[{"hash":"2234578728262992067","title":"Redox metabolism and starvation response","description":"This cluster is dominated by redox and glutathione-related processes: glutathionylation, glutathione metabolic process, and cell redox homeostasis. It also includes pathways tied to nutrient stress and detoxification, such as response to starvation and toxin catabolic process, and regulation of nitrogen utilization. The presence of L-ascorbic acid metabolism and nucleotide-excision repair suggests broader stress and damage-response roles. Overall, these terms point to a set of proteins involved in maintaining redox balance and adapting metabolism under nutrient stress.","confidence":"Medium","size":29,"edges":27,"triangles":12,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":6},{"id":"GO:0006289","count":5},{"id":"GO:0010731","count":4},{"id":"GO:0006749","count":4},{"id":"GO:0042594","count":4}]},{"hash":"1878399869234997888","title":"Mitochondrial metabolism and protein synthesis","description":"Top terms indicate mitochondrial function: cristae formation, TCA cycle, oxaloacetate metabolism, along with translation and transcription processes\u2014consistent with mitochondrial protein synthesis and gene expression. The presence of various catabolic pathways also aligns with mitochondrial metabolism. Thus, the cluster represents mitochondrial energy metabolism and protein synthesis.","confidence":"High","size":29,"edges":37,"triangles":7,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046392","count":2}]},{"hash":"452242949880542939","title":"Dopaminergic signaling and neuronal endocytic recycling","description":"The top GO terms cluster around dopamine-related signaling (cellular response to dopamine; positive regulation of dopamine receptor signaling) and vesicle trafficking (endocytic recycling), with supporting neuronal context such as negative regulation of neuron apoptosis and neuronal responses to stressors (xenobiotic stimulus, manganese ion). This suggests a cohesive theme of dopaminergic neurotransmission linked to neuronal endocytosis and maintenance, rather than a broad, non-specific stress response. ","confidence":"High","size":29,"edges":56,"triangles":41,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043524","count":5},{"id":"GO:0035690","count":5},{"id":"GO:1905289","count":4},{"id":"GO:1905279","count":4},{"id":"GO:0071287","count":4}]},{"hash":"1626954248470023403","title":"Neurodevelopment with chromatin regulation and splicing","description":"The top terms point to embryonic neural development, neuron maturation, and RNA processing (alternative splicing), with signals of chromatin-level control (histone demethylation). Metabolic terms like glutamate and guanine biosynthesis also align with neural function, supporting a theme of neurodevelopment tied to gene expression regulation and RNA processing.","confidence":"Medium","size":29,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046886","count":4},{"id":"GO:0034720","count":4},{"id":"GO:0001701","count":4},{"id":"GO:0043923","count":3},{"id":"GO:0006990","count":3}]},{"hash":"1200335850426935226","title":"RNA Splicing and DNA Repair Regulators","description":"Top terms are dominated by RNA processing (spliceosome-mediated mRNA splicing; snRNP assembly) and genome maintenance (DNA repair and replication initiation). This points to a cluster of proteins coordinating RNA maturation with DNA integrity, with some regulatory signaling roles evident in related terms.","confidence":"High","size":29,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0016242","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0032298","count":2},{"id":"GO:0000387","count":2}]},{"hash":"62143698598535678","title":"TLR-Mediated Innate Immunity","description":"The common functions center on Toll-like receptor signaling (TLR4, TLR9), inflammatory responses, macrophage activation, and production of interferon-beta and chemokines, indicating a cohesive innate immune activation module. The presence of SCF-dependent ubiquitin-proteasomal protein catabolic process suggests involvement in antigen processing as part of immune signaling. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0050830","count":8},{"id":"GO:0034142","count":6},{"id":"GO:0006954","count":6},{"id":"GO:0051607","count":6}]},{"hash":"1483186016000474773","title":"Mitotic cell cycle with translation regulation","description":"Top GO terms indicate a cohesive theme around mitosis (mitotic cell cycle, cell division) and translation control (formation of translation preinitiation complex, translation reinitiation), plus protein ubiquitination and mRNA transport, implying coordination of cell-cycle progression with proteostasis and mRNA handling. Some terms are historical or outliers, but the dominant pattern points to proteins involved in mitosis and translation regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0050774","count":3}]},{"hash":"909963183684799435","title":"TLR2-Driven innate immunity and cytoskeletal remodeling","description":"The cluster includes GO terms tied to innate immune sensing and response (TLR signaling, detection of diacyl lipopeptides, defense against Gram-negative bacteria) and to actin-related processes (lamellipodium morphogenesis, positive regulation of GTPase activity), suggesting a theme of immune activation coupled with cytoskeletal reorganization. Muscle attachment/sarcomere terms may reflect shared cytoskeletal components rather than muscle-specific function, reinforcing the cytoskeleton-immune link. Overall, the data point to coordinated TLR2-mediated defense with actin dynamics.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016203","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006915","count":3},{"id":"GO:2000394","count":2}]},{"hash":"1540053453690084794","title":"Neuronal Synaptic Signaling and Plasticity","description":"The terms point to ephrin receptor signaling and synapse structural plasticity, with excitatory postsynaptic potential and substantia nigra development highlighting neuronal and synaptic function. Cytoskeletal remodeling (actin polymerization, podosome assembly) and endocytosis further support synaptic vesicle cycling and membrane trafficking. Some xenobiotic response and Cvt pathway terms are peripheral but reflect broader cellular trafficking contexts. Overall, the cluster centers on neuronal signaling and synaptic plasticity.","confidence":"Medium","size":28,"edges":3,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048013","count":5},{"id":"GO:0051835","count":5},{"id":"GO:0035690","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0060079","count":4}]},{"hash":"2135386412512510954","title":"Stress-Responsive Morphogenesis Signaling","description":"The set combines stress-related GO terms (cellular response to xenobiotic stimulus; response to unfolded protein) with morphogenesis-related terms (branching in blood vessel morphogenesis; negative regulation of dendrite morphogenesis; positive regulation of connective tissue replacement) and calcium/NFAT signaling (dephosphorylation; calcineurin-NFAT signaling). This pattern suggests a cluster of proteins that mediate stress-activated signaling pathways that influence vascular and neural tissue remodeling, rather than a single narrowly defined process.","confidence":"Medium","size":28,"edges":19,"triangles":8,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0001569","count":3},{"id":"GO:0050774","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0060316","count":3}]},{"hash":"2125359398300248990","title":"Gonadal development and androgen biosynthesis","description":"The top GO terms point to both gonadal development (uterus development, male gonad development) and steroid hormone production (androgen metabolic process, testosterone biosynthetic process), suggesting a cluster of proteins involved in reproductive development and androgen biosynthesis. Other terms like regulation of transcription and ribosome biogenesis may reflect general gene-expression roles in these tissues, while some terms (e.g., ozone or vitamin D response) seem less directly connected. Overall, the dominant theme is reproductive development linked to androgen biosynthesis. ","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060065","count":5},{"id":"GO:0046232","count":4},{"id":"GO:0008209","count":4},{"id":"GO:0061370","count":4},{"id":"GO:0006355","count":4}]},{"hash":"1560798673740212382","title":"Ribosome Biogenesis and Translation","description":"Most of the top GO terms map to ribosome-related processes and translation, including translation, cytoplasmic translation, translation initiation, ribosome biogenesis and ribosomal large subunit biogenesis, SSU-rRNA maturation, and export of the large subunit from the nucleus. This indicates the cluster centers on ribosome assembly and the protein synthesis machinery. A few terms like cell cycle and osteoblast differentiation are more peripheral noise. ","confidence":"High","size":28,"edges":114,"triangles":247,"max_degree":24,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0042254","count":5},{"id":"GO:0000462","count":4},{"id":"GO:0006413","count":4},{"id":"GO:0002181","count":4}]},{"hash":"1290988364445727862","title":"Ubiquitin-Proteasome Regulation of Innate Immunity","description":"The cluster centers on ubiquitin-dependent protein catabolic processes and protein ubiquitination (SCF-dependent and ERAD-related), coupled with innate immune responses and TNF signaling, indicating a core theme of proteostasis shaping antiviral and immune signaling pathways; a minor mechanotransduction term is present but does not outweigh the dominant ubiquitin-proteasome/immune signal axis.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0016567","count":5},{"id":"GO:0033209","count":5},{"id":"GO:0014068","count":5}]},{"hash":"689650847018000287","title":"Ribosome biogenesis and cell cycle","description":"The terms indicate both ribosome biogenesis/translation (cytoplasmic translation, ribosomal subunit export, ribosomal biogenesis, tRNA modification) and core cell-cycle processes (DNA replication, cell division, cell cycle, septum assembly), suggesting a cluster of proteins coordinating growth and division by linking protein synthesis capacity with DNA replication and mitotic-like events.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0000055","count":4}]},{"hash":"748352511532172343","title":"MAPK and Hippo signaling in development","description":"I named this cluster MAPK and Hippo signaling in development because the top GO terms emphasize two major signaling pathways (p38 MAPK and ERK cascades) and Hippo signaling, along with developmental and differentiation processes such as multicellular organism development and keratinocyte differentiation. The combination suggests a signaling network coordinating cell proliferation, differentiation, and tissue development, including epidermal lineages, rather than a single isolated function. ","confidence":"High","size":28,"edges":30,"triangles":0,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0038066","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0070371","count":3},{"id":"GO:1904628","count":3}]},{"hash":"2278098827131236034","title":"Unknown","description":"The top GO terms span adhesion (cell adhesion and integrin-mediated adhesion), metabolism (glycogen and mycothiol biosynthesis), transcription and chromatin regulation, post-translational modification, antibiotic response, and infection-related processes, indicating a broad, heterogeneous set of functions. There are no edges or coherent connectivity among the proteins, making it hard to assign a single, meaningful label. Therefore Unknown with None. ","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007155","count":4},{"id":"GO:0010125","count":4},{"id":"GO:0006348","count":4},{"id":"GO:0018003","count":4},{"id":"GO:0046677","count":3}]},{"hash":"1964133007553680706","title":"Cold response and adipose differentiation","description":"This cluster is driven by terms related to responding to cold and fat cell differentiation, suggesting a theme of adipose tissue\u2013related stress response and differentiation. Additional terms on cell migration, ubiquitination, and kinase regulation indicate broader roles in cell remodeling and signaling during these processes, though some terms are obsolete and may reflect annotation noise. Overall, the most indicative signals are cold response and adipocyte differentiation, with supporting remodeling clues.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009409","count":10},{"id":"GO:0016477","count":9},{"id":"GO:2001275","count":9},{"id":"GO:0007205","count":8},{"id":"GO:0045736","count":8}]},{"hash":"106183842462062097","title":"Developmental signaling and cell-cycle regulation","description":"The top GO terms point to developmental processes (heart development, Schwann cell development) and cell-cycle control (mitotic cell cycle, G2/M transition), with associated signaling activities (GTPase regulation, phosphorylation). Neural activity terms (long-term synaptic potentiation, excitatory postsynaptic potential) suggest involvement in nervous system development and function, indicating a broad developmental signaling theme coordinated with cell-cycle regulation rather than a single specific pathway.","confidence":"Medium","size":28,"edges":34,"triangles":7,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0000086","count":4},{"id":"GO:0043065","count":4}]},{"hash":"2004746397768305948","title":"Bacterial Biosynthesis and Xenobiotic Response","description":"The top GO terms cluster around biosynthetic pathways for biotin, menaquinone, lipid A, and antibiotics, plus cellular responses to xenobiotics and related metabolic regulation. This suggests a microbial metabolic module involved in small-molecule biosynthesis and detoxification, rather than a single signaling pathway. While some terms appear noisy, the overall theme is biosynthesis and xenobiotic processing.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":8},{"id":"GO:0017000","count":8},{"id":"GO:0035690","count":7},{"id":"GO:0009102","count":7},{"id":"GO:0009245","count":6}]},{"hash":"1048659962351873442","title":"Tight junctions and developmental signaling","description":"This cluster has clear signals around cell junctions, especially bicellular tight junction assembly, and synaptic-type signaling (excitatory postsynaptic potential). Alongside these are developmental terms (heart development, osteoclast development) and signaling regulation (positive regulation of GTPase activity), suggesting a broader developmental signaling context that links cell adhesion with developmental regulation. Therefore, a label focusing on junctions and developmental signaling fits best.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0051291","count":3},{"id":"GO:0006348","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0070197","count":2}]},{"hash":"397166718387168121","title":"Post-transcriptional mRNA processing and translation control","description":"This cluster is dominated by GO terms related to mRNA processing and regulation of translation, including mRNA export from the nucleus, spliceosome-mediated splicing and alternative splicing, polyadenylation, translation initiation and reinitiation, preinitiation complex formation, mRNA modification, and stabilization. The convergence of splicing/processing with translation control indicates a cohesive role in post-transcriptional gene expression regulation.","confidence":"High","size":27,"edges":48,"triangles":91,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006406","count":8},{"id":"GO:0006378","count":6},{"id":"GO:0045292","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6}]},{"hash":"796260701390611380","title":"DNA replication, recombination, and genome integration","description":"Based on the prominent GO terms, the cluster is centered on genome maintenance: DNA replication, DNA recombination, DNA integration, and related repair processes, including a specific mention of double-strand break repair in meiotic recombination. A few terms about host interaction (symbiont entry, viral penetration) and biosynthesis (biotin/menaquinone) are present but less cohesive with the core theme, suggesting possible annotation noise or multifunctionality. Overall, the strongest signal is genome processing and rearrangement.","confidence":"Medium","size":27,"edges":68,"triangles":89,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0006310","count":6},{"id":"GO:1990918","count":5},{"id":"GO:0009636","count":5},{"id":"GO:0046718","count":5}]},{"hash":"1255586968373476912","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006808","count":4},{"id":"GO:0015937","count":3},{"id":"GO:0044206","count":3},{"id":"GO:0015969","count":3}]},{"hash":"1959222021026565979","title":"Innate Immune and Stress Signaling","description":"The top GO terms show a strong enrichment for innate immune processes (innate immune response, LPS signaling, dsRNA response) and cellular stress responses (cadmium ion response, DNA damage checkpoint signals, regulation of CDK activity), suggesting the cluster centers on innate immune signaling combined with stress-related pathways that modulate cell cycle and proliferation under stress.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045087","count":10},{"id":"GO:0071276","count":10},{"id":"GO:0051436","count":9},{"id":"GO:0031571","count":9},{"id":"GO:0008285","count":9}]},{"hash":"228719967542696070","title":"GTPase and TGF-\u03b2 signaling regulators","description":"The top GO terms are dominated by regulation of small GTPases (Rho) and TGF-\u03b2 signaling (receptor pathway and SMAD assembly), pointing to a core function as intracellular signaling regulators. Additional terms touch on development (oligodendrocyte development, pigmentation) and other cellular processes (translation initiation, cell division), suggesting broader regulatory roles rather than a single cohesive pathway. Because the cluster lacks connection structure (no edges), the label centers on the most consistent theme across the terms while acknowledging the broader, mixed functions.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0061179","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007179","count":2}]},{"hash":"261054030183657556","title":"Gene expression from transcription to translation","description":"This cluster is centered on core gene expression processes: transcription (DNA-templated transcription), RNA processing (alternative splicing, mRNA modification, mRNA export), and translation initiation/reinitiation (translation preinitiation complex formation, regulation of translational initiation). The presence of histone methylation terms links chromatin-level control to transcription, suggesting a cohesive group of proteins that coordinate gene expression from transcription through to translation. Some terms are historical/obsolete annotations, but the overall theme remains gene expression regulation across RNA processing and protein synthesis.","confidence":"Medium","size":27,"edges":40,"triangles":0,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0051568","count":3}]},{"hash":"1848708923097273149","title":"ER-Golgi trafficking and proteostasis","description":"The top GO terms point to vesicle transport between the endoplasmic reticulum and Golgi (retrograde and ER-to-Golgi), indicating a cluster centered on the secretory pathway. The presence of the SCF-dependent ubiquitin-proteasome\u2013mediated degradation term supports a proteostasis component, consistent with turnover of trafficking machinery or cargo. Although some terms relate to transcription or histone acetylation, these are less central to the main signal, which is ER-Golgi transport coupled with protein turnover.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006890","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0031146","count":5},{"id":"GO:0051028","count":5}]},{"hash":"43673212086562495","title":"Mitotic cycle and transcription regulation","description":"Top terms show strong enrichment for the mitotic cell cycle and DNA-templated transcription, suggesting core roles in cell division and gene expression. Additional signals for mRNA transport, protein regulation, and stress-related pathways (hypoxia response and ER-stress\u2013induced apoptotic signaling) imply these proteins may coordinate proliferation with post-transcriptional control and cellular stress responses, with some hints of tissue-specific roles such as skin development and protein complex formation.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000278","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0043547","count":8},{"id":"GO:0051028","count":7},{"id":"GO:0071456","count":7}]},{"hash":"1979666279858777025","title":"Developmental transcriptional regulation","description":"Proteins in this cluster are enriched for developmental processes across tissues (neural tube closure, forebrain and skeletal development, multicellular organism development) and for transcriptional control (DNA-templated transcription, imprinting regulation). This points to a coherent role in embryogenesis driven by transcriptional programs, with cell cycle activity reflecting proliferation during development; stress-related signals appear supplementary rather than central.","confidence":"High","size":27,"edges":26,"triangles":19,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006349","count":17},{"id":"GO:0001843","count":17},{"id":"GO:0071276","count":17},{"id":"GO:0007275","count":17},{"id":"GO:0070059","count":17}]},{"hash":"1399484918635428971","title":"Cytoskeleton signaling and synapse assembly","description":"The cluster features actin-regulating processes (barbed-end capping), Rho/GTPase signaling, Ras modulation, IP3 biosynthesis, and synapse assembly, pointing to a theme of signaling-driven cytoskeletal remodeling linked to synaptic connectivity, with additional signal transduction aspects (TGF-beta response, B cell differentiation) providing broader context.","confidence":"Medium","size":27,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0051016","count":3},{"id":"GO:0050731","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0043547","count":3}]},{"hash":"401288243797485620","title":"Nucleocytoplasmic Transport and Protein Trafficking","description":"The most represented GO terms center on nucleocytoplasmic exchange (NLS-bearing protein import into nucleus; mRNA export from nucleus) and trafficking through the Golgi and vesicles (protein retention in Golgi; anterograde dense core vesicle transport), with some signals from ribosome assembly and DNA replication that may reflect broader cellular growth processes. Some outliers (gas vesicle organization, cilium movement, ERAD) introduce noise, but the core theme appears to be intracellular transport and protein processing.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0006607","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0003341","count":7},{"id":"GO:0000027","count":7}]},{"hash":"471339545839959455","title":"GTPase-Regulated Vesicle Trafficking and Cell Migration","description":"This cluster is enriched for GO terms related to ER-to-Golgi vesicle transport, endocytosis, and positive regulation of GTPase activity, all of which point to a network coordinating vesicle trafficking and cytoskeletal dynamics. The presence of cell migration and cranial skeletal development terms suggests roles in cell movement during development, while innate immune response and cadmium-related terms may reflect broader stress-responsive trafficking and signaling pathways. Overall, the common theme centers on GTPase-regulated trafficking processes that govern vesicle flow and cell motility.","confidence":"Medium","size":27,"edges":45,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1850980659580036781","title":"Vertebrate embryonic development and organ morphogenesis","description":"Top GO terms indicate broad vertebrate development with emphasis on neural crest\u2013related processes (neural crest migration, glossopharyngeal nerve morphogenesis), brain and retina development, limb and digestive tract morphogenesis, and placenta formation, plus transcriptional regulation during development. This combination suggests a cluster of proteins involved in coordinating embryonic development and organ formation across multiple tissues, hence the label.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0007275","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0032330","count":3},{"id":"GO:0021615","count":3}]},{"hash":"1538711418080076935","title":"LPS biosynthesis and stress response","description":"It shows a strong emphasis on lipopolysaccharide biosynthesis (including lipopolysaccharide core region and ADP-L-glycero-beta-D-manno-heptose biosynthesis), pointing to bacterial outer-m membrane assembly. The additional terms for cellular responses to hydrogen peroxide and cadmium ion suggest oxidative and metal stress defense that often accompany envelope-related processes. Potassium transport appears secondary to membrane-associated biosynthesis. ","confidence":"Medium","size":27,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0071805","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0019853","count":2},{"id":"GO:0071276","count":2}]},{"hash":"250673654224780403","title":"Innate immune activation and cytokine production","description":"This cluster is dominated by GO terms related to inflammatory signaling and antigen-presenting functions, including positive regulation of TNF and IL-6 production, LPS-triggered signaling, macrophage activation, and dendritic cell antigen processing/presentation, with additional terms pointing to Th17 differentiation. This pattern suggests a coherent theme of innate immune sensing and cytokine-driven activation, with supporting roles for cytoskeletal remodeling and protein turnover during immune activation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032760","count":5},{"id":"GO:0031663","count":4},{"id":"GO:0030011","count":4},{"id":"GO:2000321","count":4},{"id":"GO:0051638","count":4}]},{"hash":"520988879857507635","title":"Golgi-based vesicle trafficking and Rab signaling","description":"Dominant GO terms point to Golgi organization and vesicle trafficking, with Rab signal transduction; CVT pathway adds vacuolar targeting context. A few mitotic terms appear but are secondary. Overall, the cluster centers on Golgi- and Rab-mediated vesicle trafficking.","confidence":"High","size":26,"edges":24,"triangles":21,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007030","count":7},{"id":"GO:0032258","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0006893","count":6},{"id":"GO:0050771","count":6}]},{"hash":"1337080757665009747","title":"Unknown","description":"The top GO terms span platelet aggregation, multiple developmental processes (cervix, atrial cardiac muscle, paramesonephric duct), growth regulation in the liver, immune signaling, sulfur metabolism, ubiquitin-SMAD protein turnover, and RNA silencing. This collection does not converge on a single clear biological function or pathway, suggesting either a highly diverse set of roles or annotation noise; therefore there is no coherent theme to name the cluster beyond Unknown.","confidence":"","size":26,"edges":65,"triangles":75,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":7},{"id":"GO:0060067","count":6},{"id":"GO:0055014","count":6},{"id":"GO:2000346","count":6},{"id":"GO:0061205","count":6}]},{"hash":"603337247176346247","title":"Cell cycle entry and DNA replication regulation","description":"The cluster is enriched for mitotic-cycle transitions (G1/S), DNA replication, transcription, kinetochore localization, and CDK regulation, pointing to coordinated cell-cycle progression and genome replication; supporting terms about membrane targeting and junction regulation are likely secondary context rather than core drivers.","confidence":"High","size":26,"edges":119,"triangles":274,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090314","count":9},{"id":"GO:0007118","count":9},{"id":"GO:2000810","count":9},{"id":"GO:0046626","count":9},{"id":"GO:0000082","count":9}]},{"hash":"1112165741175248135","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0033622","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000381","count":2}]},{"hash":"1442981800622584889","title":"Neural development and differentiation","description":"These proteins show a strong signal for neural lineage specification and differentiation: subpallium neuron fate commitment, spinal cord motor neuron fate specification, cerebral cortex GABAergic interneuron differentiation, and spinal cord oligodendrocyte cell fate specification. There are also broader development terms (bronchiole development, endocrine pancreas development, embryonic placenta development), and a general transcription term, but the neural-related GO terms predominate, suggesting a core function in neurodevelopment. Confidence: Medium","confidence":"","size":26,"edges":205,"triangles":814,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0045668","count":7},{"id":"GO:0060766","count":7},{"id":"GO:0060163","count":7},{"id":"GO:0021520","count":7}]},{"hash":"2040933173163903390","title":"Redox Stress and Developmental Signaling","description":"The top GO terms cluster around redox biology (oxidation-reduction, cellular oxidant detoxification), stress responses (hypoxia), apoptosis pathways (intrinsic ER-stress\u2013mediated and general), and developmental processes (heart and skeletal system development), with transcriptional regulation noted (DNA-templated transcription). This suggests a group of proteins coordinating redox balance and stress signaling that can influence development and cell fate.","confidence":"Medium","size":26,"edges":10,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0071456","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0070059","count":3}]},{"hash":"1701118907016738293","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0000462","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000480","count":3}]},{"hash":"848785681308693235","title":"Unknown","description":"The top GO terms span several disparate themes, including nuclear processes (DNA replication, establishment of protein localization to chromatin, maturation of LSU rRNA) and various metabolic/biogenesis pathways (glycogen biosynthesis, GPI anchor biosynthesis, oligosaccharide-lipid intermediate biosynthesis, mannosylation) as well as a few unrelated terms (response to sorbitol, feeding behavior). The lack of a single cohesive function and the presence of obsolete terms suggest no clear common theme tying these proteins together, so the cluster is best labeled Unknown.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1685235630750089675","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster\u2019s strongest signals are ribosome biogenesis and maturation of SSU-rRNA, with supporting links to GTPase-regulated assembly and protein oligomerization\u2014core features of ribosome production and nucleolar processing. While a few terms (e.g., brain development, COPII budding) are broader, the dominant theme ties to ribosome assembly and RNA processing.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0070317","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":3}]},{"hash":"874040213060641328","title":"Immune cell differentiation and cytokine signaling","description":"This cluster's top GO terms cluster around immune-related functions: interleukin-7 response, NK T cell differentiation, B cell maturation, and interleukin-4 production, along with cell migration and insulin signaling, indicating a theme of immune cell development and cytokine-mediated signaling. A couple of terms (nitrate assimilation and nitrite transport) are metabolic outliers, which may reflect annotation noise or multi-species content. Overall, the common function points to immune differentiation and signaling, hence the chosen label.","confidence":"Medium","size":26,"edges":18,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":4},{"id":"GO:0015707","count":4},{"id":"GO:0098761","count":3},{"id":"GO:0002344","count":3},{"id":"GO:0016477","count":3}]},{"hash":"67941627031279807","title":"TLR\u2013NF-\u03baB Innate Immune Signaling","description":"The cluster is dominated by terms related to Toll-like receptor signaling (including TLR4 and MyD88-independent pathways), inflammatory and antiviral defense responses, and negative regulation of NF-\u03baB signaling, plus a ubiquitin-proteasome process linked to NF-\u03baB regulation. Together these indicate a coherent theme of innate immune activation and NF-\u03baB\u2013mediated transcriptional responses, with a minor occurrence of development/transcription terms likely representing broader gene functions. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0031146","count":3},{"id":"GO:0051770","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1380409011495756541","title":"DNA replication and repair machinery","description":"This cluster is dominated by GO terms for DNA replication (GO:0006260), DNA repair (GO:0006281), and DNA-templated transcription (GO:0006351), which point to a shared function in nuclear DNA processing. While other terms (embryonic development and immune signaling) appear, the strongest and most frequent annotations center on DNA synthesis, damage repair, and transcription initiation, indicating a coherent core of DNA maintenance genes.