[{"hash":"56511983832175001","title":"Ribosome Biogenesis and Translation","description":"Predominant GO terms center on translation, ribosome assembly/biogenesis, and SSU rRNA maturation, with cytoplasmic translation also represented. The cluster is clearly enriched for components of the ribosome production and protein-synthesis machinery, indicating a ribosome-biogenesis/translation module; the antibiotic response term is ancillary noise. ","confidence":"High","size":29,"edges":392,"triangles":3367,"max_degree":28,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":26},{"id":"GO:0000027","count":8},{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000462","count":3}]},{"hash":"1011305078239138964","title":"Mitotic Regulation and Protein Degradation","description":"This cluster is dominated by mitosis-related GO terms (mitotic cell cycle, anaphase-promoting complex-dependent catabolic process) and protein turnover pathways (neddylation, ubiquitin-dependent ERAD), with a chromatin-remodeling hint from subtelomeric heterochromatin formation. While immune signaling terms are present, the overarching signal is cell-cycle control and proteostasis.","confidence":"Medium","size":28,"edges":36,"triangles":17,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006348","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0031145","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0045116","count":5}]},{"hash":"2259820596747712414","title":"Ubiquitin-related protein quality control and ribosome assembly","description":"The cluster is enriched for ubiquitin-related processes (deubiquitination, sumoylation, obsolete ERAD pathway, deglycosylation) and core protein synthesis/biogenesis (translation, ribosomal small subunit assembly). This suggests a cohesive theme of protein homeostasis and production machinery. A few terms about signaling regulation or development appear but are less central to the dominant pattern.","confidence":"High","size":25,"edges":180,"triangles":973,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":10},{"id":"GO:0016925","count":9},{"id":"GO:0034140","count":8},{"id":"GO:0045648","count":8},{"id":"GO:0006412","count":8}]},{"hash":"1320519878369372127","title":"Translation machinery and translational regulation","description":"The top GO terms are dominated by translation-related processes (initiation, elongation, termination, cytoplasmic translation, and selenocysteine incorporation), including positive regulation of translation and related mRNA decay. This suggests the cluster comprises components of the protein synthesis machinery and its regulation, with some auxiliary RNA/degradation links. Confidence: High","confidence":"","size":24,"edges":94,"triangles":256,"max_degree":17,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0006415","count":5},{"id":"GO:0002181","count":5},{"id":"GO:0006413","count":5},{"id":"GO:0014009","count":4}]},{"hash":"759309810177831193","title":"DNA Damage Response and Cell Cycle Checkpoints","description":"The cluster shows enrichment for DNA repair, mitotic spindle assembly checkpoint signaling, and apoptotic processes, with supporting terms in DNA-templated transcription and TNF signaling, suggesting a core role in genome maintenance and cell fate decisions under stress. While some terms (like obsolete annotations) are less informative, the dominant themes point to DDR and cell cycle control mechanisms.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043029","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0051092","count":2},{"id":"GO:0070535","count":2}]},{"hash":"1663445245427721834","title":"Neuronal development and synaptic signaling","description":"The proteins show strong associations with neural development (axonogenesis, substantia nigra development, visual perception) and synaptic activity/plasticity (excitatory postsynaptic potential, long-term potentiation), with signaling inputs such as cAMP, glucocorticoids, and GTPase regulation linking to activity-dependent neuronal function. The mitotic cell cycle term is likely developmental noise and does not override the dominant neuronal theme.","confidence":"Medium","size":22,"edges":20,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":8},{"id":"GO:0060079","count":7},{"id":"GO:0051591","count":7},{"id":"GO:0051384","count":7},{"id":"GO:0043547","count":6}]},{"hash":"784194197536923144","title":"Brain development, metabolism, and cell-cycle regulation","description":"This cluster centers on brain development terms (substantia nigra and hippocampus development), neuronal signaling (excitatory postsynaptic potential), core metabolism (tricarboxylic acid cycle), and cell-cycle processes (mitotic cycle, cell division, CDK activity regulation), plus transcription and protein interactions, suggesting a cohesive theme around brain development and function with metabolic and cell-cycle coordination.","confidence":"Medium","size":21,"edges":8,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0043065","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0060079","count":3}]},{"hash":"876014009178296820","title":"TNF signaling and NF-kappaB with ubiquitin regulation","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic process and TNF-mediated signaling, along with activation of the NF-kappaB-inducing kinase and regulation of the JNK cascade, which together point to inflammatory/immune signaling and protein turnover. The presence of V(D)J recombination suggests lymphocyte-related immune functions; a unifying theme is immune signaling modulated by ubiquitin-mediated proteolysis.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0033209","count":5},{"id":"GO:1903762","count":4},{"id":"GO:2000620","count":4},{"id":"GO:0007250","count":4}]},{"hash":"1402278092390591035","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":177,"triangles":984,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":15},{"id":"GO:0048026","count":15},{"id":"GO:0006369","count":10},{"id":"GO:0034475","count":10},{"id":"GO:0000467","count":10}]},{"hash":"930121430555709268","title":"Unknown","description":"The top terms span core cellular processes (DNA replication, mitotic cell cycle, cell morphogenesis) and development in animals (Schwann cell development, excitatory postsynaptic potential) together with fungal-specific processes (karyogamy, fungal-type beta-glucan biosynthesis) and stress-related apoptosis, indicating a highly heterogeneous set with no single unifying function. Unknown is therefore the most appropriate label.","confidence":"","size":19,"edges":25,"triangles":7,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":7},{"id":"GO:0006260","count":5},{"id":"GO:0000902","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0014044","count":4}]},{"hash":"595091843828441519","title":"Bacterial translation and ribosome assembly","description":"The cluster shows multiple strong signals for protein synthesis-related processes: translation, ribosome biogenesis, and small subunit assembly, along with tRNA wobble uridine modification, which collectively point to the bacterial translation machinery. While there are some other bacterial processes present (e.g., flagellum-related assembly and metabolism), the dominant theme is the core components and assembly of ribosomes and translation. Confidence: Medium","confidence":"","size":19,"edges":50,"triangles":109,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0044780","count":2}]},{"hash":"216031748442023323","title":"RNA processing and translation initiation regulation","description":"This cluster is enriched for RNA-centric processes: mRNA splicing via the spliceosome, small-subunit processome assembly, mRNA modification and stability regulation, and formation of the translation preinitiation complex, plus ncRNA-mediated gene silencing. Taken together, the proteins appear to function in RNA maturation and the control of translation initiation, with some related regulatory activities.","confidence":"High","size":19,"edges":167,"triangles":905,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":12},{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:1901407","count":11},{"id":"GO:0045292","count":10}]},{"hash":"955606446519143047","title":"RNA splicing and chromatin regulation","description":"The cluster centers on RNA processing and chromatin-related processes, with strong representation for mRNA splicing via spliceosome (GO:0000398, GO:0048026) and subtelomeric heterochromatin formation, plus regulatory ncRNA-mediated gene silencing. DNA replication appears as a related function, and several stress-response terms suggest broader genome maintenance and cellular signaling connections. Overall, RNA processing coupled with chromatin regulation best explains the dominant GO signals.","confidence":"Medium","size":19,"edges":12,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0048026","count":2}]},{"hash":"1197040202101938561","title":"Prohormone Processing and Secretion","description":"Top GO terms here largely point to the processing and maturation of secreted peptides and hormones\u2014dibasic protein processing, insulin processing, peptide pheromone maturation, and renin secretion\u2014implying a role in the secretory/prohormone pathway. Nerve growth factor production also aligns with secretion of signaling molecules. Some terms are more development- or cholesterol transport\u2013related, which are less directly tied but can involve secretory/endocytic processes. Overall, the cluster appears to group proteins involved in prohormone processing and peptide hormone secretion.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":1},{"id":"GO:0032902","count":1},{"id":"GO:0010989","count":1},{"id":"GO:0007354","count":1},{"id":"GO:0090472","count":1}]},{"hash":"1590398011263295930","title":"TGF-\u03b2/BMP Signaling Regulation","description":"The major GO terms point to regulation of transforming growth factor beta (TGF-\u03b2) and BMP signaling pathways, including cellular response to TGF-\u03b2 stimulus, negative regulation of TGF-\u03b2 receptor signaling, and negative regulation of BMP signaling, with supporting hints from SMAD-related assembly and peptidyl-threonine dephosphorylation. While a couple terms (e.g., photosystem stoichiometry adjustment) appear unrelated (likely annotation noise), the cohesive theme is modulation of TGF-\u03b2/BMP signaling.","confidence":"High","size":18,"edges":28,"triangles":18,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035970","count":5},{"id":"GO:0046827","count":5},{"id":"GO:0080005","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0000173","count":4}]},{"hash":"510431721578780967","title":"Wnt-driven skeletal morphogenesis","description":"The cluster is enriched for skeletal development terms (skeletal system development, embryonic cranial skeleton morphogenesis) and positive regulation of canonical Wnt signaling, suggesting proteins that participate in Wnt-mediated bone formation during development. While there are also general cellular processes (DNA replication, transcription, mitotic cell cycle) present, the prominent theme centers on Wnt signaling guiding skeletal morphogenesis. A few terms related to neural plasticity or metal response appear as secondary associations.","confidence":"High","size":18,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0090263","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0048701","count":4},{"id":"GO:0001501","count":4}]},{"hash":"1142135677464708894","title":"Nuclear RNA processing and transcription regulation","description":"The top GO terms cluster around RNA metabolism\u2014splicing, mRNA maturation/decay, snoRNA and rRNA processing\u2014as well as transcriptional regulation by RNA polymerase II, all core nuclear processes. While there are a couple of broader development and DNA replication terms, the dominant signal is RNA processing and transcription control in the nucleus.","confidence":"High","size":18,"edges":24,"triangles":15,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0000398","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0048701","count":6},{"id":"GO:0071042","count":5}]},{"hash":"2069378608158054141","title":"DNA Replication and Cell Cycle with Translation","description":"The cluster is dominated by nuclear DNA metabolism signals: strong representation of mitotic cell cycle, DNA replication, and DNA-templated transcription. There are also translation initiation/reinitiation terms, suggesting a subset of proteins that connect DNA processing with translation machinery. Hypoxia response and development terms appear less central but indicate broader regulatory roles. Overall, the core theme centers on DNA replication/transcription and cell cycle control, with some translation-related involvement.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0006351","count":5}]},{"hash":"1624697456165457489","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":75,"triangles":197,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0000462","count":4},{"id":"GO:0000472","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0031564","count":2}]},{"hash":"1435033899488672905","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":66,"triangles":142,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006283","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0006369","count":6},{"id":"GO:0006310","count":6},{"id":"GO:0031124","count":6}]},{"hash":"1097630894328449171","title":"ER-Golgi trafficking and ER stress response","description":"The cluster's top terms include ER-to-Golgi vesicle transport and response to ER stress, plus protein targeting to the vacuole, all pointing to intracellular trafficking and ER-associated processing. While there are also terms for metabolism and various signaling/transcription processes, the strongest signals relate to protein sorting between the ER and Golgi and the cellular coping mechanisms for ER stress, supporting a theme around ER-related trafficking and stress responses. Confidence: Medium","confidence":"","size":17,"edges":30,"triangles":18,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0034976","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1136966636147348736","title":"Golgi trafficking and chromosome dynamics","description":"The cluster includes GO terms for COPI coating of Golgi vesicles and kinetochore localization, plus mitotic chromosome movement and alignment, pointing to roles in vesicle trafficking linked to chromosome segregation. Intraciliary transport and GTPase activity regulation further support a theme of coordinated intracellular transport during mitosis and ciliogenesis, despite some sparse terms like dendritic spine development and xenobiotic response. Overall, the core function appears to lie in intracellular transport processes tied to cell division and ciliary function.","confidence":"Medium","size":17,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0048205","count":2},{"id":"GO:0060999","count":2},{"id":"GO:0007079","count":1},{"id":"GO:0035735","count":1}]},{"hash":"133080495769354053","title":"Bacterial lipid biosynthesis and cell envelope component production","description":"This cluster is dominated by fatty acid/medium-chain acyl-CoA metabolism and the biosynthesis of lipopolysaccharide and O-antigen, pointing to lipid metabolism and cell-envelope assembly in bacteria. Additional terms like poly-hydroxybutyrate biosynthesis and retinol metabolic processes broaden to lipid-associated pathways, with antibiotic biosynthesis/response suggesting antimicrobial metabolite production. The mix indicates a lipid-centric, cell-surface biosynthesis theme, despite a few obsolete GO entries. ","confidence":"Medium","size":16,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006633","count":3},{"id":"GO:1902987","count":3},{"id":"GO:0036112","count":3},{"id":"GO:0009243","count":3}]},{"hash":"1098784374332064682","title":"Heat-Induced Protein Folding and Quality Control","description":"Based on GO terms, the strongest signals are heat response, misfolded protein detection, and chaperone-mediated folding/assembly, indicating a proteostasis module active under thermal stress. Other terms (immune signaling, telomere maintenance, and sperm binding) are peripheral and do not define the main function of the cluster. ","confidence":"Medium","size":16,"edges":21,"triangles":11,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":5},{"id":"GO:0002842","count":4},{"id":"GO:0002236","count":4},{"id":"GO:0002368","count":4},{"id":"GO:1904469","count":4}]},{"hash":"1851619574250432930","title":"DNA replication and RNA processing","description":"The cluster combines processes centered on genome maintenance (DNA replication, primer synthesis, and DNA repair including transcription-coupled repair and SOS response) with RNA metabolism (mRNA splicing and export) and ribosome biogenesis, suggesting a core theme of DNA maintenance and gene-expression machinery. A couple of outlier terms (viral process and collagen catabolic process) likely reflect broader or noisy annotations rather than a unifying function. ","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0042273","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0006268","count":3},{"id":"GO:0006283","count":3}]},{"hash":"1953267953968106774","title":"Gene expression and ER\u2013Golgi trafficking","description":"The top terms show translation and transcription, pointing to gene expression, along with vesicle transport between the endoplasmic reticulum and Golgi (and retrograde ER\u2013Golgi transport) and an ERAD-related pathway, indicating a cluster of proteins involved in protein synthesis and the secretory/quality-control pathway. Some stress-response terms appear but are secondary to the core functions. ","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006351","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0030433","count":2}]},{"hash":"369974742269517660","title":"Developmental transcription and ribosome biogenesis","description":"The cluster is heavily enriched for DNA-templated transcription and ribosome biogenesis, with additional development-related terms such as mesoderm formation and dorsal/ventral neural tube patterning. This suggests a shared role in coordinating gene expression and protein production during development, even though other terms (protein targeting, redox homeostasis, stimulus responses) add broader functional context. Overall, the dominant theme points to developmental regulation of transcription and protein synthesis/processing.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0070843","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0031204","count":2}]},{"hash":"9711263212102178","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:1901917","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000447","count":1}]},{"hash":"2061828565721739566","title":"Membrane Transporters and Xenobiotics","description":"The top GO terms are dominated by various transporter activities (amino acid, carbohydrate, lipoprotein, and molybdate transport) and xenobiotic export, suggesting the proteins in this cluster function primarily as membrane transporters handling diverse substrates, with a few outlier terms related to antibiotic response and DNA/RNA processing. This indicates a cohesive theme around transport and xenobiotic management, albeit with some peripheral functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0046618","count":2},{"id":"GO:0042760","count":2},{"id":"GO:0060702","count":2}]},{"hash":"206557956513436534","title":"RNA processing and ribosome biogenesis","description":"This cluster is driven by GO terms for translation initiation/reinitiation, ribosome biogenesis, spliceosome-mediated mRNA splicing, and mRNA modification, suggesting a cohesive group involved in RNA maturation and the assembly of the translational machinery.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0042254","count":3}]},{"hash":"1123211684633615687","title":"Mitotic cell cycle and ubiquitin-mediated proteolysis","description":"This cluster centers on mitotic processes (chromatid cohesion, DNA replication, mitotic cell cycle) and ubiquitin/SUMO regulatory mechanisms (sumoylation, ubiquitin-dependent degradation including K48/K63 linkages, SCF proteasomal pathways, ERAD), suggesting a theme of coordinated cell-cycle progression with tight proteostasis. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007064","count":3},{"id":"GO:0016925","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0030433","count":3}]},{"hash":"1709012642613640022","title":"TGF-beta/BMP signaling regulation","description":"These proteins are enriched for GO terms related to regulation of TGF-beta/BMP signaling, including negative regulation of TGF-beta receptor signaling, negative regulation of BMP signaling, SMAD-related assembly regulation, and peptidyl-threonine dephosphorylation, as well as cellular responses to TGF-beta stimulus. This points to a coherent theme of modulating TGF-beta/BMP signal transduction.","confidence":"High","size":14,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035970","count":5},{"id":"GO:0046827","count":5},{"id":"GO:0080005","count":5},{"id":"GO:0071560","count":5},{"id":"GO:0000173","count":5}]},{"hash":"1663987018673823242","title":"Ubiquitin-regulated NF-kappaB/JNK inflammatory signaling","description":"The GO terms emphasize ubiquitin-dependent protein turnover (autoubiquitination, ubiquitin-protein catabolic processes) and signaling cascades such as TNF-mediated NF-kappaB activation and JNK regulation, suggesting a theme of ubiquitin-mediated control of inflammatory signaling. The presence of V(D)J recombination signals an immune context, supporting a role in immune/inflammatory responses rather than unrelated processes.