolded protein response, chaperone-related processes) may reflect host\u2013virus interactions or incidental associations but do not outweigh the viral assembly/release theme. Thus the label captures the primary functional focus of the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0051085","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0051131","count":1},{"id":"GO:0019068","count":1}]},{"hash":"2282110926239171267","title":"Ribosome biogenesis and translation","description":"The Top Terms are centered on ribosome production and function (ribosome biogenesis, ribosomal subunit assembly, translation, translational termination, and mitochondrial translation), indicating proteins involved in assembling ribosomes and carrying out protein synthesis. This cohesive theme justifies a label focused on ribosome biogenesis and translation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0006415","count":1}]},{"hash":"213166592252264514","title":"RNA processing and translational regulation","description":"The top GO terms cluster around RNA maturation and processing steps (polyadenylation, splicing, export, and mRNA stability) plus control of translation initiation, indicating proteins linked to RNA processing and subsequent translational regulation. Despite some obsolete terms, the core theme is coherent.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0006406","count":1},{"id":"GO:1902625","count":1},{"id":"GO:1903586","count":1},{"id":"GO:1905663","count":1}]},{"hash":"2035276398353279727","title":"Unknown","description":"The top GO terms span oxidative stress response, transcription regulation, various mitosis-related processes, neuron differentiation, translation regulation, and mechanosensory behavior, with no single cohesive function linking them. Given the diverse and seemingly unrelated functions, there isn\u2019t a clear, common theme to label this cluster beyond a generic, Unknown category.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0051256","count":1}]},{"hash":"393211374891227196","title":"Cardiac and Neural Signaling Regulation","description":"These proteins appear to be involved in signaling control for both muscle and nervous system functions: terms for heart contraction and atrial action potential regulation suggest cardiac signaling, while regulation of synaptic vesicle exocytosis, synaptic plasticity, and responses like cAMP indicate neural communication control. Calcium-related processes (mitochondrial Ca2+ concentration) and muscle development (myoblast fusion) further support a broader theme of signaling regulation in muscle and neural contexts, though there are some fusion-related outliers (karyogamy). Overall, a cohesive core theme around signaling regulation in muscle/nerve context with some fusion-related variance.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0008016","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0048168","count":2},{"id":"GO:0051561","count":2}]},{"hash":"1343522431108005523","title":"Protein quality control and mitochondrial function","description":"GO terms emphasize protein processing, ER unfolded protein response, oxidative processes tied to protein degradation, and assembly/hexamerization, all pointing to protein quality control and folding. Several terms also relate to mitochondrial energy production (oxidative phosphorylation, complex III assembly), suggesting a link to mitochondrial function. A few terms (microtubule depolymerization, transcription elongation) appear less directly connected and may reflect broader cellular regulation, but the dominant signal is a cluster around maintaining proteostasis with mitochondrial activity.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031117","count":3},{"id":"GO:0032968","count":3},{"id":"GO:0016485","count":3},{"id":"GO:1903862","count":3},{"id":"GO:0070987","count":3}]},{"hash":"1392157785852844696","title":"Ribosome biogenesis and translation","description":"The top GO terms concentrate on ribosome production and function (translation, ribosome biogenesis, ribosomal subunit assembly) and nucleolus organization, indicating this cluster represents ribosome assembly/translation machinery. A few terms like Notch signaling and inflammatory response appear but are likely incidental.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042274","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0060266","count":1},{"id":"GO:0007219","count":1}]},{"hash":"163284008702452373","title":"Nuclear RNA processing and export","description":"The terms cluster around RNA metabolism and trafficking within the nucleus, including rRNA maturation, tRNA transport, mRNA export, hnRNP import, and ribosomal subunit export, pointing to nuclear RNA processing and nucleocytoplasmic transport as the shared theme. Some terms touch on unrelated processes, but the dominant signal is RNA processing/transport.