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0006281","count":23},{"id":"GO:0006351","count":23},{"id":"GO:0048701","count":22},{"id":"GO:0098761","count":22}]},{"hash":"1068689667066646888","title":"DNA Replication and Cell Cycle Regulation","description":"This cluster is dominated by GO terms for DNA replication, mitotic cell cycle, DNA repair, and DNA-templated transcription, indicating a core group of nuclear proteins involved in genome duplication and cell-cycle control. Some developmental terms appear, but they likely reflect shared gene regulation or pleiotropy rather than a distinct developmental program. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0000278","count":23},{"id":"GO:0006281","count":22},{"id":"GO:0006351","count":22},{"id":"GO:0098761","count":21}]},{"hash":"2070289845282735984","title":"Polysaccharide and ubiquitin-dependent protein catabolism","description":"Top GO terms indicate strong enrichment for carbohydrate degradation (cellulose, xylan, polysaccharide catabolic) and for ubiquitin-dependent protein catabolic process, suggesting the cluster centers on macromolecule breakdown and turnover. Additional terms (diaphragm contraction, transcription regulation, cell cycle, apoptosis) are present but seem secondary; the dominant theme is catabolism and protein turnover rather than a single pathway.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0045493","count":3},{"id":"GO:0000272","count":3},{"id":"GO:0006491","count":3}]},{"hash":"1426651829634672531","title":"Unknown","description":"The GO terms span transcription regulation, metabolism (inositol and purine pathways), mitochondrial targeting (obsolete), signaling, neuronal growth, and dephosphorylation. There is no single dominant function or pathway linking these terms, so there is no cohesive theme for a specific label. ","confidence":"","size":26,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045893","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0032958","count":2},{"id":"GO:0060168","count":2},{"id":"GO:0051516","count":2}]},{"hash":"1083885074712878016","title":"Regulatory Transcription and Signaling Cluster","description":"This cluster includes GO terms spanning DNA-templated transcription, calcium signaling, regulation of SNARE complex assembly, protein ADP-ribosylation, telomere localization/regulation, and even angiogenic processes. The proteins appear to participate in broad regulatory functions rather than a single cohesive pathway, indicating a set of factors that modulate gene expression and cellular signaling, rather than a shared, well-defined molecular module.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1903589","count":4},{"id":"GO:1904357","count":4},{"id":"GO:0010745","count":4},{"id":"GO:0050968","count":4}]},{"hash":"1895540450765774366","title":"Central carbon metabolism and amino acid catabolism","description":"Dominant GO terms include glycolysis, TCA cycle, and various amino acid catabolic pathways, pointing to a cluster of proteins involved in central carbon metabolism and amino acid turnover; weaker signals from Notch signaling and cAMP response likely reflect regulatory cross-talk or annotation noise rather than a core function.","confidence":"High","size":25,"edges":273,"triangles":1827,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006099","count":10},{"id":"GO:0006096","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0033512","count":7},{"id":"GO:0019878","count":6}]},{"hash":"985564599215841712","title":"DNA replication and transcription with protein turnover","description":"The cluster\u2019s top GO terms emphasize nuclear processes (DNA replication, DNA-templated transcription, transcription by RNA polymerase II) and ribosome biogenesis, coupled with ubiquitin-dependent protein degradation (ERAD) and regulation of protein kinase activity. This suggests a cohesive theme linking gene expression with proteostasis and protein quality control, rather than a single metabolic pathway. A few peripheral terms ( xenobiotic response, LPS biosynthesis, muscle fiber transition) are less central but do not override the dominant signal. Confidence: Medium","confidence":"","size":25,"edges":9,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0042787","count":3}]},{"hash":"1819522861860107209","title":"DNA replication and cell cycle","description":"The top terms are dominated by nuclear processes: DNA replication, DNA-templated transcription, protein localization to kinetochore, and meiotic cell cycle, pointing to cell division and chromosome maintenance. Developmental and ECM-related terms appear as secondary signals, suggesting additional roles in morphogenesis, but the core theme remains cell-cycle\u2013related nuclear functions. ","confidence":"Medium","size":25,"edges":21,"triangles":10,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":14},{"id":"GO:0048701","count":12},{"id":"GO:0030212","count":12},{"id":"GO:1905050","count":12},{"id":"GO:0007229","count":12}]},{"hash":"703313866852191578","title":"RNA processing and translation machinery","description":"The cluster is dominated by translation-related terms (general translation, translational termination, mitochondrial translation, translational fidelity) and several spliceosome/RNA-processing terms, plus mRNA decay, pointing to a cohesive RNA metabolism and protein-synthesis focus. A hematopoietic differentiation term appears ancillary but does not override the central RNA-centric theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0046677","count":3},{"id":"GO:1990145","count":2},{"id":"GO:0000349","count":2},{"id":"GO:0000288","count":2}]},{"hash":"801176087214953543","title":"RNA processing and mRNA metabolism","description":"Most high-frequency GO terms in this cluster point to RNA metabolism and processing, including tRNA processing, spliceosome-mediated splicing, deadenylation-dependent decapping, mRNA cis splicing, and P-body assembly, as well as histone mRNA metabolism. A few terms relate to chromatin regulation, but the dominant signal is RNA processing machinery.","confidence":"Medium","size":25,"edges":34,"triangles":7,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0030212","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0000290","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0000245","count":2}]},{"hash":"130292088992170528","title":"Retroviral integration and latency","description":"The top GO terms cluster around retroviral processes: reverse transcription (RNA-templated DNA synthesis), DNA replication and integration, viral entry/penetration into the host nucleus, and establishment of proviral latency. Additional terms point to virus\u2013host interactions and modulation of host RNAi pathways, supporting a cohesive theme of viral genome integration and latency within the host.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006310","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0075732","count":3}]},{"hash":"1696905836812226291","title":"DNA Replication and Cell Cycle Core","description":"The top GO terms overwhelmingly point to genome maintenance and division, with strong signals for DNA replication (20), mitotic cell cycle (15), and DNA repair (14). While there are additional developmental and signaling terms present (e.g., mesoderm formation, neural patterning, and response to hormones), they appear secondary to the core theme of DNA replication, repair, and cell cycle control. This suggests a cluster of proteins central to genome duplication and cell division, possibly with ancillary roles in signaling or development.","confidence":"High","size":25,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":20},{"id":"GO:0048701","count":17},{"id":"GO:0001403","count":15},{"id":"GO:0007124","count":15},{"id":"GO:0018108","count":15}]},{"hash":"964942765321679709","title":"T cell signaling and cell cycle regulation","description":"This cluster is strongly enriched for T cell receptor signaling, alongside mitotic cell cycle, DNA repair, and related regulatory processes, suggesting a functionally coherent module where immune signaling interfaces with cell proliferation and genome maintenance. While other terms hint at broader signaling roles (angiogenesis, muscle activity), the dominant theme centers on T cell\u2013driven signaling linked to growth and repair pathways.","confidence":"Medium","size":25,"edges":11,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":21},{"id":"GO:0000278","count":21},{"id":"GO:0006281","count":20},{"id":"GO:0001324","count":20},{"id":"GO:0060044","count":20}]},{"hash":"654037398186909212","title":"Cytoskeleton Remodeling and Ubiquitin-Proteasome Turnover","description":"This cluster is dominated by GO terms related to cytoskeletal dynamics (mitotic spindle assembly, microtubule-based movement, actin cytoskeleton organization) and protein turnover via ubiquitin-proteasome pathways (SCF-dependent degradation, ERAD). Together these suggest proteins that coordinate cytoskeletal remodeling with regulated proteolysis, a common cell-cycle/structural maintenance theme. Some unrelated terms appear as annotation noise.","confidence":"Medium","size":25,"edges":27,"triangles":2,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":4},{"id":"GO:0001560","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0007605","count":2},{"id":"GO:0017000","count":2}]},{"hash":"265438206607195935","title":"Ubiquitin-mediated signaling and apoptosis in development","description":"The cluster centers on ubiquitination processes (K63-linked, autoubiquitination, monoubiquitination) and ubiquitin-dependent proteolysis, coupled with regulatory impacts on signaling pathways (JNK, Wnt, GTPase activity) and developmental processes (mesoderm morphogenesis, cardiac proliferation). This points to a cohesive theme where ubiquitin controls signaling and apoptosis during development and tissue formation.","confidence":"High","size":25,"edges":25,"triangles":10,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":5},{"id":"GO:0051865","count":4},{"id":"GO:0060044","count":4},{"id":"GO:0046328","count":4},{"id":"GO:0006915","count":4}]},{"hash":"2097127608472337501","title":"Amino acid biosynthesis cluster","description":"This cluster is characterized by GO terms across several L-amino acid biosynthetic pathways (lysine, threonine, arginine, proline, homoserine, and related diaminopimelate steps), suggesting a common function in amino acid production. Despite no edges, the convergence on multiple biosynthetic processes indicates a coherent biological theme around amino acid biosynthesis. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0019877","count":2},{"id":"GO:0055129","count":2}]},{"hash":"509142211417384668","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0035826","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0071373","count":2}]},{"hash":"1919062422203243994","title":"Cellular Regulation and Signal Transduction","description":"The cluster features diverse regulatory processes: actin capping (cytoskeletal dynamics), regulation of tyrosine phosphorylation, ubiquitination/ERAD, neuronal apoptosis, DNA-templated transcription, GTPase activity regulation, TGF-beta signaling, and cell division. These terms indicate a broad theme of cellular regulation and signal transduction, including protein turnover and gene expression control, rather than a single cohesive pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051016","count":3},{"id":"GO:0050731","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051402","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1869103555086582582","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043588","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0034316","count":4},{"id":"GO:0070734","count":3}]},{"hash":"370486539177570330","title":"Cell Cycle and Ribosome Biogenesis","description":"This cluster is driven by mitosis-related terms (G1/S transition, spindle pole body separation, cell division) and by ribosome biogenesis, with additional signals pointing to embryo development (blastocyst development). Although there are other broad terms like transcription regulation and lysosomal targeting, the dominant pattern links cell cycle progression with protein synthesis machinery, justifying a label focused on these core processes.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0010696","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0001824","count":2}]},{"hash":"1972774921629254487","title":"Innate antiviral and LPS immune signaling","description":"This cluster is dominated by GO terms for innate immune response, defense against virus, and responses to dsRNA and lipopolysaccharide, indicating a core function in antiviral and bacterial recognition/signaling. A few terms related to neuronal development appear, which may reflect annotation noise or multifunctional proteins, but the core theme remains innate immunity and PAMP sensing. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":11},{"id":"GO:0051607","count":10},{"id":"GO:0043330","count":9},{"id":"GO:1903351","count":9},{"id":"GO:0031663","count":9}]},{"hash":"1768494539703420942","title":"Insulin signaling and actin cytoskeleton regulation","description":"This cluster shows multiple GO terms centered on insulin/IGF receptor signaling and its regulation, along with several terms about actin cytoskeleton organization, actin filament bundle formation, and negative regulation of Rho/Rac signaling. The convergence of insulin signaling pathway regulation with cytoskeletal dynamics suggests proteins coordinating metabolic signaling with cytoskeletal remodeling, despite a few ancillary terms (e.g., SNARE regulation, ceramide transport) that are less central to the core theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0035024","count":3},{"id":"GO:0035544","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1540347580333329572","title":"Spliceosome and ribosome biogenesis factors","description":"This cluster is dominated by RNA-centric terms: mRNA splicing via spliceosome, general mRNA processing, and maturation of 5.8S and LSU rRNA, all pointing to spliceosomal and ribosome biogenesis activities. Additional terms touch on regulatory ncRNA-mediated silencing and polyadenylation, reinforcing an RNA-processing theme. Some unrelated processes (Rho signaling, endosome transport) are present but less represented, so the core signal remains RNA processing and ribosome assembly.","confidence":"Medium","size":24,"edges":67,"triangles":85,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0032511","count":3},{"id":"GO:0000398","count":3}]},{"hash":"119413503178624322","title":"Energy metabolism and redox balance","description":"The top GO terms point to core metabolic pathways and redox regulation: glycolytic process, ATP synthesis via proton motive force, folate and thiamine cofactor biosynthesis supporting metabolism, and redox/homeostasis including removal of superoxide. This combination indicates a cluster of proteins involved in energy production and maintaining cellular redox state, with additional links to nutrient cofactor biosynthesis.","confidence":"High","size":24,"edges":191,"triangles":634,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0015986","count":2},{"id":"GO:0036245","count":2},{"id":"GO:0046653","count":2},{"id":"GO:0009228","count":2}]},{"hash":"597664020852116496","title":"B Cell Signaling and Ubiquitin Regulation","description":"The top GO terms point to adaptive immune processes, with B cell receptor signaling and germinal center formation being prominent, plus regulators of ubiquitination (K33-linked ubiquitination and negative regulation of protein ubiquitination) and non-canonical NF-kappaB signaling, all of which fit a coherent immune signaling theme. There are a few outliers (muscle development and distal tubule morphogenesis) that may reflect annotation noise rather than core function. Overall, the cluster most plausibly centers on immune signaling modulated by ubiquitin dynamics.","confidence":"Medium","size":24,"edges":33,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:1901223","count":3},{"id":"GO:0000462","count":2},{"id":"GO:2000312","count":2},{"id":"GO:1990390","count":2}]},{"hash":"606074235173812632","title":"Unknown","description":"The cluster shows a mix of processes across apoptosis, DNA repair, RNA processing and stability, cell wall organization, corneocyte development, renal water transport, and PI signaling, with no single dominant function tying the proteins together. This heterogeneity suggests there isn\u2019t a clear, shared biological role to assign to the entire cluster.","confidence":"","size":24,"edges":40,"triangles":17,"max_degree":22,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0071555","count":5},{"id":"GO:0090502","count":4},{"id":"GO:0006284","count":4},{"id":"GO:2001153","count":4}]},{"hash":"2204919024455718257","title":"Adipogenesis and cytoskeleton-driven migration","description":"Primarily driven by fat cell differentiation and cell migration, with emphasis on cytoskeleton remodeling (actin reorganization) and mechanotransduction (response to muscle stretch). Some telomere maintenance and development terms appear but do not define the core theme; the dominant cluster is adipogenic differentiation linked to cytoskeletal dynamics and movement.","confidence":"Medium","size":24,"edges":8,"triangles":2,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045444","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0035994","count":4},{"id":"GO:0006397","count":4}]},{"hash":"1747223270977142134","title":"Mitotic Cell Cycle Regulators","description":"The strongest signals are in mitosis-related processes: metaphase/anaphase transition, mitotic cell cycle, and cell division, suggesting the cluster mainly comprises proteins involved in mitotic progression. Several other terms (response to unfolded protein, interferon response, snoRNP assembly) indicate additional roles or annotation noise, but the core theme is cell cycle regulation during division.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071357","count":4},{"id":"GO:0051348","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4}]},{"hash":"46198814809883920","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000447","count":4}]},{"hash":"422833519180336553","title":"Cell Polarity and Membrane Trafficking","description":"This cluster centers on GO terms related to maintaining cellular polarity, regulating cell migration, post-Golgi vesicle transport, and lipid biosynthesis (sphingolipids, triglycerides), plus responses to epidermal growth factor. Together these suggest a shared theme of polarized membrane organization and trafficking, supported by lipid metabolism. A nuclear-related term (Cajal body organization) is present but likely reflects multifunctional proteins or annotation noise. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030011","count":2},{"id":"GO:0030335","count":2},{"id":"GO:0030148","count":2},{"id":"GO:0006892","count":2},{"id":"GO:0071364","count":2}]},{"hash":"1563424936521268732","title":"Glycolysis Regulation and Metabolic Processes","description":"The top GO terms cluster around glycolytic activity and its regulation (glycolytic process, gluconeogenesis, fructose metabolism, negative regulation of glycolytic process, dephosphorylation), pointing to an energy metabolism\u2013focused theme. Several developmental terms are present but appear less central to the core signal, suggesting the dominant function is metabolic regulation rather than a single developmental program.","confidence":"Medium","size":23,"edges":22,"triangles":1,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0045820","count":3},{"id":"GO:0045453","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0006000","count":2}]},{"hash":"2232904921569809240","title":"Neural development and synapse assembly","description":"This cluster center appears to be driven by transcriptional regulation (RNA polymerase II transcription, regulation of transcription) coupled with neural differentiation cues (spinal cord motor neuron fate specification, skeletal muscle differentiation) and synapse formation (inhibitory synapse assembly). Additional terms touch on broader developmental processes like placenta morphogenesis and circadian rhythm, which are compatible with pleiotropic developmental gene programs but do not override the core neural-development signal. Overall, the set is best described as genes involved in neural development and synapse assembly.","confidence":"Medium","size":23,"edges":99,"triangles":308,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":6},{"id":"GO:0001892","count":6},{"id":"GO:0021520","count":5},{"id":"GO:0007623","count":4},{"id":"GO:2000323","count":4}]},{"hash":"1432040681175601103","title":"Muscle and vascular differentiation regulators","description":"Based on the top GO terms, the cluster centers on differentiation and development of muscle tissues (myoblast and cardiac muscle differentiation) and blood vessel formation (vasculogenesis), with links to transcriptional regulation (DNA-templated transcription) and signaling pathways (Notch). Obsolete hydroxylation terms likely reflect legacy annotations but do not override the central theme of developmental regulation in muscle and vascular lineages.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042264","count":3},{"id":"GO:2001214","count":3},{"id":"GO:0042265","count":3},{"id":"GO:0045663","count":3}]},{"hash":"1672870230001292186","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045944","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0000472","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1757218726762416070","title":"Regulated cellular signaling and stress responses","description":"This cluster includes GO terms spanning calcium signaling, mechanical stimulus response, pain detection, angiogenesis, telomere regulation, SNARE assembly regulation, and kinase activity control\u2014suggesting broad regulatory roles rather than a single pathway; the common thread is modulation of diverse cellular signaling and stress-related processes.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:1903589","count":3},{"id":"GO:1904357","count":3},{"id":"GO:0010745","count":3},{"id":"GO:0045736","count":3}]},{"hash":"1773670214415624666","title":"RNA Pol II Transcription Regulation and Cell Cycle","description":"This cluster is dominated by GO terms related to transcription by RNA polymerase II, DNA-templated transcription, and initiation at Pol II promoters, with additional cell-cycle terms like G1/S transition and meiosis-related chromosome pairing, suggesting a group of proteins that regulate transcription with roles in cell-cycle progression. A few terms such as brain development and X-ray response are less central but do not override the overarching transcription/ cell-cycle theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000122","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006367","count":3},{"id":"GO:0070898","count":3}]},{"hash":"1164030485824037756","title":"Axon guidance and neural development signaling","description":"The cluster is enriched for ephrin receptor signaling, axonal fasciculation, corpus callosum development, and regulation of axon regeneration, all core to neuronal pathfinding and brain development. Additional terms point to related signaling and intracellular transport processes (CAMKK-AMPK, endosome-to-Golgi retrograde transport) that support trafficking and signaling in neurons. A few immune-related terms appear but do not define the cluster\u2019s main function. ","confidence":"High","size":23,"edges":25,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0048013","count":3},{"id":"GO:1902499","count":2},{"id":"GO:0007413","count":2},{"id":"GO:0048681","count":2}]},{"hash":"4710977294964991","title":"RNA Transcription and Processing","description":"The most represented GO terms are related to transcription and processing of RNA (RNA Pol III\u2013driven tRNA transcription, RNA Pol I\u2013driven rRNA transcription, RNA-templated transcription, rRNA modification, and RNA guanine-N7 methylation). A smaller subset relates to lipid metabolism and antibiotic biosynthesis (sterol biosynthetic process, ceramide transport, antibiotic biosynthetic process), which are likely secondary associations. Overall, the cluster is best characterized by RNA synthesis and processing.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":3},{"id":"GO:0042797","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0017000","count":2}]},{"hash":"1630529396220561632","title":"Muscle growth and cellular stress signaling","description":"These proteins cluster around growth control and stress response, highlighted by Hippo signaling and regulation of cardiac muscle cell proliferation, as well as response to muscle stretch. Additional terms for DNA replication and repair, apoptosis, and endosome transport indicate concurrent maintenance of genome integrity and vesicle trafficking alongside growth signals. The mix suggests a coordinated program governing cell proliferation, survival, and mechanotransduction in muscle/heart contexts rather than a single specific function.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":14},{"id":"GO:0006260","count":14},{"id":"GO:0006915","count":14},{"id":"GO:0006281","count":13},{"id":"GO:0060044","count":13}]},{"hash":"204196279276281816","title":"TLR2-driven innate immunity and cytoskeletal remodeling","description":"The cluster is enriched for innate immune terms (innate immune response, macrophage activation, defense against Gram-negative bacteria, TLR2 signaling, LPS signaling) and cytoskeletal dynamics terms (filopodium/microspike assembly, regulation of Rho signaling), suggesting a group of proteins involved in initiating innate immune responses against Gram-negative bacteria with coordinated actin remodeling for phagocytosis or migration.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0035023","count":4},{"id":"GO:0046847","count":4},{"id":"GO:0060348","count":4},{"id":"GO:0060335","count":4}]},{"hash":"248191495894868059","title":"CDK-Regulated Cell Cycle and DNA Replication","description":"The cluster is dominated by GO terms related to negative regulation of cyclin-dependent kinase activity, cell cycle progression, DNA replication, and double-strand break repair via classical NHEJ, suggesting a core role in genome maintenance and cell-cycle control. Some terms touch on differentiation and signaling, but the prominent pattern ties to cell-cycle regulation and DNA replication/repair.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":3},{"id":"GO:0021707","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0006260","count":2}]},{"hash":"427684372531060286","title":"Unknown","description":"The top GO terms span diverse biological processes (transcription regulation, vesicle transport, DNA replication, lipid catabolism, xenobiotic response, development, dendrite morphogenesis, methylation, and ubiquitination). There is no clear, single functional theme tying the proteins together, so a cohesive label cannot be confidently assigned.","confidence":"","size":22,"edges":36,"triangles":18,"max_degree":17,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006685","count":3}]},{"hash":"136908405731894700","title":"Ubiquitin-Dependent Cell Cycle Regulation","description":"This cluster centers on mitotic cell cycle and cell division, with several terms about negative regulation of proliferation, and links to ubiquitin-mediated processes (ubiquitin-dependent ERAD, histone ubiquitination). Together these point to proteins that regulate cell cycle progression and proteostasis through ubiquitin-mediated degradation, with some oxidative stress and immune signaling components likely reflecting broader stress responses rather than a core function. ","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902564","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0071276","count":4}]},{"hash":"2286217360193367011","title":"Glial Development and Cellular Stress Responses","description":"The cluster includes oligodendrocyte development (GO:0014003), indicating neural/glial differentiation, alongside numerous stress- and toxin-response terms (e.g., responses to lithium, aluminum ions, ethanol, starvation, and toxic substances), plus cell division and a T cell receptor signaling term, suggesting a mix of developmental and broad stress/immune signaling activities. While the dominant signal appears to be glial development with concurrent stress response pathways, the immune signaling term hints at broader cross-talk or annotation breadth. Overall, a cohesive label capturing neural glial development coupled with cellular stress signaling fits best.","confidence":"Medium","size":22,"edges":14,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071285","count":5},{"id":"GO:0014003","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0010044","count":4},{"id":"GO:0045471","count":4}]},{"hash":"1081699947503270345","title":"Mitochondrial transport and metabolic regulation","description":"The terms cluster around mitochondrial processes and cellular energy metabolism, including mitochondrial membrane potential regulation, apoptotic mitochondrial changes, and transmembrane transport of citrate, CoA, and NAD, along with metabolic responses to fatty acids, insulin, and glucose. This set suggests a cohesive function in mitochondrial transport and energy regulation, which can influence insulin signaling and metabolic tissues such as liver and brain.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":4},{"id":"GO:0021762","count":3},{"id":"GO:0051881","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0035349","count":3}]},{"hash":"481386696504997397","title":"Glycan biosynthesis and GPI anchor formation","description":"The top terms cluster around glycosylation and membrane-anchoring processes: GPI anchor biosynthetic process, mannosylation, and oligosaccharide-lipid intermediate biosynthesis strongly point to glycan assembly and protein anchoring. Additional signals from glycogen biosynthesis and sugar-related responses (sorbitol, feeding behavior) hint at carbohydrate metabolism interconnected with membrane modification. Some metabolic terms (uracil catabolic process, nitrogen utilization) appear peripheral but do not outweigh the glycan/GPI signature. Confidence: Medium.","confidence":"","size":22,"edges":33,"triangles":8,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":2},{"id":"GO:0019740","count":2},{"id":"GO:0097502","count":2},{"id":"GO:0072708","count":2},{"id":"GO:0007631","count":2}]},{"hash":"634657920955455856","title":"Plant Redox Metabolism and Transcription","description":"The cluster\u2019s terms center on photosynthesis, the TCA cycle, and a cellular response to hydrogen peroxide, all pointing to redox-regulated metabolism typical of plants. It also includes DNA-templated transcription and chromatin-related activity, suggesting coordinated gene expression in response to metabolic state. Some outlier terms (e.g., keratinocyte differentiation, phagocytosis regulation) may reflect annotation noise or cross-kingdom annotations, but the dominant theme appears to be plant redox-linked metabolism and transcriptional control. ","confidence":"Medium","size":22,"edges":69,"triangles":147,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006351","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0070301","count":3},{"id":"GO:0015979","count":3}]},{"hash":"1403308864966692098","title":"Bone development and remodeling signaling","description":"The GO terms center on osteoblast fate commitment and bone development, with supporting signals for cytoskeletal remodeling (podosome assembly, cleavage furrow formation) and signaling pathways (PI signaling) that tie into bone formation and remodeling, including aspects relevant to osteoclast-mediated matrix interactions.","confidence":"High","size":22,"edges":26,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0002051","count":3},{"id":"GO:0031139","count":3},{"id":"GO:0060348","count":3},{"id":"GO:1904179","count":3},{"id":"GO:0071800","count":3}]},{"hash":"239776037551016806","title":"Rho-GTPase signaling in development","description":"The cluster centers on broad developmental processes (skeletal, nervous, heart development) and Rho GTPase signaling, suggesting proteins involved in signaling networks that regulate cytoskeletal dynamics during development. While other terms like exocytosis and stress responses appear, the dominant theme is developmental signaling modulated by Rho-family GTPases.","confidence":"Medium","size":22,"edges":44,"triangles":41,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":7},{"id":"GO:0007266","count":6},{"id":"GO:0007124","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0007507","count":6}]},{"hash":"284648048047187289","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":52,"triangles":44,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":16},{"id":"GO:0000398","count":15},{"id":"GO:0031047","count":15},{"id":"GO:0000472","count":12},{"id":"GO:0000480","count":12}]},{"hash":"323329452420301097","title":"Developmental signaling and cell proliferation","description":"The terms cluster around developmental growth and signaling (angiogenesis, mesoderm formation, neural tube patterning) and fundamental cell-cycle processes (DNA replication, mitosis, transcription), with some immune and stress response terms mixed in. There isn't a single, narrowly defined function shared by all proteins, but \u201cdevelopmental signaling and cell proliferation\u201d captures the dominant themes. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001525","count":6},{"id":"GO:0071374","count":4},{"id":"GO:1901621","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0001707","count":4}]},{"hash":"1128761509927836315","title":"Nuclear transport and RNA processing","description":"The cluster shows strong enrichment for nuclear-cytoplasmic transport processes: mRNA export, ribosomal small subunit export, nuclear pore complex assembly, and import of splicing factors and snRNPs, with supporting Ran signaling. These collectively point to a core function in nuclear transport and RNA processing, with some peripheral links to ciliary transport and microtubule organization. ","confidence":"High","size":22,"edges":20,"triangles":0,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0000056","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0035735","count":2}]},{"hash":"1865194476746554384","title":"Neural development and synapse assembly","description":"This cluster is dominated by neural development terms, including axonal fasciculation, corpus callosum development, and positive regulation of synapse assembly, with supporting terms like cell morphogenesis and DNA-templated transcription, suggesting a shared role in neural connectivity and development. Some terms (mitotic cell cycle, mitotic spindle checkpoint) indicate broader developmental or proliferative contexts, and a few terms (defense response to Gram-positive bacterium) may reflect multifunctional proteins or annotation noise. Overall, the core theme points to neural differentiation and synapse formation with supporting developmental processes.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007413","count":3},{"id":"GO:0022038","count":3},{"id":"GO:0071372","count":3},{"id":"GO:0050830","count":3}]},{"hash":"2112450028235184678","title":"Intracellular vesicle trafficking and protein turnover","description":"GO terms cluster around vesicle trafficking (synaptic vesicle exocytosis, Golgi-to-ER transport, intracellular transport) and proteasomal protein turnover (ubiquitin pathway) with GTPase activity regulation; though brain development and cell division terms appear, the common theme is vesicle movement coupled to protein turnover.","confidence":"Medium","size":22,"edges":21,"triangles":0,"max_degree":21,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":9},{"id":"GO:0031384","count":8},{"id":"GO:0010796","count":8},{"id":"GO:0007420","count":7},{"id":"GO:0051301","count":7}]},{"hash":"575155545438120228","title":"Unknown","description":"The GO terms cover diverse processes (angiogenesis regulation, telomere biology, foam cell differentiation, pain perception, SNARE regulation, calcium signaling, telomeric localization, and protein ADP-ribosylation) with no single unifying function, suggesting broad regulatory roles rather than a cohesive pathway.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903589","count":3},{"id":"GO:1904357","count":3},{"id":"GO:0010745","count":3},{"id":"GO:0050968","count":3},{"id":"GO:0070213","count":3}]},{"hash":"321073916476507676","title":"Ubiquitin-regulated TNF/NF-kappaB signaling","description":"The proteins appear to co-occur with ubiquitination-related processes (autoubiquitination, ubiquitin-dependent proteolysis) and signaling pathways central to TNF-mediated and NF-kappaB-driven responses, including JNK cascade regulation. While V(D)J recombination is present, the dominant theme is ubiquitin-mediated regulation of inflammatory signaling via TNF and NF-kappaB, with related MAPK/JNK involvement.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0046328","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0070512","count":5},{"id":"GO:1903265","count":5}]},{"hash":"1513087484304634256","title":"Ubiquitin-Proteasome Proteostasis and Metal Stress","description":"The dominant GO terms are about ubiquitin-mediated protein degradation (SCF-dependent proteasomal ubiquitin-dependent catabolic process, protein polyubiquitination, ERAD) and regulation of circadian rhythm, pointing to a core function in proteostasis. Additional terms indicate cellular responses to metal stress (arsenic, cadmium, methylmercury), which often converge on ubiquitin-proteasome pathways. Together, these suggest a cohesive cluster focused on proteostasis and metal-stress signaling, with some related neuronal stress outcomes. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000083","count":9},{"id":"GO:0031146","count":7},{"id":"GO:0042752","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0046685","count":7}]},{"hash":"1369944792135141153","title":"Bacterial quinone biosynthesis and related metabolism","description":"The cluster is enriched in metabolic pathways, notably menaquinone and phylloquinone biosynthesis, various catabolic processes (phenylacetate, valine) and fatty acid beta-oxidation, as well as antibiotic biosynthesis, indicating a cohesive bacterial metabolism theme centered on energy generation and membrane-associated electron carriers; a few terms related to endothelial regulation or nitrogen fixation may reflect annotation noise.","confidence":"High","size":21,"edges":199,"triangles":1146,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0006574","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0042372","count":4}]},{"hash":"2138843350861774602","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":19,"triangles":21,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0031146","count":3}]},{"hash":"367800863675025709","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0000472","count":3}]},{"hash":"75100144677324207","title":"Unknown","description":"The GO terms are diverse, spanning translation, transcription regulation, glycosylation, ion transport, redox-related processes, and viral processes, with no single cohesive theme. Therefore this cluster cannot be confidently assigned a specific functional label.","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":3},{"id":"GO:0017004","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006662","count":2}]},{"hash":"284140373166457689","title":"Bacterial LPS and exopolysaccharide biosynthesis","description":"Most top terms point to biosynthesis of bacterial cell envelope polysaccharides: LPS core (ADP-L-glycero-beta-D-manno-heptose), colanic acid, dTDP-rhamnose, and related sugar-nucleotide pathways. Additional terms for polyhydroxybutyrate and fatty-acyl-CoA metabolism reflect broader bacterial metabolism that commonly accompanies capsule and outer-m membrane assembly. This makes the label concise and representative of the cluster\u2019s function.","confidence":"High","size":21,"edges":9,"triangles":3,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042619","count":6},{"id":"GO:0046677","count":5},{"id":"GO:1902987","count":5},{"id":"GO:0010124","count":5}]},{"hash":"2022217418741967349","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000398","count":12},{"id":"GO:0070262","count":12},{"id":"GO:0030042","count":12},{"id":"GO:0034316","count":12},{"id":"GO:0006888","count":12}]},{"hash":"394008104753268133","title":"Mitosis and APC-dependent protein degradation","description":"The top GO terms are dominated by mitotic cell cycle and cell division, including APC-dependent catabolic processes and regulation of metaphase/anaphase transition, plus K11-linked ubiquitination linked to APC activity. This points to a core theme of mitotic progression governed by targeted protein degradation. While vesicle trafficking and immune-related terms appear, they are less central to the cluster\u2019s main signal.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0051607","count":2},{"id":"GO:2001162","count":2}]},{"hash":"1210892385491638958","title":"Unknown","description":"The top GO terms are diverse, including muscle-related terms (sarcomere organization, cardiac muscle development) but also neural differentiation, DNA repair, RNA processing, and transport processes. There is no single cohesive function linking the cluster, so a specific label cannot be derived. Confidence: None","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":2},{"id":"GO:0048714","count":2},{"id":"GO:2000811","count":2},{"id":"GO:0055013","count":2},{"id":"GO:0090502","count":1}]},{"hash":"162663142216308917","title":"Rho-Driven Filopodium Formation and Cell Migration","description":"The top GO terms strongly point to Rho GTPase\u2013regulated cytoskeletal remodeling, with filopodium assembly and cell migration as central themes. While other signaling pathways appear (insulin signaling, cytokine responses), the recurrent motifs center on actin dynamics and protrusive migration driven by Rho signaling, justifying a cohesive label focused on cytoskeletal remodeling and movement.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":7},{"id":"GO:0046847","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0060335","count":5}]},{"hash":"277160055253952351","title":"Innate immune signaling and interferon response","description":"Top GO terms point to innate immune processes, dsRNA sensing, interferon production, and NF-kB\u2013regulated signaling, with LPS signaling also present; the proteins likely function together in innate antiviral and inflammatory pathways, making this label appropriate.","confidence":"High","size":21,"edges":18,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0071300","count":3},{"id":"GO:0030097","count":3},{"id":"GO:0032869","count":2}]},{"hash":"2080461207016276793","title":"Developmental Gene Regulation and Signaling","description":"The GO terms cluster around gene expression control (mRNA processing, transcription, DNA repair) and developmental/differentiation processes (face development, fat cell differentiation, cell migration), coordinated with signaling pathways (insulin receptor signaling, JNK cascade regulation). This suggests a cohesive theme of regulating gene expression in development and associated signaling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006397","count":5},{"id":"GO:0045736","count":5},{"id":"GO:0016477","count":5},{"id":"GO:2001275","count":5},{"id":"GO:0006351","count":4}]},{"hash":"1881953639013786006","title":"Innate Immune Signaling and Lysosome Function","description":"The top terms include NOD2 signaling and phagosome-lysosome fusion, which point to innate immune sensing and lysosomal trafficking. Additional hints of calcium signaling and stress-related responses suggest broader cellular signaling connected to these processes. The strongest cohesive theme is innate immune signaling linked to lysosome function, though other terms indicate broader cellular responses, hence a medium confidence.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0035751","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0051209","count":2}]},{"hash":"125368418494633720","title":"Macrophage Activation and Inflammatory Signaling","description":"The terms point to innate immune responses (LPS signaling, macrophage activation, and NF-kappaB-related regulation) with adaptive components (Th17 differentiation) and ubiquitin-proteasome regulation, suggesting an inflammatory/immune activation program in macrophages; accompanying cytoskeletal remodeling terms (actin uncapping, cell polarity) align with immune cell movement and phagocytosis, while some terms (bone formation, cell cycle) may reflect pleiotropic roles. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0045842","count":3},{"id":"GO:0031663","count":2},{"id":"GO:0030011","count":2},{"id":"GO:2000321","count":2}]},{"hash":"917865347045730604","title":"DNA replication and repair machinery","description":"The majority of terms point to DNA replication, DNA-templated transcription, and DNA repair, with related cell cycle regulation terms, indicating a nuclear genome-maintenance module. A few developmental terms may reflect pleiotropy or annotation noise.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006260","count":21},{"id":"GO:0006351","count":21},{"id":"GO:0006281","count":20},{"id":"GO:0098761","count":20},{"id":"GO:0010571","count":20}]},{"hash":"1916227815239122575","title":"Ubiquitin-Proteasome ERAD and ER Stress Response","description":"This cluster is dominated by ubiquitin-related processes (autoubiquitination, ubiquitin chain formation, SCF-dependent proteasomal degradation) and ER-associated degradation, pointing to a core module of proteostasis and ER stress signaling. The presence of interferon responses and ER-stress\u2013induced apoptosis suggests links between protein quality control and innate immune signaling, with additional, less central ties to DNA repair and chromatin regulation. Overall, the strongest theme is ubiquitin-mediated proteolysis and ERAD in stress contexts.","confidence":"Medium","size":20,"edges":38,"triangles":31,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006348","count":6},{"id":"GO:0051865","count":5},{"id":"GO:0030433","count":5},{"id":"GO:1904153","count":4},{"id":"GO:0010994","count":4}]},{"hash":"801882720457850077","title":"Translation initiation and mRNA binding regulation","description":"This cluster is dominated by translation-related terms: translation, formation of translation preinitiation complex, regulation of translational initiation, translation reinitiation, and positive regulation of mRNA binding, pointing to a core theme of controlling how translation starts and how mRNAs engage ribosomes. Additional terms touch on transcription regulation and nucleotide-excision repair, and a proteasomal degradation process, which may reflect multifunctional proteins or annotation across related processes, but the strongest signal is translation initiation control.","confidence":"High","size":20,"edges":31,"triangles":30,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":4},{"id":"GO:0006283","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0048142","count":3}]},{"hash":"610623517387587273","title":"Hepatic mitochondrial energy metabolism and insulin signaling","description":"The terms cluster around mitochondrial function (mitochondrial membrane potential, NAD and CoA transport, mitochondrial maintenance) and energy/lipid metabolism (fatty acids, amino acid starvation responses) with insulin/ glucose signaling and liver-specific processes (liver regeneration). This suggests a coherent theme of liver-centered energy metabolism coordinated with mitochondrial activity and insulin signaling.","confidence":"Medium","size":20,"edges":31,"triangles":14,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097274","count":9},{"id":"GO:0000002","count":8},{"id":"GO:0034198","count":7},{"id":"GO:0051881","count":6},{"id":"GO:0070542","count":6}]},{"hash":"2184432544194445556","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":66,"triangles":21,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0007275","count":3}]},{"hash":"2237349905421970295","title":"Methylation and Biosynthesis Enzymes","description":"The top GO terms indicate a mix of biosynthetic processes (ubiquinone, sterol, antibiotic biosynthesis) and multiple methylation-related modifications (rRNA methylation, N-terminal peptidyl-glycine methylation, peptidyl-lysine dimethylation). Some terms also touch on ribosome export and transcription regulation, suggesting involvement in both metabolic pathways and macromolecule modification/processing. Taken together, the cluster appears to group proteins tied to biosynthesis and methylation activities, with possible links to ribosome-associated maturation and gene expression control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0090398","count":5},{"id":"GO:0016126","count":5},{"id":"GO:0018013","count":5}]},{"hash":"449758632905524358","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051209","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0051497","count":2}]},{"hash":"1053373006828035966","title":"Small-molecule biosynthesis and antibiotic response","description":"The top GO terms point to biosynthesis of diverse small molecules (antibiotics, retinoic acid, estrogen, tetrahydrobiopterin, fatty acids) and a related antibiotic response, with a transcriptional regulation term suggesting coordinated control. This indicates a broad metabolic and regulatory theme around production of signaling/metabolic compounds and related stress/response, rather than a single focused pathway.","confidence":"Medium","size":20,"edges":8,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0017000","count":9},{"id":"GO:0006355","count":9},{"id":"GO:0006729","count":7},{"id":"GO:0046677","count":7}]},{"hash":"1245180572108296042","title":"Actin Cytoskeleton Remodeling and Cell Motility Signaling","description":"This cluster is dominated by GO terms for actin filament bundle assembly and cell migration, with supporting terms for regulated Rho/Ras signaling and synaptic vesicle priming, all of which relate to actin-driven remodeling and movement. Additional terms like T cell activation death, DNA replication, and mRNA processing appear less central but may reflect broader cellular contexts. Overall, the common thread is actin-based cytoskeletal dynamics that enable motility and vesicle trafficking, rather than a single narrowly defined process.","confidence":"Medium","size":20,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0016082","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0035023","count":3}]},{"hash":"840993661189949460","title":"Innate antiviral response and interferon signaling","description":"The prominent GO terms point to innate immunity and antiviral signaling, including innate immune response, cellular response to dsRNA, and cellular response to type I interferon, which collectively define an antiviral/IFN-centric module. A few terms about chromatin organization and development appear but are less representative of the cluster\u2019s main signal. Confidence in this label is medium.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000973","count":2},{"id":"GO:0006336","count":1},{"id":"GO:0006335","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0001824","count":1}]},{"hash":"1193417189228462771","title":"Membrane Ion and Metabolite Transporters","description":"This cluster shows strong enrichment for transmembrane transport across diverse substrates (sodium, potassium, galactose, nitrate/nitrite, phosphate, and other metabolites) and a related process of neurotransmitter loading into synaptic vesicles, with metabolic regulation like glucose starvation. The common theme is membrane transporter proteins that move ions and small molecules across membranes, influencing cellular energetics and signaling.","confidence":"High","size":19,"edges":29,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0042149","count":3},{"id":"GO:0015757","count":3},{"id":"GO:1900754","count":3}]},{"hash":"1850614342109180913","title":"Steroid biosynthesis and energy metabolism","description":"The cluster is enriched for androgen-related processes (androgen metabolic process, testosterone biosynthetic process) and several energy-generating catabolic pathways (fatty acid beta-oxidation, medium-chain fatty acid catabolic process, L-leucine catabolic process) as well as regulation of gluconeogenesis and starvation response, pointing to a theme of steroid production linked to energy mobilization. While some terms like post-embryonic development and cardiac differentiation appear, the dominant signal is steroid biosynthesis coupled with metabolic catabolism. ","confidence":"High","size":19,"edges":29,"triangles":6,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0009791","count":6},{"id":"GO:0042594","count":5},{"id":"GO:0008209","count":4},{"id":"GO:0061370","count":4}]},{"hash":"1087294335517942355","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072358","count":1},{"id":"GO:0010259","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0061458","count":1},{"id":"GO:0006120","count":1}]},{"hash":"1962744423370145202","title":"Ribosome biogenesis and translation","description":"Most top terms point to protein synthesis machinery: translation, ribosome assembly, and mitochondrial translation. The tRNA methylation term fits translational control, and ITS2 rRNA cleavage relates to ribosome maturation. The antibiotic response, biotin/menaquinone biosynthesis appear peripheral but do not define the core theme. Thus the cluster likely represents ribosome biogenesis and translation.","confidence":"High","size":19,"edges":155,"triangles":769,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0042255","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0030488","count":2}]},{"hash":"1519775153508530898","title":"Diverse Small-Molecule Biosynthesis","description":"This cluster shows enrichment for a wide range of biosynthetic processes, including antibiotic biosynthesis, biotin and cobalamin biosynthesis, fatty acid and porphyrin biosynthesis, and other small-molecule precursor pathways (pyruvate, threonine, etc.). The common thread is production of diverse metabolites rather than a single pathway, suggesting a general biosynthetic module. ","confidence":"High","size":19,"edges":79,"triangles":123,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0006633","count":4},{"id":"GO:0019878","count":4}]},{"hash":"1381165862981221064","title":"Nuclear DNA replication, transcription, and chromatin assembly","description":"This cluster is dominated by nuclear processes: DNA-templated transcription, DNA replication, mitotic cell cycle, and CENP-A\u2013containing chromatin assembly, with related histone methylation signals. Some terms (mRNA processing, translation reinitiation, and the defense response term) are less coherent or likely annotation noise. Overall, the group centers on genome maintenance and gene expression in the nucleus, supporting this label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0061641","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1092931688526913693","title":"Regulation of Signaling and Protein Turnover","description":"The GO terms point to regulatory roles across multiple pathways (Wnt signaling, calcineurin-NFAT signaling) and processes affecting protein fate (proteasomal ubiquitin-dependent degradation, translation initiation/complex formation, and GTPase activity), plus trafficking (COPII cargo loading) and developmental contexts (lens morphogenesis) and cell-cycle control (CDK activity). The unifying theme is regulation of signaling outputs and protein homeostasis rather than a single, shared effector function, suggesting a regulatory network cluster.","confidence":"Medium","size":19,"edges":26,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0032435","count":2},{"id":"GO:0002188","count":2}]},{"hash":"145558576164892887","title":"Ion Homeostasis and Developmental Signaling","description":"The cluster combines clear ion-transport and homeostasis terms (potassium and sodium fluxes) with multiple development/morphogenesis processes (angiogenesis, cortex layer formation, cartilage condensation, pseudohyphal growth) and Rho signaling, suggesting proteins that integrate ion balance with developmental signaling and tissue morphogenesis. Pain perception appears but does not define the core theme, so an ion-homeostasis plus developmental-signaling label fits best.","confidence":"Medium","size":19,"edges":34,"triangles":21,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097623","count":6},{"id":"GO:0007266","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0019233","count":6},{"id":"GO:0030007","count":5}]},{"hash":"2001334314003482227","title":"Unknown","description":"The top GO terms span both mitochondrial/electron transport functions (aerobic respiration, proton transport, ubiquinol-to-cytochrome c transfer) and diverse cell-surface and polysaccharide biosynthesis processes (teichoic acid, hyaluronan, UDP-galactose metabolism, protein glycosylation). There isn\u2019t a single coherent biological theme linking these terms into a concise, specific functional label, so a generic Unknown label is most appropriate.","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":3},{"id":"GO:1902600","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0035754","count":2},{"id":"GO:0030244","count":1}]},{"hash":"1950076545342821345","title":"Ribosome biogenesis and arginine methylation","description":"This cluster\u2019s frequent terms center on ribosome assembly and RNA modification (rRNA methylation and nuclear export of the small subunit) and arginine-focused post-translational modifications (methylation and hydroxylation). A few terms are less connected (digressions like nodulation or vitamin E biosynthesis), but the dominant signal reflects ribosome biogenesis and protein arginine modification.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000056","count":2},{"id":"GO:0046690","count":2},{"id":"GO:0010189","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0016049","count":2}]},{"hash":"1894473495181886599","title":"Post-transcriptional mRNA processing and translational regulation","description":"The cluster is enriched for GO terms related to mRNA stability, splicing, modification, and control of translation initiation and reinitiation. These terms indicate a coherent theme of post-transcriptional gene expression regulation, including spliceosome-mediated alternative splicing, mRNA maturation, and mechanisms governing mRNA stability and translation. The mix of splicing, polyadenylation-related (obsolete) terms and translation control supports a function focused on mRNA life cycle and its translation rather than transcriptional regulation. Overall, the proteins likely participate in post-transcriptional mRNA processing and regulation of translation.","confidence":"High","size":19,"edges":14,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0006446","count":2},{"id":"GO:1900363","count":2}]},{"hash":"1342081632384124137","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":13,"triangles":3,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006289","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000480","count":3}]},{"hash":"1789185638846596507","title":"Lymphoid development and cytokine signaling","description":"This cluster is dominated by immune-related terms: interleukin-7 response, B cell affinity maturation, interleukin-4 production, and NK T cell differentiation, all pointing to lymphoid development and cytokine signaling. Additional terms like cell migration and apoptotic processes support immune cell dynamics, while heart and neuron development terms may reflect broader developmental programs or pleiotropy. Overall, the strongest signals align with lymphoid maturation and cytokine-mediated signaling.","confidence":"Medium","size":18,"edges":13,"triangles":0,"max_degree":6,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098761","count":7},{"id":"GO:0008286","count":7},{"id":"GO:0002344","count":7},{"id":"GO:0016477","count":7},{"id":"GO:0007507","count":7}]},{"hash":"2241387670060589991","title":"Stress and defense response cluster","description":"The top GO terms are dominated by defense response to bacterium, osmotic stress, ER unfolded protein response, and host-mediated suppression of viral genome replication, pointing to a core theme of cellular stress and innate defense. Other annotations like cell morphogenesis, choline transport, and taste perception appear as peripheral associations, suggesting additional functions for some proteins but not a single cohesive pathway. Overall, the cluster seems best described by stress- and defense-related signaling rather than a single precise function.","confidence":"Medium","size":18,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0042742","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0044828","count":2},{"id":"GO:0030968","count":2}]},{"hash":"587107269613484379","title":"Developmental Regulation and Gene Silencing","description":"The cluster shows several development-related GO terms across tissues (cervix development, paramesonephric duct development, atrial cardiac muscle cell development) and regulatory processes (miRNA-mediated post-transcriptional gene silencing, ubiquitin/SMAD-related protein catabolic process). This pattern suggests proteins involved in developmental signaling and transcriptional/post-transcriptional control, with a few peripheral terms (sulfur oxidation, actin filament regulation) that may reflect broader cellular roles. Therefore, this label is moderately representative of the cluster's function.","confidence":"Medium","size":18,"edges":75,"triangles":150,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0060067","count":2},{"id":"GO:0055014","count":2},{"id":"GO:2000346","count":2},{"id":"GO:0061205","count":2},{"id":"GO:0071657","count":2}]},{"hash":"319838587767123511","title":"Developmental signaling and stress responses","description":"The proteins appear across developmental processes (placenta/thymus development, Hippo signaling) and multiple stress/immune signaling pathways (ER-stress\u2013induced apoptosis, dsRNA response, LPS signaling, cadmium response, innate immunity, dopamine signaling) with a note of DNA replication context, suggesting a broad signaling-centric cluster rather than a single pathway.","confidence":"Medium","size":18,"edges":7,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001890","count":6},{"id":"GO:0035329","count":5},{"id":"GO:0070059","count":5},{"id":"GO:0043330","count":5},{"id":"GO:0048538","count":5}]},{"hash":"850314984415859064","title":"T Cell Receptor Signaling and Endosomal Trafficking","description":"The cluster shows enrichment for T cell receptor signaling (GO:0050852) and positive regulation of ERK1/ERK2 cascade, along with ubiquitination and endosomal transport/fusion terms, suggesting a module of T cell activation closely tied to intracellular trafficking. Additional terms for stress fiber assembly and mechanical stimulus response point to cytoskeletal remodeling during signaling, supporting a cohesive immune signaling and vesicle-trafficking function.","confidence":"Medium","size":18,"edges":9,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071260","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0043366","count":3},{"id":"GO:1905289","count":3}]},{"hash":"105773741336817853","title":"Serine-driven sphingolipid biosynthesis","description":"This cluster centers on serine metabolism feeding into sphingolipid biosynthesis: serine transport, positive regulation of serine palmitoyltransferase activity, and associated sphingolipid and phosphatidylserine metabolic processes, with myelination as a downstream theme. Translation-related terms appear but are likely ancillary noise; the dominant pattern ties serine availability to lipid production important for myelin. ","confidence":"Medium","size":18,"edges":25,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:0031365","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0043686","count":1},{"id":"GO:0006658","count":1}]},{"hash":"1050634196942639346","title":"Protein folding and secretion stress response","description":"The cluster is dominated by terms tied to protein quality control and stress signaling\u2014unfolded protein response, protein isomerization, and regulation of secretion, along with cellular responses to UV-A and heat\u2014pointing to a cohesive theme of managing protein folding and secretion under stress. Some terms (DNA replication, myelin maintenance) seem outliers, suggesting multi-function proteins or annotation noise.","confidence":"Medium","size":18,"edges":9,"triangles":2,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0006675","count":4},{"id":"GO:0032286","count":4}]},{"hash":"951802421191822576","title":"ER-Golgi trafficking proteins","description":"The top GO terms cluster around ER-to-Golgi transport, ER retention, and Golgi ribbon formation, indicating the proteins mainly participate in the secretory pathway and Golgi organization, with other terms (developmental/behavior) likely reflecting pleiotropic roles. Confidence: High.","confidence":"","size":18,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048042","count":1},{"id":"GO:0070863","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0032525","count":1},{"id":"GO:0090161","count":1}]},{"hash":"513653209904976133","title":"Protein acetylation","description":"Most of the top GO terms point to acetylation and related modifications (peptidyl-lysine N6-acetylation, N-terminal peptidyl-methionine acetylation, N-terminal protein acetylation/propionylation, spermidine acetylation), suggesting a coherent theme around protein acetylation processes. A few terms like angiogenesis or chromatin-related processes are present but far less core to the cluster\u2019s signal. Confidence: High","confidence":"","size":18,"edges":8,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":4},{"id":"GO:0017196","count":4},{"id":"GO:0045150","count":4},{"id":"GO:0019491","count":4},{"id":"GO:0006526","count":4}]},{"hash":"668635962524140030","title":"Cell-cycle and cytoskeletal regulation","description":"The cluster is driven by GO terms for cell cycle, mitotic spindle orientation checkpoint signaling, and septin ring organization, implying a shared function in cell division and cytoskeleton dynamics. Additional terms such as ubiquitination, bone/liver development, vitamin D response, heat response, and nutrient stress may reflect secondary or context-dependent roles, or annotations from multi-functional proteins; overall a coherent scaffold around cell-cycle control and cytoskeletal organization.","confidence":"Medium","size":18,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0031578","count":2},{"id":"GO:0032186","count":2},{"id":"GO:0046849","count":2},{"id":"GO:0033280","count":2}]},{"hash":"422702767518671537","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":12,"triangles":0,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0035948","count":4},{"id":"GO:0071456","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0001731","count":4}]},{"hash":"865160361001686257","title":"Autophagy\u2013lysosome targeting and degradation","description":"The top GO terms are centered on lysosomal/vacuolar targeting and autophagy-related processes (secretion of lysosomal enzymes, protein targeting to lysosome, phagophore assembly site localization, cytoplasm-to-vacuole targeting via the Cvt pathway, and autophagy of peroxisomes), with supporting ubiquitin-related regulation. Together these indicate a coherent cluster of proteins involved in autophagic flux and lysosome/vacuole degradation pathways. Some terms appear peripheral, but the dominant signal supports an autophagy\u2013lysosome function. ","confidence":"High","size":18,"edges":18,"triangles":1,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0033299","count":1},{"id":"GO:0006622","count":1},{"id":"GO:0034497","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0030242","count":1}]},{"hash":"1471701723681992554","title":"Immune Activation and Signaling","description":"Based on GO terms, the cluster centers on macrophage activation, LPS-mediated signaling, and Th17 cell differentiation, with supporting roles for ubiquitin-proteasome turnover and actin cytoskeleton remodeling\u2014overall pointing to immune response and signaling pathways. Some terms like RNA transport are less aligned but do not outweigh the strongest immune-related themes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006409","count":4},{"id":"GO:0006404","count":4},{"id":"GO:0031663","count":3},{"id":"GO:0030011","count":3},{"id":"GO:2000321","count":3}]},{"hash":"409097843987889589","title":"Cell signaling and apoptotic regulation","description":"The terms show a pattern around regulation and signaling pathways (Wnt, Hippo, Rho) together with apoptotic processes, suggesting a theme of signaling control influencing cell fate. Some terms like hippocampus development and pseudohyphal growth appear as broader or cross-species links, but the core cluster centers on signaling regulation and apoptosis rather than a single specific pathway. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030517","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0007266","count":2}]},{"hash":"1696978683102778733","title":"Unknown","description":"The terms point to diverse processes: germ cell development; establishment of protein localization to chromatin; fatty acid biosynthesis (including long-chain and methyl-branched variants); ribosome biogenesis and nuclear export; tRNA modification; cell fusion; ppGpp biosynthesis; and septum assembly. There isn\u2019t a single cohesive function tying these annotations together, suggesting either multi-functionality or annotation noise, so the cluster is labeled Unknown with no clear representative theme.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007281","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0042759","count":1},{"id":"GO:1902321","count":1},{"id":"GO:0042274","count":1}]},{"hash":"785923645546667049","title":"Embryonic cell-cycle progression and apoptosis","description":"The cluster is driven by mitotic processes (G2/M transition, chromosome segregation, exit from mitosis) and SCF-dependent proteasomal degradation, with notable translation and in utero embryonic development terms. Apoptotic signaling and neuronal projection development further suggest a developmental program coordinating cell division, protein turnover, and differentiation during early development. The dominant theme centers on cell-cycle control during embryogenesis, with supporting processes like translation and neural development.","confidence":"Medium","size":17,"edges":20,"triangles":11,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0001701","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0009229","count":3},{"id":"GO:0009228","count":3}]},{"hash":"2058765190120894092","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":40,"triangles":20,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0006417","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0000447","count":1}]},{"hash":"1661112376412510901","title":"Actin Cytoskeleton Remodeling and Signaling","description":"This cluster centers on actin-related processes (actin crosslink formation, terminal web assembly) and signaling pathways (GPCR-linked signaling, calcineurin-NFAT), with additional development and reproductive terms (axonogenesis, heart development, ascospore formation, karyogamy). The combination suggests proteins that link signaling to cytoskeletal dynamics across diverse contexts, including fungal mating and general development. Confidence: Medium.","confidence":"","size":17,"edges":27,"triangles":14,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":7},{"id":"GO:1902896","count":6},{"id":"GO:0051764","count":6},{"id":"GO:0030437","count":6},{"id":"GO:0000742","count":6}]},{"hash":"1009518640696490179","title":"Developmental signaling and cell cycle control","description":"The GO terms are dominated by nervous system development, Notch signaling, and cell cycle-related processes (cell cycle, mitotic spindle orientation), with supporting terms for transcription/translation and epithelial polarity. This suggests a cluster centered on developmental signaling pathways coordinating cell proliferation and tissue organization, rather than a single enzyme or structural function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0007219","count":3},{"id":"GO:0060766","count":3}]},{"hash":"1627950060001473450","title":"Nuclear DNA Replication and RNA Processing","description":"Most of the top GO terms are centered on DNA replication and genome maintenance (DNA replication, primer synthesis, DNA topology changes, SOS response, etc.), with additional signals from RNA processing (splicing, nonsense-mediated decay) and ribosome biogenesis (preribosome assembly). This points to a nuclear functional module focused on DNA replication/maintenance with connected RNA metabolism activities.","confidence":"Medium","size":17,"edges":24,"triangles":0,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006269","count":5},{"id":"GO:0006265","count":5},{"id":"GO:0019079","count":5},{"id":"GO:0009432","count":5}]},{"hash":"26183299586139014","title":"Central carbon metabolism","description":"The cluster\u2019s top GO terms cluster around core energy- and small-molecule metabolism: glycolysis, the TCA cycle, thiamine biosynthesis, and fatty acid beta-oxidation, with additional biosynthetic processes like prostaglandin and ascaroside production. Together they suggest enzymes and proteins tied to central carbon metabolism and energy production, rather than a single, narrow pathway. A few terms (e.g., DNA-templated transcription, corticosterone response) may reflect broader housekeeping roles, but the dominant signal is metabolic. ","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0006693","count":2}]},{"hash":"2119273175602343891","title":"Epigenetic Regulation of Development and Reproduction","description":"Top terms include rDNA heterochromatin formation, histone H3-K4 methylation regulation, and negative regulation of transcription by RNA polymerase II, pointing to chromatin remodeling and epigenetic control. The presence of brain development, spermatogenesis, male gonad development and estradiol response suggests these regulators participate in developmental and reproductive pathways. The combination of epigenetic marks and developmental/hormonal terms implies a cluster of proteins that coordinate gene expression programs during development and reproduction. The remaining terms (cell migration, keratinocyte differentiation, single fertilization) align with broader developmental contexts, supporting a shared regulatory role rather than a single pathway.","confidence":"Medium","size":17,"edges":44,"triangles":60,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":7},{"id":"GO:0007420","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0051572","count":5},{"id":"GO:0008584","count":5}]},{"hash":"307527567079629566","title":"RNA metabolism and nucleotide biosynthesis","description":"The cluster is driven by GO terms tied to RNA-related processes (translation, tRNA wobble editing) and nucleotide metabolism (uridine biosynthesis, UMP salvage, cytidine/deoxycytidine pathways), with riboflavin biosynthesis suggesting broader metabolic activity. Some terms like lung development/antibiotic response appear less connected, but the core signal is RNA metabolism and nucleotide biosynthesis.","confidence":"Medium","size":17,"edges":134,"triangles":651,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0019858","count":1},{"id":"GO:0046109","count":1},{"id":"GO:0044206","count":1}]},{"hash":"824873289075279994","title":"Heat-responsive nuclear transport","description":"Several top GO terms point to nuclear transport processes (nuclear pore organization; NLS-bearing protein import into nucleus) and heat-induced mRNA export, suggesting a module centered on nucleo-cytoplasmic trafficking during heat stress. Some terms related to vesicle trafficking and desumoylation may reflect related stress responses, while ear morphogenesis and lipid metabolism terms likely represent unrelated noise.","confidence":"Medium","size":17,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0060188","count":1},{"id":"GO:0006999","count":1},{"id":"GO:0031990","count":1},{"id":"GO:0072417","count":1}]},{"hash":"2215389690563376217","title":"Growth Factor Receptor Signaling and Actin Remodeling","description":"The Top Terms center on IGF/insulin and growth hormone receptor signaling, small GTPase\u2013driven signaling, and actin cytoskeleton organization, indicating a module that links receptor-mediated growth signals with cytoskeletal remodeling. Additional terms related to vascular and immune regulation may reflect pleiotropic roles of these signaling components, but the core theme is growth factor receptor signaling with cytoskeletal dynamics.","confidence":"Medium","size":17,"edges":16,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0048009","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0060396","count":2}]},{"hash":"862864903134275067","title":"Endomembrane trafficking and vesicle fusion","description":"Most of the top GO terms describe movements and fusion of vesicles within the endomembrane system (endosome to Golgi, recycling endosome to Golgi, plasma membrane to endosome, regulation of vesicle fusion). While there are a few terms related to ER stress-induced apoptosis or cell-cycle signaling, the dominant theme is vesicle trafficking and membrane fusion.","confidence":"Medium","size":17,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0031578","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0044829","count":2}]},{"hash":"403917062123568558","title":"Chromatin modification and transcription regulation","description":"This cluster centers on histone modification and transcription control terms (H3-K4 demethylation/trimethylation, histone deacetylase activity, and negative regulation of transcription by RNA Pol II), suggesting a theme of chromatin remodeling and gene expression regulation. Additional terms touch on related nuclear processes (DNA/RNA repair) and cell-cycle-associated events (spindle assembly), which may reflect broader coordination of nuclear functions within the cluster.","confidence":"Medium","size":17,"edges":15,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:1901726","count":2},{"id":"GO:0034720","count":2},{"id":"GO:2000864","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0000122","count":2}]},{"hash":"78881411836731905","title":"Plant transcriptional regulation and development","description":"This cluster centers on DNA-templated transcription and growth-related processes, including cytokinin signaling, multicellular organism development, and cell proliferation, along with histone modifications and ribosome biogenesis. The combination suggests proteins involved in chromatin-mediated transcriptional control that coordinates plant development and growth. Some GO terms are labeled obsolete, but the overall theme aligns with plant gene expression regulation during development.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035264","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0008283","count":2}]},{"hash":"1197254076555278884","title":"Unknown","description":"The GO terms span stress responses (cobalt, xenobiotic, respiratory burst), metabolism (glycolysis, pentose phosphate pathway, carbohydrate phosphorylation), DNA damage signaling, mitophagy regulation, and development (brain and intestinal epithelium), with no clear common function linking most proteins.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071279","count":1},{"id":"GO:0045730","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0009410","count":1},{"id":"GO:0006110","count":1}]},{"hash":"176887662389680772","title":"Ubiquitin-Proteasome Regulation and Immune Signaling","description":"The top GO terms cluster around ubiquitination/deubiquitination and proteasome-related processes (protein deubiquitination; SCF-dependent proteasomal ubiquitin-dependent protein catabolic process; proteasome core complex assembly) and immune signaling pathways (T cell receptor, Fc-epsilon receptor, C-type lectin receptor). This points to a functional group coordinating protein turnover with immune signaling, with additional links to broader defense responses (viral process, plant hypersensitive response) that may reflect shared regulatory mechanisms.","confidence":"Medium","size":16,"edges":117,"triangles":519,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":8},{"id":"GO:0010950","count":7},{"id":"GO:0060071","count":7},{"id":"GO:0038095","count":7},{"id":"GO:0050852","count":7}]},{"hash":"541223773296594235","title":"Hepatic Mitochondrial Metabolic Regulation and Insulin Signaling","description":"The terms cluster around mitochondrial functions (membrane permeability/potential regulation and transmembrane transport of citrate, NAD, and CoA) and metabolic signaling related to insulin and glucose, with a liver-related context (liver regeneration and insulin response), suggesting a cohesive theme of hepatic mitochondrial metabolism and insulin signaling.","confidence":"High","size":16,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":8},{"id":"GO:0051881","count":7},{"id":"GO:0070542","count":7},{"id":"GO:0035349","count":7},{"id":"GO:0032869","count":7}]},{"hash":"1466224107390252699","title":"Proteostasis and Heat-Stress Response","description":"The cluster is dominated by terms related to protein quality control and stress handling, including misfolded protein transport, ubiquitin-dependent ERAD pathways, ER-associated degradation, and cellular/heat stress responses. Additional terms point to membrane/mitochondrial targeting of proteins, consistent with proteostasis under stress. A few outliers (DNA replication, developmental signaling) are present but do not define the core theme. This suggests a cohesive label around proteostasis and heat-related regulation.","confidence":"Medium","size":16,"edges":98,"triangles":308,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006469","count":4},{"id":"GO:1900035","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0071374","count":3}]},{"hash":"2285814918639624277","title":"Protein complex\u2013mediated signaling","description":"This cluster's top GO terms center on protein heterooligomerization and multiple signaling pathways (Rac signaling, T cell receptor signaling, Roundabout signaling) with membrane transport, suggesting assembly of signaling complexes at the membrane that regulate growth, division, and cell behavior.","confidence":"Medium","size":16,"edges":46,"triangles":49,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":4},{"id":"GO:0016601","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0035385","count":4},{"id":"GO:0071806","count":4}]},{"hash":"251046387545501075","title":"Vesicle trafficking and transmembrane transport","description":"The top GO terms point to broad transmembrane transport activities across diverse substrates (sialic acid, phosphate, sodium, galactose, nitrite, vitamins, and related compounds) and a specific process of neurotransmitter loading into synaptic vesicles, along with a regulatory link to GTPase activity. Together, these suggest a cluster of proteins engaged in membrane transport and vesicle trafficking/ loading functions.","confidence":"Medium","size":16,"edges":14,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0015739","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0042891","count":2}]},{"hash":"2233725829214239303","title":"Lipid metabolism and energy pathways in neural/eye tissues","description":"Most frequent GO terms point to lipid and energy metabolism (response to fatty acid, triglyceride metabolic process, aerobic respiration, sphingolipid metabolism), with additional neural/eye context (retina vasculature development, CNS myelin maintenance, white fat differentiation). This suggests a cluster centered on lipid-driven metabolic processes that support neural and ocular tissue function.","confidence":"Medium","size":16,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0010193","count":2},{"id":"GO:0006641","count":2}]},{"hash":"31098640614682018","title":"Wnt-Hippo Signaling in Development","description":"Based on enriched terms, the cluster centers on canonical Wnt signaling activation and Hippo pathway signaling, both key drivers of cell growth, proliferation, and organ size control. Additional terms cover keratinocyte differentiation and dendrite morphogenesis, implying broader developmental and differentiation roles, along with apoptosis and cell-cycle processes as downstream outcomes. Together, these proteins likely function as a unit in signaling networks that govern tissue development and cell fate decisions.","confidence":"High","size":16,"edges":99,"triangles":361,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":10},{"id":"GO:0060044","count":9},{"id":"GO:0035329","count":9},{"id":"GO:0030216","count":9},{"id":"GO:0006915","count":9}]},{"hash":"2097149017130568365","title":"Neuronal dendritic spine morphogenesis and Rac signaling","description":"This cluster centers on neuronal development and synaptic maturation, highlighted by ephrin receptor signaling, Rac-mediated actin remodeling (ruffle assembly), and regulation of dendritic spine morphogenesis/development, along with hippocampus development and related protein trafficking from Golgi to the plasma membrane. These terms together point to neuronal growth, spine formation, and synaptic connectivity processes.","confidence":"High","size":16,"edges":19,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0097178","count":4},{"id":"GO:0048013","count":3},{"id":"GO:0030307","count":3},{"id":"GO:0043001","count":3},{"id":"GO:0016601","count":3}]},{"hash":"656556767675499877","title":"Macrophage Activation and Inflammatory Signaling","description":"The cluster is enriched for innate immune and cytokine-related terms, including positive regulation of IL-1\u03b2 production, macrophage activation, lipopolysaccharide signaling, and Th17 differentiation, suggesting a core function in inflammation and immune response. Additional terms related to actin dynamics and ubiquitin-proteasome\u2013mediated protein turnover support cellular activation and signaling in immune cells. Some development-related terms appear incidental rather than indicative of a shared function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050718","count":3},{"id":"GO:0061303","count":3},{"id":"GO:0031663","count":2},{"id":"GO:0030011","count":2},{"id":"GO:2000321","count":2}]},{"hash":"1150150483598289247","title":"Diverse metabolite biosynthesis and fatty acid oxidation","description":"Top GO terms indicate biosynthesis of multiple specialized metabolites (ectoine, verruculogen, polyhydroxybutyrate) and fatty acid oxidation/metabolism, along with detoxification and DNA repair activities. The proteins appear functionally diverse rather than part of a single pathway, yet the recurring theme is biosynthesis of small molecules and lipid-related metabolism. This justifies a label capturing the broad biosynthetic and fatty acid metabolism theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019491","count":2},{"id":"GO:0042400","count":2},{"id":"GO:1902181","count":2},{"id":"GO:0001561","count":2}]},{"hash":"1324599255318751602","title":"Unknown","description":"The top GO terms span very different biology\u2014from reproductive development (uterus development, Sertoli cell proliferation, luteinizing hormone stimulus) to heart morphogenesis, neural myelination, innate immunity (TLR signaling, diacyl lipoproteptide detection), and metabolism signaling (CAMKK-AMPK), plus general processes like regulation of kinase activity and intracellular transport. With no clear unifying function and no edges in the cluster, there isn\u2019t a cohesive theme to label, so the appropriate label is Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0034123","count":2},{"id":"GO:0042496","count":2},{"id":"GO:0071373","count":2}]},{"hash":"2171532610589331204","title":"NF-kappaB-Linked Immune Signaling and Endosomal Trafficking","description":"The cluster centers on NF-kappaB regulation (both positive and negative), T cell receptor signaling, and transport from the plasma membrane to endosomes, suggesting a cohesive module where receptor activation is coupled to NF-kappaB signaling and endocytic trafficking. Additional terms like ROBO signaling and nervous system development hint at broader roles in migration and development, with polarity maintenance and ubiquitin-proteasome\u2013mediated turnover supporting signaling control. Overall, it most plausibly represents immune signaling intertwined with receptor trafficking and regulation.","confidence":"Medium","size":15,"edges":20,"triangles":7,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0048227","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0030335","count":5},{"id":"GO:0045740","count":5}]},{"hash":"173660132337352538","title":"Nucleotide salvage pathways","description":"Dominant GO terms relate to salvage and interconversion of nucleotides and nucleobases (guanosine, inosine, uridine) and nucleotide-derived metabolites, indicating a coherent theme of nucleotide salvage/metabolism across purine and pyrimidine pathways. A few annotations reference ER-associated transport, which may reflect broader annotations but do not override the primary salvage signal.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006206","count":1},{"id":"GO:0006179","count":1},{"id":"GO:0019358","count":1}]},{"hash":"1468934988432244428","title":"Nuclear gene expression and chromatin assembly","description":"The cluster\u2019s top GO terms are dominated by nuclear processes: DNA-templated transcription, CENP-A chromatin assembly, mRNA splicing, and ubiquitin-proteasome\u2013dependent protein turnover, all central to gene expression and chromatin maintenance. While there are peripheral terms related to transport, development, and immunity, the strongest signal points to nuclear regulation of transcription and chromatin dynamics.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":3},{"id":"GO:0031954","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0000398","count":2}]},{"hash":"563514411398539896","title":"RNA Pol II transcription initiation","description":"This cluster is mainly characterized by transcription by RNA polymerase II and RNA Pol II preinitiation complex assembly, pointing to core transcription initiation; additional terms on chromatin modification and DNA repair are present but less representative.","confidence":"High","size":15,"edges":30,"triangles":8,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0051106","count":1},{"id":"GO:0045191","count":1},{"id":"GO:0000012","count":1},{"id":"GO:0016578","count":1}]},{"hash":"506415232377002631","title":"Developmental morphogenesis and cytoskeletal dynamics","description":"The terms cluster around tissue development and morphogenesis across neural, vascular, and germline contexts, plus microtubule-based movement, indicating cytoskeletal dynamics during development; occasional signaling terms (insulin receptor signaling, IL-7 response) support regulatory processes during these morphogenetic events.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":13,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0021510","count":4},{"id":"GO:0031641","count":3},{"id":"GO:0007018","count":3},{"id":"GO:0098761","count":2},{"id":"GO:0035904","count":2}]},{"hash":"625790576381128598","title":"Growth signaling and proliferation control","description":"This cluster's GO terms cluster around pathways that regulate cell growth, division, and fate: Wnt signaling, Hippo signaling, and the ERK cascade, plus DNA replication and apoptosis. The combination points to a core theme of growth signaling and proliferation control, with additional stress/immune signaling (PMA response, GM-CSF response) and basic cellular functions (potassium transport) providing context. Overall, the dominant pattern is signaling networks that govern cell growth and division, with apoptosis acting as a check, making the label appropriate.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0006813","count":9},{"id":"GO:0060044","count":9},{"id":"GO:0090263","count":9},{"id":"GO:0006915","count":9}]},{"hash":"100207676981913472","title":"Ubiquitin-Proteasome-Mediated Proteolysis","description":"The cluster is enriched for ubiquitination and proteasome-dependent protein degradation terms (polyubiquitination, ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal ubiquitin-dependent degradation), indicating a core function in regulated protein turnover. Additional terms reflect stress and DNA damage response connections, but ubiquitin-mediated degradation is the dominant theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":9},{"id":"GO:0071276","count":8},{"id":"GO:0042787","count":7},{"id":"GO:0031571","count":7},{"id":"GO:0031146","count":7}]},{"hash":"293571704470524816","title":"DNA Damage Response and Signaling","description":"This cluster shows GO terms centered on DNA repair (base-excision repair, gamma radiation response) and genome maintenance (DNA biosynthetic process, replication- or damage-related regulation). It also includes multiple signaling pathways (regulation of phosphorylation, GPCR signaling, interleukin-12 signaling) and broader developmental signals (brain development, meiosis activation), suggesting a set of proteins involved in coordinating DNA damage responses with diverse signaling networks. Confidence: Medium","confidence":"","size":15,"edges":15,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001932","count":3},{"id":"GO:0001302","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0071897","count":3},{"id":"GO:0010332","count":3}]},{"hash":"2179565356908224731","title":"Unknown","description":"Top GO terms are diverse, spanning cellular responses to growth factors and cytokines (EGF, GM-CSF), multiple developmental lineages (pancreatic B cells, B cells, trophoblast giant cells), cell cycle, and host\u2013pathogen interactions (symbiont entry, viral entry, DNA integration). This broad mix lacks a single cohesive function or pathway defining the cluster, so a concise, accurate label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0001782","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0060707","count":2}]},{"hash":"67262310104095626","title":"Translational initiation and TORC1 signaling","description":"The top GO terms are dominated by translation initiation and its regulation (formation of preinitiation complex, translation reinitiation, regulation of translational initiation) with TORC1 signaling also highlighted, indicating the cluster centers on control of protein synthesis via initiation pathways. Peripheral terms like neural tube closure or defense responses seem less representative but do not override the main theme. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0038202","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001843","count":3},{"id":"GO:1904668","count":3}]},{"hash":"229901782745353807","title":"Protein degradation and cell cycle regulation","description":"This cluster gathers terms tied to protein turnover (polyubiquitination, ERAD, regulation of protein catabolic processes) and growth signaling (TORC1), plus events in cell division (cell division, female meiotic nuclear division) and broader protein assembly/gene expression processes. The combination suggests a theme of coordinating protein quality control with cell cycle progression and growth signals, rather than a single narrowly defined function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000209","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2001241","count":2}]},{"hash":"1855375102874745420","title":"Nucleocytoplasmic transport and translation initiation regulation","description":"The top GO terms point to nuclear pore complex assembly and mitotic nuclear membrane reassembly, indicating nuclear envelope and transport dynamics. Additional terms about GTPase activity regulation (often linked to Ran-mediated transport) and regulation of translational initiation suggest a concurrent theme of coordinating nucleocytoplasmic transport with initiation of translation. Some terms are obsolete or peripheral (hair follicle maturation), but the core cluster seems to center on transport-related processes and translation control during the cell cycle.