[{"hash":"1880378805796434373","title":"Mitosis control via ubiquitin-mediated proteolysis","description":"Based on the top GO terms, the cluster centers on cell division and the mitotic cell cycle, including APC/C-dependent catabolic processes and K11-linked ubiquitination, which indicates regulation of mitosis through ubiquitin-mediated proteolysis. Some terms reference ribosome maturation and innate immune response, but the strongest and most frequent signals pertain to mitotic control and protein ubiquitination, supporting this label.","confidence":"High","size":29,"edges":18,"triangles":5,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:2001162","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0000278","count":4}]},{"hash":"800195593317962259","title":"Mitotic cell division and ER-Golgi transport","description":"The label reflects strong enrichment for mitotic processes (mitotic spindle assembly, mitotic cell cycle, cell division) and significant vesicle trafficking activity (COPII-coated vesicle budding, retrograde transport Golgi to ER), with accompanying growth-related signals, suggesting a module that links cell division with secretory pathway dynamics during development.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0048813","count":3}]},{"hash":"1374736878294113348","title":"Steroid and lipid metabolism","description":"The set of GO terms centers on hormone biosynthesis (testosterone biosynthetic process, androgen catabolic process) alongside lipid-related pathways (sphingolipid biosynthesis, fatty acid elongation, very long-chain fatty acid biosynthetic process, phylloquinone catabolic process, retinal metabolic process), suggesting a cohesive module for lipid and steroid metabolic processes; a couple of terms (response to methotrexate, regulation of transcription) appear secondary to this core theme.","confidence":"Medium","size":29,"edges":27,"triangles":6,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0061370","count":4},{"id":"GO:0031427","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006710","count":4}]},{"hash":"612094520266027964","title":"Membrane trafficking and ion transport","description":"The cluster shows a cohesive signal around membrane-related processes: endocytosis, ion homeostasis and export (potassium and sodium), and protein import into organelles (peroxisome) as well as ER-associated degradation, which points to intracellular transport and maintenance of ion balance. Some terms like stilbene catabolism and LPS biosynthesis appear as noisy annotations, but the dominant theme is membrane trafficking and ion transport.","confidence":"Medium","size":29,"edges":11,"triangles":2,"max_degree":4,"top_function":"establishment or maintenance of cell polarity","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006897","count":4},{"id":"GO:0030007","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0031448","count":4}]},{"hash":"418092093538249197","title":"Nuclear Transcription Regulators and Redox Signaling","description":"This cluster is dominated by GO terms related to transcription regulation and DNA binding (DNA-templated transcription, regulation of transcription by RNA Pol II, positive/negative regulation of DNA binding), suggesting nuclear transcription-modulating functions. The concurrent presence of signaling-related terms (regulation of GTPase activity, calcineurin-NFAT signaling cascade, phosphatidylinositol dephosphorylation) and redox-associated processes (cell redox homeostasis, protein deglutathionylation) indicates these proteins may also modulate signaling and redox states, linking transcription control with signaling pathways.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043388","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0045454","count":4}]},{"hash":"1751366528358060709","title":"Neural development and MAPK-regulated axon growth","description":"The top terms cluster around nervous system development (including hippocampus development), dendrite morphogenesis, and positive regulation of axon extension, plus signaling pathways such as ERK and JNK cascades and phosphorylation events. This suggests proteins involved in neuronal differentiation and neurite outgrowth regulated by MAPK signaling; the mitotic cell cycle term may reflect neurogenesis but is secondary.","confidence":"High","size":29,"edges":11,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0048813","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0045773","count":5},{"id":"GO:0001403","count":5}]},{"hash":"1066717193908375487","title":"GTPase-regulated cytoskeleton and trafficking","description":"The top GO terms point to regulation of small GTPases (Rac, Rho) and their signaling, including positive regulation of GTPase activity and regulation of Rac/Rho pathways, alongside processes involving Golgi localization, endothelial tube formation, and vascular permeability. Dendritic spine modification also ties to cytoskeletal dynamics, while ER unfolded protein response hints at integration with cellular stress responses. Together, these terms suggest a cohesive theme where GTPase signaling governs cytoskeleton remodeling and membrane trafficking across cell types. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904425","count":2},{"id":"GO:0098886","count":2},{"id":"GO:0097498","count":2},{"id":"GO:0035021","count":2},{"id":"GO:0043114","count":2}]},{"hash":"717876124465747115","title":"Innate Immune Defense and Mitochondrial Dynamics","description":"The cluster is dominated by GO terms for innate immunity and antiviral/bacterial defense (defense response to virus, innate immune response, defense response to Gram-positive bacterium, antibacterial peptide biosynthetic process), with additional connections to mitochondrial regulation (positive regulation of mitochondrial fission and depolarization) and inhibition of viral material transport. Some annotations (GPCR signaling, FSH signaling, obsolete ERAD) may be peripheral or noisy, but the core theme ties immune defense to mitochondrial dynamics. This supports labeling the group as innate immune defense with mitochondrial involvement.","confidence":"Medium","size":28,"edges":4,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":9},{"id":"GO:0045087","count":9},{"id":"GO:0030433","count":6},{"id":"GO:0050830","count":6},{"id":"GO:0007200","count":6}]},{"hash":"1349167819940669329","title":"Reproductive hormone signaling and ovarian development via cAMP","description":"The cluster is dominated by GO terms related to FSH and LH signaling, ovarian follicle growth, and uterus development, all indicating endocrine signaling governing reproductive tissues. Activation of adenylate cyclase and related signaling (cAMP, IP3) suggests a shared second-messenger framework. Some terms like defense response to virus are peripheral noise, but do not outweigh the reproductive signaling theme.","confidence":"Medium","size":28,"edges":245,"triangles":1063,"max_degree":25,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":26},{"id":"GO:0042699","count":26},{"id":"GO:0001545","count":26},{"id":"GO:0060065","count":26},{"id":"GO:0009992","count":26}]},{"hash":"551337072494675334","title":"Ribosome biogenesis and rRNA processing","description":"This cluster is dominated by GO terms related to ribosome assembly and RNA maturation, including ribosome biogenesis, translation, and maturation of LSU- and 5.8S rRNA. The presence of DNA replication and chromatin organization hints at nuclear/nucleolar coordination of ribosome production and cell-cycle processes, supporting a cohesive theme around ribosome biogenesis and RNA processing.","confidence":"High","size":28,"edges":192,"triangles":1050,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000902","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1340850563405282891","title":"Developmental transcription and stress-response cluster","description":"The top GO terms center on DNA-templated transcription and various developmental processes (multicellular development, forebrain development, neural tube closure), suggesting a theme of transcriptional regulation during development. Additional terms point to cellular stress and defense responses (ER stress\u2013related apoptosis, cadmium response, antibiotic defense, Gram-positive bacteria defense), indicating linkage between developmentally regulated transcription and stress pathways. A few items like sperm capacitation are reproductive, but they can be encompassed within broader developmental biology contexts, supporting a cohesive label focused on developmental gene regulation with stress-response links.","confidence":"Medium","size":28,"edges":18,"triangles":6,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0007275","count":4},{"id":"GO:0048240","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0006349","count":3}]},{"hash":"1617224180911803270","title":"Developmental signaling and morphogenesis","description":"The top GO terms cluster around signaling pathways and developmental processes across tissues: Wnt and neurotrophin signaling, angiogenesis, branching morphogenesis, and axon guidance, with some immune signaling (T cell differentiation, IL-7 response). This suggests a general theme of signaling directing development and tissue organization rather than a single specific function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0046638","count":3},{"id":"GO:0045056","count":3},{"id":"GO:0060068","count":2},{"id":"GO:0048011","count":2}]},{"hash":"1960208036603020213","title":"Developmental Signaling Pathways","description":"GO terms emphasize signaling cascades (Wnt, PDGF), chemotaxis, and developmental processes (cardiac morphogenesis, pro-B cell differentiation) with a few broader terms (DNA repair, apoptosis) that may reflect annotation noise; overall the cluster appears enriched for signaling pathways governing development and cell fate.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":3},{"id":"GO:0007257","count":3},{"id":"GO:0036120","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0090305","count":2}]},{"hash":"291436695182927766","title":"Endosome-Golgi Transport Regulators","description":"The frequent terms describe trafficking between endosomes, Golgi, and plasma membrane (e.g., recycling endosome to Golgi, retrograde transport), along with Rap signaling. This points to a cluster of proteins that primarily govern membrane trafficking and related signaling, with some secondary regulatory roles in cell cycle and ciliogenesis.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0071955","count":3},{"id":"GO:1902543","count":3},{"id":"GO:0051534","count":3},{"id":"GO:0032486","count":3},{"id":"GO:0048227","count":3}]},{"hash":"1749312473632291037","title":"GPCR Hormone Signaling in Reproduction","description":"Most top GO terms point to reproductive signaling and development: FSH and LH signaling, primary ovarian follicle growth, uterus development, and development of secondary sexual characteristics. Activation of adenylate cyclase and IP3 biosynthesis indicate GPCR-mediated cAMP and Ca2+ signaling pathways driving these processes. A few terms like defense response to virus or water homeostasis appear peripheral or noisy relative to the dominant reproductive signaling theme. Hence this cluster likely comprises proteins involved in hormone-driven GPCR signaling in reproductive tissues.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":9},{"id":"GO:0042699","count":9},{"id":"GO:0001545","count":9},{"id":"GO:0060065","count":9},{"id":"GO:0009992","count":9}]},{"hash":"776451052947411712","title":"Innate antiviral signaling via ubiquitination","description":"Represents antiviral innate immunity driven by ubiquitin signaling: defense/innate response to virus, ubiquitin-dependent proteolysis (including autoubiquitination and K63-linked ubiquitination), and NF-\u03baB/TNF pathways.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051607","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":5},{"id":"GO:1903265","count":5}]},{"hash":"430478471496667169","title":"Neuronal development and neurite outgrowth","description":"The top GO terms converge on nervous system development, dendrite morphogenesis, hippocampus development, and axon extension, suggesting a cluster enriched for neuronal differentiation and neurite outgrowth. Supporting terms like ERK cascade regulation and actin cytoskeleton reorganization align with signaling and structural remodeling required for neurite growth. Despite a few obsolete entries, the overall theme points to neuronal development processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043552","count":5},{"id":"GO:0031532","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0048813","count":4},{"id":"GO:0007399","count":4}]},{"hash":"1140684819367538754","title":"Cell Wall and Envelope Polysaccharide Biosynthesis","description":"The top GO terms cluster around cell wall organization, lipopolysaccharide biosynthesis, and various carbohydrate biosynthetic pathways (GDP-mannose, UDP-GlcNAc, glycogen), pointing to coordinated assembly of surface polysaccharides and envelope components. Some terms also touch on cell morphogenesis and shape regulation, supporting a theme of envelope remodeling rather than cytosolic metabolism. Consequently, the cluster seems best described as a cell wall/envelope biosynthesis module.","confidence":"High","size":27,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0009298","count":4},{"id":"GO:0006048","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0005978","count":4}]},{"hash":"644838513464731145","title":"Intracellular Transport and Localization","description":"Top GO terms cluster around transport and localization processes, including proton transmembrane transport, translocation into host cell cytoplasm, and positive regulation of protein localization to Cajal bodies and telomeres. This pattern points to proteins involved in intracellular movement and targeting to nuclear substructures, rather than external signaling. Some terms (like response to cocaine or inflammatory response) seem ancillary or noisy. Therefore the cluster is best described as Intracellular Transport and Localization.","confidence":"Medium","size":27,"edges":256,"triangles":1572,"max_degree":26,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015991","count":6},{"id":"GO:1901998","count":5},{"id":"GO:0044053","count":5},{"id":"GO:0007339","count":5},{"id":"GO:1904871","count":5}]},{"hash":"2181864375615446364","title":"Tyrosine Phosphatase\u2013Mediated Signaling Inhibition","description":"The top GO terms point to peptidyl-tyrosine dephosphorylation and the negative regulation of key signaling pathways (ERK/MAPK and PI3K/AKT), with additional associations to cell cycle, kinetochore localization, and synaptic organization. This pattern strongly suggests a cluster of tyrosine phosphatases and related regulators that dampen signaling and influence cell division and synaptic/adhesion processes. ","confidence":"High","size":27,"edges":297,"triangles":2187,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035335","count":18},{"id":"GO:0070373","count":18},{"id":"GO:0050860","count":18},{"id":"GO:0000200","count":18},{"id":"GO:0007049","count":15}]},{"hash":"505686756071862314","title":"Neural development and synaptic signaling","description":"The cluster centers on nervous system development, dendrite morphogenesis, hippocampus development, axon extension, and excitatory synaptic signaling, with supporting terms on regulation of phosphorylation and protein stability. This pattern points to proteins involved in neuronal growth, differentiation, and synapse formation/maintenance, rather than housekeeping processes. Occasional terms like mitotic cell cycle and T cell receptor signaling may reflect shared components or broad expression, but the dominant theme is neural development and synaptic function.","confidence":"High","size":27,"edges":19,"triangles":2,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":14},{"id":"GO:0048813","count":13},{"id":"GO:0007399","count":13},{"id":"GO:0045773","count":13},{"id":"GO:0033138","count":13}]},{"hash":"1467805889882330264","title":"Ubiquitin-Mediated Xenobiotic and Antibiotic Stress Response","description":"The top GO terms point to responses to antibiotic and xenobiotic stimuli and to ubiquitination/ERAD pathways, indicating a cluster focused on coping with chemical stress via ubiquitin-dependent protein quality control. While a few terms pertain to sterol metabolism, the dominant signal is external-stress response coupled with protein degradation, suggesting a cohesive theme of ubiquitin-mediated handling of xenobiotic challenges.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0042493","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0009245","count":2}]},{"hash":"327185132725996734","title":"Neurodevelopment and brain formation","description":"The top GO terms show strong enrichment for neural development-related processes, notably forebrain development, brain development, and neural tube closure, suggesting the proteins cluster around neurodevelopment. While other terms (mitotic spindle assembly, transcription, ER-Golgi transport, defense to Gram-positive bacteria) are present, they are less representative of the core theme. Therefore, naming it Neurodevelopment and brain formation captures the principal function of this cluster.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006349","count":4},{"id":"GO:0070059","count":4}]},{"hash":"2193441377407172698","title":"Embryonic Development and ER-Golgi Transport","description":"The dominant signal is ER-to-Golgi vesicle transport, suggesting a secretory pathway cluster, with gastrulation and embryonic organ development pointing to a role in early morphogenesis; cilium assembly adds a possible link to developmental ciliogenesis. Some terms (obsolete aging, histone deacetylation) may be legacy annotations and less informative.","confidence":"Medium","size":27,"edges":17,"triangles":20,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0007568","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0048568","count":3},{"id":"GO:0007369","count":3}]},{"hash":"611905804136605698","title":"Transcription, Translation, and Chromatin Regulation","description":"The top GO terms cluster around core gene expression control: transcription (DNA-templated transcription, RNA Pol II tethering to the nuclear periphery, transcription-related complexes), chromatin modification (histone methylation), translation initiation/reinitiation, and associated RNA processing and protein turnover (nuclear mRNA surveillance, ubiquitin-dependent proteolysis). This suggests a cohesive theme of regulation across transcription, translation, and chromatin states.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006511","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0051568","count":3}]},{"hash":"1952446559032117701","title":"Rap GTPase Signaling and Vesicle Trafficking","description":"The top terms center on activation/regulation of GTPase activity, especially Rap signaling, together with multiple membrane-traffic processes (endosome\u2013Golgi, recycling endosome to Golgi, plasma membrane to endosome). This suggests a coherent role in small GTPase\u2013driven vesicle trafficking within the secretory/endosomal pathways; a few terms about apoptotic signaling or spindle localization seem less central to this core function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0043547","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0071955","count":2},{"id":"GO:1902543","count":2}]},{"hash":"1243634641768093001","title":"Endocytosis and actin-cytoskeleton regulation","description":"The top terms converge on membrane trafficking via clathrin-dependent endocytosis and regulation of actin dynamics (Arp2/3), with supporting signals (ERK, Rho, TGF-beta) and ubiquitination that often accompany endocytic and cytoskeletal processes. This suggests a core theme centered on endocytosis coupled with cytoskeletal remodeling, hence the chosen label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034316","count":2},{"id":"GO:0072583","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006623","count":2}]},{"hash":"1841377996033570423","title":"Transcription Regulation and Vesicle Trafficking","description":"The cluster is enriched for transcription initiation at RNA Pol II promoters, transcription-coupled nucleotide-excision repair, and regulation of transcription via serum response element binding, plus glucocorticoid signaling, suggesting core transcriptional control elements; it also includes exocytosis, slow endocytic recycling, and actin filament depolymerization, pointing to coordination between gene regulation and vesicle trafficking/cytoskeletal remodeling. A few terms (dopaminergic differentiation, sulfur oxidation, obsolete GO) are less coherent with the rest.","confidence":"Medium","size":26,"edges":19,"triangles":16,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0030042","count":2},{"id":"GO:1904948","count":2},{"id":"GO:0010735","count":2}]},{"hash":"1699097370832076000","title":"Cell proliferation with secretory pathway activity","description":"This cluster is dominated by mitotic and proliferative terms (mitotic cell cycle, cell division, mitotic spindle assembly, cell population proliferation) and includes key components of the secretory machinery (COPII-coated vesicle budding, ER-Golgi transport, Golgi\u2013ER retrograde transport). Ribosome biogenesis also appears, supporting a growth/production axis. While brain development and cadmium ion response appear, the core theme ties cell growth and division to protein synthesis and intracellular trafficking, suggesting a cohesive growth-proliferation plus secretory pathway signature.","confidence":"Medium","size":26,"edges":18,"triangles":9,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0051301","count":8},{"id":"GO:0006888","count":8},{"id":"GO:0090307","count":7},{"id":"GO:0008283","count":7}]},{"hash":"1946655944501832155","title":"Ribosome biogenesis and translation","description":"The cluster is enriched for ribosome-related processes, including ribosome biogenesis, ribosomal subunit export from nucleus, translation initiation, formation of translation preinitiation complex, and general translation. While there are a few outliers related to transcription regulation, DNA replication and splicing, the dominant GO signals point to assembly of ribosomes and active protein synthesis, justifying a label centered on ribosome biogenesis and translation.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0045190","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1983905719365023910","title":"Mitotic control and genome maintenance","description":"Top GO terms cluster around cell cycle and genome stability: centrosome cycle, mitotic metaphase/anaphase transition, maintenance of sister chromatid cohesion, and telomere maintenance via recombination, with supporting terms for transcription regulation and microtubule localization. Although a few terms reference innate immunity or are obsolete, the dominant signal points to proteins involved in mitosis and chromatin/genome maintenance. Therefore a label like \u201cMitotic control and genome maintenance\u201d best captures the shared function. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0045842","count":2}]},{"hash":"1732103296095079116","title":"Actin Remodeling and Epithelial Cell Migration","description":"This cluster is governed by strong actin-related terms (filament bundle assembly, nucleation, polymerization, barbed-end capping, lamellipodium morphogenesis) combined with cell migration and establishment of epithelial cell polarity, and includes related signaling (EGFR) and growth factor responsiveness (TGF-beta). The co-occurrence of cytoskeletal dynamics with polarity and trafficking hints at coordinated actin remodeling during motile epithelial behavior, with vesicle trafficking (COPII cargo loading) supporting membrane delivery during movement.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051017","count":5},{"id":"GO:0016477","count":4},{"id":"GO:0090162","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0051127","count":4}]},{"hash":"1077694532606185535","title":"Neuronal translation and synaptic signaling","description":"This cluster shows enrichment in neural-related functions: brain development, ephrin receptor signaling, and regulation of synaptic vesicle exocytosis, indicating a role in neural signaling and synaptic transmission. The presence of translation initiation and reinitiation terms suggests coordinated protein synthesis control in neurons. While a few terms are broader or obsolete, the overall theme points to neuronal development and synaptic function with translation regulation as a supporting mechanism.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0031384","count":2},{"id":"GO:0048013","count":2}]},{"hash":"121003148094545149","title":"Nuclear import and intracellular trafficking","description":"This cluster centers on import of nuclear proteins (NLS-bearing proteins, ribosomal protein import), mRNA transport, and transcription regulation by RNA polymerase III, combined with multiple intracellular trafficking steps (endosome to melanosome transport, targeting proteins to lysosome). The presence of GTPase activity regulation and ciliary basal body docking suggests broader control of localization and signaling. Overall, the dominant theme is intracellular transport and nuclear RNA handling.","confidence":"Medium","size":25,"edges":10,"triangles":3,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006607","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0045945","count":5},{"id":"GO:0035646","count":4}]},{"hash":"1701908914052925626","title":"RNA processing and cell cycle regulation","description":"The cluster centers on RNA processing and gene expression control, with GO terms for mRNA splicing via spliceosome, rRNA maturation, ncRNA-mediated gene silencing, translation, and key cell cycle/replication processes (mitotic cycle, centrosome cycle, DNA replication). The presence of development-related term suggests broader roles during growth. This combination supports a cohesive theme around RNA processing linked to cell division machinery.","confidence":"High","size":25,"edges":34,"triangles":25,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0031047","count":5}]},{"hash":"1935978043250803206","title":"Ribosome biogenesis and translation initiation","description":"These proteins cluster around core ribosome assembly and translation initiation processes: ribosome biogenesis, maturation of rRNA, formation of translation preinitiation complex, translation initiation and reinitiation. Some members also relate to RNA Pol II transcription initiation complexes and rDNA chromatin organization, suggesting nucleolar co-regulation of transcription and ribosome production. Overall the dominant theme is assembly and regulation of the protein synthesis machinery.","confidence":"High","size":25,"edges":261,"triangles":1778,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1378549982824974010","title":"Developmental signaling and morphogenesis","description":"These proteins cluster around developmental processes and signaling pathways that shape tissues and organs, such as angiogenesis, axon guidance, cell-matrix adhesion, growth hormone signaling, and gonad development. The DNA-templated transcription term points to transcriptional programs driving development, while calcineurin-NFAT signaling adds a calcium-dependent regulatory layer. A few terms (sporulation, acetoin catabolic process, subtelomeric heterochromatin formation) are less directly tied to development and may reflect broader or cross-species functions. Overall, the cluster is best described as Developmental signaling and morphogenesis.","confidence":"Medium","size":25,"edges":17,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001525","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0008045","count":5},{"id":"GO:0007160","count":5},{"id":"GO:0060396","count":5}]},{"hash":"640884352642370763","title":"Neuronal Synaptic Signaling and Plasticity Regulation","description":"Based on the prominence of terms related to synaptic function and plasticity (long-term potentiation, ephrin signaling, regulation of synaptic vesicle exocytosis, ERK cascade, brain development, and plasticity regulation), the cluster appears to be centered on neuronal communication and synaptic modulation. Some terms from other kingdoms (acrosome reaction, plant ABA signaling, mating projection growth) may reflect annotation cross-talk or shared signaling components, but they do not outweigh the predominant neuronal signal theme. Therefore, the label reflects the core function of the cluster.","confidence":"High","size":25,"edges":140,"triangles":421,"max_degree":16,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0060291","count":5},{"id":"GO:0048013","count":5},{"id":"GO:0031384","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0070374","count":5}]},{"hash":"33765746064066901","title":"Gametogenesis-Linked Chromatin Remodeling","description":"The terms cluster around chromatin remodeling and epigenetic processes (chromatin remodeling; DNA methylation in gamete generation; snoRNP assembly) and reproductive development (prostate gland development; steroid hormone receptor complex assembly), suggesting a germline/chromatin regulation theme. Some terms (morphine response, interferon response) seem incidental to the core function. Overall, the cluster likely represents germline gene regulation and gametogenesis-related chromatin dynamics.