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0051031","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0006609","count":1},{"id":"GO:0000122","count":1}]},{"hash":"290367068459080821","title":"Ubiquitination and Proteasome Assembly","description":"The top GO terms are dominated by protein polyubiquitination (GO:0000209), K11-linked ubiquitination (GO:0070979), and proteasome assembly (GO:0043248), pointing to a core role in ubiquitin-mediated protein turnover and proteasome formation. Although some development- or RNA processing-related terms are present, the strongest signal centers on tagging proteins for degradation and assembling the proteasome, suggesting these proteins participate in the ubiquitin-proteasome system.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0010950","count":1},{"id":"GO:0043248","count":1},{"id":"GO:0007584","count":1},{"id":"GO:0070979","count":1}]},{"hash":"1205241876126250275","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031123","count":1},{"id":"GO:0043631","count":1},{"id":"GO:0008103","count":1},{"id":"GO:0030036","count":1},{"id":"GO:0000902","count":1}]},{"hash":"704109671746408324","title":"Unknown","description":"There are no shared GO terms or functional signals among the proteins (Top Terms empty; Edges and Triangles are zero), so a cohesive biological function cannot be inferred. Without a common theme, the cluster is best labeled Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1516588148509771581","title":"Unknown","description":"The GO terms span stress-related processes (trehalose biosynthesis, heat response) and a wide range of neural development, signaling, and trafficking functions, with no clear single theme tying all terms together. This lack of a cohesive functional topic suggests the cluster cannot be confidently assigned a specific label beyond Unknown.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0005992","count":1},{"id":"GO:0070413","count":1},{"id":"GO:0034605","count":1},{"id":"GO:0060973","count":1},{"id":"GO:0021762","count":1}]},{"hash":"649628886237982790","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0006564","count":1},{"id":"GO:0032361","count":1}]},{"hash":"2279176601400827130","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0033358","count":2},{"id":"GO:1902653","count":2},{"id":"GO:0009699","count":2},{"id":"GO:0019673","count":2}]},{"hash":"788227391219712029","title":"DNA Damage Response and Genome Maintenance","description":"This cluster\u2019s GO terms center on genome integrity: intrinsic apoptotic signaling in response to DNA damage via p53, replication fork arrest, meiotic mismatch repair and gene conversion, and regulation of helicase activity, all indicating a shared theme of DNA repair and replication stress response; additional terms for oxidative phosphorylation and lifespan may reflect general cellular maintenance, while a few immune-related terms appear as potential noise.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008340","count":1},{"id":"GO:0043570","count":1},{"id":"GO:0051096","count":1},{"id":"GO:0006119","count":1},{"id":"GO:0042771","count":1}]},{"hash":"1231262585931807767","title":"Oxidative Stress and Cell Morphogenesis","description":"The cluster\u2019s top GO terms point to responses to singlet oxygen and programmed cell death, indicating oxidative stress responses, alongside terms for cell morphogenesis and lamellipodium formation, suggesting cytoskeletal remodeling and cell shape changes. A few developmental or plasticity terms are also present but are less cohesive with the stress/morphogenesis theme, so the clear thread lies in stress-related signaling and morphogenetic remodeling.","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":1},{"id":"GO:0000304","count":1},{"id":"GO:0031571","count":1},{"id":"GO:0010343","count":1},{"id":"GO:0000902","count":1}]},{"hash":"1008977860870959049","title":"Nuclear Transcription Regulation & RNA Processing","description":"Top terms cluster around nuclear gene expression control, especially negative regulation of transcription by RNA Pol II, nuclear mRNA surveillance, and Pol II DNA tethering at the nuclear periphery. Other terms (ubiquinone biosynthesis, proteasome assembly, response to toxic substances) are less central, so the dominant theme is nuclear transcription regulation and RNA processing.