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0042787","count":6},{"id":"GO:1903762","count":5},{"id":"GO:2000620","count":5}]},{"hash":"1786528123380663500","title":"Amino acid catabolism and central energy metabolism","description":"This cluster centers on core metabolic processes: multiple amino acid catabolic pathways (lysine, threonine, alanine) and energy production via the TCA cycle, plus biosynthetic steps for heme and porphyrinogens. The presence of sphinganine biosynthesis adds a lipid metabolism angle, and regulatory terms like cellular response to insulin and DNA-templated transcription suggest coordination with metabolic regulation. Overall, the proteins seem to form a cohesive metabolic module rather than a single, narrow function.","confidence":"Medium","size":14,"edges":87,"triangles":317,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033512","count":7},{"id":"GO:0006099","count":6},{"id":"GO:0019518","count":5},{"id":"GO:0006571","count":5},{"id":"GO:0032869","count":5}]},{"hash":"1144408268470662910","title":"Spliceosome-Driven RNA Processing and Translation Initiation","description":"This cluster is dominated by GO terms tied to RNA splicing via the spliceosome, small-subunit processome assembly, and mRNA modification, along with formation of the translation preinitiation complex. Together these signals point to a core role in RNA maturation and the initiation of translation, with some peripheral links to transcriptional regulation. Therefore, a label highlighting spliceosome-mediated RNA processing and early translation steps is appropriate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1903586","count":1}]},{"hash":"192386414628258369","title":"Translation machinery and ribosome dynamics","description":"Most top GO terms cluster around translation and ribosome function (translation, initiation, termination, elongation, ribosome disassembly, and selenocysteine incorporation), with links to translational regulation. mRNA turnover terms (deadenylation-dependent decay, nuclear-transcribed mRNA catabolic process) further tie into translation control. Overall, this cluster appears focused on protein synthesis machinery and its regulation.","confidence":"High","size":13,"edges":23,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0006413","count":6},{"id":"GO:0014009","count":5},{"id":"GO:0046677","count":5},{"id":"GO:2000767","count":5}]},{"hash":"1592583653089016085","title":"Cell Wall and Polysaccharide Biosynthesis","description":"The top GO terms cluster around synthesis and organization of cell wall components and related polysaccharides (fungal-type cell wall biogenesis, cell wall mannoprotein biosynthesis, lipopolysaccharide/LPS core and lipid A biosynthesis, UDP-glucose metabolism), indicating a shared function in constructing cell wall polysaccharides. Growth-related terms like cell division and ribosome biogenesis appear as auxiliary processes during proliferation, and antibiotic response may relate to cell wall stress. Overall, the dominant theme is cell wall and polysaccharide biosynthesis.","confidence":"Medium","size":13,"edges":14,"triangles":3,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0045226","count":2},{"id":"GO:0000032","count":2}]},{"hash":"81558270420503352","title":"Nuclear Chromatin Assembly and Remodeling","description":"The top GO terms point to chromatin assembly and organization in the nucleus, including CENP-A\u2013containing chromatin assembly, DNA replication\u2013dependent chromatin assembly, transcription initiation\u2013coupled chromatin remodeling, and heterochromatin formation. These collectively suggest a cohesive role in chromatin dynamics and nuclear regulation, with supporting hints from dosage compensation and nucleolar transcription-related regulation.","confidence":"High","size":13,"edges":17,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":5},{"id":"GO:0061641","count":4},{"id":"GO:0030466","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0007549","count":3}]},{"hash":"2077900344671834094","title":"Diverse substrate membrane transporters","description":"Top GO terms point to transmembrane transport of diverse substrates (arabinose, sodium, potassium, nitrate, carbohydrate, vitamin) and related vesicular loading, suggesting the cluster comprises membrane transport proteins with broad substrate specificity rather than a single substrate.","confidence":"Medium","size":13,"edges":14,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0035461","count":1}]},{"hash":"1268557066426134541","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1}]},{"hash":"1521837688302749991","title":"Ribosome Biogenesis and Translation; Cell Cycle","description":"The top GO terms cluster around ribosome biogenesis, ribosomal subunit biogenesis, translation, and cytoplasmic translation, indicating a core role in protein synthesis. Additional terms about cell division and the cell cycle suggest a link between the translation machinery and cellular proliferation, with stress-response terms playing a secondary role.","confidence":"High","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0006412","count":5},{"id":"GO:1901001","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000747","count":4}]},{"hash":"93511808022788189","title":"Ribosome biogenesis and rRNA maturation","description":"The dominant GO terms center on ribosome biogenesis, translation, and maturation of SSU/LSU rRNA, indicating proteins involved in assembling the ribosome and processing rRNA. A few terms about transcription and antibiotic response are present but appear secondary to ribosome-related processes.","confidence":"High","size":12,"edges":26,"triangles":32,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0006412","count":5},{"id":"GO:0000462","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3}]},{"hash":"482720912625614405","title":"Ribosome biogenesis and translation","description":"The cluster shows strong representation of translation and ribosome-related GO terms (translation, cytoplasmic translation, ribosome biogenesis, small subunit biogenesis, LSU rRNA maturation), indicating a shared function in ribosome assembly and protein synthesis. Some cell-cycle/division terms are present but likely reflect growth coordination with translation.","confidence":"High","size":12,"edges":9,"triangles":1,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0007049","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000463","count":2}]},{"hash":"724464969869953861","title":"ER-Golgi-Lysosome Vesicle Trafficking","description":"The GO terms point to intracellular transport and vesicle movement across ER, Golgi, endosomes, and lysosomes, including ER-to-Golgi vesicle transport and endosome-to-lysosome pathways, plus lysosomal membrane organization. Additional signals from lipoprotein assembly and small GTPase\u2013mediated signaling support a vesicle trafficking/dynamics theme. This suggests the cluster represents components of intracellular vesicle transport machinery.","confidence":"High","size":12,"edges":8,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":3},{"id":"GO:0034379","count":3},{"id":"GO:0097212","count":3},{"id":"GO:1902824","count":3},{"id":"GO:1902953","count":3}]},{"hash":"890806196295482704","title":"Mitotic spindle and neuronal microtubule dynamics","description":"This cluster is dominated by GO terms for mitotic spindle assembly, centrosome separation, chromosome alignment, and cytokinesis, with several microtubule-related activities like plus-end depolymerization and kinetochore interactions, pointing to microtubule dynamics during cell division. The inclusion of terms about anterograde dendritic transport of neurotransmitter receptor complexes and cerebellar granular layer organization suggests a broader microtubule-related role in neuronal transport and structure. Taken together, the shared theme is microtubule dynamics across mitosis and neuronal processes.","confidence":"High","size":12,"edges":21,"triangles":11,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":4},{"id":"GO:0007100","count":4},{"id":"GO:0021685","count":3},{"id":"GO:0070462","count":3},{"id":"GO:0099607","count":3}]},{"hash":"249056356439384771","title":"ER-Golgi Trafficking and Protein Processing","description":"The GO terms cluster around components and processes of the secretory pathway, including protein localization to the Golgi, transmembrane transport, and ER stress response, with hints of redox regulation via deglutathionylation. This points to proteins involved in maturation and trafficking through the ER-Golgi network, rather than a single tight function. Some obsolete terms and a few outliers reduce specificity, so the label is plausible but only moderately confident.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0000042","count":3},{"id":"GO:0034976","count":3},{"id":"GO:0097327","count":2}]},{"hash":"1207752671748710745","title":"DNA Replication and Stress Response","description":"The cluster\u2019s top GO terms cluster around DNA replication (DNA synthesis and unwinding) and DNA damage/stress responses (response to heat, SOS response, cisplatin response), suggesting a core theme of replication machinery tied to damage repair. A few terms related to embryonic development and extracellular matrix are present but appear secondary or incidental, possibly reflecting multifunctional proteins or broader annotations. ","confidence":"Medium","size":12,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0009408","count":4},{"id":"GO:0006268","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0001701","count":4}]},{"hash":"1313284306363411438","title":"Neural development and apoptotic signaling","description":"The proteins cluster around neural differentiation and synaptic activity, with strong ties to apoptosis regulation through Wnt signaling (axonogenesis, CNS neuron development, excitatory postsynaptic potential, apoptotic process), while other terms like innate immunity and nuclear periphery localization appear as side themes. Overall, the dominant theme is neuronal development linked to programmed cell death pathways.","confidence":"Medium","size":12,"edges":12,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000751","count":3},{"id":"GO:0032092","count":3},{"id":"GO:0007409","count":3},{"id":"GO:1900086","count":3},{"id":"GO:0044337","count":3}]},{"hash":"1720746892554991698","title":"DNA damage response and translation regulation","description":"The cluster shows enrichment for translation-related processes (translation, positive regulation of cytoplasmic translation) alongside DNA damage and cell-cycle related terms (cell division, DNA repair, regulation of apoptotic process, negative regulation of DNA binding) and protein homeostasis (protein deubiquitination). This suggests a coordinated response that links protein synthesis capacity with genome maintenance and cell fate decisions under stress, with some stress- and hormone-related signals evident (dexamethasone stimulus, antibiotic response). The mix points to a theme of stress-induced regulation of translation and genome stability pathways.","confidence":"Medium","size":12,"edges":15,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006281","count":1},{"id":"GO:0071549","count":1},{"id":"GO:0042981","count":1}]},{"hash":"1789211685730961236","title":"Ribosome Biogenesis and Cell Division","description":"The top GO terms center on translation, cytoplasmic translation, and ribosome biogenesis, with several terms for cell cycle, cell division, and septum assembly. This points to a cohesive cluster of genes involved in protein synthesis and the machinery that governs cell growth and division.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0007049","count":3},{"id":"GO:1901001","count":2},{"id":"GO:0042254","count":2}]},{"hash":"362356968478766737","title":"DNA replication and chromatin maintenance","description":"The cluster centers on genome maintenance: multiple GO terms relate to replication (initiation, elongation, MCM complex assembly) and repair (break-induced replication), alongside chromatin regulation (heterochromatin formation, telomere silencing). A meiotic recombination nodule term also fits this theme, suggesting proteins involved in coordinating replication, repair, and chromatin state. Some terms like root meristem growth or xenobiotic response may reflect broader regulatory roles or annotation noise rather than a core function of the cluster.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0000727","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0042140","count":5},{"id":"GO:0006343","count":5},{"id":"GO:0072689","count":5}]},{"hash":"912289437704570160","title":"Developmental trafficking and signaling","description":"The cluster centers on intracellular logistics and signaling tied to development: ER-to-Golgi transport, intraflagellar transport and ciliogenesis, spindle orientation, and GTPase regulation all point to coordinated trafficking and cytoskeletal rearrangements during development (brain and spermatid formation). Additional terms like transcription, autophagy, and synaptic target recognition reflect broader cellular organization that supports developmental processes. Overall, trafficking-related processes are the unifying theme linking these functions.","confidence":"Medium","size":12,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007420","count":2}]},{"hash":"969531069168497318","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000466","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0036265","count":3}]},{"hash":"2017114513859718040","title":"Unknown","description":"The top GO terms span very different biology: sperm capacitation and skeletal development suggest reproduction and morphogenesis, while mRNA splicing/polyadenylation points to RNA processing, and vesicle transport plus membrane potential hints at cellular trafficking and excitability. With no clear, unified function linking these terms and no network edges, there isn\u2019t a cohesive theme to name a specific cluster here.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0060081","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3}]},{"hash":"1777563773608622428","title":"Neuronal signaling and development","description":"The cluster contains clear neuronal-related terms such as axonogenesis and excitatory postsynaptic potential, pointing to neuronal development and synaptic signaling. Additional signals include growth factor response and tyrosine autophosphorylation, and while there are broader signaling and immune terms (e.g., Wnt signaling, innate immune response), the strongest coherent theme centers on neuronal communication and development. This justifies a label focused on neuronal signaling with development aspects, though the presence of non-neuronal GO terms lowers the overall certainty.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035729","count":2},{"id":"GO:0048544","count":2},{"id":"GO:0000751","count":1},{"id":"GO:0032092","count":1},{"id":"GO:0007409","count":1}]},{"hash":"1105416724908121529","title":"Calcium signaling and contraction in skeletal muscle","description":"This cluster centers on calcium dynamics in muscle cells, with terms about ER/SR calcium regulation, calcium import into the sarcoplasmic reticulum, calcium-dependent exocytosis, and modulation of fast-twitch muscle fiber contraction and relaxation, pointing to a cohesive theme of calcium handling driving skeletal muscle function. Some biosynthetic GO terms appear incidental rather than core to the cluster.","confidence":"Medium","size":12,"edges":38,"triangles":56,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0051479","count":2},{"id":"GO:0032470","count":2},{"id":"GO:0045299","count":2},{"id":"GO:0009103","count":2}]},{"hash":"461859211280479940","title":"Redox Homeostasis and Oxidative Stress Response","description":"The cluster\u2019s top GO terms are dominated by redox-related processes: cellular redox homeostasis, oxidant detoxification, oxidative stress response, and deglutathionylation. This suggests the proteins in this group mainly function to maintain redox balance and detoxify reactive species. A few terms touch on DNA replication and cell cycle, which may reflect replication stress responses under oxidative conditions, but the redox-related terms are the strongest signal for the cluster\u2019s theme.","confidence":"High","size":11,"edges":8,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":3},{"id":"GO:0009263","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0071473","count":2},{"id":"GO:0098869","count":2}]},{"hash":"2141768768072544569","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1904571","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0042254","count":1},{"id":"GO:1900745","count":1}]},{"hash":"658976062412991265","title":"Oxidative Stress and Hormone Signaling","description":"The top GO terms point to stress-responsive pathways (response to hydrogen peroxide, apoptotic process) together with hormone-related signaling (peptide hormone stimulus, cellular response to cAMP, phosphatidylinositol signaling). A few terms also touch xenobiotic response and mRNA stability, suggesting a general stress and signaling theme rather than a single, narrow function. The absence of edges indicates no observed direct interactions in this set. Thus, a label emphasizing oxidative stress responses and hormone signaling best captures the cluster\u2019s unifying theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0070301","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0071375","count":4},{"id":"GO:0043488","count":3},{"id":"GO:0046856","count":3}]},{"hash":"1386148589121936952","title":"Mitochondrial transporters and energy regulation","description":"The cluster centers on mitochondrial metabolite transport and energy production, with GO terms for ADP/ATP transport, thiamine pyrophosphate transport, deoxynucleotide transport, magnesium export from mitochondrion, and mitochondrial ATP transmembrane transport, all pointing to inner-membrane transport supporting ATP generation. Additional terms like adaptive thermogenesis, response to fatty acids, and cellular response to insulin stimulus suggest linkage to metabolic signaling and energy homeostasis, reinforcing a cohesive theme of mitochondrial energy regulation.","confidence":"High","size":11,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990845","count":2},{"id":"GO:0030302","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0015866","count":2},{"id":"GO:0032869","count":2}]},{"hash":"35910774595718754","title":"Ribosome biogenesis and translation initiation control","description":"Top terms indicate a cohesive theme around formation of the translation preinitiation complex, regulation of translational initiation, and SSU-rRNA maturation, pointing to ribosome assembly and translation control as the cluster\u2019s core function. Peripheral terms such as cell proliferation and chromatin regulation likely reflect secondary roles or pleiotropy rather than the main theme.","confidence":"High","size":11,"edges":15,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000462","count":2}]},{"hash":"671403312103182513","title":"Viral Translation Initiation and Reinitiation","description":"The cluster is dominated by GO terms for translation initiation, preinitiation complex formation, translation reinitiation, and IRES-dependent viral translation, pointing to proteins involved in initiating or restarting translation, particularly in viral contexts. A minority of terms touch RNA processing or ncRNA-mediated silencing, but the core signal is viral translation control.","confidence":"High","size":11,"edges":9,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075522","count":3}]},{"hash":"429965698467197029","title":"ER stress\u2013linked translation and protein trafficking","description":"The Top Terms show a thread around translation regulation in response to endoplasmic reticulum stress (positive regulation of translation initiation in ER stress) and related translation processes (translational frameshifting, tRNA import into the nucleus). Additional terms point to protein trafficking and processing (regulation of nuclear export, mitochondrial targeting), with redox homeostasis indicating a broader stress-adaptation context. Together these suggest a cluster centered on how cells adjust protein synthesis and trafficking under stress, especially ER-related stress. ","confidence":"Medium","size":11,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:1900035","count":2},{"id":"GO:0035719","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0046825","count":2}]},{"hash":"1964136625433811835","title":"RNA processing and translation initiation machinery","description":"This cluster centers on RNA metabolism and the assembly/ regulation of the translation apparatus: mRNA modification and stabilization, spliceosome-mediated splicing, formation of the translation preinitiation complex, and regulatory aspects of translational initiation, plus small-subunit processome assembly and even viral termination-reinitiation contexts. Taken together, the common theme is RNA processing coupled to initiation of translation, rather than a single linear pathway.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0075525","count":2},{"id":"GO:1903586","count":2},{"id":"GO:0031047","count":2}]},{"hash":"450983511787447247","title":"Cell Cycle Transcriptional Regulation","description":"GO terms cluster around transcriptional control (DNA-templated transcription; negative regulation of transcription by RNA polymerase II) and cell cycle processes (cell cycle; negative regulation of G0 to G1 transition; G1 DNA damage checkpoint signaling; homologous chromosome segregation), with chromatin-related modification (histone H3-K27 methylation) contributing to transcriptional regulation during the cycle. This supports a cohesive theme of transcriptional regulation tied to cell cycle progression and chromatin state.