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0040022","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0071357","count":2}]},{"hash":"2290292954535867014","title":"Neural development and transcriptional regulation","description":"This cluster is dominated by neural development terms (forebrain development, neural tube closure) alongside multicellular development and DNA-templated transcription, suggesting proteins involved in vertebrate development with transcriptional control, possibly coordinating neural formation and cell cycle. ","confidence":"High","size":25,"edges":92,"triangles":176,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006349","count":22},{"id":"GO:0070059","count":22},{"id":"GO:0030900","count":22},{"id":"GO:0001843","count":22},{"id":"GO:0071276","count":22}]},{"hash":"122690401523014455","title":"Unknown","description":"The terms span DNA replication and mitotic cell cycle, neuronal development and dendritic spine morphogenesis, synaptic plasticity, innate immune response, insulin receptor signaling regulation, and metal ion response. This broad mix across cell-cycle, neural development, and immune/metal stress contexts does not point to a single cohesive function for the cluster, making a precise, representative label unlikely.","confidence":"","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0045087","count":9},{"id":"GO:0046626","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0071276","count":9}]},{"hash":"244907570537645999","title":"Ubiquitin-Mediated Innate Immune Signaling","description":"The cluster is dominated by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, autoubiquitination, K63- and K6-linked ubiquitination) and innate immune responses (defense against virus, TNF signaling, NF-\u03baB regulation). This suggests a cohesive role in regulating innate immune signaling via ubiquitination.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0051865","count":6},{"id":"GO:1903265","count":6},{"id":"GO:0051607","count":5},{"id":"GO:0070534","count":5}]},{"hash":"1397696713352962586","title":"Neural development and synapse formation with immune signaling","description":"The top terms point to neuronal development and synaptic assembly (corpus callosum development, positive regulation of synapse assembly) and pain-related behavioral responses, suggesting a neuronal development/synaptic focus. The presence of immune/stress terms (response to lipopolysaccharide, antibiotic response, dsRNA) alongside core processes (translation, DNA replication, glucose metabolism) indicates these proteins also participate in broader cellular stress responses, yielding a cohesive but multifaceted cluster.","confidence":"Medium","size":24,"edges":15,"triangles":4,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0031532","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1338306972046461215","title":"Transcription Regulation and RNA Processing","description":"The cluster is dominated by GO terms related to transcription control (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) and RNA metabolism (tRNA processing; ribosomal large subunit export from nucleus), with supporting signals of cell-cycle/ DNA damage checkpoints and growth regulation (mitotic G1 DNA damage checkpoint signaling; negative regulation of cell population proliferation) and stress response (cellular response to cadmium ion). A weaker link to ER-to-Golgi transport is present but not central. This pattern supports a cohesive theme around gene expression regulation and RNA processing, with ties to cell-cycle control and stress responses.","confidence":"Medium","size":24,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0031571","count":2},{"id":"GO:0008285","count":2}]},{"hash":"1977216798377394934","title":"Membrane transporters for nutrients and xenobiotics","description":"The top GO terms are dominated by transport and secretion across membranes, including amino acid transport, vitamin and thiamine transport, xenobiotic export, lipid-related transport, and secretion systems. This points to a cohesive theme of proteins involved in moving diverse small molecules and peptides across cellular membranes, with some related secretion activity. The outlier endoribonuclease regulation term is likely incidental. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030253","count":4},{"id":"GO:0060702","count":4},{"id":"GO:0015803","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0046618","count":4}]},{"hash":"928601158980041720","title":"Bacterial cell wall and envelope biosynthesis","description":"Top GO terms point to biosynthesis of lipopolysaccharide, peptidoglycan, and other cell wall components (lipid A, slime layer polysaccharide), as well as cell wall organization and morphogenesis. The combination indicates a cluster of proteins involved in envelope biogenesis and structural maintenance, with antibiotic response likely reflecting envelope-targeted stress. Overall, a common theme is cell wall/envelope synthesis and remodeling.","confidence":"High","size":24,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0009252","count":2},{"id":"GO:0000902","count":2}]},{"hash":"1503027526667944776","title":"DNA replication and repair stress response","description":"This cluster is driven by DNA-centric processes: DNA replication, SOS response, and nucleotide-excision repair, with additional signals of antibiotic response and stress-related transcription activities. A few terms (transcription regulation and blastocyst development) seem less cohesive with the core theme, but the dominant GO terms align with genome maintenance under stress. The low connectivity suggests a broader, multi-functional set rather than a tight complex, supporting a label focused on replication/repair stress responses.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0006289","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0019079","count":4}]},{"hash":"312755394710092541","title":"Cardiovascular development and cell proliferation","description":"The cluster shows strong enrichment for mitotic cell cycle, DNA replication, and cell division, indicating proliferative activity. Terms related to heart development and angiogenesis, along with cell migration, point to a cardiovascular development program where proliferation supports morphogenesis and vessel formation. Annotations like ABA signaling may be noise or cross-species artifacts but do not alter the overall proliferative/vascular theme.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0006260","count":5}]},{"hash":"1566961880562913620","title":"DNA Replication and Transcription Regulation","description":"This cluster\u2019s strongest, recurring annotations center on DNA replication (including primer synthesis) and regulation of DNA-templated transcription, suggesting a core association with nuclear DNA synthesis and gene expression control. Other terms like ER-Golgi transport or hormone biosynthesis appear less cohesive with the main theme, likely reflecting annotation diversity. Overall, the dominant signal points to replication and transcription regulation.","confidence":"Medium","size":24,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006269","count":2}]},{"hash":"782920940227098256","title":"ER-Golgi vesicle transport","description":"The top GO terms strongly point to endoplasmic reticulum to Golgi vesicle-mediated transport and SNARE complex disassembly, which together define vesicle trafficking within the secretory pathway. While other terms like DNA replication and SOS response appear, they seem auxiliary notes rather than core functions of the cluster. This suggests a cohesive theme around membrane trafficking and SNARE regulation, with some incidental multifunctionality among the proteins.","confidence":"High","size":24,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0035494","count":4},{"id":"GO:0035690","count":4}]},{"hash":"1274502031295280616","title":"Unknown","description":"The terms span DNA replication, transcription termination, DNA repair/maintenance, vesicle transport, and developmental processes (myelination, lymphangiogenesis), with no clear shared function linking most proteins, so no cohesive label can be assigned.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0010719","count":4},{"id":"GO:0022011","count":4},{"id":"GO:0051321","count":4},{"id":"GO:2001241","count":4}]},{"hash":"568778250945717231","title":"Membrane trafficking and receptor signaling","description":"This cluster appears to center on membrane signaling and vesicular trafficking: ephrin receptor signaling, endosome-to-Golgi transport, phagosome-lysosome fusion, and regulation of protein localization to the plasma membrane. These terms suggest coordinated signaling at the cell surface with intracellular transport and membrane remodeling; a few outliers reflect broader cellular metabolism or development but do not override the main theme.","confidence":"Medium","size":24,"edges":68,"triangles":16,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048013","count":11},{"id":"GO:0031532","count":11},{"id":"GO:0090324","count":10},{"id":"GO:0034498","count":10},{"id":"GO:0035281","count":10}]},{"hash":"877024865876144095","title":"Cytoskeletal remodeling and vascular signaling","description":"The cluster shows strong enrichment for cytoskeletal dynamics and cell-movement-related GO terms (lamellipodium assembly, podosome assembly, Rho signaling, positive regulation of cell spreading) and vascular-related processes (regulation of vascular permeability), with additional hints from cardiac morphogenesis and growth hormone secretion. Transcriptional term presence is limited and less central to the dominant theme, so a label capturing cytoskeletal remodeling coupled with vascular signaling best represents the cluster\u2019s core functions.","confidence":"Medium","size":24,"edges":29,"triangles":14,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:2000973","count":3},{"id":"GO:0003209","count":3},{"id":"GO:1900169","count":3},{"id":"GO:0007266","count":3}]},{"hash":"728448389398987530","title":"Nuclear DNA replication and chromatin assembly","description":"The cluster is enriched in nuclear processes: DNA-templated transcription, DNA replication, CENP-A\u2013containing chromatin assembly, microtubule severing, and cell division, suggesting roles in genome maintenance and mitotic chromosome dynamics. Some terms point to trafficking or stress responses, but the core theme is nuclear replication/assembly accompanying cell division.","confidence":"Medium","size":24,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0071276","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0061641","count":3}]},{"hash":"1365350298023793352","title":"Neurovascular Development and Signaling","description":"The cluster shows strong representation of brain development (brain development) and angiogenesis, along with transcriptional regulation and cytoskeletal remodeling (DNA-templated transcription, cortical actin cytoskeleton organization). Additional signals such as regulation of NFAT signaling, ER stress\u2013related apoptosis, and metabolic responses (glucose metabolism) point to neural signaling and neurovascular adaptation. While there are diverse terms (e.g., Cocaine response, glucose signaling), the core themes converge on neurodevelopmental processes tied to vascular and signaling pathways in the brain.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033138","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0051534","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007420","count":3}]},{"hash":"941396214875983083","title":"Transcription Regulation and Chromatin Modification","description":"The top GO terms are dominated by DNA-templated transcription and histone H3-K4 methylation, pointing to regulation of gene expression and chromatin state. Other terms (e.g., cAMP response, gamma radiation response) suggest ancillary signaling/stress responses, and metabolism-related terms appear less central. Thus the core theme centers on transcription control and chromatin modification, with some noise from other processes.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0001662","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009102","count":3}]},{"hash":"1012494913619932688","title":"Brain development and synaptic signaling","description":"The terms strongly point to neuronal signaling and development: brain development, excitatory postsynaptic potential, and GPCR-related kinase signaling with phosphorylation; together with regulation of GTPase activity and mRNA transport, these features suggest a neuronal/synaptic function cluster rather than general housekeeping.","confidence":"High","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0010800","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0000742","count":2}]},{"hash":"668742695597767214","title":"Stress- and growth-regulating signaling","description":"The top GO terms point to stress responses (hypoxia, astrocyte activation, cardiac hypertrophy under stress), regulation of signaling pathways (kinase activity, autophosphorylation, GTPase activity), nuclear import, and processes related to mRNA transport and cell proliferation. This suggests a coherent cluster centered on stress-induced signaling that modulates growth, division, and nuclear-cytoplasmic transport.","confidence":"Medium","size":23,"edges":9,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051028","count":6},{"id":"GO:0071456","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0008284","count":5},{"id":"GO:0071902","count":5}]},{"hash":"1172225338721937518","title":"Ribosome biogenesis and UV-induced DNA damage response","description":"The top GO terms point strongly to ribosome production and translation (ribosomal large subunit biogenesis, cytosolic ribosome assembly, translation, regulation of translation), while additional terms indicate cellular responses to UV or gamma radiation and p53-mediated DNA damage signaling. This suggests a cohesive cluster of proteins involved in ribosome biogenesis and protein synthesis, with a connected subset that participates in DNA damage/UV stress signaling, justifying a combined label that captures both themes.","confidence":"Medium","size":23,"edges":24,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:1902167","count":2},{"id":"GO:0006977","count":2},{"id":"GO:0071480","count":2},{"id":"GO:1904803","count":2}]},{"hash":"1105391352902364938","title":"Developmental Regulation and Neurogenesis","description":"The cluster is dominated by neural and broader developmental terms (forebrain development, neural tube closure, multicellular organism development, skeletal system development) and coupled with transcriptional regulation signals (DNA-templated transcription, imprinting regulation). While there are some stress/immune signals (defense response to Gram-positive bacterium, ER stress\u2013related apoptosis, cadmium response), the developmental and regulatory themes are most representative of the cluster\u2019s function.","confidence":"Medium","size":23,"edges":6,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0006349","count":8},{"id":"GO:0070059","count":8},{"id":"GO:0030900","count":8}]},{"hash":"1534182383784427950","title":"Vesicle Trafficking and Neural Development","description":"The cluster shows strong representation of vesicle trafficking terms (Golgi to plasma membrane transport, endosome transport, phagosome-lysosome fusion), indicating a core function in intracellular transport. It also contains neural and sensory organ development terms (neuron maturation regulation, midbrain dopaminergic neuron differentiation, cochlea morphogenesis) and apical junction assembly, suggesting involvement in neural/sensory tissue development and epithelial organization. Together, these terms point to a theme of vesicle trafficking supporting developmental processes in neural and sensory contexts.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006893","count":8},{"id":"GO:0090316","count":8},{"id":"GO:0048227","count":8},{"id":"GO:0090385","count":7},{"id":"GO:0036035","count":7}]},{"hash":"920644714116908819","title":"Dopaminergic signaling and neuronal development","description":"This cluster centers on dopaminergic synaptic transmission and neuron growth programs (including PI3K/Akt signaling and dendrite morphogenesis), with supporting transcriptional regulation and nuclear export terms, indicating a neuronal signaling/growth theme.","confidence":"High","size":23,"edges":51,"triangles":63,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0032435","count":8},{"id":"GO:0033138","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0001963","count":7}]},{"hash":"2184145794694799753","title":"Synaptic vesicle trafficking and synapse assembly","description":"The top GO terms cluster around synaptic vesicle exocytosis/maturation, regulation of endocytosis, and synapse assembly, with brain development also represented. This suggests the proteins work together in neuronal vesicle cycling and synapse formation/maintenance.","confidence":"High","size":23,"edges":39,"triangles":32,"max_degree":9,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0010796","count":5},{"id":"GO:0031384","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0048260","count":4},{"id":"GO:0016188","count":4}]},{"hash":"258258604700566853","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0036265","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0051567","count":4}]},{"hash":"1372027893661983673","title":"Endocytic trafficking with GTPase regulation","description":"This cluster is dominated by GO terms linking endosomal transport (early to late endosomes, endosome to lysosome) and negative regulation of endocytic recycling, plus GO:0043547 (positive regulation of GTPase activity) and regulation of Rho/Rac signaling. These points suggest a cohesive theme of intracellular trafficking governed by small GTPases, with supporting signals from autophagy-related vacuolar targeting (CVT pathway) and ER-associated processes. Some terms (like extrinsic apoptotic signaling) appear less central, but do not outweigh the trafficking/GTPase theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0045022","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0008625","count":2}]},{"hash":"758602333550589801","title":"Neural Development and Axon Growth","description":"The cluster is dominated by terms related to nervous system development and axon biology (nervous system development; positive regulation of axon extension; Rho protein signal transduction), along with DNA-templated transcription and broader multicellular development. This pattern suggests a core theme of neuronal differentiation and axon guidance/growth, with cytoskeletal signaling (Rho) and transcriptional control underpinning these processes. A secondary term on angiogenesis appears, which can be associated with neurovascular development, but the primary signal remains neural development and axon extension. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043552","count":5},{"id":"GO:0007266","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0020021","count":4}]},{"hash":"767113148452281423","title":"Ribosome biogenesis and RNA processing","description":"The strongest signals are rRNA maturation and ribosome assembly: maturation of LSU-rRNA and 5.8S rRNA from tricistronic transcripts, plus spliceosomal conformational changes related to RNA processing. Actin filament severing and ethanol response appear weaker or incidental. Overall, the cluster points to ribosome biogenesis and RNA processing, with possible ties to broader proteostasis regulation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051014","count":2},{"id":"GO:0000470","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0010950","count":1},{"id":"GO:0000393","count":1}]},{"hash":"1873314815443390605","title":"Innate Immune Signaling and Ubiquitination","description":"The cluster is enriched for innate immune and antiviral defense terms, including innate immune response and defense against virus, with a notable presence of ubiquitination-related processes (K63-linked ubiquitination) and NF-kappaB regulation, which are central to signaling in innate immunity. Microtubule localization may reflect trafficking or assembly of signaling complexes, though a few terms (development/ossification) are less directly connected. Overall, the set points to a coherent theme of immune signaling governed by ubiquitin-mediated regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0051607","count":4},{"id":"GO:0035372","count":4},{"id":"GO:0051092","count":4}]},{"hash":"1625018655205408069","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms tied to ubiquitin-mediated proteolysis: ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, autoubiquitination, and ERAD pathways. The inclusion of Wnt receptor catabolic process also aligns with receptor degradation via ubiquitin-proteasome/endocytic routes. While a few terms (dosage compensation, peroxisome import, V(D)J recombination) are less directly connected, they may reflect broader roles of protein turnover in regulation and immune-related processes. Overall, the proteins likely participate in tagging proteins for degradation and maintaining proteome homeostasis.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0060816","count":7},{"id":"GO:1900095","count":7},{"id":"GO:0038018","count":7},{"id":"GO:0051865","count":7}]},{"hash":"751088432983876790","title":"Reproductive Hormone Signaling and Ovary Development","description":"The top GO terms cluster around reproductive biology: FSH and LH signaling, primary ovarian follicle growth, and uterus development, together with activation of adenylate cyclase and IP3 biosynthesis, which point to GPCR-mediated endocrine signaling driving ovarian maturation and reproductive tissue development. A couple of terms like defense response to virus and intracellular water homeostasis are less connected but do not undermine the dominant reproductive signaling theme.","confidence":"Medium","size":22,"edges":22,"triangles":21,"max_degree":8,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":12},{"id":"GO:0042699","count":12},{"id":"GO:0001545","count":12},{"id":"GO:0060065","count":12},{"id":"GO:0009992","count":12}]},{"hash":"1106650857309176571","title":"Cell cycle, translation, and trafficking","description":"The cluster highlights core cellular processes such as cell division/mitosis, translation and its regulation, and protein transport/localization (including endosome targeting) with occasional links to protein complex assembly and basic metabolism. This suggests a broad, cohesive theme of fundamental cellular growth and protein handling rather than a single precise pathway, so a broad label capturing these connected housekeeping functions is appropriate.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0036010","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0045070","count":2}]},{"hash":"1548165891425189743","title":"RNA processing and ribosome biogenesis","description":"This cluster is enriched for RNA maturation and modification processes\u2014mRNA capping, guanine-N7 methylation, tRNA methylation, and splicing\u2014as well as rRNA maturation steps, which together point to RNA processing and ribosome assembly. A smaller subset includes Golgi/ER trafficking terms, suggesting some involvement in vesicle transport, but the dominant theme centers on RNA processing and ribosome biogenesis.","confidence":"High","size":22,"edges":108,"triangles":313,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0046677","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0000466","count":2}]},{"hash":"1428593910370526206","title":"Developmental and Stress-Response Genes","description":"The terms emphasize CNS development (neural tube closure, forebrain development) and skeletal development, alongside transcription and cell-cycle processes, plus multiple stress-related responses (ER stress-induced apoptosis, cadmium response) and immune defense. This suggests a broad cluster centered on development with intertwined stress signaling and gene regulation, rather than a single pathway.","confidence":"Medium","size":22,"edges":44,"triangles":62,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":11},{"id":"GO:0070059","count":10},{"id":"GO:0001403","count":10},{"id":"GO:0006349","count":10},{"id":"GO:0050830","count":10}]},{"hash":"643595236593061068","title":"Ciliogenesis and Cytoskeletal Dynamics","description":"Top GO terms point to cilium assembly and microtubule-based movement as the dominant themes, suggesting a core focus on cytoskeletal organization and ciliogenesis. Developmental terms (spinal cord development) and transcriptional regulation appear as additional layers, with a few apoptosis and oxidative stress-related terms as ancillary connections. Overall, the strongest signal is cytoskeletal/ciliogenesis-related processes, justifying this label.