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0071033","count":1},{"id":"GO:0034260","count":1}]},{"hash":"1646811785738052555","title":"Unknown","description":"The top GO terms span diverse, loosely related cellular processes (mitochondrial protein import, viral genome replication, mRNA export, microtubule dynamics, misfolded protein handling, transcription elongation, protein processing, vesicle formation, oxidative phosphorylation regulation, and stress granule dynamics) across multiple cellular compartments, with no clear single function tying them together. Therefore there isn\u2019t a coherent, specific label that represents the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0031117","count":1},{"id":"GO:0071712","count":1}]},{"hash":"1680025313934046140","title":"Regulation of signaling and phosphorylation","description":"The terms show broad regulatory roles, including positive/negative regulation of phosphorylation and various signaling pathways, plus cell-cycle and growth-related regulation. While the specific processes differ (bud growth, polarity, meiosis, cardiac proliferation), they share a common theme of regulation rather than a single pathway, so the label reflects a general regulatory function for this small cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007118","count":1},{"id":"GO:2000100","count":1},{"id":"GO:0042327","count":1},{"id":"GO:0031031","count":1},{"id":"GO:0000920","count":1}]},{"hash":"671473204482779550","title":"Stress and immune regulation","description":"Based on the top GO terms, the proteins appear involved in dampening immune signaling (negative regulation of NF-kappaB signaling, leukocyte proliferation, and neutrophil aggregation) and apoptosis (negative regulation of extrinsic apoptotic signaling), alongside stress-related responses (glucocorticoid stimulus response and glutathione biosynthesis). While some terms reflect plant or abiotic stress (auxin signaling, aluminum ion response), the overarching theme is modulation of stress responses with suppression of inflammatory signaling. This makes \"Stress and immune regulation\" a concise, representative label for the cluster.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2001237","count":4},{"id":"GO:1901687","count":4},{"id":"GO:0070664","count":4},{"id":"GO:0035732","count":4},{"id":"GO:0045669","count":4}]},{"hash":"1504234207627380088","title":"Pyrrolysine and Glutathione Biosynthesis","description":"The cluster\u2019s top GO terms are pyrrolysine biosynthetic process and glutathione biosynthetic process, suggesting a general link to biosynthetic activities rather than a single pathway. With minimal edges and only one annotation per term among four proteins, the label reflects a broad biosynthesis theme without overcommitting to a specific pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071524","count":1},{"id":"GO:0006750","count":1}]},{"hash":"1704393752270439068","title":"Unknown","description":"There are no GO terms or interactions to suggest a common function (Edges: 0, Triangles: 0, Max Degree: 0), so a cohesive label cannot be inferred. The ReCIPE re-addition doesn\u2019t reveal a shared biological role.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1212456884805480890","title":"Cytoskeleton remodeling and cell migration","description":"Based on the terms, the cluster is driven by cytoskeletal rearrangements (ruffle assembly, stress fiber assembly) and processes related to cell movement (positive regulation of fibroblast migration, cellular response to mechanical stimulus, response to growth factor signaling). Other terms point to broader signaling and stress responses, but the strongest pattern ties to actin dynamics and motility. Confidence: Medium","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097178","count":1},{"id":"GO:0032435","count":1},{"id":"GO:0061321","count":1},{"id":"GO:1903061","count":1},{"id":"GO:0071364","count":1}]},{"hash":"737349116959589759","title":"Ciliary Sensory Signaling","description":"This cluster is dominated by cilium and sensory-related terms (visual perception, cilium assembly, sensory neuron guidance), suggesting a shared function in ciliary structure and sensory signaling. Other terms like mitotic cell cycle and budding growth are more general, so the core theme remains cilia-related; hence a medium confidence in this assignment.