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0070317","count":1}]},{"hash":"2187314036204048072","title":"RNA processing and transcription regulation","description":"Based on GO terms centered on alternative mRNA splicing via spliceosome, regulation of mRNA splicing, and termination of RNA Pol II transcription, the cluster appears to organize around RNA maturation and transcription control. A few terms about ESCRT-mediated viral budding, symbiont entry, and plant histogenesis may reflect peripheral annotations or multifunctional proteins rather than a single cohesive function.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0006379","count":1},{"id":"GO:0039702","count":1},{"id":"GO:0051533","count":1}]},{"hash":"502489165093189253","title":"RNA processing and translation initiation regulation","description":"The proteins are enriched for spliceosome-related terms (mRNA splicing, spliceosomal conformational changes) and for formation of the translation preinitiation complex and regulation of translational initiation, pointing to a cohesive role in RNA processing and control of protein synthesis. Additional terms on protein modification (K11-linked deubiquitination, deneddylation) and stress responses (IRE1-mediated UPR) plus exosomal secretion further suggest involvement in proteostasis and cellular stress signaling. ","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000338","count":1},{"id":"GO:1903894","count":1},{"id":"GO:0035871","count":1},{"id":"GO:0001731","count":1}]},{"hash":"510449107061603052","title":"Unknown","description":"The terms span signaling, energy metabolism, protein turnover and assembly, peptide processing, and even viral processes, with no clear single function tying the cluster together. This diversity makes a cohesive, specific label difficult.","confidence":"","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0045861","count":2},{"id":"GO:0032461","count":2},{"id":"GO:0010815","count":2}]},{"hash":"1628759226224689909","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms point to ribosome production and function: ribosome biogenesis, cytoplasmic translation, and ribosomal subunit assembly, plus SRP-dependent cotranslational targeting to membrane, suggesting a cohesive group of ribosome-related proteins. Occasional transcription-related terms and a general interleukin-4 response appear but are limited and likely represent annotation noise or multifunctionality; the primary signal remains ribosome-related.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0006614","count":1}]},{"hash":"1358399834310115090","title":"Chromatin remodeling and nucleosome dynamics","description":"This cluster is dominated by GO terms related to nucleosome assembly/disassembly and histone modification (e.g., nucleosome assembly/disassembly, histone acetylation regulation, sperm DNA decondensation), suggesting proteins that function in chromatin remodeling and DNA packaging during cell cycle or development, with additional but related signals to microtubule-related aspects of cell division.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006337","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0071442","count":1},{"id":"GO:2000035","count":1}]},{"hash":"1853760736814607310","title":"Membrane Transporters (various substrates)","description":"The top GO terms are all about transmembrane transport of diverse substrates (bicarbonate, oxalate, chloride, sulfate, fructose, L-aspartate, etc.), plus related membrane-potential regulation and transport-influenced processes (gastric acid secretion, sperm capacitation). This points to a cluster of membrane transporter proteins with broad substrate specificity rather than a single, uniform function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015701","count":1},{"id":"GO:0007605","count":1},{"id":"GO:0042391","count":1},{"id":"GO:0089712","count":1},{"id":"GO:0019532","count":1}]},{"hash":"1261519446995037047","title":"Aminoacyl-tRNA Synthetases and Translation","description":"Based on the GO terms, several proteins are involved directly in tRNA charging (methionyl-, leucyl-, valyl-, isoleucyl-tRNA aminoacylation) and there is a general translation term, indicating association with the protein synthesis machinery. The other terms (e.g., heat response, prostate gland development) are minor and likely incidental. The absence of edges reinforces a functional grouping around translation rather than signaling networks.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0007286","count":1},{"id":"GO:0033674","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0006431","count":1}]},{"hash":"1539028683278311890","title":"Ribosome biogenesis and translation","description":"The GO profile is dominated by ribosome-related processes: translation, ribosome biogenesis, small subunit assembly, and maturation of SSU rRNA, indicating proteins involved in ribosome assembly and protein synthesis. The presence of responses to antibiotic and cycloheximide suggests links to translation inhibition, reinforcing a ribosome/translation-focused theme. Some unrelated terms (e.g., spermatid differentiation) appear but do not override the core ribosome/translation signal.","confidence":"High","size":10,"edges":16,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000028","count":1}]},{"hash":"318079182043587621","title":"Ribosome biogenesis and RNA methylation","description":"The terms cluster around ribosome assembly and maturation (ribosome biogenesis, small subunit biogenesis, SSU-rRNA maturation, small subunit assembly) and RNA modification (rRNA and tRNA methylation, protein methylation), with translation appearing as an associated process. This points to a functional group focused on building ribosomes and modifying their RNA components, justifying the label. ","confidence":"High","size":10,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006479","count":2},{"id":"GO:0070476","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0030490","count":1}]},{"hash":"232498575602088156","title":"Actin cytoskeleton remodeling in muscle and neurons","description":"The cluster centers on actin dynamics: Arp2/3-mediated actin nucleation, actomyosin contractility, and postsynaptic actin organization, alongside muscle fiber development and mesenchyme migration. These terms point to coordinated remodeling of the actin cytoskeleton during muscle and neural development and cell movement, with neural development terms (substantia nigra) supporting a broader neuronal context. Some atypical terms (obsolete histone acetylation) likely reflect database noise rather than core function.","confidence":"High","size":10,"edges":28,"triangles":41,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":6},{"id":"GO:0034314","count":6},{"id":"GO:0043982","count":6},{"id":"GO:0021762","count":6},{"id":"GO:0043981","count":6}]},{"hash":"313565933994323540","title":"Microtubule dynamics and mitotic spindle organization","description":"Top terms include multiple microtubule depolymerization processes (cytoplasmic, axonemal, plus-end), mitotic spindle functions (kinetochore attachment, metaphase alignment), and regulation of microtubule-based processes, plus dendritic transport of receptor complexes. A few terms touch cerebellar granular layer structure, hinting at neuronal roles that still rely on microtubule networks. Together these point to a cohesive theme of microtubule organization governing both cell division and neuronal transport.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021685","count":1},{"id":"GO:0070462","count":1},{"id":"GO:0099607","count":1},{"id":"GO:0032886","count":1},{"id":"GO:0098971","count":1}]},{"hash":"615876420540459267","title":"Unknown","description":"The GO terms span diverse processes\u2014from cell cycle and division to neural development and basic metabolic activities\u2014offering no single cohesive function to bind the cluster. This functional heterogeneity makes a reliable, specific label unlikely, so the appropriate name is Unknown with no confidence.","confidence":"","size":10,"edges":11,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0007601","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0009399","count":2},{"id":"GO:0006814","count":2}]},{"hash":"1638233263256725269","title":"Nuclear DNA Replication, Transcription, and Repair","description":"Top GO terms indicate a focus on DNA-templated transcription, DNA replication, and DNA repair, with mitotic cell cycle as a related process. This suggests the proteins function together in nuclear DNA metabolism and genome maintenance during cell division. Some secondary terms (vesicle transport, ATP metabolism) appear less central and may reflect broader cellular roles or annotation noise.","confidence":"High","size":10,"edges":9,"triangles":1,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0007118","count":3}]},{"hash":"552975891959804096","title":"Ribosome biogenesis and RNA modification","description":"The top terms cluster around ribosome-related processes: rRNA base methylation, maturation of LSU rRNA, ribosome biogenesis, and cytosolic ribosome assembly, along with tRNA wobble methylation and regulation of mitochondrial translation. This suggests a core theme of ribosome assembly and RNA modification that underpins translation, with a few other terms (e.g., transcription regulation, insulin response) that appear ancillary. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0000463","count":1},{"id":"GO:1902626","count":1}]},{"hash":"173072169295207945","title":"Nuclear transcription and RNA processing","description":"The top GO terms point to nuclear processes such as DNA-templated transcription, transcription termination, splicing regulation, and mRNA turnover/polyadenylation, with additional signals for DNA replication and genomic maintenance. This pattern suggests a cluster of proteins involved in gene expression control and RNA processing within the nucleus, rather than a single cytosolic pathway. Some developmental and neural terms may reflect broad roles in development but do not override the central theme of transcription and RNA processing.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0060291","count":3}]},{"hash":"1104054765625605191","title":"Vitamin biosynthesis and aromatic compound metabolism","description":"The top GO terms include menaquinone biosynthesis, biotin biosynthesis, antibiotic biosynthetic processes, and several aromatic compound degradation pathways (3-phenylpropionate, stilbene, beta-ketoadipate), along with oxidant detoxification. While a term like strigolactone response is plant-specific, the cluster overall centers on biosynthesis of vitamins and breakdown of aromatic compounds with redox-related processes, suggesting a cohesive theme of vitamin and aromatic metabolism with redox balance.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0046839","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0055114","count":4}]},{"hash":"1225477384912233962","title":"Neuronal synaptic exocytosis and dendrite morphogenesis","description":"The GO terms converge on neurotransmitter release and synaptic signaling (calcium-dependent exocytosis and excitatory postsynaptic potential) along with neuronal development and dendritic structure (hippocampus development, dendrite morphogenesis). Rac signaling ties to cytoskeletal changes needed for dendritic growth, while trafficking terms reflect localization of synaptic components (Golgi to endosome, vacuole targeting). This combination suggests a cluster of proteins involved in synaptic maturation and dendrite architecture in neurons.","confidence":"High","size":10,"edges":5,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045956","count":4},{"id":"GO:0021766","count":4},{"id":"GO:0051291","count":4},{"id":"GO:0060079","count":3},{"id":"GO:0006895","count":3}]},{"hash":"24762983685732585","title":"Diverse Ion and Small Molecule Membrane Transport","description":"The proteins are linked by transmembrane transport activity across a wide range of substrates, from ions like Na+, K+, and nitrate to small metabolites and even neurotransmitter loading. This suggests a general membrane transporter theme rather than a specific pathway.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0035461","count":1}]},{"hash":"41427948800695102","title":"RNA processing and translation regulation","description":"The proteins cluster around RNA metabolism and translation control: mRNA modification, spliceosome assembly and alternative splicing, formation of the translation preinitiation complex, regulation of translational initiation, and mRNA stabilization. This points to a coherent group involved in RNA processing and control of translation.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0075525","count":2},{"id":"GO:1903586","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1549844106747133679","title":"ER stress\u2013linked translation control","description":"The top GO terms point to translation and protein synthesis regulation under stress: positive regulation of translation initiation in response to endoplasmic reticulum stress; translational frameshifting; tRNA import into the nucleus; and regulation of protein export from the nucleus hint at coordinated cellular control of protein production. Additional terms like cellular redox homeostasis and response to hormones suggest an overarching stress-response context, though a few terms (mesoderm formation) appear less connected. Overall, the data support a label around translation control during ER-associated stress.","confidence":"Medium","size":10,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:1900035","count":2},{"id":"GO:0035719","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0046825","count":2}]},{"hash":"565960544692101650","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":7,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0007494","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2}]},{"hash":"61248902381842466","title":"Nuclear Transport and Stress-Responsive Translation","description":"The GO terms point to translation control (translation initiation under ER stress, translational frameshifting) and nucleus\u2013cytoplasm trafficking (tRNA import into nucleus, regulation of protein export from nucleus). Together they imply a cluster focused on coordinating protein synthesis with nuclear transport and stress signaling. A few terms (viral process, mesoderm formation) are peripheral, but the core theme is translation regulation linked to nuclear trafficking and cellular stress.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:1900035","count":2},{"id":"GO:0035719","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0046825","count":2}]},{"hash":"1943228942400794395","title":"Unknown","description":"The Top Terms span diverse processes (proton transmembrane transport, vacuolar acidification, seed growth regulation, various negative regulations, RNA splicing, innate immune signaling, and osmotic stress) with no single cohesive theme. There are only single-term hits and no edges linking functions, so a unifying biology for this cluster isn\u2019t evident. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":1},{"id":"GO:0007035","count":1},{"id":"GO:1903770","count":1},{"id":"GO:0080113","count":1},{"id":"GO:1903086","count":1}]},{"hash":"1845613617628318519","title":"Mitochondrial redox balance and cytochrome assembly","description":"The top GO terms point to redox processes and detoxification (oxidation-reduction, redox homeostasis, cellular oxidant detoxification) and to cytochrome complex assembly, which together suggest mitochondrial oxidative metabolism and maintenance of redox balance. Some terms related to extracellular matrix or immune functions appear as minor outliers, but the dominant signal supports a mitochondrial redox-focused cluster.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0017004","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0006351","count":3}]},{"hash":"267637625671228745","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:0042776","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0031124","count":1},{"id":"GO:1902775","count":1}]},{"hash":"1324399761897846540","title":"Ribosome biogenesis and RNA processing","description":"This cluster centers on RNA metabolism and ribosome assembly, with terms like translation, mRNA export from the nucleus, snoRNP/snoRNA-related modifications, snRNA pseudouridine synthesis, and ribosome biogenesis, suggesting a cohesive role in producing and preparing ribosomes for translation. Some outliers (meiotic cohesion, p38MAPK regulation) may reflect broader cellular contexts but do not override the dominant RNA-processing/ribosome theme.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051754","count":2},{"id":"GO:1904571","count":1}]},{"hash":"738746960998115838","title":"Translation initiation and ribosome biogenesis","description":"The top GO terms cluster around translation initiation and ribosome assembly (formation of translation preinitiation complex; translation reinitiation; ribosome biogenesis), suggesting these proteins participate in protein synthesis machinery. While other terms pertain to development and immune processes, the dominant signal is translation-related. ","confidence":"Medium","size":9,"edges":8,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007369","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1493392921098473958","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071039","count":1},{"id":"GO:0000460","count":1},{"id":"GO:0071031","count":1},{"id":"GO:0071030","count":1},{"id":"GO:0014033","count":1}]},{"hash":"1865243993775547727","title":"Epigenetic Transcription Regulation","description":"Top GO terms indicate regulation of transcription by RNA polymerase II (both negative and positive) and chromatin-associated processes (localization to chromatin, chromatin remodeling, histone methylation). This pattern points to proteins involved in epigenetic control of transcription rather than a single downstream pathway. Some non-core terms (liver regeneration, oligodendrocyte differentiation, cellular senescence) may reflect broader developmental and cellular contexts, but they do not outweigh the chromatin/transcription theme.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0071168","count":2},{"id":"GO:0045944","count":2},{"id":"GO:2000616","count":2},{"id":"GO:0043044","count":2}]},{"hash":"1047919010287652930","title":"Translation initiation and reinitiation regulation","description":"This cluster shows a clear enrichment for translation-related terms, notably translation preinitiation complex formation and translation reinitiation, suggesting a focus on regulating translation initiation and reinitiation. A secondary signal is proteasomal ubiquitin-dependent protein catabolic process, indicating a link to protein turnover that can accompany translation control. The presence of chromatin regulation and DNA repair terms appears less connected to the main theme, so the label centers on translational control (initiation/reinitiation) with some proteostasis context. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0032436","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000338","count":1},{"id":"GO:0075525","count":1}]},{"hash":"1481334625462298122","title":"DNA replication and chromosome segregation","description":"The top terms cluster around DNA replication and recombination, including DNA-templated replication, general DNA replication, replication fork progression, and chromosome separation, with additional meiotic recombination resolution and mitotic DNA replication terms. A single translation term is present but does not dominate the theme; overall, the proteins appear involved in DNA replication and chromosome maintenance during cell division.","confidence":"High","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0051304","count":1},{"id":"GO:1902969","count":1}]},{"hash":"335774850693184318","title":"Neuronal Development and Dendrite Morphogenesis","description":"The cluster is dominated by terms like CNS neuron development (GO:0021954) and dendrite morphogenesis (GO:0048813), which point to neuronal differentiation and dendritic structuring. Other terms such as DNA-templated transcription, response to wounding, and cellular response to peptide hormone stimulus appear peripheral but do not override the neural-development theme. Consequently, Neuronal Development and Dendrite Morphogenesis best describes the cluster's core function.","confidence":"High","size":9,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007118","count":2},{"id":"GO:0021954","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1954650756458372499","title":"Ribosome and Mitochondrial Translation","description":"This cluster is dominated by GO terms tied to ribosome function and protein synthesis, including rRNA processing, ribosomal large subunit assembly, translation, and mitochondrial translation with related electron transport. While a few terms (neuron development, granulocyte differentiation, cAMP response, isoleucine catabolism) are less connected, the core theme clearly centers on the translation machinery in both cytosolic and mitochondrial contexts.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":2},{"id":"GO:0006415","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0006412","count":1}]},{"hash":"876588811740790053","title":"Ubiquitination/SUMOylation and Autophagy","description":"Proteins in this cluster are enriched for ubiquitination and SUMOylation (including urmylation), indicating a heavy focus on post-translational modification. Autophagy-related terms (mitophagy, CVT, and piecemeal microautophagy) point to selective protein and organelle turnover. The presence of growth signaling (Wnt pathway, cell growth) and a defense term suggests these modified proteins may connect stress responses to growth regulation via autophagy and protein turnover. Overall, the cluster seems centered on post-translational modification and autophagy with links to growth signaling.