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071447","count":3},{"id":"GO:1903204","count":3},{"id":"GO:1902083","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0021510","count":2}]},{"hash":"753611834213475132","title":"Cell growth, division, and translation machinery","description":"This cluster is dominated by core cellular processes tied to growth: cell division, cell septum assembly, ribosomal biogenesis, cytoplasmic translation, and tRNA modification, with phosphorylation also fitting into regulation of these processes. Additional terms reflecting metabolism and stress response align with housekeeping functions, supporting a theme of growth and protein synthesis. The odd virus-mediated pore formation term appears as annotation noise and doesn\u2019t disrupt the main signal. ","confidence":"Medium","size":22,"edges":15,"triangles":5,"max_degree":6,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0039707","count":4},{"id":"GO:0016310","count":3},{"id":"GO:0090529","count":3},{"id":"GO:0042274","count":3}]},{"hash":"2024816865069988484","title":"Neuronal axon guidance and cytoskeleton remodeling","description":"The cluster is dominated by GO terms for motor neuron axon guidance, cell-matrix adhesion, lamellipodium assembly, and cerebellar cortex development, pointing to roles in neural development and axon pathfinding with dynamic cytoskeletal changes. Additional terms (growth hormone signaling, proteasomal degradation, serine biosynthesis, copper transport) suggest supportive metabolic/regulatory processes but do not redefine the core theme.","confidence":"Medium","size":22,"edges":35,"triangles":26,"max_degree":15,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0008045","count":9},{"id":"GO:0007160","count":9},{"id":"GO:0060396","count":9},{"id":"GO:0097194","count":6},{"id":"GO:0031532","count":6}]},{"hash":"684424306669500340","title":"Neural development and cell cycle proteins","description":"The cluster features nervous system development terms (telencephalon development, Schwann cell development) and neural signaling (excitatory postsynaptic potential), alongside cell cycle and DNA replication terms (DNA replication, G1/S transition, protein localization to kinetochore), suggesting a cohort of proteins involved in neural progenitor proliferation and maturation. This combination points to a theme of neural development intertwined with cell cycle regulation.","confidence":"Medium","size":22,"edges":34,"triangles":21,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0042220","count":6},{"id":"GO:0060079","count":6},{"id":"GO:0051321","count":6},{"id":"GO:0000082","count":6}]},{"hash":"1533858519304566116","title":"Ribosome Biogenesis and Cell Cycle","description":"The cluster shows strong enrichment for ribosome biogenesis terms (ribosome biogenesis, ribosomal subunit biogenesis, export from nucleus) alongside cell division and cell cycle terms, suggesting a group linked to ribosome production and progression through the cell cycle, with some associated trafficking processes.","confidence":"High","size":21,"edges":8,"triangles":0,"max_degree":4,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0007049","count":7},{"id":"GO:0000055","count":6},{"id":"GO:0006888","count":5},{"id":"GO:0000747","count":5}]},{"hash":"1603704943660009509","title":"Vacuolar trafficking and endosome sorting","description":"The top GO terms show a coherent theme of vesicular transport toward the vacuole/lysosome and endosomal sorting: Golgi-to-endosome transport, early endosome dynamics, multivesicular body sorting, endocytosis, phagosome-lysosome fusion, and Cvt-mediated targeting to the vacuole. This points to a cluster of proteins involved in endomembrane trafficking and vacuolar sorting rather than a single cytoskeletal or cell-cycle function. The cell cycle terms appear secondary or broader, but the dominant signal is vacuolar/lysosomal protein sorting.","confidence":"High","size":21,"edges":65,"triangles":105,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0034498","count":8},{"id":"GO:0071985","count":8},{"id":"GO:0006895","count":8},{"id":"GO:0006897","count":8}]},{"hash":"900546464545568734","title":"MHC I antigen presentation and immune signaling","description":"The cluster is enriched for antigen processing and presentation via MHC class I (TAP-dependent), along with immune receptor signaling (C-type lectin and Fc-epsilon), and deubiquitination, suggesting a core function in immune recognition and signaling; some cell-cycle related terms may reflect general protein turnover rather than a dedicated mitotic role.","confidence":"Medium","size":21,"edges":87,"triangles":190,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":9},{"id":"GO:0002479","count":8},{"id":"GO:0009651","count":8},{"id":"GO:0010950","count":8},{"id":"GO:0002223","count":8}]},{"hash":"2116531382302561242","title":"Neuronal development and axon growth signaling","description":"The Top Terms are dominated by nervous system development, dendrite morphogenesis, hippocampus development, and positive regulation of axon extension, along with MAPK signaling components (ERK1/2 and JNK cascades) and regulation of serine phosphorylation. This combination points to a cohesive theme of neural development and neurite outgrowth driven by signaling pathways, despite a couple of outlier terms (beta selection, obsolete PI3K term). Therefore, the label reflects the cluster\u2019s core function.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070374","count":7},{"id":"GO:0048813","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0045773","count":6},{"id":"GO:0033138","count":6}]},{"hash":"871244410550107941","title":"Golgi-ER trafficking and filopodium dynamics","description":"The cluster\u2019s top GO terms point to vesicle transport between the ER, Golgi, and plasma membrane (anterograde and retrograde pathways) and to actin-based protrusions (filopodia) with regulation by small GTPases. This suggests a cohesive role in coordinating intracellular trafficking with cytoskeletal remodeling and membrane protrusion, possibly extending to related cell division processes. ","confidence":"High","size":21,"edges":28,"triangles":4,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":8},{"id":"GO:0051932","count":6},{"id":"GO:0006890","count":6},{"id":"GO:0043001","count":6},{"id":"GO:0090307","count":6}]},{"hash":"1076262430386796560","title":"Neural signaling and myelination","description":"This cluster is dominated by nervous system-related terms: peripheral nervous system myelination, astrocyte activation, regulation of synaptic vesicle exocytosis, and signaling via calcium and nitric oxide, with an additional note on light-activated channel activity. While angiogenesis and cardiac-related terms appear, the strongest shared theme among the GO terms centers on neural signaling and glial support rather than muscle or cardiac specificity.","confidence":"Medium","size":21,"edges":13,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":2},{"id":"GO:0008218","count":2},{"id":"GO:0014898","count":1},{"id":"GO:0048143","count":1},{"id":"GO:0001525","count":1}]},{"hash":"1046163056279039285","title":"Zinc and heavy metal ion transport and detoxification","description":"Top terms show zinc ion transmembrane transport, cadmium and cobalt ion transport, iron ion transport, and detoxification/response to zinc, indicating a cohesive function in maintaining intracellular metal ion balance and detoxification. This pattern supports a label centered on metal ion transport and detoxification across Zn, Cd, Fe, and Co, making the name representative of the cluster\u2019s core biology.","confidence":"High","size":21,"edges":32,"triangles":22,"max_degree":10,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0071577","count":5},{"id":"GO:0006877","count":5},{"id":"GO:0006876","count":5},{"id":"GO:1903874","count":5},{"id":"GO:0070574","count":5}]},{"hash":"527756896025132078","title":"Mitotic Cycle and Cytoskeletal Dynamics","description":"This cluster centers on processes linked to cell division and cytoskeletal remodeling: mitotic cell cycle and APC-dependent catabolic events indicate mitosis; actin cytoskeleton organization and negative regulation of focal adhesion assembly point to cytoskeletal dynamics; ribosome biogenesis suggests upscaled protein synthesis to support growth and division; additional terms like neuron projection development and GCN2 signaling hint at broader growth and translation regulation that accompany proliferative states. Overall, the most coherent theme is coordination of cell division with cytoskeletal changes and growth-related processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0060733","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0031175","count":2},{"id":"GO:0030036","count":2}]},{"hash":"2287783865525759750","title":"Plant translation and ribosome biogenesis","description":"This cluster is dominated by GO terms for translation and ribosome biogenesis (each appearing twice), indicating a core association with protein synthesis machinery. The presence of several plant-specific regulatory terms (leaf formation, seed growth, secondary cell wall biogenesis) and osmotic stress response suggests a plant-context functional grouping around ribosome function and translation, possibly with developmental and stress-related regulatory roles.","confidence":"High","size":21,"edges":28,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006970","count":1},{"id":"GO:0010338","count":1},{"id":"GO:1903770","count":1}]},{"hash":"57657640873843658","title":"Neuronal axon growth and Rac-driven cytoskeletal remodeling","description":"The cluster centers on Rac signaling, axon extension, lamellipodium assembly, and nervous system development, indicating a focus on neuronal growth and actin cytoskeleton remodeling. Additional terms like ER-Golgi transport and autophagy regulation are compatible with general cellular processes, but the core theme remains Rac-mediated cytoskeletal dynamics supporting axon growth in neurons.","confidence":"Medium","size":21,"edges":27,"triangles":10,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045792","count":7},{"id":"GO:0016601","count":6},{"id":"GO:1903833","count":6},{"id":"GO:2000785","count":6},{"id":"GO:0006888","count":6}]},{"hash":"1998942590720872681","title":"Angiogenic signaling and endothelial tube formation","description":"The protein set is enriched for GO terms related to angiogenesis and endothelial signaling: endothelial tube lumen extension; positive regulation of Wnt signaling; ERK1/ERK2 cascade; small GTPase-mediated signal transduction; ephrin receptor signaling; and regulation of sprouting angiogenesis. Collectively these indicate control of vessel formation and endothelial cell behavior via multiple signaling pathways (Wnt/ERK/GTPases/ephrin). A few terms (mast cell degranulation, DNA replication) appear more peripheral, but the dominant theme is angiogenic signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097498","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0007264","count":2}]},{"hash":"314708818045535156","title":"Neural development and microtubule transport","description":"The cluster\u2019s top terms show strong links to neural development (spinal cord development, peripheral myelination) alongside microtubule-related processes (mitotic spindle assembly, microtubule-based movement, intraciliary transport). This suggests a coherent theme around neural development governed by microtubule dynamics and ciliary transport, with some supporting ion transport functions. Confidence: Medium","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0022011","count":3},{"id":"GO:0006355","count":2},{"id":"GO:1903830","count":2}]},{"hash":"1949920597978882091","title":"Carbohydrate Biosynthesis and Metabolism","description":"This cluster is enriched for carbohydrate biosynthetic and metabolic processes (glycogen, sucrose, and starch biosynthesis; carbohydrate phosphorylation), suggesting a common theme around carbohydrate metabolism. While there are additional terms related to protein targeting and bacterial structure, the carbohydrate-related terms appear most representative of the cluster\u2019s function. ","confidence":"Medium","size":21,"edges":15,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":2},{"id":"GO:0006616","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0044781","count":2},{"id":"GO:0006461","count":2}]},{"hash":"1504505364152493209","title":"Cardiac Wnt/EGFR Signaling and Angiogenesis","description":"This cluster is enriched for Wnt signaling, EGFR signaling, angiogenesis, and cardiac muscle development terms, indicating a cohesive role in cardiac vascular development. Supporting terms related to cytoskeletal remodeling and vesicle trafficking suggest accompanying structural and intracellular transport changes that often accompany heart and vessel formation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0055013","count":2},{"id":"GO:0051496","count":2},{"id":"GO:0048255","count":2}]},{"hash":"1527292684676548378","title":"Cytokinesis and actin cytoskeleton regulation","description":"This cluster is dominated by GO terms for cell division, septum digestion after cytokinesis, and Arp2/3 complex\u2013mediated actin nucleation, pointing to cytoskeletal remodeling during cytokinesis; additional signals from GTPase activity regulation and transcription/stress responses support this cohesive functional theme.","confidence":"High","size":20,"edges":20,"triangles":3,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0000920","count":4},{"id":"GO:0043981","count":3},{"id":"GO:0043982","count":3},{"id":"GO:0034314","count":3}]},{"hash":"113756130116253252","title":"Ubiquitin-Dependent Proteolysis","description":"Top GO terms are dominated by ubiquitination and ubiquitin-dependent protein catabolic processes (K48- and K6-linked ubiquitination, autoubiquitination, histone catabolic process), pointing to a cluster of ubiquitin-proteasome system components involved in targeted protein turnover. Some terms relate to signaling and chromatin remodeling but the prevalent theme is protein ubiquitination and degradation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0085020","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0036205","count":5}]},{"hash":"179378991987129134","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":75,"triangles":158,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:0000398","count":10},{"id":"GO:0071031","count":9},{"id":"GO:0009432","count":9}]},{"hash":"739860794320316314","title":"Unknown","description":"The top GO terms span distinct processes (cell division; regulation of apoptosis; megakaryocyte differentiation; host-cell peptide translocation; sperm binding; telomere maintenance; Cajal body protein localization; inflammatory response) with a couple of obsolete terms, indicating a heterogeneous or poorly cohesive cluster. No single dominant function emerges to unify these proteins.","confidence":"","size":20,"edges":21,"triangles":2,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0071866","count":3},{"id":"GO:0045654","count":3},{"id":"GO:1901998","count":2},{"id":"GO:0044053","count":2}]},{"hash":"332091759483635236","title":"Spliceosome-driven mRNA processing and silencing","description":"This cluster shows strong enrichment for splicing regulation via the spliceosome, along with multiple post-transcriptional controls such as mRNA modification and ncRNA/miRNA-mediated gene silencing, and translation initiation. Together, these terms point to a cohesive module centered on RNA processing and translational regulation.","confidence":"High","size":20,"edges":22,"triangles":19,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0009432","count":4},{"id":"GO:0006289","count":4}]},{"hash":"1680933537685088753","title":"Neural development and signaling","description":"This cluster centers on neural development features, with corpus callosum development and dendrite morphogenesis, and dopamine-related signaling, suggesting a focus on neural differentiation and connectivity. Supporting processes like angiogenesis, DNA replication, and mitotic cell cycle point to proliferation during development, while broader signaling terms (peptidyl-serine phosphorylation, protein export from nucleus) and immune response terms (dsRNA response, T cell receptor signaling) reflect shared signaling pathways and cellular regulation across tissues. Overall, the dominant theme appears to be neural development and associated signaling, with some ancillary pathways. ","confidence":"Medium","size":20,"edges":34,"triangles":39,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0033138","count":12},{"id":"GO:0046827","count":12},{"id":"GO:0050852","count":12},{"id":"GO:0000278","count":12},{"id":"GO:1903351","count":12}]},{"hash":"1417958747764863325","title":"Cytoskeleton dynamics and vesicle transport","description":"The top GO terms cluster around intracellular transport from the ER to the Golgi and cytoskeletal organization, including vesicle trafficking (ER-Golgi), actin nucleation via Arp2/3, mitotic spindle assembly, and cilium assembly. This points to a shared role in organizing cellular architecture and movement rather than a single signaling pathway. Other terms like transcription, splicing, apoptosis, and skeletal morphogenesis are more heterogeneous and less representative. Overall, the dominant theme is cytoskeleton dynamics coupled with vesicle trafficking.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0090307","count":2},{"id":"GO:2000601","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001403","count":2}]},{"hash":"1703644304652975001","title":"DNA replication and cell cycle machinery","description":"The cluster\u2019s top GO terms are dominated by DNA replication (GO:0006260) and mitotic sister chromatid separation (GO:0051306), highlighting a core cell-cycle/process replication theme. Supporting terms touch on protein targeting to membranes and chaperone-assisted folding, with iron-sulfur cluster assembly also appearing, suggesting broader basic cellular machinery. Several other terms (e.g., viral process, fungal cell wall biosynthesis) appear less cohesive with the core signals, implying a somewhat heterogeneous set with a central cell-cycle focus.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070389","count":4},{"id":"GO:0000902","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0051306","count":3}]},{"hash":"1883488105505886158","title":"Protein trafficking and localization","description":"The terms emphasize intracellular transport and placement of molecules (nuclear export of mRNA and ribosomal subunits, protein localization to chromatin, Golgi retention, transcytosis, and mitochondrial dynamics). While dopamine-related terms appear, the dominant theme is trafficking/localization rather than a single signaling pathway, suggesting a cluster of proteins involved in intracellular transport processes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090141","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0060161","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0000056","count":2}]},{"hash":"1350180358341755102","title":"ER-Golgi transport and ER stress\u2013induced apoptosis","description":"The dominant GO terms cluster around vesicle trafficking between the ER and Golgi (ER-to-Golgi and Golgi-to-ER transport) and ER-stress\u2013driven intrinsic apoptosis, indicating a core function in trafficking with stress-induced cell fate decisions. Additional terms related to development and metal stress appear as broader or contextual associations rather than core features of the cluster.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0050830","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0006349","count":4},{"id":"GO:0070059","count":4}]},{"hash":"283763517718438431","title":"DNA replication and mitotic progression","description":"This cluster's top GO terms cluster around DNA replication, the centrosome cycle, and mitotic processes (mitotic cleavage furrow ingression), indicating a core association with cell division. Supporting terms include regulation of Wnt signaling, cranial skeleton morphogenesis, and cell migration, suggesting these proteins may participate in developmental contexts that couple proliferation with morphogenesis. Thus, a concise label capturing DNA replication and mitotic progression reflects the major function of this cluster.","confidence":"High","size":20,"edges":18,"triangles":2,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045956","count":7},{"id":"GO:0016477","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0043552","count":5}]},{"hash":"157299304936213553","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster is characterized by ribosome-related processes (maturation of SSU-rRNA and formation of the translation preinitiation complex) and initiation and regulation of translation, which together reflect the core protein synthesis machinery; additional terms related to RNA processing and meiotic/cell-cycle contexts may reflect multifunctionality but do not outweigh the ribosome/translation signal.","confidence":"Medium","size":20,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007369","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0007584","count":2}]},{"hash":"135851321564270598","title":"RNA processing and translation with ER-Golgi trafficking","description":"This cluster shows enrichment for RNA-related processes (transcription termination, rRNA processing, translation, mRNA export) alongside vesicle trafficking between the ER and Golgi, and synaptic vesicle transport. The combination suggests a theme of RNA metabolism coupled with protein sorting in the secretory pathway, with some cell-cycle signals indicating broader involvement in proliferative contexts. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006353","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000447","count":2}]},{"hash":"2002481864856194969","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000753","count":2},{"id":"GO:0010636","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006888","count":2},{"id":"GO:1904263","count":2}]},{"hash":"1188373169269083940","title":"GTPase signaling and cytoskeletal dynamics","description":"The top GO terms cluster around activation of GTPase activity, Rho and Rap signaling, actin filament depolymerization, mitotic spindle assembly, and cell division, with additional links to Wnt signaling. This points to a coherent theme of signaling pathways coordinating cytoskeletal regulation and cell cycle processes, despite the virus-related term being a potential outlier. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0046726","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030042","count":2}]},{"hash":"854190189295414325","title":"DNA replication and cell cycle regulation","description":"Enriched terms center on DNA replication and regulation of mitotic processes, with additional signals for nuclear import, DNA damage response, and apoptosis. The presence of DNA replication (GO:0006260), regulation of microtubule dynamics (GO:0007026), and meiotic/metaphase-related alignment (GO:0043060), alongside nuclear import (GO:0006607) and DNA damage/apoptosis regulation (GO:1904290, GO:1902231), suggests a cohesive theme of coordinating genome duplication, spindle function, and checkpoint control during cell division.","confidence":"Medium","size":19,"edges":11,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007026","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0010804","count":1}]},{"hash":"580254852876524005","title":"Nuclear gene expression and chromatin regulation","description":"This cluster centers on nuclear processes: chromatin assembly during DNA replication, DNA-templated transcription and RNA Pol III transcription, and nuclear import of ribosomal proteins, with regulatory signals including NF-kappaB and STAT pathways and ubiquitin-dependent protein turnover. The combination suggests co-regulation of gene expression and nuclear transport, with some participation in cell signaling.","confidence":"Medium","size":19,"edges":82,"triangles":177,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0032436","count":2},{"id":"GO:0051307","count":2}]},{"hash":"898459373110155306","title":"Stress-Response and Metabolic Signaling","description":"The top GO terms cluster around cellular stress responses (cadmium ion response, innate immune response, apoptotic process), hormone- and signaling-related responses (cellular response to peptide hormone stimulus), and metabolic processes (glucose metabolic process), along with core cellular activities like mitotic cell cycle and transcription. This suggests a broad theme of stress signaling coupled with metabolic regulation, rather than a single, cohesive pathway. Some terms (angiogenesis, sporulation) may reflect annotation noise or broad functional overlaps. ","confidence":"Medium","size":19,"edges":13,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":7},{"id":"GO:0030435","count":6},{"id":"GO:0006006","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0006915","count":4}]},{"hash":"157113051129427346","title":"Vesicle trafficking and Golgi organization","description":"The terms show strong enrichment for Golgi-related processes and vesicle transport, including Golgi organization, Golgi-to-ER retrograde transport, endosome-to-Golgi and early endosome\u2013Golgi transport, and phagosome-lysosome fusion. Additional terms reference vacuole targeting (Cvt pathway) and nuclear RNA export, suggesting a broader but cohesive theme of intracellular trafficking and organelle dynamics. The angiogenesis term (endothelial tube lumen extension) may reflect context in vascular cells where trafficking is critical, but the core signal remains vesicle trafficking and Golgi function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097498","count":3},{"id":"GO:0090051","count":3},{"id":"GO:0007030","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0032258","count":3}]},{"hash":"1866681372171720573","title":"Actin-driven membrane remodeling and endocytosis","description":"The top GO terms center on actin cytoskeleton dynamics (actin polymerization, podosome/ruffle assembly, cell spreading) and membrane trafficking processes (endocytosis, engulfment of apoptotic cells, Golgi-to-plasma membrane transport). This suggests a coherent role in coordinating cytoskeletal rearrangements with membrane uptake and trafficking. The inclusion of neuronal synapse plasticity reflects actin remodeling in synaptic structures as well. Overall, these proteins likely function in actin-guided membrane remodeling and related endocytic/phagocytic activities.","confidence":"High","size":19,"edges":16,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051835","count":6},{"id":"GO:0034260","count":6},{"id":"GO:0043652","count":6},{"id":"GO:0006893","count":6},{"id":"GO:0043552","count":6}]},{"hash":"963515224491764816","title":"DNA replication and cell cycle progression","description":"Based on the top GO terms, the cluster is dominated by processes related to DNA replication, cell cycle transitions (G1/S), and chromosome segregation (kinetochore localization) as well as meiotic cell cycle activity. These associations point to a cohesive theme around cell-cycle control and replication, with a few peripheral terms (neural development, lymphangiogenesis, transcription termination) likely reflecting multifunctional proteins or annotation noise rather than a distinct alternate function in this cluster.","confidence":"High","size":19,"edges":140,"triangles":675,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":18},{"id":"GO:0042220","count":17},{"id":"GO:0060079","count":17},{"id":"GO:0051321","count":17},{"id":"GO:0000082","count":17}]},{"hash":"882438726481800489","title":"MAPK Signaling in Neural Development","description":"The top GO terms point to MAPK pathway activity (ERK1/ERK2 cascade, JUN kinase activation) and responses to growth factors (VEGF, PDGF), along with neural development processes (layer formation in the cerebral cortex, visual learning). This suggests the proteins are linked by MAPK-mediated signaling that influences neural development and associated cytoskeletal or adhesion changes, with a few terms spanning cell cycle or apoptotic regulation that may reflect broader signaling crosstalk. The lack of network edges reduces the certainty, but the recurrent MAPK-growth factor\u2013neural development theme supports a coherent label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007257","count":3},{"id":"GO:0070371","count":3},{"id":"GO:0008542","count":3},{"id":"GO:0035924","count":3},{"id":"GO:2001241","count":3}]},{"hash":"1471190396346608717","title":"DNA replication and mitotic cell cycle","description":"The top GO terms are dominated by cell cycle and chromosome segregation processes, including DNA replication (GO:0006260), mitotic cell cycle (GO:0000278), G1/S transition (GO:0000082), meiotic cell cycle (GO:0051321), and kinetochore localization (GO:0034501). This pattern indicates proteins largely participate in DNA synthesis and mitosis rather than neuronal or glial differentiation. A few terms touch on dendrite morphogenesis or Schwann cell development, but they are less represented, so the core theme is cell cycle machinery.","confidence":"High","size":19,"edges":16,"triangles":4,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0042220","count":9},{"id":"GO:0060079","count":9},{"id":"GO:0051321","count":9},{"id":"GO:0000082","count":9}]},{"hash":"1091689781479657111","title":"Immune cell signaling and differentiation","description":"GO terms are dominated by immune-related processes: cellular response to interleukin-7, interleukin-4 production, NK T cell differentiation, and B cell affinity maturation, plus general immune signaling and cell migration. While insulin receptor and Wnt signaling, heart development, and transcytosis appear, the strongest recurring theme centers on lymphocyte signaling and differentiation.","confidence":"High","size":19,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046626","count":9},{"id":"GO:0098761","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0016477","count":8},{"id":"GO:0032633","count":8}]},{"hash":"995644775810669507","title":"GTPase Regulation and Rac Signaling","description":"The GO terms point to a shared theme of modulating small GTPases: positive regulation of GTPase activity, negative regulation of Rac signaling, and negative regulation of GTP binding. Other terms in the set (DNA replication, ER unfolded protein response, endothelial lumen formation, dendritic spine modification, glucan biosynthesis) appear less related, and with no reported interactions (Edges: 0), the most coherent core of the cluster is GTPase regulation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0070389","count":2},{"id":"GO:1904425","count":1},{"id":"GO:0098886","count":1},{"id":"GO:0097498","count":1}]},{"hash":"1216492445014000456","title":"Golgi\u2013endosome vesicle trafficking","description":"The GO terms cluster around intracellular transport pathways: COPII vesicle loading, recycling endosome to Golgi transport, plasma membrane\u2013endosome and retrograde transport to the Golgi, indicating a cohesive theme of vesicle trafficking within the secretory and endocytic routes. A few terms touch cell-cycle signaling, but the dominant pattern is vesicle trafficking between Golgi, endosomes, and the plasma membrane.