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0060271","count":2},{"id":"GO:1905490","count":2},{"id":"GO:0035330","count":2}]},{"hash":"414855240893819791","title":"Chromatin Organization and Transcription Regulation","description":"Top GO terms point to chromatin organization and transcriptional control, including histone-related processes and ubiquitin signaling (K11-linked ubiquitination). Despite some obsolete annotations, the recurring themes of chromatin maintenance, transcription regulation, and ubiquitin-mediated modification suggest proteins that regulate chromatin structure and gene expression, possibly linking to DNA damage tolerance pathways.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010620","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0090089","count":3},{"id":"GO:0006344","count":3},{"id":"GO:0033128","count":3}]},{"hash":"672655429892207339","title":"Amino acids, vitamins, and metal ion transport","description":"GO terms point to transmembrane transport of amino acids (cysteine, methionine), vitamins (thiamine), and metal ions (cadmium, molybdate), plus general amino acid and vitamin transport. The SOS response term is incidental; overall the cluster seems to consist of transporters for diverse substrates across membranes.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042883","count":1},{"id":"GO:0015888","count":1},{"id":"GO:0036249","count":1},{"id":"GO:1902943","count":1},{"id":"GO:0003333","count":1}]},{"hash":"1755524271424183173","title":"Potassium Ion Transport and Homeostasis","description":"This cluster is dominated by GO terms about potassium transport and intracellular potassium ion homeostasis (and related sodium transport regulation), indicating a core role in maintaining cellular ion balance. Some adjacent terms touch on muscle contraction regulation, which can be influenced by ion channels, but the strongest signal centers on potassium ion handling.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":2},{"id":"GO:1903249","count":2},{"id":"GO:0045988","count":2},{"id":"GO:0045299","count":2},{"id":"GO:0002028","count":2}]},{"hash":"1348575929088183040","title":"Unknown","description":"The GO terms span immune-related processes (dendritic cell chemotaxis, phagocytosis, MHC class I antigen assembly) as well as general cellular processes (protein folding, ER unfolded protein response, synaptic vesicle endocytosis, cell cycle regulation, hormone signaling), with no single unifying function. Therefore a coherent, specific label is not supported.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":1},{"id":"GO:0048387","count":1},{"id":"GO:0033144","count":1},{"id":"GO:2000510","count":1},{"id":"GO:0050766","count":1}]},{"hash":"211073202302174563","title":"X-Chromosome Inactivation and Histone Modification","description":"This cluster centers on dosage compensation and X chromosome inactivation, plus histone modifications and catabolic processes, suggesting an epigenetic/regulatory theme. A few terms related to ubiquitin signaling, RIG-I regulation, and septin organization appear as broader or incidental connections.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:1903762","count":1},{"id":"GO:0070535","count":1},{"id":"GO:0070512","count":1},{"id":"GO:1900095","count":1}]},{"hash":"1631004794840885406","title":"Neuronal vesicle trafficking and endocytosis","description":"The cluster shows enrichment for regulation of synaptic vesicle exocytosis and endocytosis, plus brain development, suggesting a core role in neuronal vesicle trafficking and synaptic membrane dynamics. While some other terms point to broader processes (mitochondria-ER tethering, NF-kB signaling), the strongest, most specific signals concern vesicle exocytosis and endocytosis in the brain.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010796","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0031384","count":3},{"id":"GO:1903434","count":2}]},{"hash":"1239898561199197685","title":"Actin Cytoskeleton and Cell Polarity","description":"Top terms point to actin-based processes: patch assembly/localization, contractile ring formation, and establishment of cell polarity, with supporting links to cell migration and calcium signaling. This suggests a cohesive cluster centered on cytoskeletal dynamics driving cell shape and movement, with some neural development and meiosis terms reflecting broader cytoskeletal roles.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010628","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0000281","count":3},{"id":"GO:0051592","count":3},{"id":"GO:0016344","count":3}]},{"hash":"753409363240769943","title":"Rab-regulated vesicle trafficking and endocytosis","description":"This cluster\u2019s GO terms converge on membrane trafficking: Rab protein signal transduction, endocytosis, and synaptic vesicle budding point to Rab-driven vesicle movement and recycling, with additional terms referencing secretory pathway regulation and organelle interface (mitochondrion-ER tethering) that support membrane dynamics. Together, these suggest a cohesive theme of Rab-mediated vesicle transport and related processes.