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0016055","count":2}]},{"hash":"2289198871681879608","title":"Actin dynamics and vesicle trafficking","description":"The cluster is driven by strong signals for actin cytoskeleton regulation (positive regulation of stress fiber and actin cable assembly, and actin filament polymerization) together with vesicle transport processes (regulation of synaptic vesicle exocytosis and COPII-coated vesicle budding). This points to a shared function in coordinating actin remodeling with vesicle trafficking/secretory pathways. Other terms like ribosome export and cell cycle appear less central to the dominant theme. ","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051496","count":2},{"id":"GO:0090338","count":2},{"id":"GO:0030838","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0090114","count":2}]},{"hash":"1303247072949080994","title":"ECM assembly and skin/cuticle morphogenesis","description":"The dominant terms describe extracellular matrix organization and tissue formation\u2014collagen fibril organization, cartilage condensation, skin morphogenesis, and cuticle development\u2014along with cell adhesion, all pointing to ECM remodeling and morphogenesis. A few terms (complement activation, oxidative stress response) are less central but may reflect broader cellular contexts. ","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":2},{"id":"GO:2000534","count":1},{"id":"GO:0006958","count":1},{"id":"GO:0030199","count":1},{"id":"GO:0001502","count":1}]},{"hash":"2219305699146678234","title":"Vesicle trafficking and secretion","description":"The terms cluster around vesicle targeting, vacuolar fusion and autophagosome docking, plus general protein transport and secretion-related processes (mucus secretion, neutrophil degranulation). This points to a cohesive module of intracellular vesicle trafficking, membrane docking/fusion, and regulation of protein targeting to vacuolar membranes, with some ties to secretory pathways.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006903","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0043312","count":1},{"id":"GO:0016240","count":1},{"id":"GO:0070254","count":1}]},{"hash":"1664834052477736920","title":"Nutrient-linked transcription and ribosome biogenesis","description":"This cluster is driven by strong signals for ribosome biogenesis and DNA-templated transcription, with additional associations to nutrient signaling (glucose-mediated pathways) and responses to nutrients, suggesting growth- and metabolism-regulated nuclear processes. The presence of related terms touching cell cycle checkpoints, stress responses, and viral mRNA export reflects broader nuclear regulation but the dominant theme centers on transcriptional activity and ribosome production under nutrient conditions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007584","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0070317","count":3}]},{"hash":"284449159410467012","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0071629","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0051131","count":2}]},{"hash":"907100056079848661","title":"Stress-Driven Translation and Nuclear Transport","description":"The top GO terms point to translation regulation in stress contexts (ER stress\u2013related translation initiation, translational frameshifting) along with nucleocytoplasmic trafficking (tRNA import into nucleus, regulation of nuclear protein export). While a few terms relate to development, the dominant signals are stress-responsive translation control and nuclear transport. Confidence: Medium","confidence":"","size":9,"edges":9,"triangles":1,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1900035","count":3},{"id":"GO:0035719","count":3},{"id":"GO:0097428","count":3},{"id":"GO:0046825","count":3},{"id":"GO:0036494","count":3}]},{"hash":"2033693050355402906","title":"RNA silencing and plant immunity","description":"This cluster centers on RNA interference and RNA processing processes (miRNA processing, dsRNA-to-siRNA, regulatory ncRNA-mediated post-transcriptional gene silencing) and includes plant-specific defense terms (defense response to Gram-negative bacteria, plant-type hypersensitive response). While some terms touch broader RNA metabolism and development, the strongest signal is RNA-mediated regulation coupled with plant defense, suggesting proteins involved in RNA silencing pathways that modulate immune responses in plants.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0050829","count":1},{"id":"GO:0031053","count":1},{"id":"GO:0045071","count":1},{"id":"GO:2000011","count":1}]},{"hash":"1355810359605397476","title":"Spliceosome Assembly and mRNA Splicing","description":"The cluster is strongly enriched for events related to the spliceosome and RNA processing, including spliceosomal snRNP assembly, mRNA splicing via the spliceosome, and regulation of alternative mRNA splicing. While there are occasional cell cycle-related terms, the dominant signal points to a cohesive RNA splicing module, suggesting these proteins function together in RNA processing. ","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":2},{"id":"GO:2000825","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0006279","count":1}]},{"hash":"1966186586013439091","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0070317","count":1}]},{"hash":"400478041208698634","title":"Xenobiotic and LPS-Triggered Immune Response","description":"The top GO terms cluster around responses to toxic substances and xenobiotics, including lipopolysaccharide and cocaine exposure, plus immune signaling terms (T cell differentiation and T cell receptor signaling), suggesting a theme of xenobiotic stress response linked to immune pathway activation; biosynthetic process terms appear less central.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009636","count":5},{"id":"GO:0042220","count":4},{"id":"GO:0035690","count":4},{"id":"GO:0046638","count":4},{"id":"GO:0097011","count":4}]},{"hash":"463671323436035968","title":"Vesicle trafficking and junction remodeling","description":"This cluster is dominated by terms tied to membrane transport, SNARE complex disassembly, and apical junction assembly, pointing to a shared role in vesicle trafficking and cell\u2013cell junction dynamics that can influence tissue morphogenesis and remodeling.","confidence":"Medium","size":9,"edges":15,"triangles":4,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046909","count":4},{"id":"GO:0043297","count":3},{"id":"GO:0010963","count":3},{"id":"GO:0060047","count":3},{"id":"GO:0045453","count":3}]},{"hash":"2022027260655556549","title":"Golgi-ER vesicle trafficking and energy metabolism","description":"This cluster is driven by GO terms tied to Golgi and ER-to-Golgi vesicle transport, inter-Golgi cisterna transport, and Golgi retention, with supporting links to microtubule-based trafficking. While there are mitochondria-associated terms (oxidative phosphorylation, ATP metabolism, Complex III assembly), the strongest and most coherent signal is Golgi/ER vesicle trafficking, justifying a label focused on intracellular transport at the Golgi with a note on energy metabolism context.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0051013","count":2},{"id":"GO:1903862","count":2}]},{"hash":"1045046300509371666","title":"Mitochondrial Stress Response and Metabolism","description":"This cluster centers on stress adaptation involving mitochondria (protein import into the mitochondrial matrix and regulation of membrane permeability) and metabolic adjustments (trehalose biosynthesis and triglyceride biosynthesis), with supporting signals from heat response. Although some terms are obsolete, the core GO terms point to a coordinated stress response linked to mitochondrial function and lipid metabolism.","confidence":"Medium","size":9,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0034605","count":1},{"id":"GO:0070413","count":1},{"id":"GO:0005992","count":1},{"id":"GO:0046902","count":1}]},{"hash":"1907617424989462880","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0002188","count":2},{"id":"GO:1902416","count":2},{"id":"GO:0033081","count":2}]},{"hash":"107798325869144726","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":3},{"id":"GO:0035606","count":3},{"id":"GO:0051402","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009089","count":3}]},{"hash":"470149837820908585","title":"Heme biosynthesis and iron homeostasis","description":"Most proteins in this cluster are linked to protoporphyrinogen IX biosynthesis (heme biosynthesis) and iron-related responses/homeostasis (response to iron ion starvation, intracellular iron ion homeostasis, response to iron(II) ion). This points to a cohesive function in porphyrin/heme production coupled with iron management. A couple of development terms may be broader annotations and not essential to the core function. Confidence: High","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009097","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0001701","count":3}]},{"hash":"922351398492908263","title":"Fungal secretory pathway and ER-stress proteins","description":"The top GO terms cluster around secretion and trafficking (positive regulation of calcium ion-dependent exocytosis, protein targeting to vacuole) and fungal cell biology (beta-glucan cell wall biosynthesis), along with ER stress and unfolded protein response signals. While there are a few more general terms (DNA replication, iron-sulfur cluster assembly), the dominant theme points to secretory/vacuolar trafficking and stress-response processes characteristic of fungal cells. This supports labeling the cluster as related to fungal secretory and ER-stress functions.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0000742","count":1},{"id":"GO:1903382","count":1}]},{"hash":"981015708668910008","title":"Centrosome Cycle and Microtubule Localization","description":"This cluster is best described by terms linked to centrosome cycle, microtubule localization, and nuclear DNA replication regulation, which together point to roles in cell division and cytoskeletal organization. Although some terms reference innate immune responses or signaling, the strongest representational signals emphasize centrosome dynamics, microtubule-associated localization, and cell cycle-related DNA replication, suggesting a cohesive function in cell division and centrosome/microtubule maintenance.","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0014075","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0010571","count":2},{"id":"GO:0007098","count":2}]},{"hash":"1704636329905728834","title":"Unknown","description":"The top GO terms point to distinct, non-overlapping themes: bacterial polysaccharide biosynthesis (LPS core, O antigen, colanic acid), sterol biosynthesis, prostaglandin biosynthesis, and various signaling/development processes. This lack of a single cohesive function suggests no clear shared biology for the cluster, so an Unknown label with None confidence is appropriate.","confidence":"","size":8,"edges":9,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0048661","count":2},{"id":"GO:0001516","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0016049","count":2}]},{"hash":"816512762167779663","title":"DNA Damage Response and Cellular Stress","description":"The top GO terms point to DNA damage tolerance (error-free translesion synthesis) and cellular stress responses (oxidative stress, cell division). Although there are also vesicle trafficking and protein unfolding terms, the dominant signals are DNA damage response and general stress adaptation, suggesting a cluster of proteins involved in maintaining genome integrity and cellular homeostasis under stress.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":3},{"id":"GO:0046034","count":2},{"id":"GO:0048219","count":2},{"id":"GO:0035494","count":2},{"id":"GO:0000733","count":2}]},{"hash":"1863347941863826427","title":"Chromatin regulation and DNA replication/repair","description":"The top GO terms cluster around DNA-templated transcription and its regulation, plus chromatin-related processes (heterochromatin formation), replication licensing (MCM complex assembly), and DNA repair/recombination (break-induced replication, meiotic recombination nodules). Although there are a couple of outliers (nitrogen fixation, phosphotransferase system) that seem less connected, the dominant signal points to nuclear genome maintenance and transcription control. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0000727","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0006268","count":1}]},{"hash":"828590139197410764","title":"Neuronal development and apoptosis regulation","description":"The top GO terms emphasize nervous system development (CNS neuron development, axonogenesis) and synaptic signaling (excitatory postsynaptic potential), with a notable emphasis on apoptosis and Wnt signaling. Although a few terms refer to other contexts (e.g., mammary gland proliferation, pheromone-induced cell-cycle arrest), the neural development and apoptotic signaling signals dominate, supporting a label focused on neurodevelopment with apoptosis regulation.","confidence":"Medium","size":8,"edges":14,"triangles":11,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000751","count":7},{"id":"GO:0032092","count":7},{"id":"GO:0007409","count":7},{"id":"GO:0044337","count":7},{"id":"GO:0060079","count":7}]},{"hash":"460440102161165479","title":"Neuronal development and synapse formation","description":"This cluster is dominated by GO terms tied to neuronal development, including CNS neuron development, dendrite morphogenesis, axonogenesis, and excitatory postsynaptic potential, pointing to roles in neuron formation and synaptic connectivity. While there are additional terms (transcription, nuclear localization, Wnt signaling, apoptosis) that are broader or secondary, the central theme is neural development and synapse-related processes.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021954","count":7},{"id":"GO:0048813","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0000751","count":6},{"id":"GO:0032092","count":6}]},{"hash":"786566467752252191","title":"Broad Cellular Regulation and Signaling","description":"The GO terms point to regulatory roles across diverse processes, including regulation of gluconeogenesis, cell division, proton transport, phosphorylation state, and signaling pathways (e.g., TGF-beta related). This suggests a broad, not pathway-specific regulatory theme rather than a single function, and the absence of edges supports a general rather than tightly connected function. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090526","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0035970","count":1},{"id":"GO:0046827","count":1}]},{"hash":"1356081318651828949","title":"DNA replication, repair, and telomere maintenance","description":"This cluster is dominated by GO terms for DNA replication, DNA repair, and telomere maintenance (including telomerase activity and its positive regulation), with supporting terms like chromatin organization and protein stabilization that also relate to genome integrity. A couple of terms (cadmium response, glomerular filtration) seem less connected and may reflect broader stress responses or dataset noise.","confidence":"High","size":8,"edges":7,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0070987","count":2},{"id":"GO:0007004","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0032212","count":2}]},{"hash":"555466089260546285","title":"RNA processing and splicing regulation","description":"The cluster is enriched for GO terms related to mRNA splicing, export, and modification, plus regulation of translational initiation and processome assembly. This combination points to a coherent module involved in RNA maturation and gene expression control, spanning splicing through ribosome biogenesis and translation regulation.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0006406","count":2}]},{"hash":"967805106851221451","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0048026","count":3}]},{"hash":"90336326533700511","title":"RNA Splicing and Translation Machinery","description":"The cluster is enriched for spliceosome-related processes (conformational changes releasing U components, tri-snRNP assembly) and ribosome/translation-related processes (translation, cytoplasmic translation, ribosome export and disassembly), pointing to involvement in RNA processing and protein-synthesis machinery. Some growth-related terms exist but the recurring theme ties to RNA processing and translation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000388","count":3},{"id":"GO:1990416","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0006412","count":2}]},{"hash":"1682471064499534006","title":"Ribosome Biogenesis and Nucleolar Function","description":"This cluster centers on ribosome production and nucleolar processes: multiple GO terms for ribosome biogenesis, small subunit biogenesis/assembly, translation, and nucleolus organization. While a Notch signaling term and inflammatory chemotaxis terms appear, they are minimal compared to the ribosome-related terms, so the dominant theme is ribosome assembly and protein synthesis within the nucleolus.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007219","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0060265","count":1},{"id":"GO:0042274","count":1}]},{"hash":"193074464646169127","title":"RNA processing and ribosome biogenesis","description":"The terms cluster around RNA maturation (tRNA processing, mRNA splicing), translation and aminoacylation, and nuclear export of ribosomal subunits, pointing to a coherent role in gene expression and ribosome assembly. ER-related folding terms appear ancillary, not defining the main function. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006432","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0051290","count":1},{"id":"GO:0008033","count":1},{"id":"GO:1903026","count":1}]},{"hash":"606019875999254480","title":"Endosomal trafficking and MVB sorting","description":"The top GO terms cluster around intracellular vesicle trafficking, especially endosome transport between Golgi and endosomes, late endosome-to-vacuole/MVB sorting, and the multivesicular body sorting pathway, with an additional note on ER targeting. This points to a cohesive theme of endosomal trafficking and MVB sorting, despite some unrelated terms present in the set.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045047","count":1},{"id":"GO:0006465","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0007565","count":1}]},{"hash":"1707421500168343126","title":"Cofactor and GPI Anchor Biosynthesis","description":"The top GO terms cluster around biosynthetic processes for several essential cofactors (biotin, thiamine, lipoate, molybdopterin, menaquinone, pyrroloquinoline quinone) and include GPI anchor biosynthesis, suggesting a common theme of assembling cofactors and lipid-anchored proteins. A few terms (like ER stress regulation and antibiotic response) are less central to the core theme, but the dominant signal is biosynthetic pathways for cofactors and related modifications.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":2},{"id":"GO:0006506","count":2},{"id":"GO:0009234","count":1},{"id":"GO:0018339","count":1},{"id":"GO:0018189","count":1}]},{"hash":"2128541096899218944","title":"Ribosome Biogenesis and Translation","description":"The top GO terms converge on ribosome biogenesis (small and large subunit processes), tRNA modification, and cytoplasmic translation, pointing to a cluster of proteins involved in making and using ribosomes. Additional terms about cell cycle and septum assembly suggest a link to growth and division, but the dominant signal is ribosome assembly and protein synthesis.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0042254","count":2}]},{"hash":"159836740032135618","title":"Diverse substrate membrane transporters","description":"The proteins in this cluster are tied together by transmembrane transport activity across a range of substrates\u2014ions (sodium, potassium, phosphate, nitrate), sugars (arabinose, fucose, sialic acid), vitamins, and even neurotransmitter loading into vesicles\u2014indicating a broad set of membrane transporter functions rather than a single substrate. This supports naming as a diverse transporter cluster.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0035461","count":1}]},{"hash":"1169466112079598653","title":"Vacuolar acidification and V-ATPase assembly","description":"These proteins cluster around vacuolar functions, especially the assembly of the vacuolar H+-ATPase complex, proton translocation, and acidification, with supporting roles in polyphosphate storage and protein catabolism within the vacuole. Minor translation-related terms appear but do not define the main function. Overall, the dominant theme is vacuolar proton transport and acidification.","confidence":"High","size":8,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0006797","count":1},{"id":"GO:0007039","count":1}]},{"hash":"190996906977012290","title":"RNA processing and transcriptional regulation","description":"The cluster shows a strong tilt toward RNA metabolism and gene expression control, with GO terms for pre-miRNA processing, miRNA turnover, mRNA stabilization, rRNA maturation, and regulation of translation, alongside transcription-related terms (DNA-templated transcription, transcription antitermination, termination regulation). A few terms touch on stress-related apoptosis, but the dominant pattern is RNA processing and transcription regulation, making this label representative of the cluster's function.","confidence":"Medium","size":8,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0031054","count":1},{"id":"GO:1901724","count":1},{"id":"GO:0070934","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1}]},{"hash":"1050791972725499287","title":"Secretory pathway and vesicle trafficking","description":"The cluster is characterized by multiple vesicle-related GO terms: ER-to-Golgi transport, autophagosome docking, vacuolar membrane targeting, and neutrophil degranulation, all pointing to secretory and vesicle trafficking functions. Additional terms on intracellular protein transport and responses to insulin/hypoxia suggest broader regulation of secretion under stress, but the dominant theme is secretory trafficking machinery.","confidence":"High","size":8,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0001666","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042144","count":2},{"id":"GO:0043312","count":2}]},{"hash":"1243475172312197900","title":"Unknown","description":"The listed GO terms are highly diverse and show no single cohesive function linking the eight proteins. They touch on pH response, nutrient and toxic substance responses, various transport and lipid biosynthesis regulations, and unrelated regulatory processes, making a confident, specific label unattainable.