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":2},{"id":"GO:0090110","count":2},{"id":"GO:0071955","count":1},{"id":"GO:1902543","count":1},{"id":"GO:0051534","count":1}]},{"hash":"1696485169709032620","title":"Neuroimmune signaling and synapse development","description":"This cluster includes immune-related processes (innate immune response; interleukin-7 and interleukin-4 signaling; NK T differentiation; B cell maturation) together with neural development and signaling terms (corpus callosum development; positive regulation of synapse assembly; PI3K-AKT pathway). The convergence of immune signaling and neural development/synaptic processes suggests a neuroimmune role in synapse formation and neural responsiveness, rather than a single tissue-specific function.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098761","count":2},{"id":"GO:0022038","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0043491","count":2},{"id":"GO:0061368","count":2}]},{"hash":"2271346324259836492","title":"DNA Replication and Mitotic Machinery","description":"This cluster is dominated by GO terms for DNA replication, the G1/S transition, meiotic cell cycle, and kinetochore localization, which together point to core roles in chromosome duplication and mitosis. While there are additional terms related to neural development and signaling, they appear weaker and likely reflect broader annotations rather than a unifying theme. The prevailing signal is consistent with a cohesive cell-cycle/mitosis-associated group.","confidence":"High","size":19,"edges":12,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0042220","count":5},{"id":"GO:0051321","count":5},{"id":"GO:0000082","count":5},{"id":"GO:0034501","count":5}]},{"hash":"1957143879397704310","title":"GTPase Signaling and Cytoskeletal Remodeling","description":"This cluster is dominated by GO terms related to small GTPase signaling, particularly Rac regulation and GTPase activity, and by terms connected to cytoskeletal remodeling such as dendritic spine modification and osteoclast differentiation. These patterns suggest a shared theme around GTPase-mediated control of the cytoskeleton and related remodeling processes. Some apoptosis/vascular-related terms are present but appear peripheral to the core GTPase/cytoskeleton motif. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035021","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0008625","count":3},{"id":"GO:0045671","count":3},{"id":"GO:1904425","count":2}]},{"hash":"611427870093317070","title":"Ubiquitin-Mediated NF-kappaB/TNF Signaling","description":"The dominant GO terms cluster around ubiquitination processes (K48, K63, K6 linkages and autoubiquitination) and their regulatory roles in TNF signaling and canonical NF-kappaB transcription, with links to transcriptional control and necroptosis. This points to a group of ubiquitin pathway regulators modulating inflammatory signaling and transcription rather than a single enzymatic function.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060546","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3}]},{"hash":"1054687565054770250","title":"Cell Cycle and Mitosis Regulation","description":"The top GO terms cluster around DNA replication, regulation of CDK activity, and kinetochore localization, all core to cell cycle progression and mitosis. Additional terms on proteasomal degradation and cell shape/polarity support roles in cell division and morphogenesis, with some development-related terms (telencephalon, cardiac growth) reflecting growth control during development. The combination points to a coherent theme of cell cycle control coupled with structural changes during division and tissue formation.","confidence":"High","size":18,"edges":17,"triangles":7,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071276","count":11},{"id":"GO:0043433","count":11},{"id":"GO:0032436","count":11},{"id":"GO:0000902","count":11},{"id":"GO:0006260","count":11}]},{"hash":"1043212134990121680","title":"Unknown","description":"The cluster shows a mix of GO terms including telomere maintenance and Cajal body localization, but also terms about cell division, translocation into host cell cytoplasm, sperm binding, inflammatory response, and responses to drugs/cocaine, with some terms obsolete. There is no single cohesive function tying all terms together, so a precise, representative label cannot be confidently assigned.","confidence":"","size":18,"edges":15,"triangles":4,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:1901998","count":2},{"id":"GO:0044053","count":2},{"id":"GO:0007339","count":2},{"id":"GO:1904871","count":2}]},{"hash":"1111343223272085857","title":"Organ Morphogenesis and Remodeling","description":"The top GO terms point to organ-level development and remodeling: lung branching and morphogenesis, basement membrane disassembly, and bone formation, with supporting signals from Wnt pathway localization and thyroid hormone responsiveness. Although some terms (immune and decidualization) broaden the scope, the common theme is developmental morphogenesis and extracellular matrix remodeling across tissues.","confidence":"Medium","size":18,"edges":92,"triangles":251,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051603","count":8},{"id":"GO:0046697","count":8},{"id":"GO:0060441","count":8},{"id":"GO:0034769","count":8},{"id":"GO:0060448","count":8}]},{"hash":"391501364406631392","title":"Cell cycle, transcription, and signaling","description":"The cluster includes core proliferative and gene-expression processes (mitotic cell cycle, DNA replication, and DNA-templated transcription) alongside signaling pathways (ephrin receptor signaling, MAPKK) and cytoskeletal/adhesion regulation (protein heterooligomerization, focal adhesion regulation). It also shows cellular stress responses (unfolded protein response, cadmium ion response). This mix points to broad regulatory and signaling roles linked to cell cycle and transcription, not a single pathway. ","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0048013","count":3},{"id":"GO:0000186","count":3}]},{"hash":"137148857933491336","title":"Telomere Heterochromatin Formation and DNA Replication","description":"The top GO terms point to chromatin silencing and heterochromatin formation at telomeres and subtelomeric regions (silent mating-type cassette, subtelomeric heterochromatin formation), together with DNA replication and cell cycle processes. This suggests a theme of regulation of chromatin state during replication and cell division, likely involving multi-subunit complexes (protein tetramerization) and linked regulatory processes, with a few peripheral terms (neuron development, tyrosine dephosphorylation) that are less central to this cluster. ","confidence":"Medium","size":18,"edges":23,"triangles":5,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901998","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0035335","count":6},{"id":"GO:0031939","count":5},{"id":"GO:0030466","count":5}]},{"hash":"1354594465216167033","title":"Nuclear gene expression and developmental signaling","description":"This cluster centers on DNA-templated transcription and DNA replication, with additional signals tied to development (TGF-beta response, heart and muscle development) and regulation of DNA binding and sumoylation. The combination suggests a module of nuclear gene expression linked to developmental signaling, rather than a single enzymatic function.","confidence":"Medium","size":18,"edges":7,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0000742","count":3},{"id":"GO:0033234","count":3}]},{"hash":"1997139046943649476","title":"Neuronal Synaptic Signaling and Plasticity","description":"The top terms are dominated by neural-related functions: long-term synaptic potentiation, excitatory postsynaptic potential, visual perception, and calcium-regulated signaling in muscle or neuron contexts. Although there are outliers like heart development, angiogenesis, and cell cycle terms, the central theme points to neuronal signaling and synaptic plasticity as the core function of this cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0010800","count":2}]},{"hash":"2251647114502811274","title":"Neurodevelopment and Synaptic Signaling","description":"The cluster is dominated by neural-related processes: axonogenesis, long-term synaptic potentiation, visual perception, and excitatory postsynaptic potential, pointing to neural development and synaptic function. Although angiogenesis and heart development appear among the terms, the strongest and most frequent signals describe neural connectivity and synaptic signaling, justifying a label centered on neurodevelopment and synaptic activity.","confidence":"High","size":18,"edges":90,"triangles":249,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007409","count":16},{"id":"GO:0001525","count":15},{"id":"GO:0010800","count":15},{"id":"GO:0000086","count":15},{"id":"GO:0009738","count":15}]},{"hash":"1187356064730489275","title":"Neurite outgrowth and spine morphogenesis","description":"The top terms cluster around neuronal development and actin cytoskeleton remodeling\u2014neuron projection development, dendritic spine morphogenesis, lamellipodium assembly, and actin filament dynamics\u2014pointing to neurite extension and synaptic structure formation. Translation-related terms appear ancillary rather than defining the group.","confidence":"High","size":18,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0031643","count":1},{"id":"GO:0031175","count":1}]},{"hash":"1716298679812542264","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0097310","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1403284393432176821","title":"Developmental growth signaling and protein synthesis","description":"The proteins show GO terms spanning development (brain, skin), cell proliferation, and various processes related to protein production and trafficking (translation initiation, mRNA transport, ER-Golgi transport), plus kinase activity regulation. This points to a broad theme of developmental growth signaling coupled with translational/trafficking machinery, rather than a single specific pathway. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0001731","count":2}]},{"hash":"541759564120622278","title":"Cell proliferation and lineage differentiation","description":"The most represented GO terms are dominated by cell division, the mitotic cell cycle, and cell population proliferation, pointing to a core proliferative process. Additional terms cluster around developmental differentiation in neurons and osteoclasts, as well as vesicle trafficking and ER stress responses, suggesting a broader link to growth and quality control during development. Overall, the cluster seems to reflect proliferative capacity with some lineage-specific differentiation cues rather than a single precise function.","confidence":"Medium","size":18,"edges":19,"triangles":0,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0090385","count":2}]},{"hash":"762414374775647693","title":"Unknown","description":"The terms span ribosome biogenesis, several morphogenesis processes (midbrain, cardiac atrium, pericardium), Rac signaling and GTPase activation, immune differentiation, and glucose transport, showing no single cohesive theme. This heterogeneity makes a specific, representative label unreliable, so the cluster is best described as Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0090307","count":3},{"id":"GO:0007296","count":3},{"id":"GO:1904693","count":3},{"id":"GO:0003209","count":3}]},{"hash":"1764952434568052350","title":"RNA processing and translation regulation","description":"Dominant signals are RNA metabolism and control of gene expression, including translation (GO:0006412; eIF4F complex assembly), miRNA-mediated translation inhibition, mRNA splicing regulation, modification, and stabilization. The cluster thus represents a module coordinating RNA processing with translation initiation and silencing.","confidence":"High","size":18,"edges":11,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0000381","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0016556","count":1}]},{"hash":"1844331397015996203","title":"Cell signaling in proliferation, neural development, and immunity","description":"The Top Terms span mitotic cell cycle transitions, neuronal development and plasticity (axonogenesis, long-term potentiation), vesicle trafficking, and immune/vascular signaling (innate immunity, LPS response, angiogenesis, hormone response). This pattern suggests a broad signaling hub coordinating cell division, nervous system development, and immune/vascular responses, rather than a single cohesive function.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000086","count":3},{"id":"GO:0007190","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007409","count":3}]},{"hash":"406483101843405059","title":"Detoxification and Xenobiotic Degradation","description":"Enrichment centers on cellular oxidant detoxification and responses to toxic substances, plus catabolic activities on xenobiotics (e.g., 1,2-dichloroethane). While antibiotic and PHB biosynthesis terms appear, the common thread is metabolism geared toward detoxification and xenobiotic degradation.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0097755","count":3}]},{"hash":"204039131393630339","title":"Mitotic division and ER-Golgi vesicle trafficking","description":"The cluster is dominated by terms related to mitosis, cell division, and spindle assembly, alongside vesicle trafficking between the ER and Golgi (COPII-coated vesicles, retrograde transport, and protein transmembrane transport). Developmental terms (brain development, multicellular growth) suggest these processes are active during growth, but the core theme centers on mitotic proliferation and the secretory pathway.","confidence":"High","size":17,"edges":110,"triangles":397,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":14},{"id":"GO:0008283","count":14},{"id":"GO:0051301","count":14},{"id":"GO:0090114","count":14},{"id":"GO:0006890","count":14}]},{"hash":"1164948273105907360","title":"Neural development and brain morphogenesis","description":"The cluster is dominated by GO terms related to neural development and brain structure formation, including telencephalon development, corpus callosum development, dendritic spine morphogenesis, and establishment of bipolar cell polarity. These suggest a common theme of brain growth and neuronal morphology during development. Some terms like DNA replication and placental development appear as less central or outliers but may reflect broader developmental or proliferative processes; overall, the neural development theme best explains the term set.","confidence":"Medium","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0021537","count":4},{"id":"GO:0060044","count":4},{"id":"GO:0061246","count":4}]},{"hash":"1234444011428738275","title":"Neural Development and Signaling","description":"The enriched terms point to neural biology, with telencephalon development, establishment of bipolar cell polarity, and cocaine response highlighting nervous-system-specific processes. Cyclic nucleotide biosynthesis supports neuronal signaling, while DNA-templated transcription reflects gene regulation during development. The other terms (cell cycle and apoptosis) may reflect general cellular responses in neural progenitors during development; overall, the theme centers on neural development and signaling.","confidence":"Medium","size":17,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061246","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0000082","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0009636","count":4}]},{"hash":"1218419482948499154","title":"Spliceosome-driven mRNA processing and regulation","description":"The cluster is dominated by GO terms related to mRNA splicing via the spliceosome, regulation of alternative splicing, and other post-transcriptional mRNA processing events (modification, stability, poly(A) tail regulation) plus components involved in translation initiation, indicating a cohesive function in post-transcriptional gene expression control.","confidence":"High","size":17,"edges":33,"triangles":45,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":7},{"id":"GO:0035278","count":7},{"id":"GO:0000381","count":6},{"id":"GO:1902625","count":6},{"id":"GO:0016556","count":6}]},{"hash":"2118331863851562116","title":"Neural development and synaptic plasticity","description":"The top GO terms point to neural development (neuron development) and synaptic activity (long-term synaptic potentiation), complemented by related processes like actin filament bundle assembly and cell morphogenesis, suggesting a cluster of proteins involved in neural development and synaptic remodeling. Some terms related to heart development and DNA replication appear, but the strongest, most coherent signal centers on neural development and synaptic plasticity.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048666","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0051017","count":3}]},{"hash":"684139216451518920","title":"Golgi\u2013endosome trafficking and organization","description":"The top GO terms cluster around trafficking between endosomes and the Golgi (early endosome to Golgi transport, endocytic recycling, regulation of Golgi organization) and related vesicular transport processes. While there are also cell cycle and ribosome biogenesis terms present, the strongest signal is Golgi/endosome trafficking and organization.","confidence":"Medium","size":17,"edges":14,"triangles":5,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0034498","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000055","count":4},{"id":"GO:1903358","count":3},{"id":"GO:0051260","count":3}]},{"hash":"1251132433108708150","title":"Unknown","description":"The top GO terms span a wide range of processes\u2014from ubiquitination and poly-ADP-ribosylation to intracellular signaling, Wnt signaling, and various tissue-specific events like muscle regeneration, adipocyte differentiation, hepatocyte apoptosis, and SA node action potential regulation. There isn\u2019t a single dominant biological function or pathway unifying these proteins, making it hard to assign a specific, representative label. Therefore no well-defined cluster name can be confidently given beyond Unknown.","confidence":"","size":17,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0043403","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0070198","count":2},{"id":"GO:0007205","count":2}]},{"hash":"682615628085908128","title":"Genome maintenance and developmental signaling cluster","description":"The top GO terms point to DNA replication and repair, genome maintenance, and regulation of proliferation, complemented by developmental and neural differentiation signals (telencephalon development, cell polarity) and pathways like Wnt that modulate growth. This suggests a coherent module linking genome maintenance with developmental growth control and neural differentiation, though there is some functional diversity within the set.","confidence":"Medium","size":17,"edges":17,"triangles":6,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0090090","count":8},{"id":"GO:0006281","count":8},{"id":"GO:0008285","count":8}]},{"hash":"303506816607343776","title":"Cell cycle and developmental regulators","description":"The terms point to processes tied to cell division and development, such as DNA replication, centrosome cycle, nuclear DNA replication, and embryonic cranial skeleton morphogenesis, with additional signals for cytoskeletal/migration and transcription regulation (e.g., cell migration, GTPase activity, exocytosis, transcription by RNA Pol II). While some terms touch on migration and exocytosis, the core signal across multiple entries centers on nuclear/cell cycle control and developmental processes, making this a cohesive label. ","confidence":"Medium","size":17,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0007098","count":2}]},{"hash":"1599061949200637093","title":"Immune Signaling and Cytoskeletal Remodeling","description":"The cluster is enriched for immune signaling terms (T cell receptor signaling pathway, T-helper 1 response) alongside cytoskeletal and membrane-trafficking processes (filopodium assembly/regulation, endocytic recycling, substrate adhesion\u2013dependent spreading), implying coordination between immune signaling and cytoskeletal dynamics. The GABAergic synaptic transmission term may reflect shared signaling pathways rather than a neuron-specific role, suggesting cross-talk rather than a strictly neuronal function.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051932","count":3},{"id":"GO:1900026","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0051489","count":2}]},{"hash":"1690560026589873361","title":"Endosomal trafficking and receptor turnover","description":"Enrichment for endosome-related transport, clathrin-coated vesicle loading, neurotransmitter receptor internalization/transport, and melanosome organization suggests a core function in endosomal/vesicular trafficking that controls receptor turnover and antigen processing.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099590","count":2},{"id":"GO:0043323","count":2},{"id":"GO:0061088","count":2},{"id":"GO:0035646","count":2},{"id":"GO:0048007","count":2}]},{"hash":"184787877846874969","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0034247","count":2},{"id":"GO:0098789","count":2}]},{"hash":"1103959762344961457","title":"Ribosome biogenesis and translation regulation","description":"Dominant GO terms center on translation and ribosome assembly (translation; ribosome biogenesis; ribosomal large subunit assembly) and various aspects of translational control (regulation of translational initiation; IRES-dependent viral translation; viral termination-reinitiation). Additional terms point to RNA processing and silencing (regulation of mRNA splicing via spliceosome; regulatory ncRNA-mediated gene silencing), suggesting coordinated regulation of gene expression at the RNA level that can influence translation. Overall, the cluster appears to group components and regulators of protein synthesis and ribosome production.","confidence":"High","size":16,"edges":85,"triangles":232,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0048025","count":3}]},{"hash":"450119527512121720","title":"Diverse carbon-source catabolism","description":"The top GO terms point to catabolic and utilization pathways for a variety of carbon substrates (methanol, glycerol, fucose, chlorocatechol, butanol) and general carbon utilization, suggesting the proteins cluster around diverse carbon-source metabolism rather than a single substrate. Some terms like cell morphogenesis or antibiotic response are less central, but the dominant signal is broad carbon catabolism. ","confidence":"Medium","size":16,"edges":84,"triangles":207,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":6},{"id":"GO:0046677","count":4},{"id":"GO:0015946","count":4},{"id":"GO:1901168","count":4},{"id":"GO:0019564","count":4}]},{"hash":"538017673793018694","title":"Unknown","description":"The cluster includes diverse GO terms from protein folding/quality control (cellular response to unfolded protein, chaperone-related refolding), membrane targeting (SRP-dependent cotranslational translocation), and unrelated processes (iron-sulfur cluster assembly, DNA replication, fungal beta-glucan biosynthesis, cell morphogenesis, stem cell differentiation). This lack of a single cohesive functional theme, plus some obsolete terms, makes it difficult to assign a concise, representative label.","confidence":"","size":16,"edges":19,"triangles":10,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034620","count":5},{"id":"GO:0000902","count":4},{"id":"GO:0006616","count":3},{"id":"GO:0070880","count":3},{"id":"GO:1902037","count":3}]},{"hash":"2083524175833516544","title":"Vesicle trafficking and neuronal maturation","description":"The cluster is enriched for secretory pathway processes (COPII vesicle coating, ER-to-Golgi transport, ER stress) and neuronal maturation/dopaminergic differentiation, suggesting a module linking the secretory machinery with neuron development. Additional terms like phagosome-lysosome fusion and apical junction assembly indicate broader vesicle trafficking roles that support this theme.","confidence":"High","size":16,"edges":17,"triangles":2,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1904948","count":4},{"id":"GO:0090334","count":4},{"id":"GO:0003400","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0090385","count":3}]},{"hash":"1572983666611522648","title":"Neuro-muscular development and angiogenesis","description":"Top terms indicate neural signaling and Schwann cell development, muscle development, and angiogenesis, plus regulatory signaling processes. This pattern suggests a broad developmental program spanning nervous, muscular, and vascular tissues rather than a single, cohesive pathway.