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050771","count":2},{"id":"GO:0032482","count":2},{"id":"GO:1903434","count":1},{"id":"GO:0071851","count":1},{"id":"GO:0071389","count":1}]},{"hash":"2079853483917915676","title":"Unknown","description":"The top GO terms span metabolism (carnitine, flavonoid, L-cysteine), nutrient response, diverse signaling (guanylate cyclase, Smoothened), nitric oxide production, and immune-related activity (IL-6 production), with no obvious shared function and no observed interactions among the proteins. This lack of a cohesive theme makes a specific, informative label inappropriate, so Unknown is the safest choice.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009437","count":1},{"id":"GO:1904042","count":1},{"id":"GO:0007584","count":1},{"id":"GO:0031284","count":1},{"id":"GO:0006809","count":1}]},{"hash":"653109282021592461","title":"Ubiquitin-Mediated Chromatin Regulation","description":"This cluster centers on ubiquitination-related terms (protein ubiquitination, histone ubiquitination) and chromatin-associated processes (histone modification/catabolic processes, dosage compensation by X chromosome inactivation). The presence of these GO terms suggests the proteins participate in ubiquitin-dependent regulation of chromatin structure and X-chromosome dosage compensation, even though there are no reported edges among them in this cluster. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:1903762","count":2},{"id":"GO:0070512","count":2},{"id":"GO:1900095","count":2},{"id":"GO:0070535","count":2}]},{"hash":"2027931416281990372","title":"Fatty acid oxidation and redox homeostasis","description":"GO terms show strong emphasis on fatty-acid transport and beta-oxidation (carnitine metabolic process; beta-oxidation using acyl-CoA dehydrogenase) alongside redox-related processes (oxidative stress response; redox homeostasis; deglutathionylation). The combination suggests a cluster centered on lipid metabolism coupled with redox regulation, despite one outlier term. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009437","count":1},{"id":"GO:0033539","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0003147","count":1}]},{"hash":"1321914381729044233","title":"Testosterone biosynthesis and male reproductive development","description":"The cluster\u2019s strongest signals are testosterone biosynthetic process and male gonad development, including regulation of testosterone biosynthesis. While other terms touch on broader developmental and metabolic pathways, the core theme centers on androgen production and male reproductive development.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0072001","count":3},{"id":"GO:2000224","count":3},{"id":"GO:2000353","count":3},{"id":"GO:0070485","count":3},{"id":"GO:0018931","count":3}]},{"hash":"702253605907700769","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0007338","count":2},{"id":"GO:0001682","count":2},{"id":"GO:0000492","count":2},{"id":"GO:2000623","count":2}]},{"hash":"653746910746358164","title":"Unknown","description":"This cluster shows a mix of very different GO terms (cofactor biosynthesis for cobalamin, phylloquinone, ubiquinone; polyamine biosynthesis; aerobic respiration) plus methylation and stress/response terms, with no apparent single biological function or interaction pattern linking them. Edges are zero, suggesting no established connections, so there isn\u2019t a clear, representative label to assign.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0018027","count":1}]},{"hash":"1730837037977277457","title":"Unknown","description":"The top GO terms show two largely distinct domains: translation/ribosome assembly and various DNA replication/mitosis-related processes, with a few unrelated terms (e.g., forebrain development). There isn\u2019t a single cohesive function that ties all terms together, so a unified label cannot be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006271","count":1},{"id":"GO:0097046","count":1},{"id":"GO:0030900","count":1}]},{"hash":"1840877094610702298","title":"Neuronal signaling and cytoskeleton regulation","description":"The proteins cluster around signaling pathways that control cytoskeleton dynamics and neuronal morphology: regulation of dendrite morphogenesis, ephrin receptor signaling, and regulation of small GTPase\u2013mediated signaling. While a few terms touch unrelated processes (anoikis, chloroquine response), the dominant GO terms point to neuronal development and cytoskeletal remodeling. This suggests a function in neuronal signaling linked to cytoskeletal change.