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051452","count":1},{"id":"GO:0051180","count":1},{"id":"GO:0009268","count":1},{"id":"GO:0007584","count":1},{"id":"GO:0009636","count":1}]},{"hash":"1533222936983763184","title":"DNA damage response and chromosome segregation","description":"Top terms indicate a focus on DNA-templated transcription, double-strand break repair by homologous recombination, sister chromatid cohesion, and homologous chromosome segregation, suggesting a cluster centered on nuclear DNA damage response and chromosomal dynamics, with supporting hints from cell cycle regulation and stress responses.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0006308","count":1}]},{"hash":"1363827774087186192","title":"Proteolysis-driven tissue remodeling","description":"Most terms cluster around proteolytic processing and tissue remodeling, especially bone-related processes (bone resorption, collagen catabolic, intramembranous ossification) with additional signals of morphogenesis and remodeling in other tissues (lung branching, decidualization) and hormonal/catalytic regulation, indicating a proteolysis-centered remodeling theme across tissues.","confidence":"Medium","size":7,"edges":13,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":2},{"id":"GO:0030574","count":2},{"id":"GO:0010815","count":2},{"id":"GO:0051603","count":2},{"id":"GO:0097067","count":2}]},{"hash":"2260587572151781288","title":"Oxidative stress, hormone response, and cell cycle control","description":"The proteins cluster around stress-response processes (response to hydrogen peroxide, high light intensity, gamma radiation, heat) and regulation of ROS, together with a key cell-cycle event (G1/S transition) and microtubule dynamics. The presence of estradiol response and T cell homeostasis hints at additional hormonal and immune signaling context, suggesting a broader theme where stress signaling intersects with growth control and immune regulation rather than a single narrow pathway.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":2},{"id":"GO:0032355","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0009644","count":1}]},{"hash":"321141645689355661","title":"Unknown","description":"The top GO terms are highly diverse and include DNA recombination, necroptosis-related ripoptosome assembly, protein deubiquitination, and a spread of metabolic processes (amino acid catabolism, one-carbon metabolism, and even an obsolete plant-specific photosynthetic pathway). The lack of a coherent, shared biological function across these terms (and the presence of obsolete terms) makes it impossible to assign a concise, representative label. Therefore, the cluster is best described as Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:1901026","count":2},{"id":"GO:1990108","count":2},{"id":"GO:0071268","count":1},{"id":"GO:0000002","count":1}]},{"hash":"55173318275733366","title":"Spliceosome and RNA processing","description":"This cluster's proteins are strongly linked to mRNA splicing via the spliceosome, including snRNP and spliceosomal complex assembly, and to broader RNA processing steps such as mRNA maturation, P-body assembly, and mRNA decapping/deadenylation, plus nuclear import. The dominant GO terms point to a cohesive role in RNA processing and gene expression regulation within the nucleus.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0030490","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0000290","count":1}]},{"hash":"893586918124050682","title":"Nuclear RNA processing and transcription termination","description":"The set is dominated by GO terms for RNA Pol II transcription termination, promoter clearance, nuclear mRNA decay, snoRNA release from pre-rRNA, and maturation of rRNA, indicating a cluster of nuclear RNA processing and transcription activities. Some terms relate to meiotic recombination or viral replication, which are less central but present as potential noise.","confidence":"Medium","size":7,"edges":11,"triangles":6,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006369","count":3},{"id":"GO:0045003","count":3},{"id":"GO:0006311","count":3},{"id":"GO:0001111","count":3},{"id":"GO:0071042","count":3}]},{"hash":"2161868792115465034","title":"Purine nucleotide biosynthesis and salvage","description":"Among the top GO terms, several explicitly describe nucleotide metabolism: ADP biosynthetic process, CDP biosynthetic process, nucleoside monophosphate phosphorylation, purine ribonucleotide interconversion, and AMP salvage. Together they point to the production and interconversion of purine nucleotides and related intermediates. Some terms like lipopolysaccharide biosynthesis and development annotations may be incidental, but the core signal is nucleotide metabolism, especially purine nucleotides. Confidence: Medium","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0046705","count":1},{"id":"GO:0046940","count":1},{"id":"GO:0006172","count":1},{"id":"GO:0046041","count":1}]},{"hash":"1434683613071410835","title":"Lipid metabolism and secondary metabolite biosynthesis","description":"This cluster shows GO terms centered on lipid metabolism (fatty acid beta-oxidation, carnitine metabolism, sphingolipid biosynthesis) and broader biosynthetic processes (poly-hydroxybutyrate biosynthesis, antibiotic and alkaloid/retinoic acid biosynthesis). While diverse, the common thread is metabolic biosynthesis with a focus on lipids and secondary metabolites, supporting the label Lipid metabolism and secondary metabolite biosynthesis.","confidence":"Medium","size":7,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033539","count":2},{"id":"GO:0009437","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2}]},{"hash":"906707460819387665","title":"Mitochondrial nucleotide and energy transport","description":"These proteins cluster around mitochondrial transport of nucleotides and energy-related metabolites: ADP/ATP, deoxynucleotides, thiamine pyrophosphate, and Mg2+. The GO terms also connect to energy expenditure and insulin-related regulation (adaptive thermogenesis, response to insulin, response to fatty acids), consistent with a role in mitochondrial energy metabolism and metabolite shuttling.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990845","count":2},{"id":"GO:0030302","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0015866","count":2},{"id":"GO:0032869","count":2}]},{"hash":"1583579444077640590","title":"Neuronal development and synaptic signaling","description":"The top GO terms cluster around neuronal differentiation and growth (axonogenesis, CNS neuron development), synaptic activity (excitatory postsynaptic potential), and signaling pathways (tyrosine phosphorylation, Wnt signaling) with apoptosis regulation. This suggests a cohesive theme of neuronal development and synaptic signaling with associated regulatory signaling and cell fate processes.","confidence":"High","size":7,"edges":9,"triangles":3,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0018108","count":6},{"id":"GO:0000751","count":4},{"id":"GO:0032092","count":4},{"id":"GO:0007409","count":4},{"id":"GO:0044337","count":4}]},{"hash":"866096038698838612","title":"Microtubule dynamics in mitosis and neuronal transport","description":"These proteins show a strong emphasis on microtubule biology: plus-end depolymerization, spindle\u2013kinetochore interactions, mitotic chromosome alignment, and regulation of microtubule-based processes, plus dendritic transport of receptor complexes and neuronal structural organization. A note on stress granule disassembly aligns with cytoskeletal roles in RNA granule dynamics, particularly in neurons. Overall, the cluster centers on microtubule remodeling that supports both cell division and neuronal transport.","confidence":"High","size":7,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":5},{"id":"GO:0021685","count":3},{"id":"GO:0070462","count":3},{"id":"GO:0099607","count":3},{"id":"GO:0032886","count":3}]},{"hash":"144399222765491149","title":"Cell Cycle and Morphogenesis Signaling","description":"The top GO terms center on mitotic/meiotic cell cycle events (spindle-kinetochore attachment, meiotic cell cycle) and a range of developmental and morphogenetic processes (EMT, dendrite morphogenesis, blood vessel branching) with signaling involvement (NFAT pathway) and neuronal activity (EPSP). Together, they suggest proteins that coordinate cell division with differentiation and tissue morphogenesis, hence this label.","confidence":"Medium","size":7,"edges":13,"triangles":11,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051315","count":5},{"id":"GO:0051037","count":5},{"id":"GO:0010288","count":5},{"id":"GO:0051533","count":5},{"id":"GO:0050774","count":5}]},{"hash":"1423663262084162759","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0031664","count":2},{"id":"GO:0007026","count":2}]},{"hash":"1440394300506148601","title":"RNA Pol II transcription regulation & ribosome biogenesis","description":"This cluster centers on nuclear gene expression processes: ribosome biogenesis, mRNA export, and positive regulation of transcription elongation or preinitiation complex assembly for RNA polymerase II, suggesting a coordinated transcriptional control linked to ribosome production. The other terms (photosynthesis, xenobiotic catabolism, redox processes) are sporadic and less cohesive with the main theme, likely noise. Overall, the dominant signal supports transcription regulation and ribosome biogenesis. ","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0045899","count":2},{"id":"GO:1902600","count":1}]},{"hash":"1378232559258548360","title":"ER protein folding and Golgi vesicle trafficking","description":"Although one term relates to DNA-templated transcription, the strongest signals are ER folding, chaperone-mediated assembly, oxidative stress response, and vesicle trafficking between Golgi compartments, pointing to a cluster of ER quality-control and secretory pathway proteins.","confidence":"High","size":7,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0018279","count":3},{"id":"GO:0051131","count":3}]},{"hash":"843753965223808770","title":"Translation initiation and preinitiation complex assembly","description":"Dominant GO terms in this cluster are all related to translation initiation and the assembly of translation preinitiation complexes (e.g., translation, translational initiation, formation of translation preinitiation complex, cytoplasmic translation initiation). Other terms are sparse and do not define the cluster. Therefore, the shared function most consistent with the proteins is involvement in initiation of translation and preinitiation complex formation.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034724","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0002176","count":1}]},{"hash":"969250876043480158","title":"RNA processing and splicing machinery","description":"This cluster is dominated by GO terms related to RNA maturation and processing, including tRNA processing, maturation of SSU-rRNA, spliceosome-mediated mRNA splicing, spliceosomal complex assembly, and P-body formation. Additional terms for mRNA decapping and histone mRNA metabolism point to broader RNA turnover and processing roles. While a few terms (e.g., NF-kappaB regulation, hair cycle) are less directly tied to RNA processing, the core signature clearly centers on RNA maturation and splicing pathways.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0043124","count":2},{"id":"GO:0030490","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0000290","count":1}]},{"hash":"1702011859172690252","title":"Nucleolar Transcription and Ribosome Biogenesis","description":"This cluster is dominated by GO terms related to transcription by RNA polymerases I, II, and III, including rRNA and tRNA transcription, and by ribosome biogenesis and small-subunit processome assembly, all centered in the nucleolus. A couple of peripheral terms exist, but the primary signal is nucleolar transcription and ribosome production. ","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042254","count":1},{"id":"GO:1904750","count":1},{"id":"GO:0042797","count":1}]},{"hash":"2016899203019691251","title":"Microtubule Assembly","description":"The top GO terms point to microtubule formation and polymerization, suggesting the proteins in this cluster are involved in cytoskeletal assembly. An outlier RNA editing term is present but does not counter the dominant microtubule-related function, so a label centered on microtubule assembly fits best.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001578","count":1},{"id":"GO:0046785","count":1},{"id":"GO:0016554","count":1}]},{"hash":"1948691477297420711","title":"Proteostasis and signaling regulation","description":"The cluster mixes proteins involved in protein quality control and turnover (deglycosylation, ER-associated ubiquitin-dependent degradation, free ubiquitin chains, aggrephagy) with diverse signaling and developmental cues (Hippo signaling, GPCR internalization, cell polarity establishment, inner cell mass fate commitment, interferon signaling). This suggests a theme around maintaining cellular protein homeostasis while modulating signaling pathways that govern cell behavior and fate.","confidence":"Medium","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006517","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0060340","count":1},{"id":"GO:1904021","count":1},{"id":"GO:0035973","count":1}]},{"hash":"2250493337439934167","title":"Developmental Gene Regulation and Stress Response","description":"This cluster centers on developmental processes (forebrain development, neural tube closure, multicellular organism development) and general transcriptional regulation (DNA-templated transcription, regulation of gene expression), with additional signals of cellular stress responses (ER stress\u2013related apoptosis, cadmium response). The dominant theme is developmental gene regulation, with secondary stress-response connections, giving a moderate level of confidence.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0006349","count":2}]},{"hash":"1608724348957098800","title":"Unknown","description":"The top GO terms span diverse functions (skin development, cell-cycle regulation, transcription, chromatin modification, RNA processing) with no dominant shared pathway. The absence of edges and the diversity of processes suggest these proteins do not form a cohesive functional cluster, so a single interpretable label is not supported.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":3},{"id":"GO:0070317","count":2},{"id":"GO:0010255","count":2},{"id":"GO:0045143","count":2},{"id":"GO:0010659","count":2}]},{"hash":"1658360872516477627","title":"P-body mRNA decay and miRNA silencing","description":"The top GO terms cluster around P-body assembly, deadenylation-dependent decapping, poly(A) tail shortening, and various mRNA decay processes, as well as miRNA-mediated post-transcriptional gene silencing. Together these indicate a module focused on post-transcriptional regulation of mRNA stability and translation, localized to P-bodies and involving miRNA pathways. A few terms about transcription regulation appear less central and may reflect annotation noise, but the dominant theme is mRNA decay and silencing in a P-body context.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0035195","count":1},{"id":"GO:0000289","count":1}]},{"hash":"1870962721135817834","title":"Unknown","description":"The GO terms in this cluster are heterogeneous: translation elongation and translational fidelity point to protein synthesis, while actin filament regulation suggests cytoskeletal control, and there are separate signals for oxidative/pH stress and vascular signaling. There is no clear, single unifying function that ties all members together, so a specific functional label is not evident.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032232","count":1},{"id":"GO:0006414","count":1},{"id":"GO:1990145","count":1},{"id":"GO:0003069","count":1},{"id":"GO:0001320","count":1}]},{"hash":"143817267100501691","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015885","count":1},{"id":"GO:0051958","count":1},{"id":"GO:0000389","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0000350","count":1}]},{"hash":"471910777602675514","title":"Mitochondria-dependent apoptosis and stress response","description":"The terms cluster around mitochondrial signaling of cell death (cytochrome c release, outer membrane insertion, hydrogen peroxide\u2013induced PCD) and related stress responses (TGF-beta signaling, proteostasis regulation), suggesting a group focused on mitochondrial stress signaling and apoptosis rather than a unrelated function.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090200","count":1},{"id":"GO:1903638","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0010421","count":1},{"id":"GO:1903645","count":1}]},{"hash":"898403382988712002","title":"Unknown","description":"The terms span vesicle trafficking and organelle organization (vacuole organization, Golgi vesicle budding), structural aspects (regulation of microvillus assembly, establishment of cell polarity), and diverse sensory/neural processes (smell detection, vestibulocochlear nerve formation, neuromuscular posture), plus immune differentiation (B cell differentiation). This broad, heterogeneous set lacks a single cohesive function, so a precise label cannot be confidently assigned.","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007033","count":1},{"id":"GO:0045332","count":1},{"id":"GO:0050911","count":1},{"id":"GO:0048194","count":1},{"id":"GO:0045579","count":1}]},{"hash":"516638879161303177","title":"Endosomal vesicle trafficking and receptor transport","description":"This cluster is enriched for vesicle- and transport-related GO terms: clathrin-coated vesicle cargo loading, vesicle-mediated transport, and neurotransmitter receptor internalization/transport to endosomes and lysosomes, plus retrograde Golgi-to-ER transport. The melanosome organization term also reflects vesicle trafficking in pigment cells, while the transcription regulation term appears less representative. Overall, the core theme is endosomal/vesicular trafficking and receptor sorting.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:1900126","count":1},{"id":"GO:0035652","count":1},{"id":"GO:0032438","count":1},{"id":"GO:0099590","count":1}]},{"hash":"535834452508466419","title":"Cell Division and Spermatogenesis","description":"The cluster is dominated by GO terms for mitotic cell cycle and cell division, with spermatid development appearing prominently, suggesting a core theme around division processes in a developmental context. Additional terms touch on related developmental or signaling processes, but the strongest signal centers on mitosis and spermatogenesis, justifying a label focused on cell division-related development.","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071803","count":1},{"id":"GO:0097498","count":1}]},{"hash":"1567050801053181230","title":"Neuronal actin remodeling and GTPase signaling","description":"The GO terms cluster around actin-based structures (filopodium assembly, stress fiber assembly), adhesion/spreading, and small GTPase signaling, with hints of nervous system development and GABAergic synaptic transmission. This points to a module of proteins coordinating cytoskeletal remodeling in neurons and signaling pathways that regulate synapse formation and function.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0046847","count":2}]},{"hash":"1018307379665756828","title":"Cell cycle and chromosome maintenance","description":"Based on the top GO terms, the cluster is enriched for cell cycle processes (G1/S transition, mitotic and meiotic cycles), DNA replication, DNA repair, and kinetochore localization, suggesting these proteins function in chromosome maintenance and cell division. Some neural-related terms appear but do not derail the dominant signal toward cell cycle/maintenance.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0051321","count":3}]},{"hash":"643579366463691888","title":"Unknown","description":"The top GO terms span nuclear transcription and DNA replication, mitochondrial energy production, cytoskeletal remodeling, and Golgi trafficking, with no single cohesive function or compartment linking all terms. This spread makes it unclear what a concise, representative label would be.