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0007084","count":2},{"id":"GO:0048820","count":1},{"id":"GO:0001731","count":1}]},{"hash":"432631883477446840","title":"Amino acid and fatty acid catabolism with quinone biosynthesis","description":"Proteins in this cluster are enriched for catabolic processes of several amino acids (L-kynurenine, L-alanine, L-valine, phenylacetate), fatty acid beta-oxidation, and biosynthesis of quinones (menaquinone, phylloquinone). This combination suggests a metabolic/energy-generation theme, rather than a single signaling pathway, even though Notch signaling appears among the terms for a subset. ","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":5},{"id":"GO:0007219","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0006107","count":4},{"id":"GO:0051591","count":4}]},{"hash":"96596977826648979","title":"Hepatic mitochondrial metabolism and insulin response","description":"This cluster centers on mitochondrial function in liver, with transport of key cofactors (CoA, NAD, citrate), regulation of mitochondrial membrane potential and permeability, and responses to insulin and fatty acids, all pointing to coordinated hepatic energy metabolism and insulin-related signaling.","confidence":"High","size":15,"edges":27,"triangles":24,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":10},{"id":"GO:0051881","count":9},{"id":"GO:0070542","count":9},{"id":"GO:0035349","count":9},{"id":"GO:0035352","count":9}]},{"hash":"1979939123070512931","title":"Neural development and neuron survival","description":"This cluster is dominated by GO terms tied to neural differentiation and neuronal survival, including substantia nigra development, forebrain radial glial differentiation, bipolar cell growth, and negative regulation of neuron apoptotic processes. Additional terms about protein localization and cellular processes like lipophagy may reflect general cellular maintenance in neural cells, but the core theme centers on neural development and neuron protection.","confidence":"High","size":14,"edges":37,"triangles":17,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902570","count":7},{"id":"GO:0010738","count":7},{"id":"GO:0021762","count":7},{"id":"GO:0051291","count":6},{"id":"GO:0060047","count":6}]},{"hash":"800161791590740884","title":"Cajal body\u2013associated telomere maintenance and cell cycle","description":"This cluster is driven by GO terms around telomere maintenance via telomerase, telomerase RNA localization to Cajal bodies, and protein localization to Cajal bodies, along with cell cycle and cell division terms. These points together suggest a nuclear, RNA-processing/telomere maintenance theme centered on Cajal bodies and telomerase activity, with some peripheral housekeeping processes.","confidence":"Medium","size":14,"edges":35,"triangles":44,"max_degree":7,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0046686","count":4},{"id":"GO:1904871","count":3}]},{"hash":"99723673464131240","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by terms tied to ribosome production and function (ribosome biogenesis, small/large subunit biogenesis, rRNA maturation, cytoplasmic translation, translation, and translational termination, and tRNA modification, plus export of large subunit from nucleus). This strongly suggests a module of ribosome assembly and protein synthesis. A single outlier term (conjugation with cellular fusion) is likely noise and does not change the main theme.","confidence":"High","size":14,"edges":36,"triangles":64,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000747","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0002181","count":4}]},{"hash":"2126199989432057696","title":"Osteoblast differentiation and bone remodeling","description":"The top terms strongly point to bone biology, with osteoblast fate commitment and bone development, plus podosome assembly related to osteoclast activity and bone remodeling. Supporting terms like positive regulation of GTPase activity and protein ubiquitination suggest signaling and cytoskeletal remodeling processes that coordinate bone formation and resorption. Overall, the cluster seems centered on osteogenesis and bone remodeling dynamics.","confidence":"High","size":14,"edges":17,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0002051","count":2}]},{"hash":"1091880014267164270","title":"Filopodium formation and Rho GTPase signaling","description":"The cluster is dominated by GO terms tied to filopodium assembly and its regulation, plus positive adhesion-dependent cell spreading, all pointing to actin-driven cytoskeletal remodeling. The shared involvement of small GTPase-mediated signal transduction supports Rho-family control of these protrusive processes, making a cohesive picture of filopodial dynamics and adhesion signaling.","confidence":"High","size":14,"edges":12,"triangles":0,"max_degree":9,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:1900026","count":7},{"id":"GO:0046847","count":7},{"id":"GO:0051489","count":7},{"id":"GO:0051932","count":7},{"id":"GO:0045792","count":7}]},{"hash":"398123435692576188","title":"Unknown","description":"The GO terms are scattered across antibiotic biosynthesis/response, various translation and RNA processing processes, plus unrelated terms like hematopoietic differentiation and an obsolete oxidation-reduction term. There is no cohesive, representative function linking all proteins, so a specific label isn\u2019t justifiable.","confidence":"","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0017000","count":3},{"id":"GO:1990145","count":2}]},{"hash":"606187268585239138","title":"mRNA processing and translation regulation","description":"These proteins predominantly participate in post-transcriptional RNA processing and control of protein synthesis. Enrichment for spliceosome-mediated mRNA splicing (including alternative splicing and splice site recognition), mRNA modification and polyadenylation, mRNA stabilization, and regulation of translation initiation/reinitiation indicates a cohesive role in processing RNA transcripts and regulating their translation. The single migration term appears peripheral and does not define the cluster's core function.","confidence":"High","size":14,"edges":42,"triangles":53,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0006378","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0000380","count":2}]},{"hash":"1464558704341074762","title":"DNA replication and mitosis machinery","description":"This cluster centers on processes essential for cell division: DNA replication and nuclear DNA synthesis, plus centrosome cycle and microtubule-associated localization, indicating a core mitotic machinery theme. While there are ancillary terms related to growth signaling (TORC1), apoptosis, and development, the strongest signal is the coordination of DNA replication and mitotic/spindle functions.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0010571","count":9},{"id":"GO:0035372","count":9},{"id":"GO:0051092","count":9},{"id":"GO:0006915","count":9}]},{"hash":"403740062972091685","title":"Cysteine and sulfur amino acid metabolism","description":"The GO terms cluster around cysteine biosynthesis (via cystathionine), transsulfuration, homocysteine catabolism, and related sulfur-containing amino acid biosynthetic processes, with additional links to 2-oxobutyrate/pyruvate biosynthesis. Despite some obsolete annotations, the common thread is sulfur amino acid metabolism and associated pathways.","confidence":"High","size":14,"edges":46,"triangles":78,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0019343","count":3},{"id":"GO:0006535","count":3},{"id":"GO:0046360","count":3},{"id":"GO:0009310","count":3},{"id":"GO:0019346","count":3}]},{"hash":"1997773279573027139","title":"Neural development and gene expression regulation","description":"This cluster shows strong signals for neural development terms (forebrain development, neural tube closure) along with gene expression control (DNA-templated transcription, RNA (guanine-N7)-methylation, mRNA transport), suggesting a group enriched for brain development and transcription/RNA processing functions. Other terms like mitotic cell cycle and ER-stress\u2013related apoptosis are present but less central. Confidence: Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031954","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0051028","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0036265","count":2}]},{"hash":"175669575400289417","title":"Unknown","description":"The top GO terms span metal detox, lipid/peroxisomal transport, sperm capacitation, membrane potential, secretion systems, antigen transport, glutathione transport, DNA repair, antibiotic response, and molybdate transport. This broad and diverse mix lacks a single cohesive function or pathway linking the proteins, so there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":14,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0098849","count":3},{"id":"GO:0015910","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0060081","count":2},{"id":"GO:0030253","count":2}]},{"hash":"55882496165090199","title":"Unknown","description":"The top GO terms include DNA replication, isotype switching, hematopoietic differentiation and proliferation, plus various trafficking and apoptotic processes. There isn\u2019t a single coherent biological function that unites these terms, and with no edges connecting members, a precise, representative label cannot be confidently assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0045190","count":2},{"id":"GO:0006469","count":2},{"id":"GO:1901532","count":1},{"id":"GO:1902035","count":1}]},{"hash":"159430313842394116","title":"Ubiquitin-Dependent Proteolysis and Stress Signaling","description":"The cluster is dominated by GO terms for ubiquitin-mediated protein degradation (ubiquitin-dependent proteolysis, ERAD, autoubiquitination), suggesting a proteostasis core. Additional terms indicate stress responses and signaling that affect proliferation and transcription, such as cellular response to cadmium, JNK cascade regulation, TNF signaling, and DNA-templated transcription. The combination points to proteins coordinating ubiquitin-driven degradation with stress-responsive signaling and cell-cycle control.","confidence":"Medium","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0030433","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0006351","count":4}]},{"hash":"2235076907639178418","title":"Cellular stress response and quality control","description":"This cluster shows enrichment in processes related to cellular stress management and homeostasis, including autophagy (aggrephagy), ubiquitination, and DNA repair, as well as regulation of signaling (negative regulation of TLR3 and TNF pathways), epigenetic gene regulation, cell cycle/mitotic functions, and vesicle formation. The proteins appear to participate in broad quality-control and stress-response networks rather than a single, cohesive pathway, justifying a label centered on stress response and maintenance of cellular integrity.","confidence":"Medium","size":13,"edges":33,"triangles":56,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":8},{"id":"GO:0030474","count":7},{"id":"GO:1903265","count":7},{"id":"GO:0010216","count":7},{"id":"GO:0051865","count":7}]},{"hash":"536408966163359574","title":"Ubiquitin-Autophagy Quality Control Pathways","description":"The top GO terms cluster around ubiquitin-related modification and turnover (sumoylation, ubiquitin-dependent ERAD, deubiquitination, C-terminal lipidation) together with multiple autophagy processes (Cvt pathway targeting, nucleophagy, mitophagy, aggresome assembly, autophagosome maturation). This points to a cohesive role in cellular protein quality control and organelle turnover via ubiquitin signaling and autophagy. ","confidence":"High","size":13,"edges":55,"triangles":128,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0016579","count":4},{"id":"GO:0006501","count":3},{"id":"GO:0032258","count":3}]},{"hash":"1707753004017085285","title":"ER stress response and protein folding regulation","description":"The cluster is enriched for GO terms related to protein folding and ER-associated stress responses (unfolded protein response, cellular response to unfolded protein, SRP-dependent cotranslational targeting to membrane). This suggests a primary theme of proteostasis under stress and regulation of stress-induced signaling, including apoptosis. Some terms (DNA replication, karyogamy) are less directly aligned, but the dominant signal points to ER/protein folding and stress regulation.","confidence":"Medium","size":13,"edges":31,"triangles":35,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:1900035","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0000742","count":4},{"id":"GO:0000902","count":4}]},{"hash":"841639033790167899","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by translation and ribosome-related processes: translation itself, ribosome biogenesis, and maturation of rRNA species, plus snoRNP assembly, suggesting proteins involved in ribosome assembly and protein synthesis. A couple of outliers (single fertilization, DNA replication) are less representative and likely incidental. Confidence: High","confidence":"","size":13,"edges":71,"triangles":218,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0000466","count":3}]},{"hash":"489668288185069760","title":"Immune signaling and cytoskeletal remodeling","description":"The cluster features GO terms tied to innate/adaptive immune signaling (TLR3 signaling, NK cell regulation, IL-2 production, ERK/MAPK cascade) alongside cytoskeletal dynamics (Rho signaling, microspike assembly) and trafficking processes (transcytosis, ECM disassembly). This combination suggests proteins that coordinate signaling with cytoskeletal remodeling and cell movement, making this label representative. ","confidence":"Medium","size":13,"edges":58,"triangles":152,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0034141","count":4},{"id":"GO:0032226","count":4},{"id":"GO:0045056","count":3},{"id":"GO:0045953","count":3},{"id":"GO:0030035","count":3}]},{"hash":"33575746502360404","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006189","count":2},{"id":"GO:0006730","count":2},{"id":"GO:0018119","count":2}]},{"hash":"1275315488192038247","title":"Ribosome biogenesis and translational fidelity","description":"The cluster is dominated by translation- and ribosome-related terms: translation, ribosome biogenesis, mitochondrial translation/termination, and regulation/maintenance of translational fidelity. While there are a few outliers (DNA repair, antibiotic response, cell cycle regulation), the core signal points to protein synthesis machinery and translation quality control.","confidence":"High","size":13,"edges":13,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0015967","count":2},{"id":"GO:0070126","count":1}]},{"hash":"2256048526961708442","title":"Amino acid biosynthesis and central carbon metabolism","description":"The top GO terms point to multiple amino acid biosynthesis pathways (threonine, leucine, isoleucine), plus central carbon metabolism steps (pyruvate and 2-oxoglutarate metabolism, TCA cycle) and glutathione metabolism, indicating a cohesive metabolic module focused on amino acid production and energy/redox metabolism.","confidence":"High","size":13,"edges":51,"triangles":100,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0019878","count":4},{"id":"GO:0009088","count":3},{"id":"GO:0009097","count":3},{"id":"GO:0042866","count":3}]},{"hash":"1394502023037129484","title":"RNA processing and translation initiation control","description":"These terms cluster around mRNA processing (splicing, modification, polyadenylation) and translation initiation/reinitiation, indicating a cohesive module coordinating RNA maturation with translation.","confidence":"High","size":13,"edges":35,"triangles":22,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0016556","count":4},{"id":"GO:0000380","count":4},{"id":"GO:0006446","count":4},{"id":"GO:1900363","count":4},{"id":"GO:0048255","count":4}]},{"hash":"1683126952085745463","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0044205","count":2},{"id":"GO:0006207","count":2},{"id":"GO:0043588","count":2}]},{"hash":"1167867404690744380","title":"Lipid and acetyl-CoA metabolism","description":"The top GO terms cluster around lipid biosynthesis and acetyl-CoA\u2013related metabolic processes, including fatty acid biosynthesis and related pathways, retinol and phenylpropanoid metabolism, and acetyl-CoA\u2013dependent steps. Some terms are organism-specific (lipoteichoic acid biosynthesis, seed coat development) but still tie into lipid- or acetyl-CoA\u2013driven biosynthesis, suggesting a broad lipid/energy metabolism theme across species.","confidence":"Medium","size":13,"edges":26,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":6},{"id":"GO:0055114","count":5},{"id":"GO:1902987","count":5},{"id":"GO:0042572","count":4},{"id":"GO:0019654","count":4}]},{"hash":"2179548243984586036","title":"Ubiquitination and Proteasome-Mediated Degradation","description":"The top GO terms cluster around ubiquitination processes (autoubiquitination, various ubiquitin linkages, regulation of ubiquitin transferase activity) and proteasomal degradation (SCF-dependent, ubiquitin-dependent protein catabolic process), with links to apoptosis and NF-kappaB signaling, suggesting a cohesive function in ubiquitin signaling and proteasome-mediated protein turnover.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0043524","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0035519","count":3},{"id":"GO:0051443","count":3}]},{"hash":"1869358896947603027","title":"Unknown","description":"The top GO terms are highly diverse, including serine biosynthesis, sulfur oxidation, multiple developmental processes (cervix, paramesonephric duct, atrial cardiac muscle cell development), and gene regulation (miRNA silencing, transcription regulation), with an obsolete SMAD-related term. There is no clear, unifying function linking the cluster\u2019s terms, so a single coherent label cannot be assigned.","confidence":"","size":13,"edges":67,"triangles":185,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":6},{"id":"GO:0060067","count":4},{"id":"GO:0055014","count":4},{"id":"GO:2000346","count":4},{"id":"GO:0061205","count":4}]},{"hash":"2018271982455878465","title":"Neural and forebrain development with transcriptional control","description":"The cluster is enriched for developmental processes (neural tube closure, forebrain and skeletal system development, multicellular organism development) and transcriptional regulation (DNA-templated transcription), suggesting a group of proteins involved in neural/brain development and gene expression control. Some stress- and cell cycle\u2013related terms are present, but the dominant theme appears developmental and transcriptional. ","confidence":"Medium","size":13,"edges":8,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":8},{"id":"GO:0006349","count":7},{"id":"GO:0001843","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0070059","count":7}]},{"hash":"1120452524990546652","title":"Nucleolar ribosome biogenesis and chromatin regulation","description":"The GO terms cluster around ribosome biogenesis and rRNA maturation (LSU-rRNA processing, rRNA base methylation, ribosome biogenesis) together with chromatin-related processes (heterochromatin formation, chromatin remodeling, telomere protection, DNA-templated transcription). This suggests these proteins function in the nucleolus to coordinate ribosome production with chromatin state and genome maintenance.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000183","count":2},{"id":"GO:0071919","count":2},{"id":"GO:0035066","count":2}]},{"hash":"2123468714430707275","title":"Neuronal development and membrane trafficking","description":"The cluster shows strong signals for neuronal development (forebrain radial glial cell differentiation, bipolar cell growth, neuron apoptotic regulation) combined with membrane trafficking and localization processes (Golgi to plasma membrane transport, exocyst localization, protein localization to leading edge). While there are some unrelated terms (lipophagy, heart contraction), the dominant themes point to neuronal differentiation coordinated with vesicle targeting and membrane dynamics. ","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0060047","count":3},{"id":"GO:0051519","count":3},{"id":"GO:0061724","count":3},{"id":"GO:1902463","count":3}]},{"hash":"647067992539928545","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosome assembly and function (ribosome biogenesis, ribosomal subunit biogenesis, cytoplasmic translation) and includes related processes such as tRNA modification and export of the large ribosomal subunit from the nucleus, indicating a core role in protein synthesis. Some cell division-related terms appear but are commonly linked to growth and coordination with translation. Overall, the pattern points to ribosome assembly and translation machinery.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0090529","count":2}]},{"hash":"306902199088734792","title":"Bone development and osteoblast differentiation","description":"This cluster is dominated by bone-related terms (bone development, cranial skeletal system development, osteoblast fate commitment), suggesting a primary role in bone formation and osteoblast activity. Supporting terms point to cytoskeletal remodeling and membrane dynamics (podosome assembly, plasma membrane tubulation, GTPase activity regulation), which are important in bone remodeling and cell morphogenesis. A few neural plasticity terms appear but likely reflect shared signaling pathways rather than neuron-specific function.","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:1904179","count":2},{"id":"GO:2000463","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0097320","count":2},{"id":"GO:0060291","count":2}]},{"hash":"144787665459510545","title":"Lamellipodium Formation and Rho GTPase Signaling","description":"The terms are dominated by actin cytoskeleton remodeling and cell motility, with lamellipodium assembly, cell migration, and regulation of Rho and GTPase activity pointing to actin-driven movement; related terms about endosome organization and vesicle priming suggest trafficking linked to cytoskeletal dynamics. Overall, the cluster centers on actin dynamics governing cell movement rather than metabolic signaling.","confidence":"High","size":13,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0007205","count":3},{"id":"GO:2001275","count":2},{"id":"GO:0016082","count":2},{"id":"GO:0035023","count":2}]},{"hash":"970494924260364846","title":"Neddylation-Linked Ubiquitin-Proteasome Regulation","description":"The cluster is dominated by GO terms tied to protein modification and degradation via the ubiquitin system: neddylation, autoubiquitination, and SCF-dependent proteasomal degradation, indicating a core theme of ubiquitin-mediated proteostasis. While other terms touch on immune signaling and genome maintenance, the strongest signal is regulation of protein turnover through neddylation-activated ubiquitin pathways.","confidence":"High","size":12,"edges":50,"triangles":130,"max_degree":10,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0045116","count":11},{"id":"GO:0042138","count":10},{"id":"GO:0071347","count":10},{"id":"GO:0051865","count":10},{"id":"GO:0031146","count":10}]},{"hash":"316605883064491657","title":"Xenobiotic and hormone response with catabolic metabolism","description":"Top GO terms include responses to lipopolysaccharide and xenobiotic stimuli, hormone biosynthetic regulation, and several catabolic processes (alanine, uracil, alkane) as well as protein glutathionylation, indicating a shared theme of stress/foreign compound sensing and coordinated metabolic adjustment.","confidence":"Medium","size":12,"edges":35,"triangles":42,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0032496","count":5},{"id":"GO:0042853","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0051412","count":3}]},{"hash":"1833922902693763711","title":"Ribosome Biogenesis and rRNA Maturation","description":"This cluster is strongly associated with ribosome biogenesis and rRNA processing, especially maturation of the large subunit rRNA (LSU) and 5.8S rRNA, and assembly of preribosomes. These recurrent GO terms suggest a core theme of ribosome production and LSU rRNA maturation, with a few additional nuclear processes (e.g., mRNA export) and unrelated terms that may reflect broader cellular context but are not central to the main function.","confidence":"Medium","size":12,"edges":40,"triangles":76,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0042254","count":3},{"id":"GO:1902626","count":3}]},{"hash":"113349840758364920","title":"Chromatin and Telomere Regulation in Meiosis","description":"The top terms cluster around chromatin dynamics and genome maintenance, including rDNA heterochromatin formation, telomere D-loop regulation, and meiotic recombination-related processes. While a few terms touch on transcription and membrane trafficking, the dominant theme ties to chromatin regulation and genomic stability during meiosis and telomere maintenance.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034499","count":2},{"id":"GO:0032534","count":2},{"id":"GO:0006654","count":2},{"id":"GO:0045737","count":2},{"id":"GO:1990414","count":2}]},{"hash":"2243727188716952510","title":"Peroxisomal lipid metabolism and stress response","description":"The cluster is dominated by GO terms tied to peroxisomal/glyoxysomal lipid metabolism (glyoxysome organization, cholesterol metabolic process, ketone body biosynthesis, lipid hydroperoxide transport) and stress-related processes (response to starvation, regulation of apoptotic mitochondrial permeabilization, oxidative stress). While a few terms reference development, the strongest signal comes from peroxisome-associated lipid pathways and cellular stress responses, suggesting a cohesive theme of metabolic adaptation via peroxisomal functions.","confidence":"Medium","size":12,"edges":19,"triangles":13,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010111","count":4},{"id":"GO:0072229","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0006550","count":4},{"id":"GO:0008203","count":4}]},{"hash":"1843890947216161472","title":"Neuronal synapse formation and signaling","description":"The cluster centers on neuronal synaptic processes: synaptic vesicle targeting, dendritic spine morphogenesis, paranodal junction maintenance, NO-mediated retrograde signaling, and serotonin uptake regulation, with a behavioral cue (vocalization). Although a few terms are unrelated or obsolete, the predominant theme is synapse assembly and neurotransmission in neurons.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016080","count":1},{"id":"GO:0021694","count":1},{"id":"GO:1904924","count":1},{"id":"GO:0071625","count":1},{"id":"GO:1990227","count":1}]},{"hash":"1261476750366146845","title":"Vesicle Transport & Organelle Signaling","description":"The terms cluster around intracellular trafficking events (endosome-to-melanosome transport, retrograde Golgi-ER transport, receptor internalization) and organelle-related signaling (TORC1 signaling, ceramide metabolism, nuclear pore assembly, ciliary docking, rDNA maintenance). This suggests a cohesive theme of cargo movement between compartments coupled with inter-organelle signaling, justifying a label focused on vesicle transport and organelle communication.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099590","count":1},{"id":"GO:0051292","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0043323","count":1},{"id":"GO:0035646","count":1}]},{"hash":"185320280632219685","title":"Cell Cycle and Cytoskeleton-Driven Migration","description":"The top GO terms cluster around cell proliferation, division, and the cell cycle, with strong emphasis on cytoskeleton remodeling (stress fiber assembly) and processes related to wound healing and cell spreading. These point to a module focused on proliferative growth plus cytoskeleton-guided migration during tissue repair. Additional terms like Golgi localization and protein oligomerization appear ancillary to this core theme. ","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0043149","count":5},{"id":"GO:0033138","count":5}]},{"hash":"1091439270452359292","title":"Axon guidance and actin cytoskeleton remodeling","description":"This cluster is driven by GO terms centered on neuronal axon extension and guidance (axonal fasciculation, axon extension in guidance, radial glia migration) coupled with extensive actin cytoskeleton dynamics (actin filament and cytoskeleton organization, filopodium and caveola assembly) and small GTPase signaling, pointing to coordinated signaling and cytoskeletal remodeling that underlies axon pathfinding and neuronal migration. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0007413","count":2},{"id":"GO:0048008","count":2},{"id":"GO:0048846","count":2},{"id":"GO:0007264","count":2}]},{"hash":"1661907415934677783","title":"Neuronal Synaptic Vesicle Trafficking","description":"Based on the top GO terms, the cluster centers on endocytosis, regulation of synaptic vesicle exocytosis, and transport of neurotransmitter receptors to postsynaptic membranes, all key aspects of synaptic vesicle cycling and neuronal signaling. While a few terms are less related (e.g., T cell signaling, ossification), the dominant theme ties to neuronal endocytosis and synaptic cargo trafficking.","confidence":"Medium","size":12,"edges":17,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006897","count":5},{"id":"GO:0071963","count":4},{"id":"GO:0098887","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0051291","count":4}]},{"hash":"1796192745213820431","title":"Lipid metabolism and membrane biosynthesis","description":"The top GO terms cluster around lipid production and membrane assembly, including ergosterol biosynthesis regulation, sphingolipid metabolism (mannosyl-inositol phosphorylceramide), and unsaturated fatty acid biosynthesis. Other terms point to lipid-rich membranes (myelin maintenance, sebaceous gland differentiation), suggesting a broader role for lipid metabolism in this cluster; a few terms are less directly related, but the dominant theme is lipid biosynthesis and membrane biology.","confidence":"Medium","size":12,"edges":17,"triangles":6,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0001949","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0006636","count":2}]},{"hash":"1490822323285282173","title":"Unknown","description":"The terms are highly diverse: brain development, spindle orientation, angiogenesis, telomere maintenance, foam cell differentiation, pain sensing, SNARE regulation, telomeric chromosome localization, and calcium release. There is no clear, single function tying the proteins together, so a coherent label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0000132","count":2},{"id":"GO:1903589","count":2},{"id":"GO:1904357","count":2},{"id":"GO:0010745","count":2}]},{"hash":"278616295776285955","title":"LPS-Triggered Innate Immunity and Antigen Presentation","description":"The cluster centers on innate immune responses to Gram-negative bacteria: lipopolysaccharide signaling, macrophage activation, dendritic cell antigen processing and presentation, and IL-6 production, with supporting links to Th17 differentiation and general proteasomal/ubiquitin regulation and actin remodeling that facilitate signaling and antigen handling. Together these terms define an LPS-driven immune activation and antigen presentation program.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031663","count":3},{"id":"GO:0030011","count":3},{"id":"GO:2000321","count":3},{"id":"GO:0051638","count":3},{"id":"GO:0031146","count":3}]},{"hash":"1639587391168541233","title":"Cell Cycle and DNA Repair","description":"The top GO terms are dominated by nuclear processes: DNA repair, regulation of nuclear DNA replication, and mitotic spindle organization, pointing to cell cycle control and genome maintenance as the core theme of this cluster. Some developmental or signaling terms appear (face/mesoderm development, IL-7 response), which may reflect pleiotropy or annotation overlap rather than core function. Therefore, the label captures the principal theme with medium confidence.","confidence":"Medium","size":11,"edges":12,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006281","count":4},{"id":"GO:0098761","count":4},{"id":"GO:0010571","count":4},{"id":"GO:0001324","count":4},{"id":"GO:0048320","count":4}]},{"hash":"1619272859476318653","title":"DNA replication and cell division proteins","description":"This cluster is driven by GO terms for DNA replication, DNA replication initiation, and cell division, suggesting proteins involved in the DNA synthesis machinery and cell cycle progression. The other terms (bradykinin catabolic process, thyroid hormone response, collagen catabolic and basement membrane-related processes, and T cell cytotoxicity) appear only once or are peripheral, so they do not indicate a coherent alternative primary function. Therefore, the most representative label is DNA replication and cell division proteins.","confidence":"Medium","size":11,"edges":13,"triangles":7,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006270","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0010815","count":1},{"id":"GO:0097067","count":1}]},{"hash":"633591616083312209","title":"Ribosome Biogenesis and Translation","description":"The cluster\u2019s terms cluster around translation and ribosome biogenesis/assembly (translation, cytosolic ribosome assembly, ribosome biogenesis, rRNA processing and methylation, tRNA wobble methylation) and even mitochondrial translation regulation, indicating a cohesive group of proteins involved in ribosome production and protein synthesis across cellular compartments.","confidence":"High","size":11,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":2},{"id":"GO:0042256","count":2},{"id":"GO:0006407","count":1},{"id":"GO:0006450","count":1}]},{"hash":"131657128899344207","title":"Amino acid, vitamin, and heme biosynthesis","description":"The proteins are enriched for multiple biosynthetic processes: protoporphyrinogen IX biosynthesis, biotin biosynthesis, histidine and alanine biosynthesis, and heme biosynthesis, with additional signals of antibiotic biosynthesis. This indicates a shared role in producing diverse small-molecule metabolites rather than degradation or signaling. A couple of terms (systemic acquired resistance signaling and cellular response to insulin) are less directly related, but do not outweigh the core biosynthetic theme. Overall, the cluster seems to represent a metabolic biosynthesis module focused on amino acids, vitamins, and heme-related pathways.","confidence":"Medium","size":11,"edges":48,"triangles":112,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006782","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0009862","count":3}]},{"hash":"1619960601230151536","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":15,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0019305","count":3},{"id":"GO:0009242","count":3},{"id":"GO:0009244","count":3},{"id":"GO:0097171","count":3}]},{"hash":"1302668690198131859","title":"Unknown","description":"The GO terms span ribosome biogenesis, ubiquitination, development (brain and smooth muscle), dsRNA response, telomere regulation, amyloid-beta clearance, and mRNA decay, with no single unifying function. Because the functions are highly diverse and do not converge on a common theme, there isn\u2019t a coherent label to assign beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0051865","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0010735","count":1},{"id":"GO:1904357","count":1}]},{"hash":"2101654622589588541","title":"Translational initiation and mRNA regulation","description":"This cluster is dominated by translation initiation and reinitiation processes (including IRES-dependent viral initiation) and by post-transcriptional mRNA regulation (stability, modification, and splicing). The shared GO terms indicate a cohesive role in controlling mRNA fate from initiation through processing.","confidence":"High","size":11,"edges":9,"triangles":3,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0075522","count":4},{"id":"GO:0075525","count":4}]},{"hash":"2152615875396692177","title":"Cell Cycle and RNA Modification Regulation","description":"This cluster is dominated by terms related to the mitotic and meiotic cell cycle, cell division, and centrosome-related protein localization, suggesting a core theme of cell-cycle control and centrosome regulation. The accompanying RNA/metabolism signals (ribosome disassembly; mRNA pseudouridine synthesis; tRNA modification; translational fidelity) indicate coordinated regulation of translation and RNA processing during or around cell division. The innate immune and cadmium response terms appear as additional stress-related signals but do not define the primary function of the cluster.","confidence":"Medium","size":11,"edges":14,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0032790","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1515110658161817733","title":"RNA processing and ribosome biogenesis","description":"The top terms are heavily skewed toward RNA maturation (mRNA splicing, rRNA processing) and ribosome assembly (ribosomal subunit biogenesis, rRNA maturation), suggesting the proteins cluster around RNA processing and ribosome biogenesis functions. Other terms like DNA replication, viral replication, and microtubule severing appear secondary and do not define a cohesive alternative theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070417","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1677752232680890840","title":"ECM-Integrin Adhesion and Cell Migration","description":"This cluster is dominated by GO terms tied to adhesion to the extracellular matrix and integrin signaling (substrate adhesion-dependent cell spreading, calcium-independent cell-matrix adhesion, hemidesmosome assembly, integrin-mediated signaling), along with collagen organization and fibroblast migration, all pointing to cell-ECM interactions and movement. Some terms about axon regeneration appear, likely reflecting common membrane-ECM adhesion mechanisms, but the core theme is adhesion and ECM signaling. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034446","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0048692","count":2},{"id":"GO:0060739","count":2},{"id":"GO:0007161","count":2}]},{"hash":"1313448716152229519","title":"Neural signaling and myelin maintenance","description":"The top GO terms cluster around nervous system-related processes: retrograde trans-synaptic signaling by nitric oxide, CNS myelin maintenance, and prostaglandin secretion, all suggesting neural signaling and myelination roles. Some terms appear peripheral (mitochondrial inheritance, general lipid metabolism), but the dominant theme is neural signaling and myelin maintenance in the CNS, making this a coherent label for the cluster.","confidence":"Medium","size":11,"edges":10,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0043154","count":2},{"id":"GO:0000001","count":1},{"id":"GO:0014806","count":1}]},{"hash":"823884272708121281","title":"Neural development and myelination signaling","description":"The terms cluster around nervous system development and myelination (peripheral nervous system development, oligodendrocyte differentiation, myelination) and associated signaling/adhesion processes (PI3K/AKT pathway, tyrosine autophosphorylation, cell-matrix adhesion). Some outliers exist (extrinsic apoptotic signaling, hemidesmosome assembly), but the dominant theme is neural development and myelin formation driven by growth factor/RTK signaling and adhesion cues.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0097192","count":3},{"id":"GO:0043491","count":3},{"id":"GO:0031581","count":2},{"id":"GO:0048172","count":2},{"id":"GO:0048709","count":2}]},{"hash":"756843504849327368","title":"Lymphocyte Activation and Immune Signaling","description":"The cluster\u2019s GO terms center on B cell differentiation and B cell receptor signaling, with additional immune-related functions like NK cell cytotoxicity, IL-7 response, and regulation of signaling pathways (Ras, Rho, PI3K) and phagocytosis. This pattern suggests a broad theme of immune cell activation and signaling across lymphoid and innate cells rather than a single, specific pathway.","confidence":"Medium","size":11,"edges":17,"triangles":6,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002316","count":11},{"id":"GO:0050861","count":11},{"id":"GO:0050764","count":11},{"id":"GO:0046580","count":11},{"id":"GO:0032959","count":11}]},{"hash":"984273845516456858","title":"Metabolic Catabolism and Detoxification","description":"These terms cluster around catabolic processes (triglyceride, uracil, and cellulose catabolic processes) with supportive roles in lipid signaling (phospholipid dephosphorylation) and detox/oxidant responses (cellular oxidant detoxification, response to toxic substance). A few terms relate to plant hormone biosynthesis (strigolactone) and regulatory pathways (endocannabinoid signaling), but the dominant theme is metabolism via catabolic/detoxification processes. Confidence: Medium","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":4},{"id":"GO:0019433","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006212","count":3}]},{"hash":"2126143646975007773","title":"Angiogenesis and Renin-Angiotensin Signaling with Immunity","description":"The top GO terms center on vascular biology (renin-angiotensin regulation of blood pressure, angiotensin maturation, angiogenesis) and immune involvement (adaptive immune response, cell-cell signaling, leukotriene biosynthesis), suggesting a cluster tied to cardiovascular signaling coupled with immune/modulatory processes.","confidence":"Medium","size":10,"edges":13,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0003081","count":2},{"id":"GO:0019370","count":2},{"id":"GO:0002003","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0007275","count":2}]},{"hash":"2143850607707872899","title":"GTPase-Driven Actin Remodeling and Cell Adhesion","description":"Top GO terms point to small GTPase\u2013mediated signaling, filopodium assembly and its regulation, and substrate-adhesion\u2013dependent cell spreading, all hallmarks of actin cytoskeleton remodeling. While other terms (mitochondrial fission, immune and developmental signals) are present, the core theme is actin dynamics governed by GTPases and adhesion cues.","confidence":"High","size":10,"edges":7,"triangles":0,"max_degree":6,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0045792","count":5},{"id":"GO:1900026","count":5},{"id":"GO:0007264","count":5},{"id":"GO:0051932","count":5},{"id":"GO:0000266","count":5}]},{"hash":"798184151147689901","title":"Cell cycle and cytoskeleton remodeling","description":"The cluster is dominated by GO terms related to the cell cycle and cell division, alongside actin cytoskeleton remodeling (Arp2/3-mediated nucleation and actin bundle assembly). This suggests proteins involved in mitotic progression together with dynamic cytoskeletal changes. Additional terms point to genome maintenance and organelle/nuclear trafficking, but the core theme centers on cell proliferation coupled with cytoskeletal dynamics.","confidence":"Medium","size":10,"edges":27,"triangles":37,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0009408","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0034314","count":4}]},{"hash":"449853210989228508","title":"Nucleotide metabolism in developing brain and liver","description":"GO terms are dominated by nucleotide biosynthesis, salvage, and interconversion (CDP, ADP, AMP salvage, phosphorylation, purine interconversion) alongside brain and liver development, suggesting nucleotide metabolism is active during these developmental processes; proteasome regulatory particle assembly appears less central.","confidence":"Medium","size":10,"edges":27,"triangles":30,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046041","count":3},{"id":"GO:0001889","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0046705","count":3},{"id":"GO:0046939","count":3}]},{"hash":"1103662783542674032","title":"Viral Translation Initiation and Reinitiation","description":"The most represented GO terms point to initiation and reinitiation of translation, including IRES-dependent viral translation and related termination-reinitiation. This makes the cluster representative of viral translation control mechanisms. A few terms relate to transcription regulation and DNA repair, but their lower prevalence suggests they are less characteristic of this cluster, so the primary theme remains translation initiation/viral translation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075522","count":3},{"id":"GO:0075525","count":3}]},{"hash":"1437123937005003607","title":"Translational Regulation and Ubiquitin-Mediated Proteolysis","description":"This cluster is enriched for GO terms on initiation and regulation of translation (formation of translation preinitiation complex, translation reinitiation, regulation of translational initiation) and on ubiquitin-proteasome\u2013mediated protein turnover (polyubiquitination, SCF-dependent proteasomal degradation, ERAD). While some transcription/splicing terms are present, the strongest signal connects gene expression control at the level of translation with protein degradation, and the cadmium response suggests stress-related proteostasis adjustments. Overall, the label captures the link between translation initiation control and ubiquitin-mediated proteolysis in this set.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0031146","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006351","count":3}]},{"hash":"767957145715796480","title":"Unknown","description":"The top GO terms cover very different biology (GPCR signaling, cardiac action potential regulation, NF-kappaB signaling, vitamin D response, ubiquitination, T cell differentiation, RNA maturation and splicing, and plant development). No single functional theme ties these terms together, suggesting the proteins do not share a common, well-defined process; thus a coherent label can't be assigned.","confidence":"","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0016567","count":2}]},{"hash":"395211077177244922","title":"Cytoskeleton dynamics and cell adhesion","description":"The top GO terms converge on desmosome assembly, localization to the cortical microtubule cytoskeleton, and cell migration, with supporting signals in GTPase activity, TORC1 signaling, and endothelial proliferation. This points to a shared role in cytoskeletal remodeling and cell\u2013cell adhesion that underpins migratory and morphogenetic behavior, rather than a single isolated function. The broader regulatory terms (apoptosis, Wnt signaling, transcription) sit alongside these core themes but do not overturn the central cytoskeleton/adhesion\u2013migration pattern.","confidence":"High","size":10,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0043547","count":3}]},{"hash":"22753361661571281","title":"Neural development and transcriptional regulation","description":"This cluster prominently features brain development terms: forebrain development, neural tube closure, and cerebral cortex development, suggesting a role in neural differentiation. Coupled with DNA-templated transcription, these terms imply regulation of gene expression during neural development. The other terms (mitotic cell cycle, ER-stress\u2013related apoptosis, metal/defense responses) are broader or secondary and do not override the neural development signal, so the label is representative though not exclusive. ","confidence":"Medium","size":10,"edges":14,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1590802790844160908","title":"Heat stress\u2013related protein quality control (ERAD)","description":"The top GO terms cluster around heat response and protein quality control: response to heat, negative regulation of cellular response to heat, misfolded protein transport, and ubiquitin-dependent ERAD pathway, plus post-translational targeting to membranes and translocation. This pattern points to a coordinated set of processes handling proteotoxic stress and targeting misfolded proteins for degradation in the ER (ERAD) or membrane-associated pathways. Some unrelated terms (e.g., DNA replication, developmental signaling) may reflect broad or ambiguous annotations, but the core theme supports proteostasis under heat stress.","confidence":"Medium","size":10,"edges":19,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1900035","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0071374","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0031204","count":1}]},{"hash":"505303991082966100","title":"Cytoskeletal Protrusions & GTPase Signaling","description":"The GO terms emphasize actin-based protrusions (filopodium/microspike assembly), and activation/regulation of GTPases, pointing to cytoskeletal remodeling and signaling for cell migration. Developmental and signaling terms (Wnt signaling, midbrain morphogenesis) appear supportive but are less central, making the protrusion/GTPase pattern the most representative theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0030035","count":2},{"id":"GO:1904693","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0002408","count":2}]},{"hash":"208391357888997739","title":"Golgi-ER vesicle trafficking and Golgi organization","description":"The top GO terms cluster around Golgi and ER-to-Golgi vesicle transport, intra-Golgi trafficking, vesicle fusion with the Golgi, and Golgi ribbon formation, indicating proteins mainly involved in Golgi apparatus function and vesicle trafficking. A few terms touch sphingolipid metabolism, oxidative stress response, and autophagy-related targeting, which are supportive or peripheral. Overall, the dominant signal is Golgi trafficking and organization.","confidence":"High","size":10,"edges":6,"triangles":1,"max_degree":3,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006891","count":6},{"id":"GO:0090161","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0048280","count":6},{"id":"GO:0006896","count":6}]},{"hash":"930887119364749296","title":"Hepatic Mitochondrial Metabolism and Insulin Signaling","description":"The GO terms cluster around mitochondrial metabolite transport (CoA, NAD, citrate) and insulin/glucose responses, with a liver-related process (liver regeneration) also represented. This supports a cohesive theme of hepatic mitochondrial metabolism tied to insulin-regulated energy homeostasis.","confidence":"High","size":10,"edges":14,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":6},{"id":"GO:0051881","count":5},{"id":"GO:0070542","count":5},{"id":"GO:0035349","count":5},{"id":"GO:0032869","count":5}]},{"hash":"702881709363692879","title":"Neuroimmune Signaling and Neural Development","description":"Top GO terms show innate immune responses (dsRNA, LPS, interferon-beta), alongside neural development and function (axonogenesis, corpus callosum development, dopamine response, pain behavior), suggesting these proteins participate in neuroimmune crosstalk during CNS development.","confidence":"Medium","size":10,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043330","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0031663","count":2},{"id":"GO:0071222","count":2}]},{"hash":"818724464552640738","title":"Yeast filamentous growth and secretory remodeling","description":"The GO terms highlight nutrient-stress\u2013driven morphological changes (pseudohyphal/invasive growth in response to glucose limitation) and related remodeling of the secretory pathway (ER exit, protein localization to the cell surface, secretion of lysosomal enzymes). While some terms (DNA transcription, viral process, telomere-related) are broader, the combination of filamentous growth signals with secretion/trafficking suggests a yeast stress response involving morphological change and secretory adjustments.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0061820","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0033299","count":1}]},{"hash":"2214542755153605973","title":"LPS-driven innate immune activation and antigen presentation","description":"The terms cluster around LPS signaling, macrophage activation, dendritic cell antigen processing and presentation, and cytokine production (notably IL-6) with TH17 differentiation, pointing to an immune response to Gram-negative bacteria and bridging to adaptive immunity. Supporting terms on actin dynamics and nuclear export reflect additional cellular processes in activated immune cells.","confidence":"High","size":10,"edges":8,"triangles":0,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031663","count":3},{"id":"GO:0030011","count":3},{"id":"GO:2000321","count":3},{"id":"GO:0051638","count":3},{"id":"GO:0031146","count":3}]},{"hash":"1383668768985379329","title":"ER stress response and protein folding","description":"The cluster\u2019s GO terms center on unfolded protein response and ER stress (response to unfolded protein; positive regulation of translation initiation in response to ER stress), along with protein folding via peptidyl-prolyl isomerase and related trafficking. This suggests a common theme of maintaining protein quality under stress, with supporting links to autophagy regulation and trafficking between endosomes and the Golgi. Plant-specific signaling and defense terms (cytokinin signaling, viral process, innate immunity) may reflect broader stress and defense cross-talk, but the core pattern points to ER stress\u2013related quality control. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042147","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1649479479625725039","title":"Glutamate and lipoate metabolism","description":"The top GO terms cluster around amino-acid and cofactor metabolism, notably L-glutamate biosynthesis, 2-oxoglutarate metabolism, and dihydrolipoamide/lipoate metabolism, pointing to central carbon and energy metabolism. Some unrelated terms (sperm capacitation, gastrulation) likely reflect annotation noise or cross-species artifacts, and there are no edges connecting the proteins, suggesting a loose or non-modular grouping. Overall, a metabolism-focused label best fits the core signal.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0016575","count":4},{"id":"GO:0097054","count":4},{"id":"GO:0048240","count":4},{"id":"GO:0051068","count":4}]},{"hash":"1286763605031092735","title":"Dopamine signaling in neurons","description":"I labeled this Dopamine signaling in neurons because two GO terms directly reference dopamine (cellular response to dopamine; regulation of dopamine receptor signaling) and a third relates to nerve branching morphogenesis, suggesting a neuronal functional context. While other terms touch on general signaling regulation and trafficking, the dopamine-neuron theme is the most prominent.","confidence":"Medium","size":10,"edges":6,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1905289","count":3},{"id":"GO:1905279","count":3},{"id":"GO:0071287","count":3},{"id":"GO:0043124","count":3},{"id":"GO:0043304","count":3}]},{"hash":"736256816086955587","title":"Golgi-ER vesicle trafficking in mitosis","description":"Proteins in this cluster are enriched for ER\u2013Golgi transport steps (COPII vesicle budding, retrograde Golgi-to-ER transport) and general vesicle trafficking, alongside mitotic processes (mitotic cell cycle, spindle assembly), suggesting roles in coordinating intracellular transport with cell division and growth.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0090114","count":6},{"id":"GO:0008283","count":6}]},{"hash":"1999582467124913986","title":"Ribosome Biogenesis and RNA Transcription","description":"The top terms cluster around nuclear RNA synthesis (RNA Pol I/III transcription, RNA-templated transcription, tRNA transcription by Pol III, and Pol III transcription termination) and ribosome assembly (ribosomal small subunit assembly), pointing to nucleolar processes that assemble ribosomes and process RNA. A few terms about shoot meristem regulation or hemidesmosome assembly appear less connected and may reflect broader or incidental annotations. Overall, the dominant theme is ribosome biogenesis coupled with RNA transcription in the nucleus.","confidence":"Medium","size":9,"edges":13,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090506","count":1},{"id":"GO:0034198","count":1},{"id":"GO:0031581","count":1},{"id":"GO:2000032","count":1},{"id":"GO:0000028","count":1}]},{"hash":"2056030980459056973","title":"Cellular redox homeostasis and oxidative stress response","description":"This cluster shows multiple GO terms tied to managing reactive oxygen species, detoxification of oxidants, and redox regulation (e.g., cellular oxidant detoxification, cellular redox homeostasis, cellular response to oxidative stress, protein deglutathionylation). While a few other terms are less directly related (metabolic and transcriptional regulation), the redox-focused terms are the strongest signal tying the proteins together.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":1},{"id":"GO:0055114","count":1},{"id":"GO:2000651","count":1},{"id":"GO:0009263","count":1},{"id":"GO:1903026","count":1}]},{"hash":"1387984535183930516","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006189","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0006412","count":2}]},{"hash":"356965918141020118","title":"Ribosome Biogenesis and Translation","description":"The dominant GO terms cluster around ribosome production and function: rRNA processing, 90S preribosome assembly, formation of translation preinitiation complex, nuclear export of ribosomal subunits, and cytoplasmic translation. A few terms (heart development, GTPase activity regulation) appear peripheral to this core, suggesting these proteins primarily participate in ribosome assembly and protein synthesis rather than development. ","confidence":"High","size":9,"edges":12,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1290161130753640259","title":"Epigenetic control of antibody diversification","description":"Top GO terms point to histone methylation regulation (H3K9, H3K36, H3K4) alongside immunoglobulin gene maturation processes (somatic hypermutation and isotype switching to IgA), suggesting a theme where epigenetic modifications influence antibody diversification. Some terms are obsolete, but the shared signal ties epigenetic regulation to B cell antibody maturation.","confidence":"Medium","size":9,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051573","count":1},{"id":"GO:0048298","count":1},{"id":"GO:0003289","count":1},{"id":"GO:0051096","count":1},{"id":"GO:0000414","count":1}]},{"hash":"1348841911998929676","title":"Ubiquitin-dependent proteolysis and histone turnover","description":"The cluster is characterized by GO terms centered on ubiquitination and protein degradation (autoubiquitination, ubiquitin-dependent proteolysis, and K6-linked ubiquitination) as well as histone catabolism, pointing to protein turnover and chromatin-related regulation as the core function. Some metabolic and developmental terms appear less prominently, likely as contextual associations rather than core functions. Confidence: High","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0085020","count":2},{"id":"GO:0036205","count":2}]},{"hash":"2203937001627499583","title":"Membrane Transport and Related Functions","description":"The top GO terms are dominated by transmembrane transport activities (xenobiotic, vitamin, molybdate, and long-chain fatty acid import into peroxisomes) and secretion-related transport, suggesting the cluster centers on membrane transport roles. Some terms (DNA repair, antigen processing) are less aligned, possibly reflecting annotation noise, but the strongest signal is transport across membranes.","confidence":"Medium","size":9,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":9},{"id":"GO:0035461","count":9},{"id":"GO:0042891","count":7},{"id":"GO:0015910","count":5},{"id":"GO:0030253","count":5}]},{"hash":"2184658546964878016","title":"RNA processing and translational regulation","description":"The cluster is dominated by post-transcriptional and translational terms: translation (GO:0006412), mRNA decay (GO:0000288), spliceosome-related activity (GO:0000349), and maintenance of translational fidelity (GO:1990145). While some terms touch on signaling and membrane trafficking, the strongest, recurring themes relate to RNA processing and control of protein synthesis, justifying this label.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0032088","count":1},{"id":"GO:1902306","count":1},{"id":"GO:1902072","count":1},{"id":"GO:0048227","count":1}]},{"hash":"536647112124047995","title":"Copper homeostasis and mitochondrial respiration","description":"The top GO terms point to copper ion homeostasis and transport, along with respiratory chain complex IV assembly, suggesting a link between copper metabolism and mitochondrial function and redox balance. A couple of terms (oocyte construction, regulation of mRNA stability) seem peripheral, but the core signal is copper handling connected to mitochondrial respiration.","confidence":"Medium","size":9,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0006878","count":1},{"id":"GO:0007308","count":1},{"id":"GO:0006825","count":1},{"id":"GO:0008535","count":1}]},{"hash":"972470727434129556","title":"Small-molecule biosynthesis and catabolism","description":"The top GO terms span synthesis and breakdown across multiple small-molecule categories: antibiotics, vitamins/quinones (menaquinone, phylloquinone), fatty acids (biosynthesis and beta-oxidation), sugars (fructose), retinol, and amino-ac acid catabolic pathways (valine, phenylacetate). This mix points to a general metabolic cluster rather than a single pathway, centered on production and degradation of diverse small molecules and lipids. ","confidence":"Medium","size":9,"edges":21,"triangles":21,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0006574","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0042372","count":3}]},{"hash":"218517204853535680","title":"Mitochondrial dynamics and ER-Golgi trafficking","description":"The top GO terms cluster around mitochondrial membrane organization and fission, plus ER-to-Golgi vesicle transport and protein localization to endosomes/ER membranes, pointing to a module of organelle remodeling and intracellular trafficking. While a couple of terms are more general (cell growth, brain development), the clearest connection is between mitochondrial dynamics and vesicular transport within the secretory pathway.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:1902953","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0007006","count":2}]},{"hash":"1512685310839578256","title":"Splicing and Translation Initiation Regulation","description":"These proteins cluster around post-transcriptional gene expression control, with enrichment for mRNA splicing (spliceosome), mRNA modification and stabilization, polyadenylation-related terms, and assembly of the eIF4F complex. The co-occurrence of spliceosomal processing and translation initiation terms suggests a coordinated role in mRNA maturation and the switch to translation, indicating a cohesive function in regulating mRNA fate from processing to initiation.","confidence":"High","size":9,"edges":9,"triangles":1,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0016556","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0006446","count":3},{"id":"GO:1900363","count":3},{"id":"GO:0048255","count":3}]},{"hash":"1512983356335065611","title":"LPS-Triggered Innate Immune Activation","description":"The GO terms cluster around lipopolysaccharide signaling, macrophage activation, dendritic cell antigen processing and presentation, and IL-6 production, all pointing to an innate immune response to Gram-negative bacteria. Additional terms on actin remodeling and ubiquitin-dependent turnover support immune cell activation and trafficking, reinforcing a cohesive LPS-driven immune activation signature.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031663","count":2},{"id":"GO:0030011","count":2},{"id":"GO:2000321","count":2},{"id":"GO:0051638","count":2},{"id":"GO:0031146","count":2}]},{"hash":"1610608125542321506","title":"Translation Initiation and Regulation","description":"The top GO terms are centered on translation initiation, formation of the preinitiation complex, and regulation of translational initiation, suggesting these proteins cluster around the protein synthesis initiation machinery. Other terms (redox homeostasis, glycosylation, amino acid transport) appear as non core annotations, but do not override the clear translation initiation theme.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0006446","count":1}]},{"hash":"253361670920757375","title":"Unknown","description":"Top GO terms are highly heterogeneous, including obsolete oxidation-reduction, RNA/DNA processing, DNA catabolic, heme biosynthesis, plant-type cell wall assembly, fatty acid transport, mitochondrial electron transport, and proton transport. There is no clear common function linking these proteins, so the cluster remains Unknown.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0090503","count":1},{"id":"GO:0006308","count":1},{"id":"GO:0070453","count":1},{"id":"GO:0006783","count":1}]},{"hash":"1206014937468132983","title":"Unknown","description":"The top terms cover a wide range of unrelated processes (redox, neurotransmitter metabolism, histone demethylation, hormone response, immune defense, spliceosome splicing, nucleotide metabolism, neuron maturation, erythrocyte differentiation, and hormone biosynthesis), with no clear single function or pathway tying the proteins together. The absence of edges and the presence of obsolete GO terms further suggest there is no cohesive theme, so a specific label cannot be assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042135","count":3},{"id":"GO:0034720","count":3},{"id":"GO:0051412","count":2},{"id":"GO:0042742","count":2}]},{"hash":"1283632045834508643","title":"Nuclear stress response and proteostasis","description":"The cluster centers on genome maintenance and protein quality control, with DNA repair (nucleotide-excision repair), nuclear body organization (PML body), and processes like aggrephagy and autoubiquitination. Additional terms for oxidant detoxification, heat acclimation, and TNF signaling point to a broader cellular stress response that interfaces stress adaptation, transcription/translation, and cell-cycle-related functions (spindle pole duplication). Confidence reflects the cohesive but broad theme across nuclear and proteostasis-related processes.","confidence":"Medium","size":8,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0006289","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0030578","count":1},{"id":"GO:0030474","count":1}]},{"hash":"1318556615176580299","title":"Vertebrate Development and Cell Cycle Control","description":"The cluster centers on developmental processes (axial mesoderm formation, face development, osteoblast differentiation) combined with core cell cycle and genome maintenance functions (DNA repair, mitotic spindle organization, regulation of DNA replication). This pattern suggests proteins that coordinate embryonic development with controlled cell proliferation and genome integrity. Some terms like interleukin-7 response and aging/oxidative stress appear less central but may reflect broader signaling contexts; overall, the dominant theme is development paired with cell cycle control.","confidence":"Medium","size":8,"edges":16,"triangles":14,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006281","count":8},{"id":"GO:0098761","count":8},{"id":"GO:0010571","count":8},{"id":"GO:0001324","count":8},{"id":"GO:0048320","count":8}]},{"hash":"789491795680708151","title":"Negative regulation of differentiation across tissues","description":"This cluster is dominated by GO terms about inhibiting differentiation in several contexts (osteoblast, pancreatic A cell, glucocorticoid signaling, androgen signaling) and notably neural development terms (subpallium neuron fate, spinal cord motor neuron specification). The shared theme is suppression of differentiation processes across multiple tissues, with a strong emphasis on neural development timing and fate decisions.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":5},{"id":"GO:0060766","count":5},{"id":"GO:2000227","count":4},{"id":"GO:2000323","count":4},{"id":"GO:0060163","count":4}]},{"hash":"1593627118036183918","title":"Ribosome biogenesis and translational regulation","description":"Dominant terms center on ribosome assembly and protein synthesis, including translation, tyrosyl-tRNA aminoacylation, and regulation of translational fidelity and initiation. The presence of transcription-related terms appears ancillary, possibly reflecting bacterial coupling of transcription with translation or annotation noise. Overall, the cluster represents components and regulators of the translation machinery and ribosome function.