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903697","count":1},{"id":"GO:0043276","count":1},{"id":"GO:1990792","count":1},{"id":"GO:0031532","count":1},{"id":"GO:1902350","count":1}]},{"hash":"1520004807322312317","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0000467","count":1},{"id":"GO:0090394","count":1},{"id":"GO:0048568","count":1}]},{"hash":"1413004600596440908","title":"Unknown","description":"The top GO terms span mitochondria-related processes (protein import into mitochondrial intermembrane space, oxidative phosphorylation) as well as RNA metabolism and stress responses (mRNA export, transcription elongation, stress granule disassembly) and vesicle trafficking, with an outlier term for viral genome replication. This mix does not reveal a single cohesive function for the cluster of three proteins, so a specific label isn\u2019t supported. ","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045041","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0031117","count":3},{"id":"GO:0071712","count":3}]},{"hash":"1243721373794740518","title":"RNA Polymerase III Transcription and 5S rRNA Synthesis","description":"These proteins are linked to RNAP III transcription, especially 5S rRNA synthesis, via terms for RNAP III transcription, preinitiation complex assembly, and termination. Some RNAP I/II terms appear, but RNAP III signals dominate, suggesting a cluster focused on RNAP III transcription machinery and 5S rRNA production.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001041","count":1},{"id":"GO:0001009","count":1},{"id":"GO:0006359","count":1},{"id":"GO:0001021","count":1},{"id":"GO:0042791","count":1}]},{"hash":"1878070800938925512","title":"Ribosome Biogenesis and Translation","description":"This cluster centers on translation and rRNA maturation, with GO terms for translation, SSU rRNA maturation, and RNA processing (folding, intron/splicing regulation). The combination of translation-related processes and rRNA maturation points to a ribosome-focused theme, with translational fidelity and antibiotic response further supporting this connection.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0034337","count":1},{"id":"GO:0000372","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0033120","count":1}]},{"hash":"1198672318495139905","title":"Insect Developmental Fate Specification","description":"The top GO terms point to developmental differentiation and cell fate decisions in insects, with spermatid differentiation, cone cell fate commitment, and wing cell fate specification forming a coherent theme. Other terms (unfolded protein response, ER-to-cytosol proteolysis, EGF ligand maturation, NK cell regulation) are less central and may reflect broader cellular processes or noise. Overall, the strongest signal is developmental fate specification, so this label is a reasonable, but not perfect, summary of the cluster.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048515","count":1},{"id":"GO:1904211","count":1},{"id":"GO:0042676","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0034620","count":1}]},{"hash":"1367518051763969078","title":"Unknown","description":"The GO terms are highly heterogeneous: insect cuticle pigmentation, Leydig cell differentiation, alkaloid metabolism, various neurotransmitter-related processes, and growth factor responses span development, neurochemistry, and metabolism. With no edges and little overlap among terms, there is no cohesive shared function linking these proteins, so a confident, specific label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048085","count":1},{"id":"GO:0033327","count":1},{"id":"GO:0071312","count":1},{"id":"GO:0042136","count":1},{"id":"GO:2001120","count":1}]},{"hash":"1040128895418244619","title":"Mitochondrial apoptosis and ROS regulation","description":"The cluster centers on mitochondria-related processes: apoptotic signaling (apoptotic process, cysteine-type endopeptidase activity linked to cytochrome c), cytochrome c linkage, and mitochondrial electron transport. Hydrogen peroxide metabolism and regulation of its biosynthesis further tie the set to reactive oxygen species management. One outlier term (photosynthesis) is likely annotation noise, but the cohesive theme points to mitochondrial apoptotic pathways and oxidative stress control.