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0051013","count":1},{"id":"GO:1903862","count":1},{"id":"GO:0009399","count":1}]},{"hash":"713591176600144029","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0045901","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0014009","count":1},{"id":"GO:0046677","count":1}]},{"hash":"1080450018099386302","title":"Unknown","description":"The GO terms are diverse and do not reveal a single cohesive function for the cluster: ubiquitination (K11-linked), unfolded protein response, innate immunity, and various developmental and cell-cycle processes appear together without a unifying theme.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0035457","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0038108","count":2}]},{"hash":"2015318389213034008","title":"G1/S Cell Cycle Regulation and Chromatin Signaling","description":"The terms point to control of cell cycle progression (negative regulation of G0 to G1 transition, G1 DNA damage checkpoint signaling, chromosome segregation) and chromatin-state modulation (DNA-templated transcription, histone H3-K27 methylation). These aspects form a coherent theme of cell cycle regulation intertwined with transcriptional and chromatin regulation, with a few ribosome biogenesis terms likely incidental. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":1},{"id":"GO:0010255","count":1},{"id":"GO:0045143","count":1},{"id":"GO:0010659","count":1},{"id":"GO:0072432","count":1}]},{"hash":"612476852460609380","title":"Ubiquitin-Proteasome Regulation","description":"The cluster\u2019s top GO terms cluster around ubiquitination and proteasome-mediated degradation (SCF-dependent proteasomal ubiquitin-dependent catabolic process, K29-linked ubiquitination), along with neddylation and nuclear protein turnover. This points to a shared function in regulating protein stability via ubiquitin tagging and degradation, with other terms touching chromatin modification and signaling as broader connections. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070076","count":6},{"id":"GO:0002223","count":6},{"id":"GO:0060340","count":6},{"id":"GO:0010976","count":6},{"id":"GO:1901044","count":6}]},{"hash":"1043105292307426211","title":"Ribosome Biogenesis and Translation","description":"Most top GO terms cluster around ribosome production and function: cytoplasmic translation; ribosome biogenesis; ribosomal small and large subunit biogenesis; and export of ribosomal subunits from the nucleus. This indicates the proteins are part of ribosome assembly and protein synthesis machinery. Some unrelated terms (cell cycle, septum assembly) may reflect broader cellular coordination, but the dominant signal is ribosome-related.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0042254","count":1},{"id":"GO:1903833","count":1}]},{"hash":"1154521549779554172","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904571","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0042254","count":1},{"id":"GO:1900745","count":1}]},{"hash":"1707706682423075973","title":"Muscle calcium signaling and development","description":"The cluster consistently features GO terms tied to skeletal muscle fiber development, calcium handling (ryanodine receptor regulation, calcium import into mitochondria), and signaling pathways (calcineurin-NFAT) that govern muscle gene expression and contraction. While some terms touch on neuronal processes, the strongest shared themes are muscle-related calcium signaling and development, including mitochondrial calcium dynamics and calcium-dependent transcription.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048741","count":5},{"id":"GO:0060315","count":4},{"id":"GO:0006479","count":4},{"id":"GO:0036444","count":4},{"id":"GO:0090151","count":4}]},{"hash":"652478537185808158","title":"Ubiquitin-Dependent Degradation and NF-kB Signaling","description":"The cluster\u2019s top GO terms center on ubiquitin-mediated pathways (ERAD, proteolysis), autophagy, and NF-kB\u2013related signaling, paired with immune regulation (T cell proliferation, chemokine production) and chromatin modification. This suggests a shared role in protein quality control linked to immune signaling and transcriptional regulation, despite no direct interactions among proteins in this cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:1903762","count":2},{"id":"GO:2000620","count":2},{"id":"GO:1903883","count":2},{"id":"GO:0007250","count":2}]},{"hash":"2103681192700017812","title":"tRNA Charging and Translation Machinery","description":"This cluster centers on translation and tRNA charging, with multiple aminoacyl-tRNA synthetases (glutaminyl-, glutamyl-, and prolyl-tRNA synthetases) and tRNA modification; a few stress-response terms are present but the core signal is the translation machinery.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006412","count":2},{"id":"GO:1990355","count":1},{"id":"GO:0070301","count":1},{"id":"GO:0030091","count":1}]},{"hash":"2263834721960516007","title":"Mitochondrial respiration and DNA repair","description":"Despite some terms tied to Golgi trafficking and transcription, the strongest signals are mitochondrial: oxidative phosphorylation, ATP metabolism, and complex III assembly. The presence of DNA biosynthetic process and base-excision repair further suggests genome maintenance roles that can intersect with mitochondrial function. Together, these point to a cluster centered on mitochondrial energy production with supporting genome maintenance functions.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071897","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0006284","count":2},{"id":"GO:0051013","count":1},{"id":"GO:1903862","count":1}]},{"hash":"472043968489802618","title":"Unknown","description":"With only sparse, single-term signals across very different biological areas (glycolysis and metabolic pathways; chloroplast organization and iron-sulfur cluster assembly; hypoxia response, plasminogen activation, and epithelial differentiation), there is no clear, shared function uniting these proteins. Therefore a cohesive label cannot be confidently assigned.","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":1},{"id":"GO:0071456","count":1},{"id":"GO:0031639","count":1},{"id":"GO:0030855","count":1},{"id":"GO:0016525","count":1}]},{"hash":"32291705766568147","title":"Cytokinesis and Microtubule Organization","description":"The top GO terms are dominated by cell division and cytoskeletal functions: cell cycle, mitotic cytokinesis, spindle pole body duplication, FtsZ-dependent cytokinesis, microtubule nucleation, and cell septum assembly. These collectively point to proteins involved in coordinating cytokinesis and microtubule dynamics across organisms. Some terms related to neuronal or immune signaling appear as secondary annotations and do not define the core cluster function. ","confidence":"Medium","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0090529","count":4},{"id":"GO:1905789","count":4},{"id":"GO:1902408","count":4}]},{"hash":"854244370566859501","title":"Unknown","description":"The GO terms span wildly diverse functions from energy metabolism (ferredoxin metabolism, ATP synthesis-coupled electron transport, xanthine catabolism) and ion transport to nitrogen fixation and regulation of vascular development, with no single cohesive biological theme linking all six proteins. Therefore a confident, cohesive label cannot be assigned. ","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0009399","count":1},{"id":"GO:2001213","count":1},{"id":"GO:0045602","count":1},{"id":"GO:0006814","count":1}]},{"hash":"535824480511129226","title":"Unknown","description":"The top terms span cell-cycle regulation and kinetochore/nuclear localization alongside neuronal development and innate immunity, with no clear, cohesive theme tying the proteins together. Thus there is no confident single function to assign. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":4},{"id":"GO:0034501","count":4},{"id":"GO:0000751","count":3},{"id":"GO:0032092","count":3},{"id":"GO:0007409","count":3}]},{"hash":"1784771238323842089","title":"Nuclear transcription and genome maintenance","description":"This cluster centers on RNA polymerase II\u2013mediated transcription regulation (positive regulation, promoter clearance, termination) and chromatin-related processes (heterochromatin formation) alongside DNA-centric events (DNA replication, double-strand break repair via SDSA, meiotic gene conversion) and RNA processing (mRNA catabolism, rRNA maturation). The overarching theme is nuclear genome metabolism, combining transcriptional control, DNA transactions, and RNA processing. ","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070869","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0021553","count":1}]},{"hash":"1400453892359196256","title":"Dopaminergic Synaptic Transmission and AKT Signaling","description":"This cluster centers on dopaminergic synaptic activity and active PI3K/AKT signaling, with protein phosphorylation and transcription-related processes suggesting downstream gene regulation in neurons. The presence of terms for dopaminergic synaptic transmission, AKT activation, and phosphorylation regulation points to a neuronal signaling module, while ideas about proteasome regulation and deglycosylation reflect post-translational control of neuronal proteins.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046826","count":2},{"id":"GO:0032148","count":2},{"id":"GO:0001963","count":2},{"id":"GO:0033138","count":2}]},{"hash":"576440856093677329","title":"Neurodevelopmental signaling and apoptosis regulation","description":"The cluster is dominated by terms related to neural development (CNS neuron development, axonogenesis, excitatory postsynaptic potential) and signaling pathways that influence apoptosis (Wnt signaling involved in positive regulation of apoptotic process). There are also hints of nuclear localization and protein binding regulation, which can accompany developmental signaling. Some cell cycle terms appear, but the neural development and synaptic terms provide the clearest, most cohesive theme for naming this cluster.","confidence":"Medium","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0051321","count":6},{"id":"GO:0000751","count":5},{"id":"GO:0032092","count":5},{"id":"GO:0007409","count":5}]},{"hash":"579776594378603087","title":"Wnt signaling in neural development","description":"The terms point to Wnt pathway activity with neural development-related processes such as axonogenesis and excitatory synaptic signaling; these suggest a cohesive theme around Wnt-regulated neural development, with other terms (glucose response, angiogenesis) likely representing broader signaling context rather than core function. Confidence: Medium","confidence":"","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071333","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0014068","count":2},{"id":"GO:0045766","count":2}]},{"hash":"2177551704437247630","title":"Unknown","description":"The GO terms span a wide range of unrelated cellular processes (metabolism, vesicle trafficking, SNARE complex activity, transcription, DNA-related processes, transformation competence, microtubule dynamics, protein folding/unfolding, oxidative stress response, and cell division) with no clear unifying function for the cluster. This lack of a cohesive shared function leads to an Unknown label rather than a specific, representative name.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0048219","count":1},{"id":"GO:0035494","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0000733","count":1}]},{"hash":"300327093946107658","title":"RNA splicing and processing machinery","description":"This cluster is dominated by GO terms related to RNA processing and splicing (mRNA processing, RNA splicing, spliceosomal assembly, snoRNP assembly), indicating proteins that function in RNA maturation and spliceosome assembly; a couple terms touching on stress responses are minor context rather than core functions.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0072423","count":1},{"id":"GO:0098789","count":1},{"id":"GO:0000354","count":1}]},{"hash":"588699368888895946","title":"Developmental signaling and cytoskeletal dynamics","description":"This cluster centers on multiple signaling pathways (EGFR, Rab GTPases, CAMKK-AMPK) and processes linked to cytoskeletal remodeling and cell polarity (podosome assembly, endothelial lumen extension, neuron precursor migration). While one term (RNA polymerase III transcription) is less connected, the dominant theme is coordinated signaling and cytoskeletal organization driving development and tissue morphogenesis.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071803","count":1},{"id":"GO:0097498","count":1},{"id":"GO:0021831","count":1},{"id":"GO:0032482","count":1},{"id":"GO:0060079","count":1}]},{"hash":"1357870441849823413","title":"Lipid biosynthesis and ER-Golgi transport","description":"The top GO terms show fatty-acid biosynthetic processes and long-chain fatty-acyl-CoA metabolic activity, indicating lipid synthesis. They also include ER-to-Golgi vesicle-mediated transport, pointing to involvement in the secretory pathway. A single term about positive regulation of phagocytosis hints at a possible link to phagocytic function, but the evidence is limited. Overall, the cluster centers on lipid production with vesicle trafficking, justifying the label.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035336","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0050766","count":1}]},{"hash":"1076346289060560564","title":"Nuclear transcription and cell cycle regulation","description":"The top GO terms cluster around DNA-templated transcription and chromatin-related processes (including histone methylation), along with cell-cycle related Regulation of the G0 to G1 transition and G1 DNA damage checkpoint signaling, plus some RNA processing terms. This points to a nuclear program coordinating gene expression with chromatin state and cell-cycle checkpoints, rather than a cytosolic signaling pathway, hence the label focusing on transcription and cell-cycle regulation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0070317","count":3},{"id":"GO:0010255","count":3},{"id":"GO:0045143","count":3},{"id":"GO:0010659","count":3}]},{"hash":"1818268705201649119","title":"Ubiquitin-mediated regulation of cell cycle and trafficking","description":"The cluster features GO terms centered on protein ubiquitination, cell cycle, and vesicle/trafficking pathways (ER-Golgi and endosome-Golgi transport), with additional hints of apoptosis and epithelial polarity. This points to a cohesive role in ubiquitin-dependent regulation of cell division and intracellular transport; the terms together suggest a functional theme around regulation of proliferation and trafficking rather than a single redundant process.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0090162","count":2}]},{"hash":"1039328636473697579","title":"Mitochondrial Transport and Energy Metabolism","description":"The GO terms cluster around mitochondrial metabolite transport (ADP, ATP, magnesium, thiamine pyrophosphate, nucleotides) and energy-related processes (adaptive thermogenesis, fatty acid response, insulin/glucose signaling), indicating a cohesive role in mitochondrial transport and energy regulation.","confidence":"High","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990845","count":1},{"id":"GO:0030302","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0015866","count":1},{"id":"GO:0032869","count":1}]},{"hash":"669715188269467025","title":"Translation control and spliceosome machinery","description":"The cluster includes multiple terms tied to regulation of translation (positive regulation of cytoplasmic/elongation, mitochondrial translation, translational fidelity) and key steps in spliceosome assembly/activation, suggesting a cohesive theme around RNA-based gene expression processes; a few terms related to cell proliferation/differentiation appear as low-frequency outliers.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045901","count":1},{"id":"GO:1990416","count":1},{"id":"GO:0017183","count":1},{"id":"GO:0014009","count":1},{"id":"GO:0002244","count":1}]},{"hash":"1545431526352065097","title":"Golgi Localization and Reassembly","description":"This cluster\u2019s top GO terms include establishment of Golgi localization and Golgi reassembly, which point to a shared involvement in Golgi apparatus organization and maintenance. While there are also terms related to insulin signaling, cell growth, ion transport, and neural development, they are less central to the core Golgi theme. Thus, a Golgi-focused label fits best with moderate confidence.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900740","count":1},{"id":"GO:0086010","count":1},{"id":"GO:0051683","count":1},{"id":"GO:0090168","count":1},{"id":"GO:0030307","count":1}]},{"hash":"754690974314716116","title":"Neural development and signaling","description":"This cluster is characterized by GO terms centered on neural processes and signaling, notably axonogenesis and excitatory postsynaptic potential, alongside related signaling activities such as activation of adenylate cyclase and regulation of GTPase activity. While there are broader cellular processes present (protein methylation, N-glycan processing, stress response), the strongest recurring theme ties to neural development and neuronal signaling pathways. The lack of edge connections suggests the label is inferred from GO term themes rather than direct protein\u2013protein associations. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006479","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0033555","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1891776335048348232","title":"Mitochondrial Transport and Energy Metabolism","description":"The cluster centers on mitochondrial processes: transport of key substrates and cofactors (ADP/ATP, dNTPs, Mg2+, thiamine pyrophosphate), protein import into the mitochondrial matrix, and energy-related responses including adaptive thermogenesis and insulin/glucose signaling. This cohesive theme points to mitochondrial transport and energy homeostasis as the core function.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":3},{"id":"GO:0030150","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0030302","count":2},{"id":"GO:0015866","count":2}]},{"hash":"1577687512479888662","title":"Chromatin remodeling and transcription regulation","description":"Top GO terms point to a coherent theme of chromatin structure modification and transcription control, including transcription initiation-coupled chromatin remodeling, DNA-templated transcription initiation, replication-dependent chromatin assembly, and heterochromatin formation, with some emphasis on negative regulation of RNA Pol II transcription. The presence of protein heterotetramerization supports the idea of multi-subunit complexes functioning in chromatin dynamics and transcription regulation, making this label representative of the cluster\u2019s function.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045815","count":3},{"id":"GO:0006335","count":2},{"id":"GO:0051290","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0000122","count":2}]},{"hash":"2013788651905857595","title":"RNA and Protein Methyltransferases","description":"The top GO terms are dominated by methylation activities: peptidyl-lysine dimethylation, N-terminal methylations, RNA methylation (rRNA, tRNA wobble uridine, guanine-N7), and related modifications, suggesting a core function in methyltransferase-mediated modification of proteins and RNAs. A few terms touch on microtubule organization and stress responses, but the strongest signal centers on methylation enzymes and their RNA/protein substrates.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0035690","count":2},{"id":"GO:1903087","count":2}]},{"hash":"1412033705317082307","title":"Regulatory Metabolism and Autophagy","description":"The top terms revolve around regulation of metabolic pathways (glycogen synthesis/catabolism, lipid homeostasis, ubiquinone/tocopherol biosynthesis) and negative regulation of signaling and autophagy, suggesting a theme of cellular metabolic regulation and organelle maintenance. A single neuronal development term appears as an outlier but doesn\u2019t define the cluster\u2019s core function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005979","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0005981","count":1},{"id":"GO:0050849","count":1},{"id":"GO:0000079","count":1}]},{"hash":"2205035817302310564","title":"ER-Golgi Transport and ER Stress Response","description":"These proteins cluster around intracellular trafficking between the ER and Golgi (ER-to-Golgi and retrograde transport) and general protein transport, with some hints of ER-stress\u2013driven regulation of translation initiation. The dominant theme appears to be membrane trafficking linked to ER function and stress signaling, rather than a single specific process.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0015031","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0035719","count":1}]},{"hash":"198428757908832913","title":"Viral translation initiation and mRNA export","description":"This cluster is dominated by GO terms related to translation initiation and viral RNA processing, including IRES-dependent viral translational initiation, formation of translation preinitiation complex, and viral mRNA export from the host nucleus, as well as regulation of translational initiation. These points suggest a shared function around controlling translation in viral contexts. A few terms (mitotic cell cycle, follicle cell development, ubiquitin ligase regulation) appear as outliers, possibly reflecting multi-functional proteins or annotation noise, but the core theme centers on translation initiation and viral RNA processing.