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0014044","count":3},{"id":"GO:0014898","count":2},{"id":"GO:0001525","count":2},{"id":"GO:1903799","count":2}]},{"hash":"445379365504252507","title":"Metal Ion Transport and Homeostasis","description":"The top GO terms center on zinc, copper, cadmium ion transport, and intracellular calcium ion homeostasis, suggesting a core theme of ion transport and metal ion regulation. Other terms (menaquinone and serine biosynthesis, P450 pathway, testosterone response) are less directly connected, indicating these proteins may also participate in broader metabolism but the dominant signal is metal ion transport. ","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":4},{"id":"GO:0071577","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0006874","count":3}]},{"hash":"1226759827727849836","title":"Endomembrane trafficking in neural development","description":"The cluster\u2019s top GO terms emphasize vesicle trafficking and fusion (synaptic vesicle exocytosis, phagosome-lysosome fusion, apical junction assembly) alongside neural development and morphogenesis (neuronal maturation, midbrain dopaminergic neuron differentiation, cochlea morphogenesis). This pattern suggests proteins involved in membrane trafficking that influence neural differentiation and tissue morphogenesis, rather than a single static function. Thus, a label combining endomembrane trafficking with neural development best captures the shared themes.","confidence":"Medium","size":16,"edges":41,"triangles":27,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":6},{"id":"GO:0031384","count":6},{"id":"GO:2000300","count":6},{"id":"GO:0090385","count":5},{"id":"GO:0036035","count":5}]},{"hash":"1982974460768335400","title":"RNA splicing and silencing regulators","description":"The cluster strongly centers on post-transcriptional control: multiple terms for splicing regulation (including alternative splicing via the spliceosome), mRNA stability, mRNA modification, and RNA silencing pathways (ncRNA- and miRNA-mediated). The inclusion of translation initiation factor complex assembly further links to RNA processing and expression control, suggesting these proteins function together in RNA processing and gene-silencing networks.","confidence":"High","size":16,"edges":51,"triangles":84,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0010610","count":7},{"id":"GO:0000381","count":6},{"id":"GO:1902625","count":6}]},{"hash":"1016320116983840310","title":"Cytoskeletal Dynamics and Morphogenesis","description":"The cluster is driven by themes of actin cytoskeleton remodeling, microspike formation, and Rho signaling that govern cell shape changes and movement, with a note of mitotic spindle assembly linking to broader cytoskeletal processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0090307","count":2}]},{"hash":"775660250171441965","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1376371025197090957","title":"Immune signaling and insulin-PI3K pathways","description":"The cluster\u2019s terms cluster around immune/hematopoietic processes (interleukin-4 production, GM-CSF response, hemopoiesis) and metabolic signaling (insulin receptor signaling, PI3K-Akt signaling, glucose import), with a broader note on GTPase activation in signaling networks. This suggests a shared theme of immune/hematopoietic signaling coupled with insulin/PI3K pathway activity, even though the proteins are not connected in this network.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0021510","count":2},{"id":"GO:0001893","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0032633","count":2}]},{"hash":"300199476884572317","title":"Negative regulation of leukocyte extravasation and vascular remodeling","description":"The cluster\u2019s top GO terms consistently describe dampening processes that would limit immune cell trafficking (negative regulation of extravasation and neutrophil degranulation) and modulate blood vessel behavior (regulation of vascular permeability and negative regulation of remodeling/angiogenesis), suggesting a shared role in restraining immune cell movement and vascular changes. A few outliers (e.g., imaginal disc morphogenesis) are present but do not derail the main theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002692","count":3},{"id":"GO:0043314","count":3},{"id":"GO:0060313","count":3},{"id":"GO:0043114","count":2},{"id":"GO:0007480","count":2}]},{"hash":"2185599337540495133","title":"Reproductive Hormone Signaling and Ovarian/Uterine Development","description":"Dominant GO terms center on reproductive hormone signaling (FSH/LH, cAMP and IP3 signaling) and ovarian/uterine development (follicle growth, uterus development), pointing to GPCR-mediated regulation of female reproductive biology. A single antiviral defense term is an outlier.","confidence":"Medium","size":15,"edges":10,"triangles":4,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":15},{"id":"GO:0042699","count":15},{"id":"GO:0001545","count":15},{"id":"GO:0060065","count":15},{"id":"GO:0009992","count":15}]},{"hash":"558648061637450141","title":"Mitotic cell cycle and ER-Golgi trafficking","description":"The top GO terms center on cell division and mitosis (mitotic spindle assembly, cell division, mitotic cell cycle, cell population proliferation), while COPII-coated vesicle budding and Golgi-to-ER retrograde transport point to secretory pathway trafficking. Some neural-development terms (brain development, dendrite morphogenesis) are present, but the dominant shared function appears to be mitotic progression coupled with ER-Golgi trafficking in growth/development contexts.","confidence":"Medium","size":15,"edges":81,"triangles":250,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":10},{"id":"GO:0008283","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0090114","count":7},{"id":"GO:0006890","count":7}]},{"hash":"1078183461976488519","title":"RNA processing and translation initiation","description":"Most top GO terms point to RNA metabolism\u2014splicing, mRNA export, polyadenylation, and snoRNA processing\u2014and to translation initiation events (reinitiation and preinitiation complex formation). A few entries are peripheral or obsolete annotations (e.g., antibiotic response, ERAD), but the dominant theme supports RNA processing together with translation initiation.","confidence":"High","size":15,"edges":21,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0006406","count":3},{"id":"GO:0030420","count":3},{"id":"GO:0046677","count":3}]},{"hash":"1562311907195137266","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to ribosome assembly and rRNA maturation (large subunit biogenesis, preribosome assembly, and maturation of LSU/SSU/5.8S rRNA) as well as translation, pointing to proteins involved in ribosome production and protein synthesis. Some terms on mRNA processing and stress granules are present but secondary to the core ribosome/rRNA processing signals.","confidence":"High","size":15,"edges":38,"triangles":44,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0009432","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0000462","count":3}]},{"hash":"689243487758721538","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0021762","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0061732","count":3},{"id":"GO:0006099","count":3}]},{"hash":"1056419053954652487","title":"Sphingolipid signaling and phospholipid metabolism","description":"This cluster is enriched for sphingolipid-related processes (regulation of sphingolipid mediated signaling, sphinganine-1-phosphate metabolic process) and various phospholipid metabolism steps (phospholipid catabolic process, phospholipid dephosphorylation, phosphatidylglycerol biosynthesis), indicating a lipid signaling and membrane remodeling theme. Some peripheral terms (glucose-6-phosphate transport, germ cell repulsion) may reflect broader cellular processes but do not override the lipid-centric pattern.","confidence":"Medium","size":15,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1902068","count":4},{"id":"GO:0009395","count":4},{"id":"GO:0044329","count":4},{"id":"GO:0044328","count":4},{"id":"GO:0006668","count":4}]},{"hash":"1011051635134609875","title":"Neural development and innate immune signaling","description":"This cluster features neural connectivity terms (corpus callosum development; positive regulation of synapse assembly) alongside innate immune and antimicrobial responses (innate immune response; cellular response to lipopolysaccharide; response to exogenous dsRNA; interferon-beta production; defense against Gram-positive bacteria), suggesting a neuroimmune/signaling theme rather than a single pathway.","confidence":"Medium","size":15,"edges":16,"triangles":6,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0046827","count":11},{"id":"GO:0022038","count":9},{"id":"GO:0043330","count":9},{"id":"GO:0051965","count":9},{"id":"GO:0071222","count":9}]},{"hash":"1469207010804373974","title":"Unknown","description":"The GO terms cover neural development (neuron maturation, dopaminergic differentiation, cochlea morphogenesis), vesicle and membrane processes (phagosome-lysosome fusion, apical junction assembly), ER stress response, mineral homeostasis (copper), and immune/bone-related processes (osteoclast development, defense against protozoan). There isn\u2019t a single cohesive function that connects all terms, so a precise label is not identifiable.","confidence":"","size":15,"edges":24,"triangles":9,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090385","count":15},{"id":"GO:0036035","count":15},{"id":"GO:0034976","count":15},{"id":"GO:0014041","count":15},{"id":"GO:0006878","count":15}]},{"hash":"824353010520705735","title":"Transmembrane solute transporters","description":"This cluster is dominated by GO terms for transmembrane transport of diverse substrates (ions like K+, Na+, nitrite, nitrate; sugars like arabinose; molecules such as sialic acid, fucose, phosphate, and vitamins), indicating a cohesive group of membrane transporter proteins with broad substrate scope rather than a single specific ligand.","confidence":"High","size":15,"edges":15,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":4},{"id":"GO:0035435","count":4},{"id":"GO:0015707","count":4},{"id":"GO:0015751","count":4},{"id":"GO:0035461","count":4}]},{"hash":"1676210072039605654","title":"Actin Cytoskeleton Regulation and Cellular Transport","description":"This cluster is driven by actin cytoskeleton organization and positive regulation of GTPase activity, indicating proteins involved in cytoskeletal dynamics. Additional single-term annotations (mRNA transport, ribosomal protein import into nucleus, ciliary basal body docking, receptor internalization) suggest related intracellular trafficking and localization roles that often accompany cytoskeletal regulation, supporting a cohesive theme of cytoskeletal control coupled with transport processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0051307","count":1},{"id":"GO:0006610","count":1},{"id":"GO:0042518","count":1}]},{"hash":"2098697098090335852","title":"Insulin Secretion and Secretory Granule Localization","description":"The top terms are dominated by secretory pathway functions, particularly insulin secretion and secretory granule localization, suggesting vesicle trafficking and exocytosis as the main theme for this cluster. The other terms (DNA replication, spindle orientation, and translesion synthesis) appear only once or twice and likely reflect annotation noise or multifunctionality rather than a core shared function of the cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030073","count":2},{"id":"GO:0032252","count":2},{"id":"GO:0034316","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0042276","count":1}]},{"hash":"2042254384555732354","title":"Rho/Rac GTPase signaling cluster","description":"The Go terms are dominated by Rho/Rac GTPase signaling and activation of GTPase activity, indicating a cohesive theme around small GTPase pathways (Rho and Rac) and their regulation. Other terms (translation, morphogenesis, pro-B cell differentiation) appear as related processes but do not override the core Rac/Rho signaling pattern.","confidence":"Medium","size":14,"edges":9,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":2},{"id":"GO:0016601","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0043547","count":2},{"id":"GO:2000973","count":2}]},{"hash":"78701993613893695","title":"Plant development and signaling regulation","description":"The GO terms point to post-translational control of signaling pathways (deubiquitination, dephosphorylation) and regulation of growth-related signaling (TGF-beta/NF-kappaB pathways), plus plant-specific processes like meristem identity maintenance and photosystem stoichiometry adjustment, suggesting a cohesive theme of signaling regulation in plant development via ubiquitination and phosphorylation mechanisms.","confidence":"Medium","size":14,"edges":37,"triangles":37,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":4},{"id":"GO:0035970","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0080005","count":3},{"id":"GO:0010074","count":3}]},{"hash":"634991798092923475","title":"Development Across Tissues","description":"The top GO terms cluster around development and growth across multiple tissues (brain, gonads, bone), fertilization, and ciliogenesis, with supporting general cellular processes like translation initiation and chromatin assembly. This suggests a broad developmental program rather than a single specific function, reflecting multi-tissue differentiation and growth themes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0050830","count":2}]},{"hash":"2256714302021929184","title":"Developmental biosynthesis and fatty-acid metabolism","description":"The cluster shows a mix of developmental terms (multicellular development, blastocyst development, mitotic cell cycle) alongside fatty-acid and other biosynthetic processes (long-chain fatty-acyl-CoA metabolism, fatty acid biosynthesis, sporopollenin/chalcone biosynthesis, DIF-1 biosynthesis). This suggests proteins involved in developmental regulation together with lipid and secondary metabolite biosynthesis across species, hence a label reflecting development linked to biosynthesis. Some terms are species-specific or outdated, but the overall signal points to developmental processes coupled with lipid/secondary metabolism.","confidence":"Medium","size":14,"edges":8,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0032508","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0001824","count":3},{"id":"GO:0009715","count":3}]},{"hash":"1252092155012306324","title":"Developmental signaling and apoptosis regulators","description":"This cluster shows enrichment for developmental and signaling-related GO terms across tissues (muscle development, placenta development), along with modulation of signaling pathways (ERK cascade, serine phosphorylation) and apoptosis/synaptic regulation. The combined pattern suggests proteins that broadly regulate development and cell fate through signaling and apoptotic control rather than a single, confined function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060044","count":2},{"id":"GO:0001893","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0007520","count":2}]},{"hash":"1331825303722393338","title":"Neural development and morphogenesis","description":"The top GO terms cluster around neural development and neuronal structure, including telencephalon development, dendritic spine morphogenesis, motor neuron axon guidance, bipolar cell polarity, and cell\u2013matrix adhesion, suggesting a theme of neural development and neuronal morphology. Some terms (mitotic spindle organization, fatty acid oxidation, growth hormone signaling) are broader or peripheral, and the lack of edges indicates uncertain connectivity, so the label is a best-fit overall. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007052","count":3},{"id":"GO:0008045","count":3},{"id":"GO:0007160","count":3},{"id":"GO:0060396","count":3},{"id":"GO:0021537","count":2}]},{"hash":"1057981227051780259","title":"Osteoclast Differentiation and Bone Resorption","description":"The top GO terms are dominated by bone resorption and osteoclast development, with phagosome-lysosome fusion supporting osteoclast bone-dissolving activity. Other terms include general cellular processes like cell division and ribosomal export, which may reflect precursor proliferation, while a subset points to neural development (midbrain dopaminergic neuron differentiation, cochlea morphogenesis), suggesting broader developmental roles. Overall, the strongest signal is osteoclast-related functions tied to bone remodeling.","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0090385","count":2},{"id":"GO:0036035","count":2}]},{"hash":"1947562151999543132","title":"Multisystem Developmental Processes","description":"The top GO terms cluster around development and differentiation across tissues: myoblast fusion, heart development, Schwann cell development, angiogenesis, and visual perception. This suggests a common theme of tissue formation and maturation. Some terms (abscisic acid-activated signaling, bipolar bud site selection) come from non-animal systems and may reflect annotation noise, but the dominant signal points to multicellular development and tissue-specific differentiation.","confidence":"Medium","size":14,"edges":61,"triangles":131,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007520","count":14},{"id":"GO:0000086","count":14},{"id":"GO:0014850","count":14},{"id":"GO:0007121","count":14},{"id":"GO:0007601","count":14}]},{"hash":"1373725855729670830","title":"DNA replication and cell cycle cluster","description":"The top GO terms are dominated by DNA replication and cell cycle-related processes (DNA replication; G1/S transition; meiotic cell cycle; kinetochore localization), suggesting a core function in cell cycle regulation. While other terms touch on development and neural signaling, they appear secondary to the primary cell cycle theme, so a concise label focusing on DNA replication and cell cycle best captures the cluster's core function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0035690","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0030324","count":3}]},{"hash":"1008028531422986880","title":"Vesicle Trafficking and Nuclear RNA Export","description":"This cluster is dominated by intracellular transport terms: protein transmembrane transport (GO:0071806), early endosome to Golgi transport (GO:0034498), phagosome-lysosome fusion (GO:0090385), and pre-miRNA export from the nucleus (GO:0035281), indicating vesicle trafficking and nuclear RNA export activities; other terms touch localization to the plasma membrane or regulation of oxidative phosphorylation and neuron maturation but are less central.","confidence":"High","size":14,"edges":15,"triangles":4,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000060","count":10},{"id":"GO:0071806","count":10},{"id":"GO:0090324","count":9},{"id":"GO:0034498","count":9},{"id":"GO:0035281","count":9}]},{"hash":"698129528650986212","title":"Ubiquitin-Mediated Signaling and Turnover","description":"Top GO terms center on ubiquitination and ubiquitin-dependent protein degradation, including K48-linked ubiquitination and ubiquitin-dependent catabolic processes, together with Notch and Wnt signaling. This points to a coherent theme of ubiquitin-driven regulation of signaling pathways and protein turnover, with some auxiliary links to metabolism and organelle dynamics. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":1},{"id":"GO:1901315","count":1},{"id":"GO:0090141","count":1},{"id":"GO:0045071","count":1},{"id":"GO:0034389","count":1}]},{"hash":"591815685438198016","title":"Ribosome biogenesis and translation","description":"Dominant terms center on ribosome assembly and function (ribosomal subunit biogenesis, cytoplasmic translation, ribosomal export, tRNA modification), which together define a clear theme of the protein cluster as part of the protein synthesis machinery. Additional terms related to cell division and septum formation may reflect growth-related coordination with translation, while a few metabolic or stress-related terms appear as broader cellular context. Overall, the cluster is best characterized by ribosome-related assembly and translation processes.","confidence":"High","size":13,"edges":8,"triangles":4,"max_degree":4,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0090529","count":4},{"id":"GO:0042274","count":4},{"id":"GO:0051301","count":4},{"id":"GO:1901001","count":4},{"id":"GO:0006007","count":4}]},{"hash":"637622356398416965","title":"Proteostasis and RNA Processing","description":"Proteostasis-related GO terms dominate, with ubiquitin-mediated turnover (polyubiquitination, ERAD, SCF-proteasomal degradation) suggesting a core proteasome/ubiquitin cluster. Translational control terms (translation initiation, translation preinitiation complex formation, translation reinitiation) plus spliceosome-mediated mRNA splicing indicate a link to RNA processing and translation regulation. A few additional terms (cilium assembly, protein homooligomerization) appear less central but fit within broader protein-assembly contexts. Overall, the group seems to center on proteostasis intersecting with RNA processing and translation. ","confidence":"Medium","size":13,"edges":9,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3}]},{"hash":"531954096162172168","title":"Proteostasis and Protein Quality Control","description":"The cluster\u2019s top GO terms center on maintaining protein homeostasis: ER-stress\u2013related regulation of translation initiation, ubiquitin-proteasome\u2013mediated protein degradation, nuclear and misfolded protein quality control, and transport of misfolded proteins. While there are a few developmental terms present, the shared theme is proteostasis and proteolytic handling of proteins. ","confidence":"Medium","size":13,"edges":16,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0097428","count":2},{"id":"GO:1905259","count":2},{"id":"GO:0035719","count":2}]},{"hash":"418057643502432658","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0043552","count":2}]},{"hash":"2298999463041760794","title":"Developmental differentiation and gene expression regulation","description":"This cluster\u2019s top GO terms point to tissue development and differentiation (lymphangiogenesis, neuron and skeletal muscle fiber development, regulation of EMT) alongside robust control of gene expression (RNA polymerase II transcription termination, miRNA processing regulation) and metabolic processes (glycogen metabolism). The mix suggests proteins involved in developmental programs that coordinate growth with gene expression regulation and metabolism, rather than a single canonical pathway. Confidence: Medium","confidence":"","size":13,"edges":67,"triangles":220,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001946","count":12},{"id":"GO:0014898","count":12},{"id":"GO:0030846","count":12},{"id":"GO:0030182","count":12},{"id":"GO:0005981","count":12}]},{"hash":"1106009160517986554","title":"ER-Golgi-to-plasma membrane vesicle transport","description":"The cluster centers on vesicular trafficking from the ER through the Golgi to the plasma membrane, including ER-Golgi transport, Golgi-to-plasma membrane transport, and vesicle fusion with the Golgi, with examples of exocytic insertion of receptors and related signaling. This pattern suggests a cohesive role in intracellular transport and surface delivery of proteins, rather than unrelated pathways.","confidence":"High","size":13,"edges":13,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090316","count":2},{"id":"GO:0043001","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0006893","count":2}]},{"hash":"1892755454678624201","title":"Hormone signaling and cell cycle control","description":"The top GO terms include estrogen response, growth hormone receptor signaling, and core cell-cycle/DNA replication processes (G1/S transition, DNA replication, meiosis, kinetochore localization), suggesting a functional theme where hormonal signaling interfaces with cell growth, replication, and genome maintenance, with apoptosis as a regulatory balance. Some terms for neural development (axon guidance, cell-matrix adhesion) appear peripheral but do not dominate the cluster\u2019s theme. Confidence: Medium","confidence":"","size":13,"edges":14,"triangles":5,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043627","count":7},{"id":"GO:0043065","count":7},{"id":"GO:0008045","count":6},{"id":"GO:0007160","count":6},{"id":"GO:0060396","count":6}]},{"hash":"754013142451586319","title":"Unknown","description":"The terms include translation, diverse developmental processes, immune cytotoxicity, hormone response, and various catabolic processes, with no clear common function binding the proteins. Therefore no coherent label can be assigned.","confidence":"","size":13,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046697","count":1},{"id":"GO:0060448","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0001913","count":1}]},{"hash":"391114062265248784","title":"Golgi-lysosome trafficking and organelle homeostasis","description":"The cluster is enriched for terms tied to intracellular trafficking and organelle function, notably protein localization to the Golgi, phagosome\u2013lysosome fusion, ER stress response, and copper ion homeostasis. While there are also development-related terms (neuron maturation, dopaminergic neuron differentiation, osteoclast development), the strongest signals point to vesicular trafficking, Golgi/ER maintenance, and lysosomal pathways, suggesting a core theme of intracellular transport and organelle homeostasis with ancillary differentiation roles.","confidence":"Medium","size":13,"edges":68,"triangles":190,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000042","count":13},{"id":"GO:0090385","count":12},{"id":"GO:0036035","count":12},{"id":"GO:0034976","count":12},{"id":"GO:0014041","count":12}]},{"hash":"1028424459761947635","title":"Nucleolar transcription and ribosome biogenesis","description":"This cluster is dominated by GO terms for transcription by RNA polymerases I\u2013III, nucleolar rRNA transcription, nucleologenesis, and ribosome biogenesis, plus regulatory ncRNA-mediated heterochromatin formation, which together point to nucleolar transcription and ribosome assembly as the core function. Some sulfate metabolism terms appear as peripheral exceptions.