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":3},{"id":"GO:1990145","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0006353","count":2}]},{"hash":"2227961827483880924","title":"Proteostasis and RNA Processing","description":"These proteins cluster around two interconnected themes: protein homeostasis (proteasome-mediated degradation, COP9 signalosome/deneddylation, autophagy regulation) and RNA metabolism (splicing, translation initiation control, ribosome biogenesis, and pseudouridine synthesis). The presence of both proteostatic and RNA-processing terms suggests a coordinating role in maintaining cellular protein and RNA quality.","confidence":"High","size":8,"edges":20,"triangles":23,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1903146","count":1},{"id":"GO:0060625","count":1},{"id":"GO:0043161","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0010387","count":1}]},{"hash":"996343967923466000","title":"Peroxisomal Protein Import and Ubiquitination","description":"The top terms show focused enrichment for peroxisome matrix protein import (and receptor recycling) and ubiquitin-related processes (ubiquitin-dependent ERAD pathway, autoubiquitination), suggesting a shared role in peroxisomal protein trafficking and protein quality control via ubiquitination. Other terms appear noisy, but the peroxisomal/ubiquitination theme is the most coherent.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0006260","count":3}]},{"hash":"817148470810797791","title":"Redox metabolism and biosynthetic pathways","description":"The GO terms show a strong emphasis on oxidation\u2013reduction processes, redox homeostasis, electron transport, and detoxification, indicating a core redox/metabolic activity. Additional terms point to various biosynthetic activities (thiamine, choline catabolism, antibiotic biosynthesis, deoxyribonucleotide synthesis), which are common in metabolically active microbes. Taken together, this cluster appears to reflect redox-associated metabolism with concurrent biosynthetic capabilities rather than a single, narrowly defined function.","confidence":"Medium","size":8,"edges":13,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0042426","count":2},{"id":"GO:0009228","count":2}]},{"hash":"353068628077918057","title":"Lipid catabolism and remodeling","description":"This cluster is dominated by GO terms for triglyceride catabolic processes, triglyceride mobilization, and acyl-chain remodeling, along with phospholipid catabolism (phosphatidylcholine and phosphatidylethanolamine). The presence of regulatory signaling terms (negative regulation of PKA) and an inflammatory signaling term (TLR4) suggests a link between lipid metabolism and cellular signaling/inflammation. A few outliers (nerve impulse transmission, embryo implantation) may reflect broader roles of lipids in membranes and development, but the lipid-centric terms dominate. ","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019226","count":2},{"id":"GO:0007566","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0036153","count":2},{"id":"GO:2000480","count":2}]},{"hash":"1555372267540469248","title":"Neural development and vesicle trafficking","description":"The cluster\u2019s terms cluster around neural development and membrane/vesicle dynamics: forebrain radial glial differentiation, neuron survival regulation, Rac-mediated signaling, protein localization to the leading edge, exocyst localization regulation, and multivesicular body sorting. Lipophagy also ties to membrane-associated autophagy and vesicle turnover, supporting a cohesive theme of neural cell differentiation with vesicle trafficking and cytoskeletal remodeling. Some terms (heart contraction, beta selection) are less directly linked, but the dominant signals point to neural development and membrane trafficking processes.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0060047","count":3},{"id":"GO:0061724","count":3},{"id":"GO:1902463","count":3},{"id":"GO:0021861","count":3}]},{"hash":"844215603487797093","title":"Unknown","description":"The top GO terms span biotin and menaquinone biosynthesis, multiple catabolic processes (chlorophyll, uracil, phosphatidylserine), an epoxygenase P450 pathway, regulation of endocannabinoid signaling, and general responses to toxic substances, with some obsolete biosynthetic terms. This mix shows no single coherent function or pathway characterizing the entire cluster, suggesting heterogeneous or multi-species content rather than a shared biological role. Therefore no specific, representative label can be reliably assigned.","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0019373","count":3},{"id":"GO:0006212","count":3}]},{"hash":"439202142114861572","title":"B/T Cell Receptor Signaling","description":"The top GO terms are dominated by adaptive immune functions, including B cell receptor signaling, B cell affinity maturation, T cell receptor signaling, and IL-7 response, suggesting a cohesive theme of lymphocyte activation and receptor-mediated signaling. Some non-immune terms appear, but the core signal points to adaptive immune receptor pathways.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098761","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0048320","count":2},{"id":"GO:0002344","count":2},{"id":"GO:0071380","count":2}]},{"hash":"2062335723755619858","title":"Rho-driven cytoskeletal remodeling","description":"The top GO terms center on Rho signaling and actin-related processes (Rho protein signal transduction, positive regulation of Rho signaling, microspike and stress fiber assembly) and link to cell morphogenesis, indicating a cluster of proteins involved in cytoskeletal dynamics governed by Rho pathways. Nuclear import terms are present but less representative, so the main theme remains cytoskeletal organization. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0006606","count":1},{"id":"GO:0061015","count":1}]},{"hash":"656380413820695977","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1116802505621432360","title":"DNA replication and centrosome cycle regulators","description":"The most represented terms are DNA replication and centrosome cycle, with supporting DNA repair and cell cycle involvement. While there are developmental terms (cranial skeleton morphogenesis, axial mesoderm formation, osteoblast differentiation) suggesting roles in embryogenesis, the core signal points to regulation of DNA replication and the centrosome cycle, with some ancillary functions in gene expression and development.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0007098","count":6},{"id":"GO:0006397","count":6},{"id":"GO:0048701","count":6}]},{"hash":"638768206111094625","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0061158","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0001825","count":2}]},{"hash":"270235640916880223","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098504","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0098506","count":1},{"id":"GO:0042769","count":1},{"id":"GO:1904355","count":1}]},{"hash":"234227050963355025","title":"Mitochondrial Complex Assembly and ATP Synthesis","description":"These proteins cluster around mitochondrial biogenesis and energy production: assembly of respiratory chain complexes I and IV, mitochondrial protein import, cristae formation, and proton-motive ATP synthesis. Other terms reflect mitochondrial maintenance (oligomerization, proteolysis, glutathione turnover) and a seedling development context.","confidence":"High","size":8,"edges":10,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0032981","count":1},{"id":"GO:0090351","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0042407","count":1}]},{"hash":"1169492246264492131","title":"Neural signaling and ion transport","description":"The cluster\u2019s top GO terms emphasize excitatory synaptic transmission (glutamatergic), calcium ion transport, and membrane depolarization related to ion channels, suggesting a shared theme of neuronal signaling and ion-channel\u2013mediated processes. While a few terms relate to immune signaling or other cellular processes, the dominant pattern supports neural excitability and synaptic function.","confidence":"High","size":8,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051968","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0019933","count":2},{"id":"GO:0046037","count":2}]},{"hash":"1473921291609023896","title":"Chromatin Silencing and DNA Replication Initiation","description":"This cluster centers on chromatin silencing/heterochromatin formation alongside core DNA replication and cell cycle processes (pre-replicative complex assembly, DNA replication, mitotic initiation, and overall cell cycle), suggesting a unifying role in chromatin-mediated control of replication and division. Some terms reflect meiosis (female gamete generation) and an unrelated annotation (bacteriochlorophyll biosynthesis), but the dominant signal is chromatin-driven replication initiation and cell-cycle regulation.","confidence":"Medium","size":8,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":3},{"id":"GO:0042127","count":2},{"id":"GO:0007292","count":2},{"id":"GO:0006267","count":2},{"id":"GO:0007049","count":2}]},{"hash":"440769209114314673","title":"Cell envelope polysaccharide and lipid biosynthesis","description":"This cluster centers on biosynthetic pathways for cell surface and envelope components, including lipopolysaccharide, colanic acid, and sugar nucleotide\u2013dependent polysaccharides (rhamnose, arabinose), as well as related polymers like wax and PHB. The common theme is the synthesis of polysaccharides and lipids that build or modify the bacterial cell surface and storage polymers.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0017000","count":3},{"id":"GO:1902987","count":2}]},{"hash":"1635267149628407388","title":"TLR/NOD2-NF-\u03baB Innate Immunity","description":"These proteins cluster around innate sensing and signaling via TLRs and NOD2, converging on NF-\u03baB and inflammatory cytokine production (LPS/TLR4 signaling, antiviral defense, chemokine and IL-1\u03b2 regulation).","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0043124","count":2},{"id":"GO:0002756","count":2},{"id":"GO:0006954","count":2}]},{"hash":"1174821277878965010","title":"Melanosome transport and pigment granule organization","description":"Based on the GO terms, this cluster is dominated by lysosome-related processes and pigment cell biology, including lysosome localization, lysosomal lumen acidification, secretion of lysosomal enzymes, and endosome-to-melanosome transport, plus eye pigment granule organization and melanocyte differentiation. The combination points to a coherent theme of melanosome/lysosome-related organelle trafficking in pigment cells, with broader vesicle transport in neurons as a supporting motif. Confidence: High.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032418","count":2},{"id":"GO:0048490","count":2},{"id":"GO:0033299","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0032816","count":1}]},{"hash":"749377791923384411","title":"Extrinsic apoptosis and inflammatory signaling","description":"The cluster centers on immune/inflammatory pathways with several GO terms tied to inflammatory response, extrinsic apoptotic signaling in the absence of ligand, activation-induced T cell death, NF-kappaB signaling, and TNF production. This combination points to a group of proteins involved in inflammatory signaling that can promote extrinsic apoptosis, supported by prostaglandin metabolism as part of inflammatory biology. A plant-specific term appears among the annotations, but the dominant pattern is inflammation-associated apoptosis signaling.","confidence":"High","size":8,"edges":10,"triangles":5,"max_degree":4,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":3},{"id":"GO:2001241","count":3},{"id":"GO:0006924","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0010311","count":2}]},{"hash":"2044485511901032761","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by translation- and ribosome-related terms: cytoplasmic translation, translation, and maturation of rRNA, plus mitochondrial translational termination and ribosomal large subunit assembly. This pattern suggests a group of proteins involved in ribosome biogenesis and protein synthesis. A few terms (immune responses, DNA repair) are present but appear peripheral to the main theme.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000027","count":3},{"id":"GO:0071353","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0071549","count":1}]},{"hash":"2129092205243236549","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":7,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006413","count":1},{"id":"GO:0009258","count":1},{"id":"GO:0009245","count":1}]},{"hash":"1258485762415784118","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017001","count":1},{"id":"GO:0098789","count":1},{"id":"GO:0031126","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0019243","count":1}]},{"hash":"1003904104271709506","title":"Nucleotide salvage and nucleoside catabolism","description":"The Top Terms are dominated by nucleotide salvage pathways (UMP salvage, AMP salvage) and nucleoside catabolic processes (guanosine, deoxyguanosine, uridine), with related urate biosynthesis and a glucose-starvation response, suggesting a cluster centered on nucleotide metabolism and nucleoside turnover rather than a specific signaling pathway. ","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019284","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0044206","count":1},{"id":"GO:0006161","count":1},{"id":"GO:0006218","count":1}]},{"hash":"1644001641440318345","title":"Unknown","description":"The GO terms are diverse: transcription elongation regulation, protein folding, tubulin complex assembly, immunity/cytotoxicity, development, locomotor rhythm, and oxidative stress regulation. There is no single coherent theme linking most of these terms across the seven proteins, so a concise, representative label cannot be inferred.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0007021","count":2},{"id":"GO:1903984","count":1},{"id":"GO:0044324","count":1}]},{"hash":"1174290120854685307","title":"Chromatin regulation and telomere maintenance","description":"Top GO terms cluster around chromatin modification (H4 deacetylation), rDNA heterochromatin formation, telomere loop/D-loop dynamics, and DNA repair/recombination (SCE, meiotic recombination). This suggests a module focused on chromatin state and genome stability, including telomere maintenance and rDNA chromatin; some metabolic terms appear incidental. ","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043457","count":2},{"id":"GO:1990414","count":2},{"id":"GO:1905839","count":2},{"id":"GO:0070933","count":2},{"id":"GO:0009301","count":2}]},{"hash":"358652262116000592","title":"Actin Cytoskeleton Remodeling and Motility Regulation","description":"The top GO terms are dominated by actin-related processes (actin cortical patches, filament debranching, lamellipodium and ruffle assembly) and their regulation, including both promotion and negative control of cell motility, which points to a cohesive theme of actin-driven remodeling of the cytoskeleton and controlled cell movement. A few terms (transcription by RNA polymerase II, IL-1 response, imaginal disc segmentation) are less central but may reflect broader functional contexts of the proteins.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0000147","count":2},{"id":"GO:0071846","count":2},{"id":"GO:0071347","count":2},{"id":"GO:0045862","count":2}]},{"hash":"445877921456181465","title":"Innate Immune Response and TLR Signaling","description":"Most top GO terms point to innate immune defense, including defense responses to Gram-positive bacteria and to viruses, an innate immune response, lipopolysaccharide-mediated signaling, and detection of diacyl lipoproteptides, with positive regulation of Toll-like receptor signaling. A few terms related to chromatin localization and morphogenesis appear but do not define the core theme; the dominant signal is innate immunity and pathogen recognition via TLR pathways. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007200","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0071169","count":4}]},{"hash":"1537389023493534703","title":"Unknown","description":"The GO terms are a broad mix of metabolism, development, stress response, and RNA processing with no single cohesive function uniting the proteins, so there isn\u2019t a clear common theme to name a specific cluster function.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042208","count":4},{"id":"GO:0048240","count":3},{"id":"GO:0045793","count":3},{"id":"GO:0021987","count":3},{"id":"GO:0051412","count":2}]},{"hash":"1730271657711279087","title":"Unknown","description":"The top GO terms span unrelated biological contexts (behavior, immune signaling and cell death, cell adhesion, cytokine production, photosynthesis, neural development, and coagulation/complement). There is no clear, shared function or pathway tying these proteins together, suggesting a heterogeneous or noise-driven cluster. ","confidence":"","size":7,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071625","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0006924","count":2},{"id":"GO:0033623","count":2},{"id":"GO:0032613","count":2}]},{"hash":"835570057082935956","title":"Embryonic and Neural Morphogenesis","description":"The cluster shows a mix of developmental and differentiation GO terms, including brain development, dendritic spine formation, limb and skeletal morphogenesis, episomal proliferation, and hematopoietic progenitor differentiation, suggesting proteins involved in broad embryonic development with notable neural morphogenesis components; other terms (synaptic targeting, ectodomain proteolysis, ER calcium homeostasis) may reflect supporting processes during development.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016080","count":1},{"id":"GO:0031149","count":1},{"id":"GO:0050673","count":1},{"id":"GO:0051563","count":1},{"id":"GO:0002244","count":1}]},{"hash":"1462092796068920402","title":"Osteoclast differentiation and cytoskeletal remodeling","description":"The cluster is dominated by osteoclast-related processes (osteoclast fusion and regulation of osteoclast development) and cytoskeletal remodeling activities (actin filament polymerization, centrosome localization, caveola assembly), with associated signaling inputs (NO, endothelin, IL-7, insulin receptor signaling), suggesting a focused theme on osteoclast differentiation driven by cytoskeletal and signaling changes.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0072675","count":2},{"id":"GO:0071732","count":2},{"id":"GO:1990859","count":2},{"id":"GO:0098761","count":2},{"id":"GO:1903760","count":2}]},{"hash":"1818403748214710111","title":"Unknown","description":"The GO terms show highly diverse roles\u2014defense response, cell wall metabolism, sensory perception (umami and light), GPCR signaling, electron transport, and development-related cytoskeleton changes\u2014without a single cohesive function connecting the proteins. Because there is no clear theme, I can't assign a meaningful label.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042742","count":1},{"id":"GO:0016998","count":1},{"id":"GO:0050917","count":1},{"id":"GO:0071257","count":1},{"id":"GO:0007196","count":1}]},{"hash":"1887187495810554724","title":"Dopamine-responsive neuronal signaling and dendrite morphogenesis","description":"The cluster's GO terms predominantly point to neuronal processes: cellular response to dopamine, dendrite morphogenesis, positive regulation of axon extension, and related signaling pathways, with additional notes on neuronal trafficking such as regulation of retrograde transport from endosome to Golgi and CAMKK-AMPK signaling. There are a couple of immune-related terms (T cell receptor signaling, mast cell degranulation), but these are less represented, so the label centers on neuronal signaling and development as the main theme.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903351","count":3},{"id":"GO:0043366","count":2},{"id":"GO:1905289","count":2},{"id":"GO:1905279","count":2},{"id":"GO:0048813","count":2}]},{"hash":"1191101518463201930","title":"Proteostasis and genome maintenance","description":"This cluster aggregates proteins involved in protein quality control (ubiquitination, ERAD, aggrephagy) and stress responses (heat acclimation, insecticide response), along with nucleotide-excision DNA repair. The shared emphasis on maintaining protein and genome integrity under cellular stress supports a cohesive theme around proteostasis combined with genome maintenance.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0070911","count":6},{"id":"GO:0030578","count":3},{"id":"GO:0030474","count":3}]},{"hash":"879170078974886462","title":"Actin Dynamics in Dendritic Spines","description":"Based on the top GO terms, this cluster centers on actin cytoskeleton remodeling, including polymerization, capping, lamellipodium and bundle assembly, and specifically dendritic spine morphogenesis and regulation of excitatory postsynaptic potential, suggesting proteins that drive actin-driven spine growth and synaptic plasticity.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":3},{"id":"GO:0060997","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0030032","count":2}]},{"hash":"488887062900962298","title":"ER stress response and innate immune activation","description":"The cluster centers on ER stress-related processes (unfolded protein response, protein folding) and immune signaling (innate immune activation, NF-kappaB, MHC class I antigen assembly, and protein trafficking to the cell surface), suggesting a coordinated response linking ER quality control to antigen presentation and immune activation, with downstream effects on cell cycle and senescence.","confidence":"Medium","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0006457","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0071805","count":2},{"id":"GO:2000010","count":2}]},{"hash":"2038976444796634068","title":"Ribosome Biogenesis and Translation","description":"The cluster is centered on translation and ribosome maturation; four proteins map to translation (GO:0006412) and three to maturation of SSU rRNA, suggesting a role in ribosome assembly and protein synthesis. Additional hints toward translation regulation and ER targeting are present but weak. Overall, the proteins likely participate in ribosome biogenesis and translation.","confidence":"Medium","size":6,"edges":12,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0033119","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0006378","count":1}]},{"hash":"1368494340627085393","title":"Light sensing and circadian rhythms","description":"The cluster\u2019s GO terms cluster around light perception and timekeeping\u2014photoprotection, photoperiodism, locomotor rhythm, and magnetoreception/detection of light stimulus\u2014suggesting a group of proteins involved in light sensing and circadian regulation. A few terms about root development are minor outliers and do not detract from the dominant light- and rhythm-related theme. ","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000323","count":1},{"id":"GO:0010117","count":1},{"id":"GO:0050958","count":1},{"id":"GO:0009646","count":1},{"id":"GO:0018298","count":1}]},{"hash":"1137621774222622503","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by translation-related terms (translation, mitochondrial translational termination, preribosome large subunit assembly, and positive regulation of ribosome biogenesis) plus tRNA modification (wobble thiolation), pointing to ribosome assembly and protein-synthesis machinery. A few terms reflect cellular responses to translation-inhibiting antibiotics (response to antibiotic, response to cycloheximide), which aligns with the same translation-focused context but represents stress rather than a separate pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0070126","count":1},{"id":"GO:0006259","count":1}]},{"hash":"1581342398894111284","title":"Fermentation and amino acid metabolism","description":"The GO terms point to central carbon metabolism with emphasis on pyruvate processing (fermentation to ethanol, pyruvate catabolic), alongside branched-chain amino acid pathways (valine) and related catabolic/biosynthetic processes. The mix, including glyoxylate and other metabolic processes, suggests a cohesive cluster of fermentation-linked and amino-acid\u2013related enzymes, likely from a microorganism.","confidence":"High","size":6,"edges":12,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019310","count":2},{"id":"GO:0000950","count":2},{"id":"GO:0019655","count":2},{"id":"GO:0009099","count":2},{"id":"GO:0034077","count":2}]},{"hash":"755236948767598299","title":"Stress-Responsive Signaling and Transcription","description":"The cluster centers on oxidative stress response, regulation of transcription, and signal transduction pathways (including MAPK/ERK and T cell signaling), suggesting a theme of stress-related signaling coupled to transcription control; a few annotations (like PTS and retina development) may reflect broader or cross-species annotations.","confidence":"Medium","size":6,"edges":6,"triangles":2,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":3},{"id":"GO:0035335","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0009401","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1866521180806721349","title":"Ear development and hearing","description":"The prominent terms point to ear and skeletal development and sensory perception of sound (middle ear morphogenesis, axial mesoderm development, ossification, skeletal system development, sensory perception of sound). While a few terms relate to general cellular processes (translation, preribosome assembly, ESCRT), the strongest signal ties to ear formation and hearing, justifying this label with moderate confidence.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042474","count":1},{"id":"GO:0048318","count":1},{"id":"GO:0001503","count":1},{"id":"GO:0007605","count":1},{"id":"GO:0001501","count":1}]},{"hash":"830439077478038047","title":"TLR Signaling and Inflammatory Response","description":"The cluster is enriched for toll-like receptor signaling terms (including TLR4 and MyD88-independent pathways), LPS-mediated signaling, NF-kappaB regulation, and inflammatory outputs such as chemokine and IL-1\u03b2 production, along with antiviral defense. This points to a cohesive set of proteins involved in innate immune sensing and the ensuing inflammatory response.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043124","count":2},{"id":"GO:0002756","count":2},{"id":"GO:0006954","count":2},{"id":"GO:0034142","count":2},{"id":"GO:0051607","count":2}]},{"hash":"497807013123602621","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster is dominated by GO terms for ribosome biogenesis and maturation of rRNA (LSU and SSU), with multiple entries indicating ribosomal subunit biogenesis. This points to a core role in assembling and processing ribosomes. Other terms like mRNA splicing, innate immune response, and mitotic cell cycle appear less represented, suggesting they are secondary associations rather than the primary function of the group.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1864660777093256608","title":"Unknown","description":"The GO terms span DNA replication and repair, neural development (dendrite morphogenesis, axon extension), immune signaling (T cell receptor signaling, mast cell degranulation), and signaling pathways (Wnt, dopamine response). With only one edge and no clear functional cohesion across these processes, there isn\u2019t a single representative function for the cluster. This mixture makes a confident, specific label unlikely.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0043366","count":4},{"id":"GO:0048813","count":4}]},{"hash":"41712058491145027","title":"Transcriptional Regulation and Signaling","description":"The top GO terms point to control of gene expression (DNA-templated transcription, mRNA transport) alongside signaling processes (TORC1 signaling, positive regulation of GTPase activity, serine dephosphorylation). The cluster therefore appears to group proteins involved in coordinating transcription with cellular signaling, rather than a single enzymatic function. Some terms like fertilization or immune responses may be incidental. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0038202","count":2}]},{"hash":"1306336708115742610","title":"Unknown","description":"The six proteins show an assortment of GO terms spanning plant development (flower development, leaf morphogenesis), general metabolism (carbohydrate, glycoside/glycosylceramide catabolic processes), nitric oxide regulation, and even angiogenesis-related processes, with no single cohesive function tying them together. Additionally, there are no edges in the cluster, suggesting little direct functional linkage. This makes a single interpretable label unlikely.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009911","count":1},{"id":"GO:0016139","count":1},{"id":"GO:0051001","count":1},{"id":"GO:0046477","count":1},{"id":"GO:0009965","count":1}]},{"hash":"1549380559349271853","title":"Cell wall and capsule polysaccharide biosynthesis","description":"The GO terms are dominated by polysaccharide biosynthesis and protein O-linked glycosylation, including cell wall, teichoic acid, capsule, and hyaluronan biosynthetic processes, plus UDP-galactose metabolism feeding these pathways. This pattern points to enzymes and steps involved in assembling and modifying glycan structures on the bacterial cell envelope. Therefore, a cohesive label centered on bacterial cell wall/capsule glycan biosynthesis fits well.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030244","count":1},{"id":"GO:0052573","count":1},{"id":"GO:0036108","count":1},{"id":"GO:0016266","count":1},{"id":"GO:0019350","count":1}]},{"hash":"402345980474230799","title":"Protein Folding and Microtubule Assembly","description":"The cluster\u2019s dominant terms point to proteostasis\u2014chaperone activity, protein folding, and ubiquitin-proteasome\u2013mediated quality control\u2014together with tubulin complex/tubulin-driven cortical microtubule organization. While a few terms touch on transcription regulation or stress responses, the prevailing signals are folding and microtubule/cytoskeleton assembly, justifying this focused label.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0071629","count":1},{"id":"GO:0043622","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1898396767001083734","title":"Diverse substrate catabolism","description":"Based on GO terms, the proteins are linked to breakdown of triglycerides, chlorophyll, uracil, and phosphatidylserine, with other terms indicating broad metabolism and detox responses. This suggests a cluster centered on diverse catabolic processes rather than a single pathway.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0019373","count":1},{"id":"GO:0006212","count":1}]},{"hash":"1832959402470580078","title":"Translation Initiation and Ribosome Quality Control","description":"The cluster shows strong signals for cytoplasmic translational initiation, regulation of translational initiation, and nonfunctional rRNA decay, which together point to ribosome-related translation control and quality surveillance. Some unrelated terms like ethylene response and oligodendrocyte development appear but do not outweigh the translation-centric pattern.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019284","count":2},{"id":"GO:0014003","count":2},{"id":"GO:0071369","count":2},{"id":"GO:0071732","count":2},{"id":"GO:0019509","count":2}]},{"hash":"1448010825949680460","title":"Ribosome biogenesis and translation","description":"The top GO terms are centered on ribosome production and function\u2014cytoplasmic translation, ribosome biogenesis, and ribosomal large subunit assembly\u2014along with SRP-dependent cotranslational targeting to the membrane, all of which point to the protein synthesis machinery and ribosome assembly. While there are a few adjacent terms (ER unfolded protein response, IL-4 response) that are less central, the dominant pattern clearly reflects translation and ribosome-related processes. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0002181","count":1}]},{"hash":"116625381058960827","title":"Epigenetic transcriptional repression and histone methylation","description":"Top GO terms point to epigenetic control of gene expression, especially negative regulation of transcription by RNA polymerase II and histone arginine methylation, suggesting chromatin-state\u2013mediated regulation. The inclusion of cellular senescence and methylation-related terms reinforces a link between histone modification and transcriptional repression affecting cell fate.","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0031427","count":2},{"id":"GO:0006729","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1682003880164187689","title":"Unknown","description":"The top GO terms are highly diverse (lung development, myelination, steroid and retinoic acid biosynthesis, fatty acid metabolism, and even cell cycle and antibiotic response) with no clear single function tying the cluster together, and the cluster has no edges or interactions. This suggests no coherent, identifiable theme across these proteins.