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0000189","count":2},{"id":"GO:0006446","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0075522","count":1}]},{"hash":"1565783596042488638","title":"Lipid and secondary metabolite biosynthesis","description":"The GO terms cluster around biosynthesis and metabolism of lipids and related small molecules (sphingolipid biosynthesis, very long-chain fatty acid biosynthesis, 3-keto-sphinganine metabolism), plus secondary metabolite pathways (retinoic acid, tropane alkaloid biosynthesis) and storage polymers (poly-hydroxybutyrate). Some terms reflect broader metabolic or stress-related processes (propylene catabolic, antibiotic response, sporulation). The shared theme is lipid and small-molecule biosynthesis/metabolism rather than a single tight pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042208","count":2},{"id":"GO:0030148","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006710","count":1},{"id":"GO:0009710","count":1}]},{"hash":"923297037678450085","title":"Chaperone-mediated proteostasis","description":"These proteins are enriched for terms related to protein quality control and folding, including detection of misfolded protein, chaperone-mediated protein folding, and chaperone complex assembly. While there are immune signaling terms and a few unrelated processes, the proteostasis-related terms dominate, suggesting a role in chaperone-assisted protein folding and quality control.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0002842","count":2},{"id":"GO:0002236","count":2},{"id":"GO:0002368","count":2},{"id":"GO:1904469","count":2}]},{"hash":"330031383802748838","title":"Unknown","description":"The top GO terms cover broad areas from metabolism (valine biosynthesis, galactitol and formate catabolism, mitochondrial electron transport) to signaling (cellular response to cAMP) and development (neuron projection development, granulocyte differentiation, stem cell proliferation), including photosynthetic pathways. The lack of a unifying biological process or pathway across these terms suggests no cohesive functional theme for the cluster. ","confidence":"","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071268","count":1},{"id":"GO:0019404","count":1},{"id":"GO:0009099","count":1},{"id":"GO:0042183","count":1},{"id":"GO:0071320","count":1}]},{"hash":"1070963963598079190","title":"Immune Activation and Cytokine Regulation","description":"The most represented GO terms are immune-related, including positive regulation of T cell mediated immune response to tumor cell, B cell cytokine production, and positive regulation of TNF production, which together point to immune signaling and cytokine control as the cluster\u2019s core function. Some terms involving misfolded protein detection, chaperone-associated folding, and RNA localization to Cajal bodies suggest ancillary roles or annotation noise, but the dominant theme remains immune activation.","confidence":"Medium","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002842","count":3},{"id":"GO:0002236","count":3},{"id":"GO:0002368","count":3},{"id":"GO:1904469","count":3},{"id":"GO:0007339","count":3}]},{"hash":"39152434774814156","title":"Ubiquitin-Proteasome Regulation","description":"The cluster\u2019s GO terms strongly point to ubiquitination and proteasome-mediated protein degradation (neddylation, SCF-dependent ubiquitin-proteasome pathway, and K29-linked ubiquitination), suggesting a shared function in protein turnover. While other terms touch on immune signaling, neuron development, and meiosis-related processes, they appear ancillary to the dominant ubiquitin-proteasome theme. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070076","count":5},{"id":"GO:0002223","count":5},{"id":"GO:0060340","count":5},{"id":"GO:0010976","count":5},{"id":"GO:1901044","count":5}]},{"hash":"1480067029915927427","title":"RNA processing and ribosome biogenesis","description":"This cluster shows GO terms tied to RNA folding, splicing regulation, rRNA maturation, translation, and small-subunit processome assembly, which together point to RNA processing and ribosome biogenesis; the antibiotic response term likely reflects antibiotic effects on ribosome function rather than a separate pathway. Overall, the terms align around RNA maturation and ribosome assembly processes.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034337","count":1},{"id":"GO:0033120","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0000372","count":1},{"id":"GO:0046677","count":1}]},{"hash":"1821947579955834192","title":"Bacterial cell wall synthesis and division","description":"This cluster centers on GO terms related to Gram-negative cell wall biogenesis, cell wall organization, peptidoglycan biosynthesis, and cell division, suggesting proteins involved in envelope construction and cytokinesis in bacteria. The presence of regulation of cell shape further supports a link to cell envelope remodeling during division. A few RNA modification terms appear but are likely incidental noise rather than core drivers of this cluster\u2019s function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0043164","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0019408","count":1}]},{"hash":"778788199023620615","title":"Unknown","description":"The top GO terms are highly diverse\u2014ranging from muscle contraction and cardiac regulation to hormone responses, pheromone signaling, bacterial lipopolysaccharide biosynthesis, and Cytochrome P450 pathways\u2014showing no clear, single theme binding the cluster's proteins together.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990938","count":1},{"id":"GO:0033574","count":1},{"id":"GO:0045822","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0019373","count":1}]},{"hash":"466787384415511949","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055121","count":1},{"id":"GO:0010099","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0080022","count":1},{"id":"GO:0070481","count":1}]},{"hash":"442870856286575351","title":"Neddylation and Ubiquitination Regulation","description":"The top GO terms cluster tightly around protein neddylation (and its positive/negative regulation), along with protein catabolic processes and ubiquitin-protein transferase activity, indicating a shared theme of post-translational modification and protein turnover. The other terms are from minor or unrelated overlaps, especially given the small cluster size, but overall the dominant signal is neddylation/ubiquitination control.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000436","count":1},{"id":"GO:0044254","count":1},{"id":"GO:0045116","count":1},{"id":"GO:2000435","count":1},{"id":"GO:0010225","count":1}]},{"hash":"1508898916703691074","title":"Ubiquinone and isoprenoid biosynthesis","description":"GO terms point to terpenoid/isoprenoid biosynthesis (IPP/DMAPP via the MEP pathway) and ubiquinone biosynthesis, with a link to mitochondrial respiratory chain complex assembly, suggesting a cluster of proteins involved in CoQ/isoprenoid production and its role in respiration.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016114","count":1},{"id":"GO:0019288","count":1},{"id":"GO:0050992","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0033108","count":1}]},{"hash":"652030585088302251","title":"Central carbon metabolism with one-carbon flow","description":"The cluster shows core metabolic pathways (glycolysis and TCA cycle) alongside serine biosynthesis/catabolism, one-carbon metabolism through folate/tetrahydrofolate interconversion, and links to methylation and purine biosynthesis. Together these terms point to a coordinated metabolism that feeds energy production with one-carbon unit generation for nucleotide synthesis and methylation reactions, anchored by serine/glycine interconversion. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033512","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0019264","count":1},{"id":"GO:0006564","count":1}]},{"hash":"99896678775408365","title":"Mitochondrial ATP Production","description":"The terms cluster around oxidative phosphorylation, ATP biosynthesis, and assembly of the mitochondrial respiratory chain (complex III), indicating a primary theme of mitochondrial energy metabolism. A few terms relate to Golgi transport and SNARE disassembly, but the dominant signal is mitochondrial energy production.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051013","count":3},{"id":"GO:1903862","count":3},{"id":"GO:0034551","count":3},{"id":"GO:0046034","count":3},{"id":"GO:0032968","count":3}]},{"hash":"836925562800488344","title":"ER stress\u2013regulated calcium homeostasis and anti-apoptotic signaling","description":"The cluster Centers on negative regulation of multiple apoptotic pathways (intrinsic ER-stress\u2013related, extrinsic Fas/death receptor\u2013mediated) and on endoplasmic reticulum calcium homeostasis and calcium transport into the cytosol, suggesting a cohesive role in promoting cell survival under ER stress via calcium signaling. A cerebellar granule layer development term appears only once, indicating it is not the main theme.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021681","count":1},{"id":"GO:0060702","count":1},{"id":"GO:1903298","count":1},{"id":"GO:0032469","count":1},{"id":"GO:1902236","count":1}]},{"hash":"1089140975403175930","title":"Diverse stress response and signaling","description":"This cluster shows terms spanning xenobiotic/stress responses (response to cocaine, cellular response to xenobiotic stimulus), signaling regulation (TGF-beta receptor signaling, nitric oxide biosynthesis, interferon signaling), and genome maintenance (telomerase-mediated telomere maintenance, mismatch repair). The functions are varied rather than pointing to a single cohesive pathway, suggesting a broad stress-response/signaling cluster.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0032516","count":1},{"id":"GO:0030511","count":1},{"id":"GO:0043524","count":1}]},{"hash":"1455860829037481649","title":"Calcineurin-NFAT signaling in hypertrophy and morphogenesis","description":"The cluster's top GO terms cluster around the calcineurin-NFAT pathway and processes of tissue morphogenesis (cardiac hypertrophy, EMT/EMT regulation, angiogenesis, dendrite morphogenesis, excitatory synaptic signaling). This suggests a common theme of calcium-dependent signaling guiding morphological and functional changes across cell types. Some terms (mitotic spindle attachment, lead ion response) appear peripheral or stress-related, but the presence of positive regulation of calcineurin-NFAT signaling supports a cohesive interpretation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014898","count":3},{"id":"GO:0051315","count":2},{"id":"GO:0051037","count":2},{"id":"GO:0010288","count":2},{"id":"GO:0051533","count":2}]},{"hash":"1905134888730582376","title":"Spliceosome Assembly and mRNA Splicing","description":"The top GO terms are dominated by spliceosome-related processes (spliceosomal snRNP assembly, spliceosomal complex assembly, and mRNA splicing via spliceosome), indicating the proteins likely participate in the splicing machinery. Other terms (xenobiotic response, sporulation, insulin processing, etc.) appear less central and may reflect broader or incidental annotations.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0009410","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0030435","count":1}]},{"hash":"685415713421238442","title":"Arabinogalactan Protein Glycosylation","description":"The GO terms are dominated by arabinogalactan protein (AGP)\u2013related processes and plant-specific glycosylation, including AGP metabolic process, poly-N-acetyllactosamine biosynthesis, and O-linked glycosylation via hydroxyproline, along with seed coat mucilage biosynthesis and root hair development. These point to AGP glycosylation and AGP-type cell surface glycoproteins driving plant cell wall remodeling and development. Some insect-related terms appear as outliers, likely annotation noise, but do not outweigh the AGPglycosylation theme. Confidence: High","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030311","count":1},{"id":"GO:0075015","count":1},{"id":"GO:0007299","count":1},{"id":"GO:0048354","count":1},{"id":"GO:0010405","count":1}]},{"hash":"1106719555956344361","title":"Chromatin remodeling and transcription regulation","description":"Top GO terms cluster around chromatin assembly during DNA replication, chromatin remodeling linked to transcription initiation, nucleus organization, and regulation of rRNA transcription, as well as chromosome condensation. This points to a cohesive theme of chromatin dynamics governing transcription and nuclear architecture, with RNA quality control as a related, but secondary, process.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007549","count":2},{"id":"GO:0006335","count":2},{"id":"GO:0045815","count":2},{"id":"GO:0070481","count":2},{"id":"GO:1901837","count":2}]},{"hash":"2039565070788532311","title":"Negative Regulation of Inflammatory Signaling","description":"The cluster is dominated by GO terms describing downregulation of inflammatory cytokines and pathways (TNF, IL-8, IFN-beta, IL-1, LPS) and suppression of TLR signaling, indicating a theme of anti-inflammatory or immunomodulatory regulation. A couple of terms (embryo axis specification and mRNA splicing) appear to be less related, likely annotations of a broader set of proteins, but the core pattern strongly points to suppression of innate immune signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032720","count":1},{"id":"GO:0032717","count":1},{"id":"GO:0008595","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0071356","count":1}]},{"hash":"1151239084346031079","title":"Insect developmental patterning and Notch signaling","description":"These proteins cluster around GO terms tied to imaginal disc leg segmentation, compartment pattern specification, follicle cell adhesion during oogenesis, and positive regulation of Notch signaling, suggesting a shared role in developmental patterning and morphogenesis in insects. Some plant-associated terms appear in the set, which may reflect cross-species annotations or noise, but the core theme is insect development and signaling. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036011","count":1},{"id":"GO:0048354","count":1},{"id":"GO:0007143","count":1},{"id":"GO:0032092","count":1},{"id":"GO:0030311","count":1}]},{"hash":"919610173806694258","title":"Mitotic spindle assembly and microtubule dynamics","description":"This cluster centers on GO terms for mitosis and microtubule-based processes\u2014mitotic spindle assembly, mitotic cell cycle, and microtubule movement with related activities like kinetochore attachment and microtubule depolymerization\u2014suggesting proteins involved in spindle formation and microtubule regulation. A couple of terms referencing neuronal structures appear tangential, but the dominant signal points to cell division machinery. ","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0021685","count":1},{"id":"GO:0070462","count":1}]},{"hash":"1677886965092382934","title":"RNA Pol II Transcription Machinery","description":"The top GO terms cluster around transcription by RNA polymerase II, including initiation, preinitiation complex assembly, and elongation, plus related processes like transcription-coupled repair and fidelity maintenance, indicating these proteins are core components of the Pol II transcription machinery. The presence of apoptotic signaling and histone acetylation regulation terms may reflect broader regulatory links but do not overshadow the primary Pol II transcription theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0006379","count":1},{"id":"GO:0032968","count":1}]},{"hash":"1490224389490397475","title":"Unknown","description":"The GO terms span mitotic cell cycle and cell division, RNA splicing (spliceosome), ubiquitin-dependent protein turnover, and even plant-specific processes like phototropism, plus muscle development; with only one edge and no coherent shared function, there is no unifying theme to label this cluster confidently (one term appears anomalous, female analia development).","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0000398","count":1},{"id":"GO:1904431","count":1}]},{"hash":"1237846767775129605","title":"TGF-beta/BMP signaling regulation","description":"Top terms show clear emphasis on regulating TGF-beta and BMP signaling (negative regulation of TGF-beta receptor signaling and BMP signaling) with SMAD-related processes, suggesting a cluster centered on the TGF-beta/BMP pathway regulation. Some listed terms are unrelated or broad, but the core signal supports this theme.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0035970","count":1},{"id":"GO:0080005","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0000173","count":1}]},{"hash":"2260073697713043159","title":"Cytoskeleton remodeling and endocytosis","description":"The top GO terms repeatedly point to actin filament bundle assembly and positive regulation of pinocytosis, suggesting a core role in cytoskeletal dynamics and membrane trafficking. Other terms touch on signaling and development but are less central, making the actin/endo motif the best unifying theme. ","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060743","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0010745","count":2},{"id":"GO:0003213","count":2},{"id":"GO:0032088","count":2}]},{"hash":"1892079785393830039","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0046677","count":1},{"id":"GO:1990145","count":1},{"id":"GO:0045903","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1373263065133670264","title":"Ribosome Biogenesis and Translation with Cell Cycle Regulation","description":"The top GO terms center on translation and ribosome biogenesis, indicating core roles in protein synthesis. Additional terms point to regulation of the cell cycle, p53-mediated signaling, and ubiquitin-related protein stability, suggesting a coordinated program that links ribosome production and translation with cell-cycle checks and stress responses. The mix implies a function in assembling and regulating the protein-synthesis machinery while ensuring proper cell-cycle progression and protein quality under stress.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0071158","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0050821","count":1},{"id":"GO:1901798","count":1}]},{"hash":"2292897903652162891","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006295","count":1},{"id":"GO:0042787","count":1},{"id":"GO:1902104","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0045116","count":1}]},{"hash":"1373181979261044087","title":"Embryonic cell cycle and DNA replication","description":"The cluster\u2019s top GO terms center on DNA replication, centrosome cycle, and regulation of nuclear DNA replication, with additional developmental processes like mesoderm formation and neural tube patterning, indicating a group of proteins coordinating cell division/DNA synthesis during embryogenesis alongside morphogenesis signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0048701","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0010571","count":3},{"id":"GO:1901621","count":3}]},{"hash":"758761831899110068","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":3},{"id":"GO:0006695","count":2},{"id":"GO:0000453","count":1},{"id":"GO:0017183","count":1},{"id":"GO:0050843","count":1}]},{"hash":"1418428662762944466","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0014718","count":2},{"id":"GO:0033234","count":2},{"id":"GO:0042274","count":1}]},{"hash":"1170441298595056345","title":"Spliceosome Assembly and mRNA Processing","description":"This cluster centers on nuclear RNA processing: spliceosome assembly, mRNA splicing, and related maturation/decay steps, including nuclear import of RNA and rRNA maturation, reflecting a cohesive RNA processing module.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0045292","count":1}]},{"hash":"1242596105139109152","title":"RNA processing and ribosome biogenesis","description":"The GO terms center on RNA maturation (rRNA/LSU processing) and tRNA modification, along with ribosome biogenesis, with a few cell-cycle and telomere-related terms. This points to a cohesive theme of ribosome production and RNA processing during cell proliferation, rather than disparate functions.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1904816","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1024154941959223372","title":"Cell Cycle and Genome Integrity Signals","description":"The GO terms point to processes governing cell cycle control (negative regulation of G0 to G1, G1 DNA damage checkpoint signaling, chromosome segregation) and transcriptional regulation, with additional hints from histone modification and signal transduction. Developmental and organ-specific terms are less central to the core theme but present as peripheral associations. Overall, the cluster appears to reflect proteins involved in coordinating cell cycle progression with genome integrity and transcriptional control.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0070317","count":1},{"id":"GO:0010255","count":1},{"id":"GO:0045143","count":1},{"id":"GO:0010659","count":1}]},{"hash":"395416328947998909","title":"RNA metabolism and translation","description":"The top terms point to post-transcriptional RNA handling (mRNA processing, splicing regulation, mRNA catabolism, mitochondrial mRNA polyadenylation) and translation, suggesting a cluster tied to RNA metabolism and gene expression control at the translational level. Some viral transport and sex-determination terms appear incidental and do not define the core theme. Confidence: Medium.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:1901254","count":1},{"id":"GO:0039702","count":1},{"id":"GO:0030238","count":1},{"id":"GO:0033129","count":1}]},{"hash":"1925797345708106337","title":"RNA processing and translation initiation","description":"The set of GO terms points to RNA metabolism and translation control. Terms include mRNA modification, spliceosome-mediated splicing, preinitiation complex formation, and regulation of translational initiation, as well as mRNA stabilization and small-subunit processome assembly. This pattern suggests the cluster comprises factors involved in RNA processing and the initiation of translation, representing a single functional module bridging transcript processing and translation.