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0000103","count":2},{"id":"GO:0001172","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0042790","count":1}]},{"hash":"1526339949312342987","title":"Developmental Chromatin Remodeling","description":"The top GO terms cluster around developmental processes (brain development, male gonad development, spermatid development, multicellular organism growth) and core chromatin-related activities (nucleosome assembly, transcription initiation-coupled chromatin remodeling, negative regulation of transcription by RNA polymerase II). This suggests the proteins collectively participate in regulating gene expression through chromatin architecture during development and germline maturation. An outlier term (antibiotic biosynthetic process) may reflect annotation noise rather than a true functional theme. Overall, a label emphasizing developmental regulation linked to chromatin remodeling fits best.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0008584","count":3},{"id":"GO:0000183","count":2},{"id":"GO:0045815","count":2}]},{"hash":"1390867211192323730","title":"Proteostasis and ER stress response","description":"The GO terms cluster around protein folding/unfolding (protein unfolding, ER unfolded protein response), quality control (aggresome assembly), and oligomerization, plus broader cellular maintenance like ribosome assembly and ATP metabolism. The dominant theme is protein homeostasis and ER stress response, with a more peripheral link to neuronal transport. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0002943","count":1},{"id":"GO:0046034","count":1},{"id":"GO:0031117","count":1}]},{"hash":"288111315604648707","title":"Neurodevelopment and inner-ear morphogenesis","description":"The top GO terms center on neural development (midbrain dopaminergic neuron differentiation, regulation of neuron maturation) and sensory organ formation (cochlea morphogenesis), with supporting roles like apical junction assembly in developing epithelia; ER stress response, phagosome-lysosome fusion, and copper homeostasis reflect general cellular maintenance during development. An outlier term (osteoclast development) is likely noise, but the overall pattern points to neurodevelopment and sensory organ formation.","confidence":"Medium","size":13,"edges":34,"triangles":71,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090385","count":3},{"id":"GO:0036035","count":3},{"id":"GO:0034976","count":3},{"id":"GO:0014041","count":3},{"id":"GO:0006878","count":3}]},{"hash":"585223688681584120","title":"Cell Division and Cytoskeleton Regulation","description":"The enriched GO terms point to mitotic processes and cytoskeletal control (mitotic spindle assembly, cell polarity establishment/maintenance, Rho signaling, and actin cytoskeleton reorganization). While ribosome biogenesis/export and some metabolic terms appear, the dominant signal ties cell cycle progression to cytoskeletal dynamics.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0031532","count":2}]},{"hash":"1823898003909917601","title":"Chromatin Remodeling and Developmental Processes","description":"The top GO terms emphasize chromatin remodeling and DNA geometry changes, while also showing diverse development-related terms across multiple tissues (tongue, lacrimal gland, bronchus cartilage) and endothelial activity. This suggests a cluster centered on chromatin regulation integrated with broad developmental pathways, rather than a single tissue-specific function, hence a label that captures both aspects.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0060532","count":1},{"id":"GO:0001935","count":1},{"id":"GO:2001237","count":1},{"id":"GO:0045063","count":1}]},{"hash":"1584294559709845359","title":"Meiosis-associated telomere maintenance","description":"The terms strongly point to telomere maintenance via telomerase and telomere capping, with explicit meiosis-related processes (male meiosis I, chiasma assembly) suggesting a role in meiotic telomere dynamics; other terms like TORC1 signaling and angiogenesis are less central, but do not override the core telomere-meiosis theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007004","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0016233","count":1},{"id":"GO:0006310","count":1}]},{"hash":"11139344535357767","title":"Ribosome Biogenesis and Translation","description":"This cluster is enriched for ribosome-related processes: small and large subunit biogenesis, cytoplasmic translation, tRNA modification, and export of ribosomal subunits from the nucleus, alongside cell cycle/division terms. The shared emphasis on ribosome assembly and protein synthesis supports a cohesive functional theme around ribosome production and function, with possible links to cell cycle progression.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0090529","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0051301","count":3},{"id":"GO:1901001","count":3},{"id":"GO:0000747","count":3}]},{"hash":"2116932170665319467","title":"Fatty acid and lipid metabolism","description":"Dominated by fatty acid biosynthesis and transport terms (fatty acid biosynthetic process, long-chain/medium-chain fatty-acyl-CoA metabolism, transport), with supporting signals from lipid-derived metabolite pathways (bile acids, menaquinone) and general small-molecule biosynthesis. Some outliers exist (phenylpropanoid, siderophore, malonate), but the core theme is lipid metabolism.","confidence":"Medium","size":12,"edges":21,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":6},{"id":"GO:0008206","count":5},{"id":"GO:0009698","count":5},{"id":"GO:0044539","count":5},{"id":"GO:0019654","count":5}]},{"hash":"1898539488303457283","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms tied to ribosome assembly and function: cytosolic ribosome assembly, ribosome biogenesis, maturation of LSU-rRNA, assembly of large subunit precursors, and cytoplasmic translation, along with rRNA and tRNA methylation. The inclusion of positive regulation of mitochondrial translation also aligns with translation across compartments. These recurring themes indicate a cohesive group focused on making and using ribosomes. A few terms like arsenite transport and transcription regulation appear as minor outliers.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0002127","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0070131","count":2},{"id":"GO:1902626","count":2}]},{"hash":"148166782407191412","title":"DNA replication and double-strand break repair","description":"The cluster is dominated by GO terms related to DNA replication (GO:0006260), responses to ionizing radiation and X-ray (GO:0010212, GO:0010165), and regulation of double-strand break repair via homologous recombination (GO:0010569), with supporting links to iron-sulfur cluster assembly (GO:0016226) that often participate in DNA-processing enzymes. Although there are a few outlier terms (cell morphogenesis, fungal beta-glucan biosynthesis, chaperone-related refolding, hematopoietic differentiation, SRP targeting to membrane), the strongest shared theme centers on genome maintenance and DNA repair. Confidence: Medium","confidence":"","size":12,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0010212","count":2},{"id":"GO:0010165","count":2}]},{"hash":"650981586894096008","title":"Unknown","description":"The top GO terms span phototransduction, transcription regulation, proteasome regulation, stress and immune signaling, telomerase assembly, DNA topology, cell growth, and protein trafficking, with no clear, shared function tying the proteins together. This lack of a cohesive theme makes it difficult to assign a specific, representative label, so the cluster is best termed Unknown. ","confidence":"","size":12,"edges":14,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0009585","count":1},{"id":"GO:0009651","count":1},{"id":"GO:1905323","count":1}]},{"hash":"2301544068286601283","title":"Ribosome biogenesis and translation machinery","description":"This cluster is dominated by GO terms tied to ribosome production and function: translation (GO:0006412), ribosome biogenesis (GO:0006270? but provided as GO:0042254), and ribosome assembly (GO:0042255), along with rRNA processing steps (ITS1/ITS2 cleavages). The presence of mitochondrial and general tRNA aminoacylation terms (glycyl, prolyl, threonyl) supports translation-related activity, including organellar translation. The antibiotic response term further echoes ribosome-targeting mechanisms. Overall, the functions converge on ribosome construction and protein synthesis. ","confidence":"High","size":12,"edges":14,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0000448","count":2},{"id":"GO:0042255","count":2},{"id":"GO:0000447","count":2}]},{"hash":"808531555264478750","title":"Ribosome biogenesis and translation quality control","description":"The cluster\u2019s terms center on protein synthesis and ribosome assembly (translation; ribosomal large subunit assembly) and on regulating translation under ER stress, plus components of protein quality control (ubiquitin-proteasome system, misfolded protein transport). While a developmental term appears, the dominant pattern is ribosome/translation with stress-related quality control, supporting this label.","confidence":"Medium","size":12,"edges":15,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0032781","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0001707","count":1}]},{"hash":"2080956924191795053","title":"GTPase-driven actin remodeling and cell migration","description":"The top terms cluster around small GTPase signaling and actin cytoskeleton dynamics (filopodium assembly, cytoskeleton organization, and GTPase activity regulation), pointing to coordinated cytoskeletal remodeling and cell movement. Immune-related terms appear but seem secondary to the core cytoskeletal/motility theme. ","confidence":"High","size":12,"edges":11,"triangles":2,"max_degree":4,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007264","count":7},{"id":"GO:1900026","count":6},{"id":"GO:0046847","count":6},{"id":"GO:0030036","count":6},{"id":"GO:0043547","count":6}]},{"hash":"1713697056628827113","title":"Neural development and MAPK signaling","description":"This cluster centers on neural development terms (dendrite morphogenesis, nervous system/hippocampus development, axon growth) and regulation of signaling pathways (ERK/JNK cascades, phosphorylation, protein stability), suggesting proteins involved in neural differentiation and MAPK-mediated signaling.","confidence":"High","size":12,"edges":7,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048813","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0045773","count":5},{"id":"GO:0070374","count":5},{"id":"GO:0033138","count":5}]},{"hash":"210162670659516394","title":"Dopaminergic neuron differentiation and actin remodeling","description":"This cluster is dominated by GO terms linked to neuronal development and cytoskeletal dynamics, notably positive regulation of lamellipodium assembly, Rac protein signaling, neuron maturation, and midbrain dopaminergic neuron differentiation, all pointing to Rac-driven actin remodeling during neuronal differentiation. Additional terms about Golgi to plasma membrane transport fit with membrane expansion needed for neurite outgrowth, while other terms (ER stress, copper homeostasis, phagosome-lysosome fusion, osteoclast development) are less central but may reflect broader cellular stress, trafficking, or metal handling contexts. Overall, the strongest signal is neuronal differentiation coupled with cytoskeletal remodeling.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010592","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0016601","count":3},{"id":"GO:0043001","count":3},{"id":"GO:0090385","count":2}]},{"hash":"1329252826450650411","title":"Nuclear RNA Processing and Protein Quality Control","description":"The cluster is driven by RNA processing terms (mRNA, miRNA, siRNA processing) and nuclear protein quality control via the ubiquitin-proteasome system, plus related processes like tRNA import into the nucleus and ER stress\u2013associated regulation of translation initiation. Some developmental terms appear as outliers, but the core signal is nuclear RNA metabolism and proteostasis.","confidence":"Medium","size":12,"edges":16,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":1},{"id":"GO:0035196","count":1},{"id":"GO:0030422","count":1},{"id":"GO:0010087","count":1},{"id":"GO:0036494","count":1}]},{"hash":"2006395364567234413","title":"Secretory Pathway and ER Stress Response","description":"This cluster is enriched for GO terms linking endoplasmic reticulum to Golgi vesicle transport and cellular responses to unfolded proteins, oxidative stress (diamide), and hypoxia, pointing to proteins involved in secretory trafficking and ER stress signaling. A few terms about placental development and pregnancy appear but are likely annotation noise; the core theme is vesicle transport in the secretory pathway combined with stress-responsive regulation.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:1990910","count":1},{"id":"GO:0060136","count":1},{"id":"GO:1904843","count":1},{"id":"GO:0043497","count":1}]},{"hash":"1077280454281225136","title":"Ribosome Biogenesis and Cell Cycle","description":"Most terms point to ribosome biogenesis and cytoplasmic translation (ribosomal subunit biogenesis, export, translation) and to cell cycle/division (cell cycle, cell division, septum assembly). This indicates a cluster representing growth-related protein synthesis machinery coordinated with cell division, hence the label.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0042254","count":3},{"id":"GO:1901001","count":3},{"id":"GO:1903833","count":3}]},{"hash":"1576010153583431070","title":"Ribosome biogenesis and translation during cell division","description":"This cluster centers on ribosome production and function: terms like ribosome biogenesis, ribosomal subunit biogenesis, and cytoplasmic translation point to synthesis and maturation of ribosomes, while tRNA modification supports translation fidelity. The presence of cell cycle, cell division, and septum assembly suggests coordination of ribosome production with cell division, and the amino acid starvation regulation term hints at translational control under nutrient stress. Overall, the proteins likely participate in ribosome assembly and protein synthesis tied to cell division.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:1903833","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0042274","count":4}]},{"hash":"238426959646267536","title":"Ribosome Biogenesis and Cell Division","description":"The strongest terms are about translation machinery and ribosome assembly (cytoplasmic translation, ribosomal subunit biogenesis, ribosomal subunit export from nucleus, tRNA modification), which point to protein synthesis. The presence of cell septum assembly and cell division suggests coordination of translation/biogenesis with cytokinesis. Peripheral terms like glucose catabolic process and negative regulation of salt-stress response may reflect broader metabolic/regulatory roles or annotation noise (virus-related term appears obsolete). Overall, the cluster centers on ribosome production and its link to cell division.","confidence":"High","size":11,"edges":21,"triangles":18,"max_degree":8,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":5},{"id":"GO:0090529","count":4},{"id":"GO:0042274","count":4},{"id":"GO:0051301","count":4},{"id":"GO:1901001","count":4}]},{"hash":"698283410906191230","title":"Transmembrane solute transport","description":"Top GO terms indicate transport of a variety of solutes across the plasma membrane (ions, sugars, vitamins, and other nutrients) and related osmotic/nutrient stress responses. Together these suggest a functional cluster of membrane transport proteins focused on transmembrane solute movement.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":1},{"id":"GO:0097080","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0071805","count":1},{"id":"GO:1904659","count":1}]},{"hash":"2094225384761327325","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around ribosome production and use\u2014ribosome biogenesis, ribosomal subunit export from the nucleus, and translational initiation/termination\u2014indicating the proteins primarily participate in ribosome assembly and the translation machinery, with a few secondary processes such as mRNA splicing or cytoskeletal assembly.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0007021","count":2}]},{"hash":"1036050264965875545","title":"Nuclear RNA export and vesicle trafficking","description":"Top GO terms center on nuclear export of RNA and ribosomal subunits and on intracellular vesicle transport processes (endosome-Golgi, phagosome-lysosome fusion, protein localization to plasma membrane). This points to a cohesive theme of intracellular transport and RNA export, despite some unrelated terms present. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000055","count":5},{"id":"GO:0090324","count":4},{"id":"GO:0034498","count":4},{"id":"GO:0035281","count":4}]},{"hash":"767969115372510336","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097498","count":2},{"id":"GO:0090334","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0090051","count":2},{"id":"GO:0098887","count":2}]},{"hash":"643919291547400021","title":"Rac-Driven Cytoskeleton Remodeling","description":"This cluster centers on Rac signaling and actin-based structures, with terms for Rac-mediated signal transduction, stress fiber and filopodium assembly, and cell spreading, indicating a common function in cytoskeleton remodeling. The inclusion of endocytic trafficking terms suggests coordination between cytoskeleton dynamics and membrane trafficking, consistent with Rac-regulated cellular remodeling.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":2},{"id":"GO:0051496","count":2},{"id":"GO:0016601","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0090307","count":2}]},{"hash":"1293894659149898497","title":"Neural Development and MAPK Signaling Regulation","description":"The cluster is dominated by neural development terms (dendrite morphogenesis, nervous system development, hippocampus development, axon extension) and by signaling regulation terms (positive regulation of JNK and ERK cascades, peptidyl-serine phosphorylation, regulation of protein stability). This points to a coherent theme of neural maturation with modulation of MAPK signaling pathways, with some overlap onto general signaling and cell cycle terms likely due to shared components. High confidence that this label captures the core function of the cluster.","confidence":"High","size":11,"edges":17,"triangles":4,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048813","count":8},{"id":"GO:0007399","count":8},{"id":"GO:0045773","count":8},{"id":"GO:0033138","count":8},{"id":"GO:0031647","count":8}]},{"hash":"847591567619829265","title":"Neural development and synaptic vesicle regulation","description":"This cluster is dominated by terms related to brain development and synaptic vesicle processes (synaptic vesicle priming and exocytosis regulation), with additional signals for negative regulation of angiogenesis and vascular remodeling. While a few terms touch on immune-related processes, the strongest signals point to neural development and synaptic function, with some cross-talk to vascular regulation.","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043314","count":4},{"id":"GO:0002692","count":4},{"id":"GO:0060313","count":4},{"id":"GO:0016082","count":3},{"id":"GO:2000300","count":3}]},{"hash":"1564580148743291971","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0071037","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0036450","count":1},{"id":"GO:0071076","count":1}]},{"hash":"1171264099110021335","title":"RNA processing and mRNA turnover","description":"The top GO terms cluster around RNA metabolism: splicing (mRNA cis splicing via spliceosome), tRNA processing, rRNA maturation, mRNA decapping/decay, and P-body assembly, with additional nuclear import and histone mRNA metabolism terms. Together these suggest a functional group focused on RNA maturation, export, and turnover, despite a few broader or stress-related terms.","confidence":"Medium","size":10,"edges":27,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":5},{"id":"GO:0008033","count":4},{"id":"GO:0009414","count":4},{"id":"GO:0033962","count":4},{"id":"GO:0030490","count":4}]},{"hash":"356433347749211700","title":"Nuclear transcription regulation and ER protein folding","description":"The cluster centers on nuclear control of gene expression (DNA-templated transcription; negative regulation of transcription by RNA Pol II; RNA Pol II regulatory region binding) and on ER-associated protein folding and related redox processes (protein folding in ER; deglutathionylation; oxidative stress response). This suggests a coordinated module linking transcriptional regulation with ER proteostasis and stress responses, though some terms are obsolete. Overall, the themes cohere around transcriptional control and ER-focused folding/redox processes.","confidence":"Medium","size":10,"edges":10,"triangles":7,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070389","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0006260","count":2}]},{"hash":"655192544858433448","title":"Redox Homeostasis and DNA Replication/Cell Cycle","description":"This cluster combines strong signals for cellular redox balance and oxidative stress responses with key nuclear processes like DNA replication, transcription, and cell-cycle transitions (G1/S and meiosis) plus kinetochore localization. The convergence of redox-related GO terms with replication/repair and cell-cycle terms suggests a coherent theme of maintaining genome integrity under oxidative conditions and coordinating replication with cell division.","confidence":"High","size":10,"edges":11,"triangles":3,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045454","count":6},{"id":"GO:0006260","count":4},{"id":"GO:0046826","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0006351","count":4}]},{"hash":"1378178992275190749","title":"Actin-driven cell edge remodeling and adhesion","description":"This cluster centers on actin cytoskeleton dynamics and associated signaling, including podosome/filopodium assembly, actin polymerization, and cell polarity, plus pathways like small GTPase signaling, ephrin and Wnt pathways, and endocytosis, all tying to adhesion-dependent spreading and cell migration processes.","confidence":"High","size":10,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0043652","count":3},{"id":"GO:0071803","count":3},{"id":"GO:0007264","count":3}]},{"hash":"397546764220819967","title":"Transcription Initiation and Chromatin Regulation","description":"This cluster shows strongest enrichment for transcription-related functions: DNA-templated transcription initiation, RNA polymerase II preinitiation complex assembly, and regulation of transcription of Notch target genes, along with histone H3 acetylation. Other terms touch on endosomal transport and immune signaling, but the dominant signal points to transcriptional control and chromatin modification.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042098","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0032435","count":1},{"id":"GO:0060760","count":1},{"id":"GO:0000492","count":1}]},{"hash":"1128183795702547812","title":"Actin Cytoskeleton Dynamics and Cell Adhesion","description":"The top terms converge on actin-related processes (cell migration, bleb regulation, actin cytoskeleton reorganization, myofibril assembly) and cellular interactions (cell-cell adhesion, phagocytosis), suggesting a theme of cytoskeleton-driven movement and adhesion. A few terms (DNA replication, sporocarp differentiation) are peripheral and do not define the cluster, so a cytoskeleton/motility focus is most representative.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0016477","count":1},{"id":"GO:1904171","count":1},{"id":"GO:0055003","count":1},{"id":"GO:2000251","count":1}]},{"hash":"706571336853910960","title":"DNA replication and chromosome maintenance","description":"The cluster shows strong representation of DNA replication (GO:0006260), double-strand break repair via homologous recombination (GO:0000724), and mitotic chromosome condensation and sister chromatid cohesion (GO:0007076, GO:0007064), pointing to genome integrity maintenance during cell division. Some outliers (tRNA gene clustering, SOS response, obsolete renaturation) are present but do not outweigh the core theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903342","count":1},{"id":"GO:0000733","count":1},{"id":"GO:0070058","count":1},{"id":"GO:0071960","count":1},{"id":"GO:0070550","count":1}]},{"hash":"1391403824656183508","title":"Angiogenesis and endothelial tube formation","description":"The top GO terms cluster around vascular development and endothelial cell behavior, notably negative regulation of sprouting angiogenesis and endothelial tube lumen extension, with supporting signals from small GTPase\u2013mediated signaling and Golgi trafficking that underpin migration and secretion during tube formation. Some terms (e.g., xylan/galactosylceramide catabolism) appear more peripheral or annotational noise, but the core theme centers on angiogenesis and endothelial morphogenesis.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0090051","count":4},{"id":"GO:0097498","count":4},{"id":"GO:0090334","count":3},{"id":"GO:0098887","count":3},{"id":"GO:0051683","count":3}]},{"hash":"1142470726049710643","title":"Unknown","description":"These proteins show a highly diverse set of GO terms spanning vitamin B12 biosynthesis, plant defense (camalexin), cell wall remodeling, various signaling pathways, and general cellular processing. The terms do not converge on a single coherent function or pathway, and some annotations (e.g., endocannabinoid signaling) may reflect cross-kingdom noise or generic terms. Therefore, there isn\u2019t a clear, representative label to assign.","confidence":"","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1901183","count":2},{"id":"GO:0071327","count":2},{"id":"GO:0045490","count":2}]},{"hash":"1146899897785010371","title":"GTPase-regulated cytoskeletal remodeling","description":"This cluster is driven by GO terms related to cytoskeletal organization and small GTPase signaling (septin ring assembly, Rac regulation, and positive regulation of GTPase activity), with links to dendritic spine modification and vascular remodeling (endothelial lumen extension, vascular permeability). The ubiquitin-dependent catabolic term is a general background process, but the shared thread appears to be cytoskeletal dynamics governed by GTPase signaling. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0000921","count":2},{"id":"GO:1904425","count":2},{"id":"GO:0098886","count":2},{"id":"GO:0097498","count":2}]},{"hash":"1232245867059027569","title":"Immune cell development and signaling","description":"Based on the Top Terms, the cluster is enriched for immune system processes: hematopoiesis, interleukin-2\u2013mediated signaling, activated T cell proliferation, and regulation of integrin-mediated cell adhesion, pointing to roles in immune cell development, activation, and trafficking. While neural development terms and pollen recognition appear among the terms, they are less represented and do not define the cluster\u2019s core function. Overall, the strongest signal is immune-related, hence this label.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030097","count":8},{"id":"GO:0009190","count":7},{"id":"GO:0060997","count":7},{"id":"GO:0022038","count":7},{"id":"GO:0020021","count":7}]},{"hash":"1757997696963880422","title":"Neural development and synaptic signaling","description":"The cluster is driven by nervous system development terms (neuron differentiation, Schwann cell development) and synaptic activity (excitatory postsynaptic potential), with additional neural-phenotype terms like response to cocaine. The presence of cell cycle-related terms may reflect proliferative neural progenitors or general cellular processes, but the dominant theme centers on neural development and synaptic function.","confidence":"Medium","size":9,"edges":14,"triangles":10,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030182","count":4},{"id":"GO:0071353","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0060079","count":3}]},{"hash":"1906811225634083522","title":"Membrane trafficking and cell division","description":"The cluster is dominated by GO terms for intracellular vesicle transport (ER-Golgi and COPII budding, endocytosis), indicating a core function in membrane trafficking. In addition, several terms relate to the cell cycle (mitotic spindle assembly, mitotic cell cycle, cell division, cell proliferation), suggesting a link between vesicle trafficking and cell-cycle regulation. Brain development appears as a broader context rather than a core motif. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0006897","count":4},{"id":"GO:0033138","count":3},{"id":"GO:0090307","count":3}]},{"hash":"1011754355284716015","title":"DNA Replication and Cell Cycle with Stress Response","description":"This cluster centers on core cell division and DNA replication processes (GO:0051301, GO:0006260, GO:0007049), indicating a cell-cycle\u2013related module. Additional terms for oxidative stress and interferon response suggest the proteins operate under cellular stress, with some chaperone/refolding and ERAD-related terms adding a protein quality-control angle. Overall, the dominant theme is DNA replication and cell cycle regulation, with associated stress responses.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0030433","count":2}]},{"hash":"4600597480745009","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":5,"triangles":1,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0071031","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0000398","count":2}]},{"hash":"139989685109295857","title":"Plant development and genome maintenance","description":"The cluster centers on chromatin remodeling and DNA replication/repair, indicating genome maintenance during growth. It also includes leaf formation and plant-specific metabolism (sinapate esters), plus osmotic stress response and ER-Golgi transport, pointing to active plant growth, development, and cellular trafficking under stress. Taken together, these terms suggest a Plant development and genome maintenance theme with associated stress signaling.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0014883","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051533","count":2}]},{"hash":"1495172845970583993","title":"Post-transcriptional mRNA processing and regulation","description":"The GO terms cluster around splicing regulation, mRNA modification, poly(A) tail dynamics, mRNA stabilization, translation initiation factor assembly, and miRNA-mediated silencing, all pointing to post-transcriptional control of mRNA fate and translation.","confidence":"High","size":9,"edges":18,"triangles":14,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":6},{"id":"GO:1902625","count":6},{"id":"GO:0016556","count":6},{"id":"GO:0048025","count":6},{"id":"GO:0035278","count":6}]},{"hash":"607023474977074985","title":"Nutrient and xenobiotic membrane transport","description":"The proteins in this cluster are linked to multiple GO terms involving transport across membranes and secretion, including sterol transport, amino acid and vitamin transport, xenobiotic export, and peroxisomal fatty acid import. This collective signal points to a shared role in membrane transport of nutrients and xenobiotics, with a possible outlier term related to ribosome disassembly that may reflect annotation noise or secondary function.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032366","count":1},{"id":"GO:0060702","count":1},{"id":"GO:0030253","count":1},{"id":"GO:0015803","count":1},{"id":"GO:0032790","count":1}]},{"hash":"710250664637726478","title":"Endomembrane transport and protein localization","description":"The top GO terms point to vesicle trafficking steps (early endosome to Golgi transport; phagosome-lysosome fusion) and regulated protein localization to membranes, plus RNA export and related processes. While there are ancillary terms related to gene expression and development, the strongest shared theme among the terms is intracellular transport and membrane targeting, suggesting a cluster of proteins involved in endomembrane trafficking and protein localization. ","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010628","count":4},{"id":"GO:0071963","count":4},{"id":"GO:0000001","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0090324","count":3}]},{"hash":"374090776172544597","title":"Cell Cycle and Ribosome Biogenesis","description":"The cluster shows strong representation of cell division and cell cycle terms (cell division, cell cycle, cell septum assembly) together with several ribosome-related processes (ribosomal small/large subunit biogenesis, cytoplasmic translation, tRNA modification, export of large subunit from the nucleus). This points to a cohesive theme of growth-related cellular machinery coordinating division with protein synthesis. Some terms relate to stress responses or conjugation, which are less central to the core theme, hence the label focuses on the dominant link between cell cycle progression and ribosome biogenesis.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0090529","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0002181","count":3}]},{"hash":"1003145600572912868","title":"Neural development and dendrite morphogenesis","description":"These top GO terms mostly describe brain development and neuronal morphology (telencephalon and corpus callosum development, dendrite and dendritic spine morphogenesis, and bipolar cell polarity). A couple of terms (placental development, symbiont-mediated host transformation) are present but solitary and do not define the core function. Overall, the proteins likely participate in neural development and the shaping of neuronal processes.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021537","count":1},{"id":"GO:0060044","count":1},{"id":"GO:0061246","count":1},{"id":"GO:0009190","count":1},{"id":"GO:0060997","count":1}]},{"hash":"551314299757661477","title":"Signal transduction and cell fate regulation","description":"The proteins appear enriched for intracellular signaling pathways (including Wnt and GPCR-related signaling) and post-translational modification (PARylation), alongside tissue-specific processes such as skeletal muscle regeneration, fat cell differentiation, hepatocyte apoptosis, and SA node action potential regulation. This suggests a broad set of signaling mechanisms that regulate cell proliferation, differentiation, and survival across different tissues, rather than a single, tightly focused function.","confidence":"Medium","size":9,"edges":14,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043403","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0070198","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0070212","count":3}]},{"hash":"197621784839831411","title":"Cell cycle and development regulation","description":"These terms cluster around regulation of fundamental cellular processes: mitotic cell cycle and stem cell division; regulation of DNA damage checkpoint; ubiquitin-dependent protein catabolic process; and developmental differentiation (cell differentiation, cotyledon development, granulocyte differentiation). A subset also hints at neuronal connectivity regulation (dendrite morphogenesis, synaptic plasticity), suggesting broader regulatory roles in development and cell fate. Taken together, the label 'Cell cycle and development regulation' best reflects the common theme of controlling proliferation and differentiation, with proteostasis supporting these processes.","confidence":"Medium","size":8,"edges":16,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:2000623","count":2},{"id":"GO:0050775","count":1},{"id":"GO:0031915","count":1},{"id":"GO:2000001","count":1}]},{"hash":"1974537386003489357","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to ribosome assembly and function\u2014ribosomal small subunit biogenesis, translation, ribosome biogenesis, and SSU-rRNA maturation\u2014indicating a cohesive group of proteins involved in ribosome production and protein synthesis. Some miscellaneous terms (TOR signaling, cell cycle, apoptosis, development) appear but do not override the strong ribosome-focused signal, supporting a core theme of ribosome biogenesis and translation.","confidence":"High","size":8,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0033077","count":1}]},{"hash":"2082386909861039574","title":"Fungal cell wall biosynthesis and morphogenesis","description":"The cluster\u2019s strongest signal is fungal-type beta-glucan biosynthetic process, paired with SRP-dependent cotranslational targeting to membranes and cell morphogenesis, suggesting a fungal secretory/membrane-associated program active in cell wall production and shape changes. Some terms (e.g., DNA replication, iron-sulfur cluster assembly) are broader or noisy, but the fungal cell wall/morphogenesis theme is the most coherent among the dominant terms.","confidence":"Medium","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006616","count":4},{"id":"GO:0070880","count":4},{"id":"GO:0000902","count":4},{"id":"GO:1902037","count":4}]},{"hash":"463220272117730219","title":"Post-transcriptional mRNA regulation","description":"The top GO terms cluster around splicing regulation, mRNA modification, poly(A) tail control, mRNA stability, and translation initiation factor assembly, all pointing to post-transcriptional control of gene expression. The absence of edges suggests no known interactions in this network view, but the functional theme remains cohesive around RNA processing and translation regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2}]},{"hash":"1635840227031139366","title":"Neural Development and Synaptic Signaling","description":"The cluster shows a strong tilt toward brain development and neuronal structure/function: telencephalon and corpus callosum development, dendritic spine morphogenesis, and bipolar cell polarity, combined with signaling and ion transport processes (potassium ion transport, cyclic nucleotide biosynthesis, and NFAT pathway regulation). While a couple of terms (placental development, symbiont-host transformation) are less related, the core theme clearly points to neural development and synaptic signaling.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006813","count":6},{"id":"GO:0051534","count":6},{"id":"GO:0021537","count":5},{"id":"GO:0060044","count":5},{"id":"GO:0061246","count":5}]},{"hash":"1700275194120118726","title":"Metal Ion Transport and Broad Metabolic Biosynthesis","description":"The GO terms show metal ion transport (copper, zinc, cadmium) and calcium homeostasis, plus diverse biosynthetic and lipid-related processes (serine, N-acetylneuraminate, N-acetylglucosamine biosynthesis; phospholipid dephosphorylation) and a P450 epoxygenase pathway, suggesting proteins with roles in ion handling alongside broader metabolic and lipid-processing functions rather than a single pathway.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":2},{"id":"GO:0006825","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0006874","count":2},{"id":"GO:0019373","count":2}]},{"hash":"1814792470700247348","title":"Unknown","description":"GO terms cover reproductive remodeling, immune cytotoxicity, neural proliferation, collagen/peptide catabolism, thyroid hormone response, and mitochondrial autophagy, pointing to diverse, largely unrelated processes rather than a single shared function. There isn\u2019t a cohesive theme tying the eight proteins together, so Unknown is appropriate.","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046697","count":1},{"id":"GO:0060448","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0001913","count":1},{"id":"GO:2000179","count":1}]},{"hash":"1017781120931028883","title":"Carbohydrate biosynthesis and catabolism","description":"Many terms describe both synthesis and degradation of various sugars and storage polysaccharides (sucrose, starch/amylopectin, glycogen, maltose, trehalose), plus related catabolic processes. This combination points to a general carbohydrate metabolism cluster rather than a narrow pathway.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0005985","count":3},{"id":"GO:0019252","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0044245","count":2},{"id":"GO:0005992","count":2}]},{"hash":"1590196386939948820","title":"Cross-Species Developmental Processes","description":"The GO terms cluster around broad developmental roles across organisms, including muscle and organ development in animals (lung smooth muscle, ventricular and skeletal muscle differentiation, bronchus cartilage), a signaling pathway (ERK5 cascade), and various plant developmental processes (inflorescence morphogenesis, floral organ abscission) as well as gastrulation-related events (primitive streak formation) and germinal center formation. The common theme is developmental biology rather than a single tissue, pathway, or species, indicating a group of proteins associated with diverse developmental programs.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061145","count":1},{"id":"GO:0070375","count":1},{"id":"GO:0060532","count":1},{"id":"GO:0080155","count":1},{"id":"GO:0048283","count":1}]},{"hash":"2260931217515624413","title":"Plant development and osmotic stress response","description":"Most GO terms point to plant development (leaf formation, seed growth, cell differentiation, secondary cell wall biogenesis) and stress/hormone signaling (osmotic stress, ethylene). Together they suggest proteins involved in plant growth and regulatory responses to environmental cues. Some terms are negative regulation of biosynthetic processes, which adds noise, so overall confidence is moderate.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":2},{"id":"GO:0010338","count":2},{"id":"GO:1903770","count":2},{"id":"GO:1990414","count":2},{"id":"GO:1903086","count":2}]},{"hash":"1793539443668925010","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0071166","count":1},{"id":"GO:0000244","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0000154","count":1}]},{"hash":"127735994570504809","title":"Deoxyribonucleotide Biosynthesis and Salvage","description":"The cluster centers on nucleotide metabolism and DNA precursor generation: TMP biosynthesis, deoxycytidine and deoxyguanosine salvage, dGTP metabolism, and deoxyribonucleoside monophosphate biosynthesis, which together indicate a shared function in producing and recycling DNA building blocks. The mitochondrial electron transport term is less directly connected to this theme. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071897","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0046092","count":2},{"id":"GO:0006230","count":2},{"id":"GO:0016310","count":2}]},{"hash":"900365924891823710","title":"Cytoskeletal remodeling and cell migration","description":"The cluster features actin filament polymerization and regulation of endocytosis, plus mesenchyme migration and skeletal muscle fiber adaptation, pointing to a shared theme of cytoskeletal remodeling driving movement and membrane trafficking. Neural-related terms like retina homeostasis and substantia nigra development are less coherent but can reflect neuronal actin dynamics; several terms are obsolete, suggesting heterogeneous signals. Overall, the dominant signals center on cytoskeletal dynamics and cell movement.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046196","count":2},{"id":"GO:0043503","count":1},{"id":"GO:0001895","count":1},{"id":"GO:0000011","count":1},{"id":"GO:0042766","count":1}]},{"hash":"36421210547736292","title":"Vesicle trafficking and secretion","description":"The top GO terms emphasize synaptic vesicle budding and priming and platelet secretion, with protein tetramerization commonly involved in multimeric trafficking complexes. Although there are also terms related to metabolism and signaling, the strongest signal centers on vesicle formation and secretory processes, suggesting a cluster of proteins involved in vesicle trafficking and secretion.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":3},{"id":"GO:0016185","count":2},{"id":"GO:0016082","count":2},{"id":"GO:0032000","count":2},{"id":"GO:0098761","count":2}]},{"hash":"143025655464801307","title":"Proteostasis and Stress Signaling Regulation","description":"The top GO terms center on protein quality control under stress (ERAD, unfolded protein response, aggresome assembly) and broad negative regulation of signaling pathways (HIPPO, TLR3, calcium channels, glucokinase, translation). This suggests a coordinated role in maintaining cellular homeostasis during stress by regulating proteostasis and dampening multiple signaling axes, with links to apoptosis via ER stress. Confidence: Medium","confidence":"","size":7,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035329","count":4},{"id":"GO:0070059","count":4},{"id":"GO:1905366","count":3},{"id":"GO:1904378","count":3},{"id":"GO:0034140","count":3}]},{"hash":"1948639747007640580","title":"Unknown","description":"The GO terms span DNA replication, protein targeting, fungal cell wall biosynthesis, morphogenesis, and iron-sulfur cluster assembly with outliers, showing no single cohesive function for the cluster. This diversity suggests no coherent cluster-level theme.","confidence":"","size":7,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006616","count":4},{"id":"GO:0070880","count":4},{"id":"GO:0000902","count":4},{"id":"GO:1902037","count":4}]},{"hash":"1986268968852196738","title":"Ribosome Biogenesis and Translation","description":"The cluster's top GO terms cluster strongly around ribosome biogenesis, rRNA processing, cytosolic ribosome assembly, and translation, indicating a cohesive function in making and initiating protein synthesis. While there are a few transcription-related terms, the dominant theme is ribosome assembly and translation.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0031564","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0042254","count":2}]},{"hash":"477041445985683753","title":"RNA processing and ribosome biogenesis","description":"This cluster is enriched for rRNA maturation (SSU and LSU) and ribosomal large subunit biogenesis, plus spliceosome-mediated mRNA splicing, suggesting a core role in RNA processing and ribosome assembly. The additional terms related to stress responses and neural development may reflect broader cellular contexts or annotation noise rather than a defining function of the cluster.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0001843","count":2}]},{"hash":"1596197547426042168","title":"Placental and cardiac development with insulin signaling","description":"The top GO terms point to maternal and embryonic placenta development, placental differentiation, and heart development, complemented by insulin receptor signaling and the PI3K/AKT pathway, suggesting a developmental program focused on placental and cardiac formation regulated by insulin signaling. Additional terms like glycogen cell differentiation in placenta and cellular signaling support this developmental theme, with immune/hematopoietic terms likely reflecting placental milieu. Overall, the dominant theme is embryonic placental and heart development coordinated with insulin/PI3K signaling.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001893","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0032633","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0008286","count":2}]},{"hash":"1619973852372124557","title":"Ribosome assembly and translation initiation","description":"This cluster centers on translation-related processes: initiation and reinitiation, preinitiation complex formation, and even viral-specific initiation/termination-reinitiation, indicating a focus on ribosome assembly and translation machinery. The presence of tRNA and rRNA pseudouridine synthesis terms and rRNA processing (ITS2 cleavage) further supports a link to ribosome biogenesis and function, with some viral-context terms suggesting context-specific translation. Confidence: High","confidence":"","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0002188","count":2}]},{"hash":"923696502673904998","title":"Amino acid catabolism and biosynthesis","description":"The cluster is enriched for amino acid metabolism terms, including various catabolic processes (amine, serine, homocysteine, threonine) and biosynthesis (tryptophan, 2-oxobutyrate) as well as hydrogen sulfide production linked to sulfur-containing amino acid pathways, indicating a group of proteins involved in amino acid turnover and related metabolic steps. One term (response to morphine) is likely incidental noise and does not alter the main theme.","confidence":"High","size":7,"edges":15,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009310","count":3},{"id":"GO:0006565","count":3},{"id":"GO:0070814","count":3},{"id":"GO:0019343","count":3},{"id":"GO:0019499","count":3}]},{"hash":"2224267602247330840","title":"Chromatin remodeling during cell division","description":"The top terms highlight chromatin dynamics (nucleosome assembly/disassembly, histone acetylation) closely tied to cell division processes (budding growth, microtubule polymerization, stem cell division), suggesting a cluster centered on chromatin remodeling coupled with cell cycle progression.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007117","count":1},{"id":"GO:0006337","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0015031","count":1}]},{"hash":"1699035076781402005","title":"Diverse bacterial metabolism and translation genes","description":"The GO terms show a mix of translation-related processes (tRNA processing, queuosine biosynthesis, ribosome disassembly) and various energy/metabolism pathways (TCA cycle, formate/formate oxidation, lactate oxidation, photosynthesis) plus other bacterial-specific processes (flagellum assembly, sulfate reduction). The cluster appears germane to diverse bacterial functions rather than a single cohesive pathway, justifying a broad label that emphasizes bacterial origin and functional diversity.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008616","count":1},{"id":"GO:0060702","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0032790","count":1},{"id":"GO:0006099","count":1}]},{"hash":"2172019136012205842","title":"Plant development and polyamine metabolism","description":"This cluster shows signals of plant growth and development, notably regulation of leaf formation, and polyamine metabolism (putrescine acetylation/catabolism and arginine biosynthesis), suggesting a developmental/metabolic program in plants. Additional terms for transcription and protein folding reflect general cellular processes that accompany growth, while glucosamine metabolism aligns with broader metabolism. Together, the strongest theme is plant development linked to polyamine pathways.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0034975","count":2},{"id":"GO:0017198","count":2},{"id":"GO:0006041","count":2},{"id":"GO:0001525","count":2}]},{"hash":"1304993817491598644","title":"Protein acetylation and polyamine metabolism","description":"The top GO terms are dominated by acetylation-related processes (N-terminal, peptidyl-lysine, putrescine acetylation, histone acetylation) and polyamine metabolism (putrescine catabolic process, arginine biosynthesis). This points to a cohesive theme around post-translational protein modification via acetylation and the metabolism of polyamines, with a few unrelated terms (like leaf formation) likely reflecting broader organismal contexts. ","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":4},{"id":"GO:0017198","count":3},{"id":"GO:0006041","count":3},{"id":"GO:0018003","count":3},{"id":"GO:0006526","count":3}]},{"hash":"442565854310478973","title":"Acetylation-driven chromatin modification","description":"The terms repeatedly point to acetylation events (histone H4 acetylation, peptidyl-lysine N6-acetylation, N-terminal serine acetylation, putrescine acetylation) and subtelomeric heterochromatin formation, suggesting a shared function in chromatin regulation via acetylation. Some metabolic terms appear as secondary associations or annotation noise, but the core pattern supports chromatin modification through acetylation.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":4},{"id":"GO:0017198","count":3},{"id":"GO:0006041","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0018003","count":3}]},{"hash":"1972911555228074951","title":"DNA repair and proteostasis regulation","description":"This cluster is dominated by a DNA repair term (global genome nucleotide-excision repair) and proteostasis-related terms (negative regulation of proteasomal protein degradation, ERAD), pointing to a theme of coordinating genome maintenance with protein quality control. The additional regulatory GO terms (e.g., signaling and metabolism regulation) suggest a broader regulatory role rather than a single pathway.","confidence":"Medium","size":6,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":4},{"id":"GO:1905366","count":3},{"id":"GO:1901799","count":3},{"id":"GO:1904378","count":3},{"id":"GO:0051572","count":3}]},{"hash":"2049986937912764849","title":"FSH/LH Hormone Signaling in Follicle Maturation","description":"The top terms point to hormonal control of female reproduction, with FSH/LH signaling, follicle-stimulating hormone stimuli, and primary ovarian follicle growth, suggesting a cluster centered on hormonal regulation of follicle maturation and related uterine development. Some immune-related terms are present, but the dominant signal is hormone-driven follicular processes.