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":3},{"id":"GO:0000082","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0006706","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1210502021428752890","title":"TLR-Mediated Macrophage Activation","description":"Most of the top GO terms point to innate immune signaling via Toll-like receptors and macrophage activation (TLR signaling, LPS signaling, detection of diacyl lipopeptides). A few terms about morphogenesis and bone remodeling may reflect broader or secondary annotations rather than a cohesive non-immune function. Overall, the cluster appears to represent a TLR-driven inflammatory/immunomodulatory program with macrophage involvement.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034123","count":4},{"id":"GO:0042496","count":4},{"id":"GO:0032474","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0036303","count":4}]},{"hash":"656376954264247989","title":"Aminoacyl-tRNA synthetases (mitochondrial & cytosolic)","description":"The cluster is dominated by GO terms for tRNA aminoacylation, including several mitochondrial and cytosolic lysyl-, aspartyl-, and asparaginyl-tRNA synthetase activities, plus tRNA wobble modification. This points to a core function in charging tRNAs for translation in both compartments. Some additional terms (DNA repair, telomere maintenance) may reflect moonlighting roles or annotation overlap, but the central theme is aminoacylation of tRNAs. ","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006422","count":3},{"id":"GO:0070154","count":3},{"id":"GO:0070146","count":3},{"id":"GO:0006430","count":3},{"id":"GO:0007093","count":3}]},{"hash":"1977342947954941877","title":"Vertebrate development and cell cycle regulation","description":"The proteins cluster around developmental processes such as face development, axial mesoderm formation, and regulation of osteoblast differentiation, while also showing signals tied to cell cycle control and genome maintenance (mitotic spindle organization, DNA replication regulation, and DNA repair). Although there are some immune-related terms like interleukin-7 response and beta selection, the dominant theme is morphogenesis linked with cell division/repair activities.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006281","count":5},{"id":"GO:0098761","count":5},{"id":"GO:0010571","count":5},{"id":"GO:0001324","count":5},{"id":"GO:0048320","count":5}]},{"hash":"872014457354090721","title":"Cell envelope polysaccharide biosynthesis and morphogenesis","description":"The top GO terms cluster around biosynthesis of cell wall and surface polysaccharides (lipopolysaccharide, slime layer, GDP-mannose) and include cell shape and morphogenesis processes, indicating these proteins likely participate in constructing or remodeling the cell envelope. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":3},{"id":"GO:0006535","count":3},{"id":"GO:0045228","count":3},{"id":"GO:0019877","count":3},{"id":"GO:0009272","count":3}]},{"hash":"2148321326203018085","title":"Spliceosome-driven RNA processing","description":"This cluster is dominated by GO terms for mRNA splicing via the spliceosome, spliceosomal complex assembly, and regulation of splicing, along with related mRNA metabolism activities (deadenylation-dependent decapping, mRNA processing, and regulatory ncRNA-mediated silencing). The consistent presence of splicing and RNA decay terms suggests proteins involved in RNA processing and gene expression regulation at the RNA level, with a few chromatin-related terms that may reflect broader nuclear RNA biology. Overall, the theme is best captured by spliceosome-mediated RNA processing functions.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0006369","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000290","count":2}]},{"hash":"652376415536773233","title":"Inflammasome-driven cytokine production","description":"The top terms cluster around NLRP3 inflammasome assembly and cytokine production (including IL-18) with additional links to broader inflammatory regulation and glial differentiation, suggesting a cohesive inflammatory signaling module. Other terms about ER/Golgi organization and microtubule dynamics may support trafficking and cytoskeletal changes linked to inflammasome activation, but the strongest theme is inflammasome-mediated cytokine output.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900025","count":2},{"id":"GO:1900017","count":2},{"id":"GO:0007019","count":2},{"id":"GO:0016320","count":2},{"id":"GO:0007030","count":2}]},{"hash":"1208630435675332446","title":"Ubiquitin-Dependent Degradation and ERAD","description":"The cluster's top GO terms cluster around ubiquitin-dependent protein catabolic processes and ERAD, indicating a focus on ubiquitin-tagged protein degradation and ER-associated degradation pathways. The viral process term hints at possible involvement in host\u2013virus interactions that exploit ubiquitin signaling. Other terms like peroxisome import or spindle checkpoint signaling are less representative. Overall, the dominant theme is ubiquitin-dependent degradation and protein quality control.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0031578","count":1}]},{"hash":"1411855404881967620","title":"Proteostasis and Metabolic Stress Responses","description":"The GO terms cluster around protein quality control and stress responses (response to cold, cellular response to misfolded protein, monoubiquitinated protein deubiquitination, ERAD-related processes), alongside various catabolic metabolism terms (leucine catabolic process, fatty acid beta-oxidation, prostaglandin metabolism). This combination suggests roles in proteostasis with linked metabolic activity, justifying a combined label rather than distinct, unrelated functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":2},{"id":"GO:0070932","count":1},{"id":"GO:0035520","count":1},{"id":"GO:0071218","count":1},{"id":"GO:0035640","count":1}]},{"hash":"978010120016539294","title":"Chromatin Remodeling and Nucleosome Dynamics","description":"The cluster is dominated by nucleosome assembly/disassembly terms and histone modification regulation, pointing to chromatin remodeling. Additional terms related to microtubule polymerization and cell division hint at a broader role in cell-cycle\u2013associated chromatin changes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007117","count":1},{"id":"GO:0006337","count":1},{"id":"GO:0031116","count":1},{"id":"GO:2000617","count":1},{"id":"GO:0035041","count":1}]},{"hash":"708021249558384234","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0071031","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0031047","count":3}]},{"hash":"2078572829081077460","title":"Sterol transport and lipid metabolism","description":"The top GO terms cluster around cholesterol and lipid trafficking (intracellular cholesterol transport, cholesterol import, cholesterol transport involved in cholesterol storage, ER to Golgi ceramide transport) and bile acid biosynthesis, along with related lipid signaling (positive regulation of PPAR signaling pathway). This points to a core function in sterol/lipid transport and metabolism. Some terms related to plant development appear but are likely incidental or reflect broad lipid-associated roles rather than a common developmental pathway.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035360","count":1},{"id":"GO:0070859","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0010879","count":1},{"id":"GO:0071378","count":1}]},{"hash":"1266844753312010249","title":"Vesicle trafficking and endocytosis","description":"The cluster\u2019s GO terms cluster around movement and sorting of vesicles inside the cell, including ER-to-Golgi transport, intracellular protein transport, clathrin-dependent endocytosis, and synaptic vesicle coating. These terms collectively point to a shared function in membrane trafficking and vesicle dynamics, with additional terms like cell cycle and apoptosis regulation appearing tangentially. Thus, the label captures the main theme of the cluster.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0007049","count":1},{"id":"GO:1900118","count":1},{"id":"GO:0090156","count":1},{"id":"GO:0006886","count":1}]},{"hash":"2140542843567844329","title":"Unknown","description":"This cluster shows two disparate GO terms (bone resorption and response to chloroquine) each supported by a single protein. There is no clear shared process, function, or pathway linking the proteins, so a cohesive, specific label cannot be assigned.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":1},{"id":"GO:1902349","count":1}]},{"hash":"1801715036211826791","title":"Ubiquitin\u2013proteasome regulation and immune signaling","description":"The cluster centers on proteostasis-related processes: protein deubiquitination, SCF-dependent proteasomal degradation, and proteasome core complex assembly, suggesting active ubiquitin\u2013proteasome regulation. It also shows enrichment for immune receptor signaling pathways (Fc-epsilon receptor, T cell receptor, C-type lectin receptor) indicating immune signaling involvement. The combination implies a functionally coherent theme around proteostasis intersecting with receptor-mediated signaling, though broader signaling contexts like Wnt PCP are also present.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":4},{"id":"GO:0010950","count":2},{"id":"GO:0060071","count":2},{"id":"GO:0038095","count":2},{"id":"GO:0050852","count":2}]},{"hash":"1891141550623411225","title":"Ribosome biogenesis and translation","description":"Most top GO terms cluster around translation and ribosome biology (translation, ribosomal large subunit assembly, translation reinitiation, rRNA/mRNA pseudouridine synthesis), indicating a role in ribosome biogenesis and protein synthesis. Telomerase/telomere-related terms appear at low frequency, suggesting they are secondary associations. Overall, the cluster is centered on ribosome assembly and translation processes.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":2},{"id":"GO:1904874","count":1},{"id":"GO:0055129","count":1},{"id":"GO:0007049","count":1}]},{"hash":"880885686388330145","title":"Unknown","description":"The four proteins show a mix of GO terms from oxidative stress response, detoxification, immune signaling, and even cardiac/muscle and bone remodeling processes, with no shared pathway or interaction (Edges 0). This scattered functional profile suggests no single cohesive function for the cluster, so Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0072675","count":1},{"id":"GO:0071732","count":1},{"id":"GO:0098761","count":1}]},{"hash":"992725093190957111","title":"Ribosome Biogenesis and Translation","description":"The top GO terms center on ribosomal large subunit biogenesis and assembly, plus translation, implying this cluster is about ribosome production and protein synthesis. Additional terms related to protein stabilization and targeting may reflect regulation of translational machinery, with a few ancillary ubiquitin-related terms likely incidental.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032092","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0000027","count":1},{"id":"GO:1904667","count":1}]},{"hash":"737570290823136495","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000472","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0035315","count":2},{"id":"GO:0006369","count":2}]},{"hash":"2038165924405951486","title":"Chromatin Regulation and Transcription Control","description":"The top terms converge on chromatin state and transcription processes, including histone modification (H2B ubiquitination), transcription termination, and mRNA export, with additional vernalization and chloroplast-related GO terms hinting at plant-specific epigenetic regulation. Together, these suggest a cluster centered on chromatin-mediated control of gene expression and RNA processing rather than a single metabolic pathway.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071894","count":1},{"id":"GO:0010048","count":1},{"id":"GO:2000104","count":1},{"id":"GO:0016584","count":1},{"id":"GO:0045038","count":1}]},{"hash":"1251080722926685229","title":"Mitochondrial respiration and energy metabolism","description":"The top terms cluster around mitochondrial electron transport, proton transmembrane transport, and aerobic respiration, with related protein oligomerization suggesting assembly of respiratory complexes. These collectively point to mitochondrial energy production and respiratory chain function; a few terms (insulin signaling, lifespan) reflect broader metabolic context but don\u2019t overwhelm the core theme.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0008340","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0045861","count":1}]},{"hash":"1180647836278283712","title":"Craniofacial and hindbrain patterning","description":"GO terms concentrate on hindbrain, face, and nucleus accumbens development, plus anterior/posterior and proximal/distal pattern formation, suggesting a developmental patterning theme; metabolic biosynthetic terms appear less central to the cluster's function.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019413","count":4},{"id":"GO:0030902","count":4},{"id":"GO:0055129","count":4},{"id":"GO:0021768","count":4},{"id":"GO:0009952","count":4}]},{"hash":"1742831908773608789","title":"Neural differentiation and brain fate specification","description":"The GO terms are dominated by neural development and neuron/glial fate specification (subpallium neuron fate commitment, spinal cord motor neuron fate specification, glial fate commitment, midbrain-hindbrain boundary morphogenesis, regulation of timing of neural differentiation), pointing to brain regional development as the cluster\u2019s core function, despite a few non-neural differentiation terms. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000227","count":4},{"id":"GO:2000323","count":4},{"id":"GO:0045668","count":4},{"id":"GO:0060163","count":4},{"id":"GO:0061100","count":4}]},{"hash":"277661694879810879","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007292","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0070060","count":1},{"id":"GO:0051295","count":1},{"id":"GO:0070649","count":1}]},{"hash":"1302084029996336488","title":"Unknown","description":"The Top Terms show a scattered mix of functions (protein complex formation, various metabolic and transcription processes, ERAD, and several obsolete terms) with no single cohesive theme and no observed interactions between proteins. This makes it unclear to assign a specific, representative label. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051289","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006729","count":1},{"id":"GO:0006351","count":1}]},{"hash":"455277500774934729","title":"Cell cycle control and apoptosis regulation","description":"This cluster centers on cell cycle progression and mitosis (regulation of cell cycle, DNA replication, kinetochore-microtubule attachment) and on apoptosis/necroptosis signaling (negative/positive regulation of apoptotic pathways, extrinsic signaling). Ubiquitination accompanies cell-cycle control, reinforcing the theme. A few terms related to TLR signaling and locomotion are present but don\u2019t alter the core focus on cell cycle and programmed cell death regulation.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1722906474311006745","title":"Ubiquitin-Dependent DNA Damage Response","description":"The top GO terms are dominated by ubiquitination-related processes (autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent protein catabolic process) and by DNA damage response/repair (DNA repair, response to ionizing radiation, replication-born double-strand break repair). This points to a module of proteins involved in ubiquitin signaling that governs DNA damage response. The signal is coherent despite the small cluster size and one obsolete term, making the label plausible and representative.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0030579","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0042787","count":2}]},{"hash":"165479501150220752","title":"Immunometabolic stress response","description":"The top GO terms include immune-related responses (lipopolysaccharide, copper ion, prostaglandin metabolism, drug response) alongside carbohydrate metabolism and PPP-related processes, suggesting a cluster tied to immune signaling coupled with metabolic or energetic adjustments. This points to an immunometabolic role rather than a single, narrow pathway.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0032496","count":4},{"id":"GO:0097327","count":3},{"id":"GO:0003016","count":3},{"id":"GO:1901159","count":3},{"id":"GO:0006693","count":3}]},{"hash":"1710915310656536835","title":"DNA Damage Response and Repair","description":"The prominent GO terms point to UV-C induced damage response, DNA replication and nucleotide-excision repair, and translesion synthesis, all characteristic of genome maintenance pathways. While a couple of terms are unrelated (collagen catabolism, glomerular filtration), the core signal is DNA damage recognition and repair.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071494","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0006297","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0070987","count":1}]},{"hash":"1146843274980043406","title":"Gluconeogenesis and glycerol metabolism","description":"This cluster centers on metabolic processes connected to carbon flux and energy/redox balance, with explicit terms for gluconeogenesis, glycerol-3-phosphate catabolism and glycerol accumulation, as well as related pathways like pantothenate biosynthesis and NADPH regeneration. While there are a few regulatory terms present, the dominant theme is central metabolism tied to glycerol handling and glucose production.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010765","count":2},{"id":"GO:0016558","count":1},{"id":"GO:0015940","count":1},{"id":"GO:0006973","count":1},{"id":"GO:2000010","count":1}]},{"hash":"1135047156861810159","title":"Immune Response and Protozoan Defense","description":"This cluster is driven by immune-related terms: defense response to protozoan and myeloid dendritic cell differentiation, along with T-helper 2 cell differentiation and host-mediated suppression of viral transcription. While a couple of terms touch on unrelated processes like wound healing and osteoblast differentiation, the strongest signals point to immune activation and protozoan defense functions.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042832","count":2},{"id":"GO:0043011","count":2},{"id":"GO:0035470","count":1},{"id":"GO:0045669","count":1},{"id":"GO:1903984","count":1}]},{"hash":"530124796614680677","title":"Notch-regulated neural development","description":"The top GO terms are centered on Notch signaling and neural differentiation/morphogenesis in brain regions (e.g., subpallium neuron fate commitment, spinal cord motor neuron fate, midbrain-hindbrain boundary morphogenesis, labyrinthine layer morphogenesis). This suggests the proteins participate in Notch-mediated neurodevelopment and regional neuronal patterning. A few terms on osteoblast differentiation and glucocorticoid signaling appear as minor outliers, but the prevailing signal is neural development governed by Notch. ","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007219","count":2},{"id":"GO:2000227","count":1},{"id":"GO:2000323","count":1},{"id":"GO:0045668","count":1},{"id":"GO:0060163","count":1}]},{"hash":"1331378105842650636","title":"Brain and craniofacial development","description":"The cluster is enriched for neural and craniofacial developmental terms (hindbrain development, nucleus accumbens development, face development, anterior/posterior pattern specification, proximal/distal pattern formation), suggesting a shared role in brain and facial morphogenesis. Some metabolic biosynthesis terms appear, but the dominant theme ties to developmental patterning in neural/craniofacial contexts.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019413","count":4},{"id":"GO:0030902","count":4},{"id":"GO:0055129","count":4},{"id":"GO:0021768","count":4},{"id":"GO:0009952","count":4}]},{"hash":"1779324389334380256","title":"Unknown","description":"The GO terms are diverse (iron transport and homeostasis, endocytosis, proteolysis, plant stomatal development, folate metabolism, etc.) with little cohesive functional theme across the cluster, so a specific, representative label cannot be determined.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098707","count":1},{"id":"GO:0035609","count":1},{"id":"GO:0006898","count":1},{"id":"GO:0031293","count":1},{"id":"GO:0045830","count":1}]},{"hash":"206409032142768888","title":"RNA splicing and processing","description":"This cluster is dominated by GO terms for spliceosome-mediated mRNA splicing, tRNA processing, deadenylation-dependent decapping, and P-body assembly, with supporting signals for nuclear import and histone mRNA metabolism. Together these terms point to a cohesive role in RNA maturation and turnover, spanning nuclear processing to cytoplasmic decay; some chromatin-related terms appear but are secondary to RNA processing. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000290","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0000245","count":2},{"id":"GO:0042633","count":2},{"id":"GO:0045292","count":2}]},{"hash":"2132533403677583231","title":"Unknown","description":"Top GO terms include general translation and regulation of translation initiation alongside meiosis-specific processes like chromosome pairing and chiasma assembly, with no clear functional linkage among them. The mixed, disparate functions and lack of network connectivity suggest there is not a single coherent function defining this cluster. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1901194","count":1},{"id":"GO:0007129","count":1},{"id":"GO:0051026","count":1}]},{"hash":"2117360732304569249","title":"Translation Initiation Regulation & Amino Acid Starvation","description":"The GO terms point to translational initiation regulation and responses to amino acid starvation, implying a shared function in controlling protein synthesis under nutrient stress; some peripheral terms (metabolic salvage, development, plant-specific responses) appear as noise.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019284","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0071369","count":1},{"id":"GO:0071732","count":1},{"id":"GO:0019509","count":1}]},{"hash":"99480935905788539","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050709","count":3},{"id":"GO:0042068","count":3},{"id":"GO:1905869","count":3},{"id":"GO:0031291","count":3},{"id":"GO:0007601","count":3}]},{"hash":"1296622372985150481","title":"RNA processing and splicing machinery","description":"The cluster is dominated by terms tied to RNA maturation and post-transcriptional regulation: deadenylation-dependent decapping of nuclear-transcribed mRNA, tRNA processing, spliceosomal complex assembly, mRNA splicing via spliceosome, and P-body assembly, plus histone mRNA metabolism and nuclear import. Together these suggest proteins that participate in RNA processing, splicing, and mRNA turnover, with some involvement in nucleocytoplasmic transport. A few unrelated terms may be incidental noise. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000290","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0042633","count":3},{"id":"GO:0045292","count":3}]},{"hash":"1735501246367111333","title":"Nuclear RNA processing and splicing","description":"The top GO terms cluster around mRNA maturation and splicing (deadenylation-dependent decapping, cis-splicing via spliceosome, spliceosomal assembly, histone mRNA metabolism) and nuclear import, indicating a focus on RNA processing in the nucleus. Additional terms like tRNA processing and P-body assembly support broader RNA metabolism, but the strongest signal is nuclear RNA maturation and splicing.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000290","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0042633","count":3},{"id":"GO:0045292","count":3}]},{"hash":"2102559299353650994","title":"Virus entry and proviral latency","description":"The top GO terms indicate viral infection processes: entry into host, membrane fusion with host cells, and establishment of integrated proviral latency, along with related host responses like leukocyte migration. This points to a cohesive theme of viral entry, genome activation, and latency rather than a single host pathway. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":2},{"id":"GO:0050714","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0019064","count":2},{"id":"GO:2000276","count":2}]},{"hash":"594314127933073751","title":"Unknown","description":"The top GO terms are a highly diverse mix\u2014ribosomal subunit export, glucose-regulated transcription, chromatin formation, various methylation/modification processes, vitamin E biosynthesis, and general stress/metabolic responses\u2014without a clear, single pathway or function linking them. This scattered set suggests no cohesive theme for the cluster. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000056","count":1},{"id":"GO:0046015","count":1},{"id":"GO:0046690","count":1},{"id":"GO:0000183","count":1},{"id":"GO:0042149","count":1}]},{"hash":"1269252955695282217","title":"Central carbon metabolism and development signals","description":"The cluster shows clear enrichment for core metabolic processes, notably glycolysis (canonical glycolysis) and gluconeogenesis, along with an acyl-CoA metabolic process, pointing to central carbon metabolism. In addition, developmental contexts are hinted by post-embryonic development and skeletal muscle tissue regeneration terms, suggesting metabolic activity linked to growth. Other terms (vacuole fusion regulation, hypoxia-related apoptotic signaling) indicate broader cellular regulation and stress responses that can intersect with metabolic state. Taken together, the proteins appear connected by energy metabolism with developmental/regenerative contexts.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0032889","count":1},{"id":"GO:1903298","count":1},{"id":"GO:0061621","count":1}]},{"hash":"581942953891341306","title":"Mitochondrial lipid remodeling and metabolism","description":"This cluster is dominated by lipid biosynthesis and remodeling terms (ether lipid biosynthesis, phosphatidylcholine and cardiolipin remodeling, triglyceride biosynthesis) and includes a mitochondrial ATP synthesis term, pointing to mitochondrial lipid homeostasis as the core function. Immune-related terms (IL-2 production, regulation of T cell death) are present but far less represented, suggesting they are secondary associations rather than the primary theme.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070970","count":3},{"id":"GO:0008611","count":3},{"id":"GO:0016024","count":3},{"id":"GO:0070236","count":3},{"id":"GO:0021587","count":3}]},{"hash":"1385691876769695298","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0070734","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0007064","count":1}]},{"hash":"2168784268007239584","title":"Translation initiation and mRNA processing","description":"The cluster is defined by GO terms for translation initiation and preinitiation complex formation, plus SSU-rRNA maturation and multiple mRNA processing steps (splicing, modification, polyadenylation, stabilization, splice-site recognition), indicating a cohesive role in assembling the translation machinery and coordinating RNA maturation.","confidence":"High","size":3,"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:0000462","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0000380","count":1}]},{"hash":"1326291459384697187","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070734","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0007064","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0007420","count":1}]},{"hash":"1398132293601396437","title":"RNA and protein methylation enzymes","description":"This cluster is dominated by GO terms related to methylation: rRNA methylation, peptidyl-lysine methylation (trimethylation and dimethylation), and N-terminal peptidyl-glycine methylation, plus rDNA heterochromatin formation, all pointing to methyltransferase activity impacting RNA, proteins, and chromatin. The remaining terms are sparse and diverse, suggesting noise rather than a cohesive alternate pathway. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":1},{"id":"GO:0018023","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0018027","count":1}]},{"hash":"1941891586827406385","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0035315","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006369","count":1}]},{"hash":"543669427792761871","title":"Developmental Growth Signaling and Differentiation","description":"The top GO terms point to developmental signaling (Hippo, Wnt), growth control (negative regulation of cardiac muscle proliferation), and differentiation processes (keratinocyte differentiation, axial mesoderm formation), with supporting roles in apoptosis and DNA repair tied to cell fate decisions.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060044","count":3},{"id":"GO:0035329","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0006915","count":3}]},{"hash":"486267375680422526","title":"Brain Region and Neuron Development","description":"This cluster is driven by GO terms pointing to development of multiple brain regions (subthalamus, pons, midbrain, thalamus, hypothalamus, hippocampus) and neuron-specific development (pyramidal neuron development), indicating a coherent theme of brain-region\u2013 and neuron-lineage development. The presence of mitochondrial electron transport and proton transmembrane transport terms likely reflects energy requirements common to developing neurons rather than a separate pathway. Overall, the terms cohere around brain development with neuronal differentiation.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021539","count":1},{"id":"GO:0021548","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0030901","count":1},{"id":"GO:0021794","count":1}]},{"hash":"182320677485737276","title":"Mitochondrial inner membrane protein insertion","description":"The GO terms point most strongly to mitochondrial membrane processes (insertion into the inner membrane and targeting to mitochondrion), suggesting the cluster centers on mitochondrial protein handling. Some terms like eye pigment granule organization and synaptic/olfactory processes are more divergent, but they may reflect broader vesicular transport roles. Overall, the mitochondrial membrane protein import/insertion theme best explains the cluster.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0008057","count":1},{"id":"GO:0048490","count":1}]},{"hash":"1715648956684376246","title":"Mitochondrial phospholipid metabolism","description":"The top GO terms are dominated by mitochondrial-related lipid processes: cardiolipin metabolic process, phospholipid transport and translocation, phosphatidylcholine biosynthesis, and regulation of mitochondrial membrane potential, suggesting a group of proteins involved in mitochondrial lipid handling and membrane dynamics. A few outlier terms (germarium-derived oocyte differentiation, T cell apoptotic process) do not define the cluster, so the core theme remains mitochondrial lipid metabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030706","count":1},{"id":"GO:0090201","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0010917","count":1},{"id":"GO:2001140","count":1}]},{"hash":"1204493993473024812","title":"Gram-positive cell wall biosynthesis","description":"The GO terms cluster around synthesis of cell envelope components\u2014peptidoglycan, lipoteichoic acid, glycolipids, and dolichol-linked oligosaccharide pathways\u2014typical of Gram-positive bacteria. The presence of antibiotic metabolic processes and cell shape/division terms further supports a theme of cell-wall-associated biosynthesis and envelope remodeling. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0016999","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0030259","count":1},{"id":"GO:0009247","count":1}]},{"hash":"1285496489159479623","title":"Dendrite morphogenesis and ephrin signaling","description":"The top terms point to neuronal development with direct references to dendrite morphogenesis and ephrin receptor signaling, supported by actin cytoskeleton dynamics and small GTPase\u2013mediated signaling. While some terms are broader or peripheral (TOR regulation, microvillus assembly), the core cluster aligns with dendrite formation and cytoskeletal remodeling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":2},{"id":"GO:0048013","count":2},{"id":"GO:1904442","count":1},{"id":"GO:0048814","count":1},{"id":"GO:1990792","count":1}]},{"hash":"1524542028457000528","title":"Unknown","description":"The GO terms span immune signaling (TLR3 pathway activation, dsRNA response, IL-2 production) as well as extracellular matrix remodeling and mitochondrial/metabolic processes, with no clear unifying function for all three proteins. Because there is no coherent theme linking these terms to a single specific function, the cluster cannot be assigned a precise label beyond Unknown.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902992","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0034141","count":1},{"id":"GO:0032623","count":1},{"id":"GO:1900210","count":1}]}]