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008635","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0042743","count":1},{"id":"GO:0034465","count":1},{"id":"GO:0006915","count":1}]},{"hash":"1245455597905818773","title":"Unknown","description":"The GO terms point to chromatin and nuclear organization (nucleolar rDNA localization, heterochromatin and telomere maintenance) but also include unrelated pathways (acetoin metabolism, androgen receptor signaling, calcium-regulated muscle contraction). This dispersion makes it hard to define a single cohesive function for the cluster.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034503","count":3},{"id":"GO:0060766","count":3},{"id":"GO:0045149","count":3},{"id":"GO:0051038","count":3},{"id":"GO:0010882","count":3}]},{"hash":"1546376909589122314","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0006564","count":1},{"id":"GO:0032361","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0019373","count":1}]},{"hash":"1264395956873140630","title":"Unknown","description":"The Top Terms span immune activation (T cell activation), cell adhesion and integrin-regulated adhesion, ECM remodeling, host-symbiont interaction, hypoxia response, cell proliferation, and even behavior-related processes. This broad and divergent set of functions does not converge on a single coherent biological theme, making it inappropriate to assign a specific, representative label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042110","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0010716","count":1},{"id":"GO:0008284","count":1}]},{"hash":"1429739626982437839","title":"Steroid and lipid biosynthesis","description":"The top GO terms are dominated by biosynthetic and metabolic processes related to steroids and lipids (testosterone and glucocorticoid biosynthesis, retinoic acid biosynthesis, fatty acid elongation, sphinganine metabolism), indicating a metabolic cluster centered on lipid/hormone biosynthesis; a few terms (poly-hydroxybutyrate, phylloquinone catabolism) appear as outliers but do not negate the overall theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042619","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006666","count":2},{"id":"GO:0008207","count":2},{"id":"GO:0061370","count":2}]},{"hash":"667409011300209444","title":"Unknown","description":"The GO terms span highly diverse processes (metabolism, cell signaling, immune activation, neurobehavior, hypoxia response, detoxification, and hormone regulation) with no clear shared function or dominant pathway, and there are no edges linking proteins, so a cohesive label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1},{"id":"GO:0097325","count":1},{"id":"GO:0033632","count":1},{"id":"GO:0036343","count":1},{"id":"GO:0019608","count":1}]},{"hash":"392909426336851178","title":"Carbohydrate Metabolism and Peptidoglycan Turnover","description":"Dominant signals are carbohydrate metabolic processes (glucose-6-phosphate, N-acetylglucosamine/mannosamine, glycolysis) with a peptidoglycan turnover term, pointing to bacterial sugar processing and cell-wall remodeling; additional methionine salvage and pteridine metabolism terms broaden the scope but do not override the carbohydrate-centric connection.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051156","count":1},{"id":"GO:0019316","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0019262","count":1},{"id":"GO:0009254","count":1}]},{"hash":"2027715873556197942","title":"Glycan biosynthesis and cell wall organization","description":"The GO terms are dominated by carbohydrate and polysaccharide biosynthetic processes (UDP-N-acetylglucosamine, GDP-mannose, glucose-1-phosphate, galactose catabolic, glycogen biosynthesis) and cell wall organization, pointing to proteins involved in glycan assembly/remodeling and cell wall biosynthesis; a couple of signaling terms (peptidyl-tyrosine dephosphorylation, gravity detection) may reflect broader roles or annotation noise, but the core theme is glycan/wall biosynthesis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0035335","count":1},{"id":"GO:0030389","count":1},{"id":"GO:0006048","count":1},{"id":"GO:0019255","count":1}]},{"hash":"230697940888792919","title":"Amino acid biosynthesis","description":"The top GO terms point to multiple amino acid biosynthetic processes (methionine, isoleucine, threonine, and diaminopimelate/lysine) and related metabolic steps, suggesting these proteins are involved in amino acid production pathways. Some terms are obsolete, but the core theme remains amino acid biosynthesis, consistent with a small cluster of proteins linked to these pathways. Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009086","count":1},{"id":"GO:0019310","count":1},{"id":"GO:0006742","count":1},{"id":"GO:0009097","count":1}]}]