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1903586","count":1},{"id":"GO:0031047","count":1}]},{"hash":"904571131424027218","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around mRNA modification, splicing and spliceosome activity, mRNA stabilization, formation of translation preinitiation complex, regulation of translational initiation, and small-subunit processome assembly, plus ncRNA-mediated gene silencing. Together these reflect RNA maturation and metabolism plus the assembly and control of translation machinery (ribosome biogenesis/translation initiation). This makes a cohesive theme of RNA processing and translation regulation.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1903586","count":1},{"id":"GO:0031047","count":1}]},{"hash":"897073776169405465","title":"Unknown","description":"The cluster has no Top Terms listed, so there is no shared GO signal to define a common function among the four proteins. With a small network (3 edges, no triangles) and no functional annotations guiding a theme, the safe label is Unknown.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"1236467613070775439","title":"Diverse Metabolic Catabolic and Biosynthetic Processes","description":"The top GO terms span several different catabolic and biosynthetic pathways (e.g., chlorophyll degradation, prostaglandin and glucuronoside metabolism, biotin and poly-hydroxybutyrate biosynthesis) with no single dominant function. This suggests the cluster comprises enzymes involved in general metabolism rather than a specific pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0015996","count":1},{"id":"GO:1905344","count":1},{"id":"GO:0019391","count":1},{"id":"GO:0019373","count":1}]},{"hash":"2070521431633071075","title":"Peptidoglycan Biosynthesis and Cell Shape","description":"The GO terms cluster tightly around bacterial cell wall biogenesis and morphology, notably cell wall organization, regulation of cell shape, and peptidoglycan/D-alanine biosynthesis, pointing to a group of enzymes involved in cell-wall synthesis and structural remodeling. Some other terms (e.g., xenobiotic response, insulin-related) appear incidental and do not alter the central theme. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0030632","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0070178","count":1}]},{"hash":"1665482547849101374","title":"Spliceosome and Translation Initiation Components","description":"The GO terms point strongly to RNA processing: regulation of alternative mRNA splicing via the spliceosome, processome assembly, formation of the translation preinitiation complex, and mRNA stabilization/modification. Together these suggest proteins involved in spliceosome-driven splicing plus early steps of translation initiation, justifying a label for spliceosome and translation initiation components.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":4},{"id":"GO:0016556","count":3},{"id":"GO:0034462","count":3},{"id":"GO:0075525","count":3},{"id":"GO:1903586","count":3}]},{"hash":"1359600525640458063","title":"Regulatory signaling and transcription control","description":"These proteins are linked to multiple regulatory processes across signaling pathways, transcription, and immune/metabolic responses (e.g., regulation of PPAR signaling, transcription from DNA, NLRP3 inflammasome regulation, MHC II biosynthesis regulation, and responses to various stimuli). The diverse, regulation-focused GO terms suggest a broad regulatory role rather than a single concrete function, hence the label.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035358","count":1},{"id":"GO:0031940","count":1},{"id":"GO:0071872","count":1},{"id":"GO:0045348","count":1},{"id":"GO:0061428","count":1}]},{"hash":"2282005232572812030","title":"Unknown","description":"The terms cover disparate biological themes\u2014from immune regulation and spermatogenesis to developmental patterning and cellular stress\u2014without a unifying function across the cluster, so a concise, representative label cannot be determined.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032815","count":1},{"id":"GO:0048515","count":1},{"id":"GO:0038005","count":1},{"id":"GO:0034620","count":1},{"id":"GO:1904211","count":1}]},{"hash":"1101991775104469321","title":"Unknown","description":"No shared GO terms or protein interactions are evident for these four proteins, and no top terms are given, so a common, interpretable function cannot be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1034489307627295361","title":"Unknown","description":"The listed GO terms are highly diverse, spanning epithelial development, immune regulation, cardiac morphogenesis, actin assembly, signaling, pinocytosis, and hepatocyte apoptosis, with no single coherent function dominating the set. The small cluster size and lack of cohesive functional signal make a reliable, specific label unlikely.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060743","count":1},{"id":"GO:1901594","count":1},{"id":"GO:0010745","count":1},{"id":"GO:0003213","count":1},{"id":"GO:0032088","count":1}]},{"hash":"850194403656420777","title":"Oogenesis and germ plasm assembly","description":"These proteins are linked to oocyte development, with terms for oogenesis, oocyte microtubule cytoskeleton organization/polarization, and pole plasm assembly, indicating roles in germ plasm establishment and egg maturation. The presence of translation-related terms (ribosome biogenesis, translation, mRNA export) suggests concurrent protein synthesis capacity during oogenesis, supporting a cohesive theme of oocyte development coupled with germ plasm organization. Some terms appear peripheral, but the core signal aligns with oogenesis and germ plasm assembly.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0007315","count":1},{"id":"GO:0000335","count":1}]},{"hash":"1778225431612075693","title":"DNA Damage Response and Translational Regulation","description":"The proteins are linked to DNA damage sensing/response (including p53-mediated signaling, gamma radiation, and UV-related responses) and to transcriptional control (elongation/termination), as well as translation regulation and ribosome biogenesis. This combination points to a theme of coordinating gene expression during DNA damage response, justifying a label around DNA damage response with translational regulation.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902167","count":1},{"id":"GO:0006354","count":1},{"id":"GO:0071480","count":1},{"id":"GO:0045727","count":1},{"id":"GO:0042273","count":1}]},{"hash":"1478291295219997026","title":"Ubiquitin\u2013Proteasome Regulation and Cell Cycle","description":"The cluster is dominated by GO terms related to the ubiquitin-proteasome system\u2014deubiquitination and proteasome core complex assembly\u2014as well as regulation of ubiquitin ligase activity and G2/M cell cycle transitions. This suggests a cohesive theme around protein turnover governing signaling and cell cycle control, with indirect links to pathways like Wnt signaling. The limited number of proteins and some divergent terms mean the link is plausible but not exhaustively supported, hence a medium confidence.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0043488","count":2},{"id":"GO:0010043","count":2},{"id":"GO:0010363","count":2},{"id":"GO:0090263","count":2}]},{"hash":"427759582560416143","title":"RNA and protein methylation enzymes","description":"The GO terms are dominated by RNA modification (tRNA wobble uridine modification; RNA guanine-N7-methylation) and various protein methylation events (protein methylation; N-terminal peptidyl-serine dimethylation), suggesting a core theme of RNA and protein methylation/modification enzymes. Other terms like regulation of mitochondrial transcription and cellular senescence may reflect broader stress-related roles, but the central signal is methylation-related modification activities.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":1},{"id":"GO:0046685","count":1},{"id":"GO:0052046","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0090398","count":1}]},{"hash":"1401365831590050862","title":"Chromatin assembly and cell cycle regulation","description":"This cluster centers on chromatin dynamics and transcription in the context of the cell cycle, highlighted by CENP-A\u2013containing chromatin assembly, DNA-templated transcription, and regulation of G0 to G1 transition and G1 DNA damage checkpoint signaling. It also includes related chromatin-modifying processes (e.g., histone methylation) and supportive terms like ribosome biogenesis, suggesting a broader nucleolar/nuclear context. Overall, the proteins appear linked to chromatin organization intertwined with cell cycle control.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0070317","count":1},{"id":"GO:0010255","count":1},{"id":"GO:0045143","count":1},{"id":"GO:0010659","count":1}]},{"hash":"1386449977914285683","title":"Ribosome biogenesis and translation","description":"Top GO terms indicate translation and maturation of SSU-rRNA from a tricistronic transcript, pointing to ribosome assembly/biogenesis coupled with protein synthesis. The proteins likely participate in ribosome maturation and function, justifying the chosen name.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000462","count":1}]},{"hash":"313543074241671987","title":"Oxidative Stress Response and Redox Homeostasis","description":"The GO terms are dominated by redox-related processes\u2014cellular redox homeostasis, oxidant detoxification, and protein deglutathionylation\u2014pointing to a coherent cluster centered on managing oxidative stress and maintaining redox balance, with a few peripheral metabolic terms.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009263","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0071473","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0080058","count":1}]},{"hash":"630114745748974703","title":"Actin Cytoskeleton Assembly and Cell Motility","description":"The top GO terms cluster around actin cytoskeleton organization and dynamics (cell migration, gliding, and actin assembly in cortices, budding and mating projections, brush border, and muscle fibers), suggesting a common theme of actin-based structural assembly supporting motility and morphogenesis across contexts.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006930","count":1},{"id":"GO:0051295","count":1},{"id":"GO:0071976","count":1},{"id":"GO:0021592","count":1},{"id":"GO:0055003","count":1}]},{"hash":"1469259339290810674","title":"Photorespiration and related plant metabolism","description":"The terms strongly point to photorespiration and glycolate processing (GO:0009853, GO:0009854, GO:0046296), with related carbon metabolism in plants (e.g., glycine betaine transport, isoprenoid biosynthesis). The presence of a protein homotetramerization term is generic and not defining. Overall, the cluster centers on plant photorespiration and associated metabolic processes.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009854","count":1},{"id":"GO:0006144","count":1},{"id":"GO:0018924","count":1},{"id":"GO:0031460","count":1},{"id":"GO:0008299","count":1}]},{"hash":"2061939338919611403","title":"Cell-cycle and morphogenesis signaling","description":"This cluster includes terms tied to mitotic spindle-kinetochore attachment and meiotic cell cycle, EMT/morphogenesis, and vascular branching, plus signaling contexts like NFAT and excitatory synaptic potential. The combination points to roles in both cell division and developmental remodeling rather than a single precise pathway, so a label encompassing both domains fits best.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051315","count":3},{"id":"GO:0051037","count":3},{"id":"GO:0010288","count":3},{"id":"GO:0051533","count":3},{"id":"GO:0050774","count":3}]},{"hash":"1811663997322740998","title":"Neural development and synaptic signaling","description":"The top GO terms are dominated by neuronal development and synaptic activity, including axonogenesis, CNS neuron development, and excitatory postsynaptic potential, indicating a cluster centered on neural differentiation and synaptic function. Wnt signaling related to apoptosis also ties into developmental regulation, supporting a theme of neural development with apoptosis modulation. Some terms like innate immune response or pheromone-induced cell cycle arrest appear peripheral, but do not override the core neural theme.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000751","count":3},{"id":"GO:0032092","count":3},{"id":"GO:0007409","count":3},{"id":"GO:1900086","count":3},{"id":"GO:0044337","count":3}]},{"hash":"678032786462041205","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0006310","count":1},{"id":"GO:0031124","count":1},{"id":"GO:1902775","count":1}]},{"hash":"1659903782523518668","title":"DNA Damage Response and Recombination","description":"The top GO terms cluster around DNA recombination, meiosis-specific chromatid cohesion, and responses to DNA-damaging conditions (X-ray, cisplatin, xenobiotics), together indicating a function in sensing and repairing DNA damage and managing recombination events during meiosis and mitosis.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007066","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0010165","count":1},{"id":"GO:0072719","count":1},{"id":"GO:0007141","count":1}]},{"hash":"571854253461568454","title":"Spliceosome Components and RNA Processing","description":"The GO terms are dominated by mRNA splicing via the spliceosome and spliceosomal assembly (snRNP assembly, spliceosomal complex assembly), indicating core components of the splicing machinery. Additional terms point to RNA metabolism (P-body assembly, deadenylation-dependent decapping, histone mRNA metabolism) and nuclear import, suggesting these proteins function within RNA processing pathways in both the nucleus and cytoplasm, with a focus on splicing-related roles.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0030490","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0070317","count":1}]},{"hash":"904191117409183127","title":"Mitotic cell cycle regulation","description":"These proteins show a cohesive theme around cell cycle control and mitosis: negative regulation of G0 to G1 transition, G1 DNA damage checkpoint signaling, mitotic cell cycle progression, and chromosome segregation. Additional terms related to transcription and chromatin modification fit into the broader regulatory context of cell division. Some outlier terms (glucose signaling, viral mRNA export) exist, but the dominant signal points to cell cycle control and chromosomal processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0010255","count":1},{"id":"GO:0045143","count":1},{"id":"GO:0046784","count":1},{"id":"GO:0010659","count":1}]},{"hash":"1793498735640918476","title":"Cell Cycle and Kinase Signaling Regulators","description":"GO terms show regulation of GTPase and serine/threonine kinase activity, mitotic cell cycle processes, and control of G0 to G1 transition, indicating a theme of signaling and cell-cycle regulation. Additional terms (mRNA transport, hypoxia response, autophosphorylation, chromosome segregation, cardiac apoptotic processes) reflect broader regulatory roles but still point to modulating cellular signaling and division rather than forming a structural complex.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0071456","count":2}]},{"hash":"1159570472640308467","title":"DNA damage response and repair","description":"This cluster's GO terms point to DNA damage response and repair pathways (DNA recombination, replication fork unwinding, and responses to DNA-damaging agents like X-ray and cisplatin). The meiosis-specific terms likely reflect related chromatid cohesion/maintenance roles, but the overarching theme is genome integrity maintenance.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0007066","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0010165","count":1},{"id":"GO:0072719","count":1}]},{"hash":"1133159170274821501","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000447","count":1}]},{"hash":"589852330333955242","title":"RNA processing and translation initiation","description":"GO terms center on RNA metabolism (mRNA modification, spliceosome, mRNA stability) and translation initiation/pri\u00admary ribosome assembly, suggesting a functional cluster in RNA processing linked to translation control.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1903586","count":1},{"id":"GO:0031047","count":1}]},{"hash":"460789044594167107","title":"Calcium-Driven Muscle Signaling","description":"The cluster appears focused on calcium signaling related to muscle activity and neurotransmitter release. Go terms such as positive regulation of ER calcium concentration, calcium transport from cytosol to ER, regulation of calcium ion-dependent exocytosis of neurotransmitter, and regulation of fast-twitch skeletal muscle fiber contraction point to a shared calcium-mediated control of muscle function and synaptic processes. Some related terms (biosynthetic processes and otolith mineralization) may reflect annotation noise or broader calcium-related roles, but the dominant theme is calcium-dependent regulation of muscle activity.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051479","count":1},{"id":"GO:0051473","count":1},{"id":"GO:0032470","count":1},{"id":"GO:0045299","count":1},{"id":"GO:0009103","count":1}]},{"hash":"221935927266129472","title":"Oxidative Stress Response and Redox Metabolism","description":"The terms cluster around responses to oxidative and electrophilic stress (hydrogen peroxide, methylglyoxal) and redox detoxification pathways (glutathione, ascorbic acid biosynthesis), plus a stress-activated signaling cascade. Drug metabolism terms (daunorubicin/doxorubicin) also tie into oxidative stress, while a few terms like arabinose catabolism and potassium transport are peripheral. Overall, the set points to a redox/stress-response functional theme for the group.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0044597","count":1},{"id":"GO:0097238","count":1},{"id":"GO:0019568","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0070301","count":1}]},{"hash":"467899458370255321","title":"Transcription initiation by RNA polymerases I\u2013III","description":"The Top Terms are dominated by processes related to DNA-templated transcription initiation and preinitiation complex assembly for RNA polymerases I, II, and III, plus regulation of transcription initiation by these polymerases, pointing to a cluster centered on transcription initiation machinery across multiple polymerases. Some terms like spermatogenesis and translation initiation appear as minor outliers, but the core signal is multi-polymerase transcription initiation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006352","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0045893","count":1},{"id":"GO:0006413","count":1}]},{"hash":"1643994101158791642","title":"RNA Pol II transcription and chromatin regulation","description":"This cluster\u2019s top GO terms center on RNA polymerase II\u2013driven transcription (elongation and termination) and chromatin-related processes (histone modifications and heterochromatin assembly), suggesting a nuclear regulatory role. Some terms related to development appear incidental, but the dominant theme ties to transcriptional control and chromatin dynamics.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0071441","count":2},{"id":"GO:0006369","count":2},{"id":"GO:0048752","count":2}]},{"hash":"436544382040688793","title":"Nuclear stress response and transcription regulation","description":"The top GO terms point to transcriptional control activities in the nucleus (DNA-templated transcription, negative regulation of transcription by RNA polymerase II, and negative regulation of protein export from the nucleus) alongside stress response pathways (response to ER stress, cellular response to oxidative stress, and redox-related processes like deglutathionylation). This suggests a small cluster of proteins involved in coordinating transcriptional responses to cellular stress within the nucleus, rather than a single, narrowly defined process.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046826","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0080058","count":1},{"id":"GO:0006662","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1640370635958744397","title":"Unknown","description":"The GO terms are highly diverse (translation fidelity, interferon response, metal and oxidative stress, chlorophyll and histone-related processes, cell cycle transition) with no clear common function or pathway linking the proteins, and there are no interactions among them, so a cohesive label isn\u2019t supported.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":2},{"id":"GO:0035457","count":1},{"id":"GO:0010288","count":1},{"id":"GO:0070301","count":1},{"id":"GO:0061087","count":1}]},{"hash":"1012482178774892224","title":"Clathrin-mediated endocytosis and GPCR internalization","description":"The top GO terms show strong signals for endocytosis, especially clathrin-dependent routes and GPCR internalization, indicating a membrane trafficking-focused cluster. Additional terms related to Golgi retention and vesicle/tubule dynamics support a broader vesicle trafficking theme, with some peripheral connections to organelle dynamics.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0002031","count":1},{"id":"GO:0072583","count":1},{"id":"GO:1901387","count":1},{"id":"GO:1900063","count":1}]}]