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0071372","count":6},{"id":"GO:0051607","count":5},{"id":"GO:0042699","count":5},{"id":"GO:0001545","count":5}]},{"hash":"287138718003627074","title":"Proteostasis and protein quality control","description":"Most terms point to protein folding/unfolding and degradation pathways (ER UPR, proteasome, aggresomes) and chaperone-associated refolding, with some notes on oligomerization. A single DNA replication term appears incidental. Thus, a proteostasis/quality-control label best fits this cluster.","confidence":"High","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0070389","count":6},{"id":"GO:0046034","count":4},{"id":"GO:0031117","count":4},{"id":"GO:0070842","count":4}]},{"hash":"1650388584269272559","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006367","count":3},{"id":"GO:0071031","count":3},{"id":"GO:1904570","count":3},{"id":"GO:0035640","count":3}]},{"hash":"1401706766040049001","title":"Organelle maintenance and core cellular processes","description":"The shared GO terms cluster around fundamental intracellular housekeeping, including mitochondrial inheritance and membrane organization, ribosome biogenesis, and protein targeting to the vacuole, suggesting a focus on organelle maintenance and basic cell biology rather than a single pathway. Some terms (heart contraction, GABAergic synaptic transmission) are outliers but do not override the core theme.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0051932","count":2}]},{"hash":"633582730985114058","title":"Rac-Regulated Neuronal Actin Remodeling","description":"The top GO terms converge on actin cytoskeleton dynamics (lamellipodium assembly, actin polymerization and severing) and neuronal development processes (dendritic spine morphogenesis, neuron projection development), all of which are typically driven by Rac signaling. This points to a coherent module of Rac-mediated actin remodeling in neurons, with osmotic stress response as a broader context, but not altering the core neuronal actin theme.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010592","count":2},{"id":"GO:0016601","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0031643","count":1},{"id":"GO:0031175","count":1}]},{"hash":"1638968773753515704","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for ribosome assembly/biogenesis and translation (including large subunit biogenesis, ribosome biogenesis, translation, and initiation complex formation), with one term for nuclear export of the large subunit. A few cell cycle and cytoskeletal terms are present but likely peripheral, making ribosome machinery the core theme.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0030036","count":1},{"id":"GO:0007049","count":1}]},{"hash":"94041362541763843","title":"Neuronal Morphogenesis and Signaling","description":"The cluster shows terms centered on neuronal structure and function, including dendritic spine morphogenesis, visual perception, and cell morphogenesis, along with Rho-mediated signaling and cAMP/PKA regulation, all pointing to neuronal development and signaling. Some terms (e.g., mitotic cell cycle, senescence) are less connected, but the dominant themes are neuronal morphogenesis and signaling. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060997","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0000278","count":2}]},{"hash":"535653812730047967","title":"Unknown","description":"The terms span diverse, largely unrelated processes (angiogenesis; ABA plant signaling; myoblast fusion; cell cycle G2/M; synaptic plasticity and visual perception), with no single cohesive function binding them. There isn\u2019t a clear, representative theme to assign a specific, informative cluster label with confidence. ","confidence":"","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":5},{"id":"GO:0010800","count":5},{"id":"GO:0000086","count":5},{"id":"GO:0009738","count":5},{"id":"GO:0014850","count":5}]},{"hash":"1229997659347384995","title":"Neural development and neuronal morphogenesis","description":"The top GO terms cluster around brain development and neuronal structure, including telencephalon development, corpus callosum development, dendritic spine morphogenesis, and bipolar cell polarity. While some broader cellular processes (transcription, DNA replication) appear, the strongest recurring theme is neural development and neuronal morphology, suggesting the cluster represents proteins involved in brain formation and neuron structure.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046826","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0021537","count":4},{"id":"GO:0060044","count":4}]},{"hash":"313191500340609775","title":"Developmental morphogenesis and tissue remodeling","description":"The top GO terms point to tissue development and remodeling across multiple systems (lung morphogenesis, decidualization, bone ossification, basement membrane remodeling), with supporting signaling (Wnt, hormone responses) and some immune-related processes. This suggests the cluster collects proteins involved in shaping and remodeling tissues during development, rather than a single, narrow pathway. ","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051603","count":2},{"id":"GO:0046697","count":2},{"id":"GO:0060441","count":2},{"id":"GO:0034769","count":2},{"id":"GO:0060448","count":2}]},{"hash":"453095843605987040","title":"Brain development and neuronal signaling","description":"This cluster is dominated by terms related to brain development (cerebral cortex, telencephalon) and neural processes (cell migration, bipolar cell polarity, calcium-dependent exocytosis), suggesting a coherent theme of neural development and signaling. A few outliers touch on reproduction, but the strongest pattern aligns with brain formation and neuronal communication.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0045793","count":3},{"id":"GO:0021987","count":3},{"id":"GO:0016477","count":3}]},{"hash":"1002101749326376650","title":"Unknown","description":"There are no Top Terms provided to define a functional theme, so we cannot infer a shared molecular function or process for these six proteins based on GO annotations; the connectivity alone does not reveal a clear common function.","confidence":"","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"1210230070351841543","title":"Mitotic progression and ubiquitin-dependent proteolysis","description":"The dominant GO terms point to mitotic control and chromosome dynamics (exit from mitosis, G2/M transition, chromosome segregation) and to ubiquitin-proteasome\u2013mediated protein turnover (SCF-dependent, K27-linked, and histone ubiquitination). This suggests the proteins cluster around regulation of mitosis via targeted degradation. Some terms (viral process, TRIF-dependent Toll-like receptor signaling) appear peripheral to the core theme.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0010458","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0000086","count":5},{"id":"GO:0007059","count":5},{"id":"GO:0016032","count":5}]},{"hash":"1499949422593725703","title":"Ubiquitination in immune signaling and chromatin","description":"Top terms are dominated by various forms of ubiquitination (polyubiquitination, K27- and K63-linked, histone H2B ubiquitination) and immune signaling (TRIF-dependent TLR signaling, interferon-beta response), indicating a theme of ubiquitin-regulated signaling and chromatin regulation. Some related terms (autoubiquitination, chromosomal/chromatin processes) appear as secondary influences. This supports a concise label focused on ubiquitin-mediated signaling and chromatin regulation.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902916","count":5},{"id":"GO:0035666","count":5},{"id":"GO:0044314","count":5},{"id":"GO:0071894","count":5},{"id":"GO:0035458","count":5}]},{"hash":"1641514996202607271","title":"Diverse carbon-source catabolism","description":"GO terms indicate enzymes involved in breaking down a range of substrates: ethanol, methanol, glycerol, glycol, fucose, and 3-chlorocatechol, plus general carbon utilization. This points to a cluster of proteins participating in broad carbon-source metabolism in microbes. One outlier term (peptidyl-tyrosine sulfation) is not aligned with catabolism, but it\u2019s minor relative to the overall theme.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006068","count":2},{"id":"GO:0006478","count":2},{"id":"GO:0015946","count":1},{"id":"GO:1901168","count":1},{"id":"GO:0019564","count":1}]},{"hash":"720252052503310914","title":"mRNA splicing and translation regulation","description":"This cluster shows strong signals for splicing regulation (including alternative splicing via spliceosome), mRNA modification and stabilization, and components involved in translation control (miRNA-mediated silencing and EIF4F assembly), pointing to a shared function in post-transcriptional RNA processing and gene expression regulation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000269","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0000381","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0016556","count":1}]},{"hash":"235479361098448442","title":"Unknown","description":"The GO terms span several distinct biological areas (SRP-dependent membrane targeting, fungal beta-glucan biosynthesis, iron-sulfur cluster assembly, DNA replication) and include several regulation-related and obsolete terms, with no clear shared pathway or function tying the proteins together. Given the small size (5 proteins), sparse edges (3) and lack of a coherent theme, there isn\u2019t a distinct, representative function for this cluster. Unknown","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":1},{"id":"GO:0070880","count":1},{"id":"GO:1902037","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0006260","count":1}]},{"hash":"194355554819487133","title":"RNA processing, export, and transcription regulation","description":"Top terms indicate a focus on RNA processing, transcription initiation, and mRNA export, with a minor signal for ER-Golgi vesicle trafficking. This suggests the proteins form a cluster linked to gene expression control at transcription and RNA maturation/export steps, potentially responsive to stress.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0031990","count":1},{"id":"GO:0006383","count":1},{"id":"GO:0045948","count":1}]},{"hash":"653898710477678231","title":"Stress and innate immune signaling","description":"This cluster centers on cellular stress and immune-related processes, including responses to amino acid starvation, innate immune response, defense against virus, and regulation of TORC1 signaling, plus apoptosis. Some terms (e.g., meiotic DSB formation, telencephalon development) are less related, but the dominant themes are stress response and immune signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":3},{"id":"GO:1903343","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051092","count":3},{"id":"GO:1904262","count":3}]},{"hash":"1528130497009564745","title":"Cholesterol metabolism and bile acid transport","description":"The cluster is dominated by GO terms related to cholesterol handling and lipid transport, including positive regulation of cholesterol esterification, cholesterol import and transport/storage, and bile acid secretion/biosynthesis regulation, with supporting terms on peroxisome proliferator-activated receptor signaling and ceramide transport. A few unrelated annotations appear, but the core signal strongly points to cholesterol homeostasis and bile acid metabolism.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010873","count":1},{"id":"GO:0035360","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0070508","count":1},{"id":"GO:0032782","count":1}]},{"hash":"356429213457027173","title":"Large subunit ribosome biogenesis and export","description":"The top GO terms cluster around assembly and maturation of the large ribosomal subunit (LSU): preribosome assembly, LSU rRNA maturation, and export of the LSU from the nucleus, indicating a cohesive function in LSU biogenesis. A few unrelated terms appear in the list, but the dominant signal points to ribosome biogenesis, specifically the LSU. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902626","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000027","count":1}]},{"hash":"1106317408631138381","title":"Neural development and dendrite morphogenesis","description":"The top GO terms cluster around brain development (telencephalon, corpus callosum) and neuronal structure (dendrite, dendritic spine morphogenesis, bipolar cell polarity). Although a couple terms are broader (cyclic nucleotide biosynthesis, ER-stress\u2013related apoptosis), the dominant theme is neural development and neuronal morphology, so this label reflects the core shared function of the proteins. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021537","count":5},{"id":"GO:0060044","count":5},{"id":"GO:0061246","count":5},{"id":"GO:0009190","count":5},{"id":"GO:0060997","count":5}]},{"hash":"1741888170348885211","title":"Nucleotide metabolism and cofactor biosynthesis","description":"The cluster shows shared involvement in nucleotide-related pathways: AMP salvage, ADP biosynthesis, CDP biosynthesis, purine ribonucleotide interconversion, and cofactors like NAD+ and coenzyme A biosynthesis. Although two developmental terms appear (brain and liver development), they are single annotations and do not define the group\u2019s core function; overall, the proteins appear linked by nucleotide metabolism and energy cofactor production.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":1},{"id":"GO:0046940","count":1},{"id":"GO:0044209","count":1},{"id":"GO:0015937","count":1},{"id":"GO:0046939","count":1}]},{"hash":"1196341982527225717","title":"Unknown","description":"The GO terms span antiviral defense and TLR signaling, multiple hormone signaling pathways (FSH and TSH), reproductive development (uterus and follicle growth), and even water homeostasis. These diverse processes lack a single cohesive function linking the proteins, so a unified label isn\u2019t supported.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":5},{"id":"GO:0042699","count":5},{"id":"GO:0001545","count":5},{"id":"GO:0038194","count":5},{"id":"GO:0002755","count":5}]},{"hash":"1628146279512198633","title":"Unknown","description":"The top GO terms span retinal/retinol metabolism, several distinct biosynthetic pathways (bile acid, testosterone, fructose), drug metabolism, and apoptosis/regulation, plus a transport term. There isn't a clear, single functional theme tying all four proteins together, so a cohesive, specific label is not supported.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":4},{"id":"GO:0042572","count":4},{"id":"GO:0043066","count":3},{"id":"GO:0061370","count":3},{"id":"GO:0006699","count":3}]},{"hash":"962139263986746238","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is enriched for ubiquitin-related proteolysis, notably ubiquitin-dependent protein catabolic process and K11-linked ubiquitination, suggesting a shared function in the ubiquitin-proteasome system; the other GO terms may reflect broader roles of ubiquitination in development and differentiation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0050775","count":2},{"id":"GO:0031915","count":2},{"id":"GO:2000001","count":2}]},{"hash":"1709359903977367401","title":"Unknown","description":"The top GO terms are highly diverse, spanning DNA repair, protein quality control, vesicle formation regulation, immune signaling, metabolism, hormone biosynthesis, plant development, and ion channel regulation, with several obsolete terms as well. With only four proteins and no clear shared pathway or function, there is no coherent theme to name a specific cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014070","count":2},{"id":"GO:0006289","count":2},{"id":"GO:1905366","count":1},{"id":"GO:1901799","count":1},{"id":"GO:1904378","count":1}]},{"hash":"2276247509824708418","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0000480","count":2}]},{"hash":"1408012327540618840","title":"Nuclear DNA Replication and Pol II Transcription Regulation","description":"The terms point to nuclear processes involving DNA replication and transcription by RNA polymerase II, including DNA-templated transcription and the negative regulation of Pol II activity, suggesting a theme of coordinated control of genome expression and replication in the nucleus (despite some obsolete terms in the set).","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018142","count":1},{"id":"GO:0019071","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0046826","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1082191740564969828","title":"Endomembrane trafficking and secretory processing","description":"The cluster's GO terms heavily point to vesicle trafficking within the endomembrane system (endosome\u2013lysosome, endosome\u2013Golgi, ER\u2013vacuole tethering) and secretory-related steps (dense core granule maturation, ectodomain proteolysis, membrane remodeling like vesicle/plasma membrane tubulation). Although eye development stands out, the shared theme is intracellular transport and processing along secretory and endocytic routes, with some extracellular remodeling terms extending the functional context.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":1},{"id":"GO:1990854","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0051044","count":1},{"id":"GO:0022617","count":1}]},{"hash":"2144107817806432586","title":"RNA Processing and Ribosome Biogenesis","description":"The top GO terms cluster around cytoplasmic translation, mRNA splicing, and ribosome biogenesis/export (with tRNA modification), indicating a shared involvement in gene expression machinery from RNA processing to ribosome assembly and protein synthesis. A few terms touch on cell division and other processes, but the dominant signals point to RNA processing and ribosome construction.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0090529","count":1},{"id":"GO:0042274","count":1}]},{"hash":"2251936964705535492","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":1},{"id":"GO:1990116","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0030260","count":1},{"id":"GO:1902167","count":1}]},{"hash":"1459198077366072903","title":"Post-transcriptional mRNA processing and regulation","description":"The proteins cluster around RNA-level regulatory processes, including spliceosome-regulated splicing, mRNA modification and stability, poly(A) tail regulation, and links to translation initiation and miRNA silencing, indicating a focus on post-transcriptional control of gene expression.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0035278","count":1}]},{"hash":"1773345391842442954","title":"Actin filament assembly and myofibril formation","description":"Most of the top GO terms relate to actin cytoskeleton dynamics and muscle fiber assembly (actin filament polymerization, actin nucleation, muscle thin filament and cardiac myofibril assembly). While other terms touch on gene expression and hypoxia response, the dominant signal is actin remodeling and myofibrillogenesis, suggesting this cluster represents proteins involved in actin-based structure formation in muscle/cardiac tissue.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904171","count":1},{"id":"GO:0055003","count":1},{"id":"GO:2000251","count":1},{"id":"GO:0010467","count":1},{"id":"GO:0072092","count":1}]},{"hash":"3974052781474164","title":"Lipid metabolism and cell envelope assembly","description":"This cluster is best explained by a central theme of lipid metabolism and cell envelope processes: multiple terms point to lipid remodeling and metabolism (acylglycerol remodeling, ether lipid metabolism) and mycolate cell wall layer assembly, with regulation of endocannabinoid signaling reinforcing the lipid-signaling angle. Additional terms reflect general catabolic metabolism and iron transport that support cellular metabolism but are less specific to the lipid/cell-envelope core. Overall, the lipid- and envelope-focused theme is the most cohesive interpretation.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":1},{"id":"GO:2000124","count":1},{"id":"GO:0006826","count":1},{"id":"GO:0071769","count":1},{"id":"GO:0046294","count":1}]},{"hash":"1415599662873504536","title":"Unknown","description":"Top Terms are not provided, so there is no clear shared function to base a label on.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"2185376204253618430","title":"Ubiquitin-dependent innate immune signaling","description":"This cluster is dominated by GO terms for ubiquitination (polyubiquitination, K27- and K63-linked, autoubiquitination) and innate immune signaling (TRIF-dependent Toll-like receptor pathway and interferon-beta response). The common theme is ubiquitin-mediated regulation of immune signaling, though some terms also touch on meiosis and synaptic assembly.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902916","count":3},{"id":"GO:0035666","count":3},{"id":"GO:0044314","count":3},{"id":"GO:0071894","count":3},{"id":"GO:0035458","count":3}]},{"hash":"694113996684499090","title":"Hormone signaling and immune response cluster","description":"The terms indicate both hormone signaling (FSH/TSH pathways, adenylate cyclase activation, IP3 biosynthesis) and immune signaling (defense against virus, MyD88-dependent TLR). Reproductive development terms (ovarian follicle growth, uterus development, secondary sexual characteristics) reinforce a reproductive-endocrine context. Together these terms suggest a set of proteins involved in general signal transduction that integrates endocrine and immune/reproductive pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0042699","count":3},{"id":"GO:0001545","count":3},{"id":"GO:0038194","count":3},{"id":"GO:0002755","count":3}]},{"hash":"750655471591653881","title":"Proteostasis Regulation and ERAD","description":"The top GO terms cluster around negative regulation of proteasomal protein degradation, ER-associated degradation (ERAD), and aggresome assembly, all pointing to protein quality control and cellular proteostasis. Although a few terms (like transcription regulation and rRNA maturation) are less directly related, the dominant theme is proteostasis and ER quality-control pathways, which justifies this label.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1905366","count":3},{"id":"GO:1901799","count":3},{"id":"GO:1904378","count":3},{"id":"GO:0014070","count":3},{"id":"GO:0034140","count":3}]},{"hash":"784198480114131035","title":"Proteostasis and stress-response factors","description":"The GO terms cluster around protein quality control and stress responses, including aggresome assembly, ER unfolded protein response, protein unfolding, and stress granule disassembly, all energized by ATP metabolism. While there are outliers like chromatin assembly and vesicle transport, the dominant theme is proteostasis and cellular stress management.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0031117","count":1},{"id":"GO:0070842","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0043335","count":1}]},{"hash":"433924058330963705","title":"Ribosome biogenesis and RNA processing","description":"This cluster's annotations cluster around preribosome assembly (90S), rRNA processing steps (ITS1 cleavage and 5.8S rRNA maturation), and RNA metabolic processes including spliceosome assembly and antisense RNA metabolism, indicating a shared role in RNA maturation and ribosome biogenesis. Despite some deprecated terms, the core theme is RNA processing linked to ribosome production.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042868","count":1},{"id":"GO:0034463","count":1},{"id":"GO:0072423","count":1},{"id":"GO:0000464","count":1},{"id":"GO:0006378","count":1}]},{"hash":"88504783775019637","title":"DNA replication and transcription machinery","description":"The cluster is dominated by nucleic acid metabolism and genome maintenance terms: DNA recombination, DNA-templated transcription, DNA topological change, helicase activity, and replication fork dynamics. While there are a couple of terms related to viral protein processing and symbiont-induced host autophagy, the core theme centers on DNA replication and transcription processes. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0039520","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0019082","count":2},{"id":"GO:0032508","count":2}]},{"hash":"632463426838964244","title":"Neural development and eye morphogenesis","description":"The terms cluster around neural morphogenesis and visual system development, including retinal ganglion cell axon guidance, camera-type eye morphogenesis, corpus callosum development, and branching morphogenesis of nerves, with supporting processes like dendritic spine morphogenesis and retinoic acid/thyroid hormone signaling that can influence neural differentiation and growth.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048671","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0042403","count":1},{"id":"GO:0071300","count":1},{"id":"GO:0048593","count":1}]},{"hash":"1177118761948350039","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0034247","count":1},{"id":"GO:0098789","count":1},{"id":"GO:0019243","count":1}]},{"hash":"670725504600383779","title":"RNA processing and translation regulation","description":"This cluster\u2019s GO terms cluster around RNA metabolism and post-transcriptional control, including splicing (regulation of alternative splicing, mRNA splicing), mRNA modification and stabilization, ribosome biogenesis, and translation initiation (EIF4F complex assembly) as well as miRNA-mediated silencing. Although a protein kinase activation term appears, the dominant themes point to RNA processing and regulation of translation, rather than a single enzymatic pathway, justifying this label.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000381","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0016556","count":1}]},{"hash":"377996424635467049","title":"Glycolysis and sugar catabolism (PTS)","description":"The top GO terms show strong emphasis on glycolytic processes and gluconeogenesis, with associated pyruvate metabolism and several sugar-specific catabolic pathways (fructose-1,6-bisphosphate, tagatose-6-phosphate, galactitol) as well as a phosphotransferase system for sugar uptake. This points to a cohesive cluster of proteins involved in carbohydrate metabolism and energy generation in bacteria, centered on sugar catabolism and glycolytic flux.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0016310","count":1},{"id":"GO:0006090","count":1},{"id":"GO:0009401","count":1}]},{"hash":"193469592292818005","title":"Neuronal development and dendritic morphogenesis","description":"Top terms are dominated by neural development and neuron morphology: telencephalon development, corpus callosum development, dendrite morphogenesis, and dendritic spine morphogenesis, plus bipolar cell polarity. While there are also terms related to phagocytosis, placental development, and host-cell transformation, the strongest and most consistent signals point to neuronal development and dendritic architecture as the cluster's theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006909","count":2},{"id":"GO:0021537","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0061246","count":2},{"id":"GO:0009190","count":2}]}]