[{"hash":"228715695003400678","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071560","count":5},{"id":"GO:0050731","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0051260","count":4}]},{"hash":"1308688296589602718","title":"T-cell signaling and cytoskeletal remodeling","description":"The top GO terms show a strong emphasis on T cell receptor signaling, IL-4 production, and various signaling pathways (Wnt, ephrin receptor) with concurrent cytoskeletal changes (actin filament binding and cell spreading), indicating a cluster of proteins coordinating immune signaling with cytoskeletal remodeling and adhesion processes, potentially reflecting cross-talk with growth factor and developmental pathways.","confidence":"High","size":29,"edges":6,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":26},{"id":"GO:0090263","count":26},{"id":"GO:0043552","count":26},{"id":"GO:0048013","count":26},{"id":"GO:0071300","count":25}]},{"hash":"1605106671507050675","title":"Neural Developmental Transcription Factors","description":"The terms cluster around development in neural contexts (hippocampus, cerebellar cortex) and transcriptional regulation (DNA-templated transcription, transcription factor activity, JUN phosphorylation, retinoic acid response, serine phosphorylation). This suggests the proteins function as transcription regulators governing neural developmental programs, with some overlap into broader developmental processes (e.g., heart development) but still centered on developmental transcription control in neural tissues.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021766","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0043433","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0021695","count":4}]},{"hash":"2093392498169035749","title":"RNA Pol II Transcription Regulation & RNA Processing","description":"This cluster's top GO terms are dominated by transcription-related processes tied to RNA polymerase II regulation, including regulation of DNA-templated transcription, transcription-coupled repair, and mRNA processing, plus ubiquitin-dependent protein catabolism. A few terms like heme transport or antibiotic response are outliers, but the core signal points to transcriptional control and RNA processing as the shared theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1344709284280930984","title":"Unknown","description":"The GO terms in this cluster cover a wide range of unrelated processes\u2014cell cycle and chromatin-related events (mitotic spindle organization, DNA replication initiation, histone phosphorylation, p53 signaling) alongside membrane trafficking (caveolin-mediated endocytosis), signal regulation (JUN phosphorylation), and various development topics (visual perception, trachea and placenta formation). The lack of a single cohesive theme and no network connections (Edges/Triangles = 0) make it unlikely to reflect a unified biological function, so a precise, representative label cannot be assigned beyond Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901925","count":3},{"id":"GO:0007052","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0032298","count":2},{"id":"GO:0072584","count":2}]},{"hash":"3882653781824856","title":"Immune signaling and cellular regulation","description":"The cluster includes innate immune and antiviral defense terms (innate immune response, defense response to virus) and a regulatory modification (K63-linked ubiquitination), suggesting a core focus on signaling and immune regulation. Other terms point to broader cellular regulation (cell growth, mitotic transition, lipid metabolism, ion response), indicating a mixed set of signaling and general regulatory roles. The balance centers on immune signaling with broader cellular regulation, giving a moderate level of confidence in the label.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0046475","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0007091","count":2},{"id":"GO:0017000","count":2}]},{"hash":"241569463821603973","title":"Synaptic Vesicle Exocytosis Regulation","description":"The cluster centers on synaptic vesicle exocytosis and neurotransmitter secretion, with strong signals for vesicle maturation and presynaptic exocytosis. It also includes regulators of small GTPase signaling (Rho, Ras, GTPases), reflecting control of vesicle trafficking and cytoskeletal dynamics; some auxiliary terms touch broader neuronal signaling (autophagy and Wnt pathways), but the dominant theme is vesicle release regulation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":8},{"id":"GO:0007269","count":7},{"id":"GO:0035023","count":6},{"id":"GO:0016188","count":6},{"id":"GO:0099525","count":6}]},{"hash":"426983913017329119","title":"Neural development and synaptic signaling","description":"This cluster's top GO terms are heavily weighted toward nervous system processes, including visual perception, long-term potentiation, myelination in the peripheral nervous system, and regulation of kinase activity, which together point to neural development and synaptic signaling roles.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0071902","count":3}]},{"hash":"2122195761234772159","title":"Cell Cycle Checkpoints and DNA Replication Regulation","description":"The cluster centers on mitotic and G2 DNA damage checkpoints and regulation of replication initiation, with connected themes in transcriptional regulation (RNA Pol II) and some nuclear RNA processing and ribosome export. This suggests a cohesive theme of cell-cycle\u2013coupled control of DNA replication and gene expression, with ancillary nuclear processes.","confidence":"Medium","size":29,"edges":55,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0032298","count":2},{"id":"GO:1903026","count":2}]},{"hash":"1523660636797287642","title":"Antiviral Ubiquitination and Autophagy","description":"This cluster centers on ubiquitin-related processes (polyubiquitination, autoubiquitination, ubiquitin-dependent ERAD) together with antiviral innate immune responses (defense response to virus, innate immune response) and autophagy. These functions commonly coordinate to tag and degrade viral components and manage intracellular viral material, forming a cohesive module of ubiquitin-mediated defense and autophagic clearance. Some terms like microtubule localization may reflect transport roles but do not redefine the main theme.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0000209","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0051865","count":5}]},{"hash":"963592142689010860","title":"Transcriptional Regulation and Vesicle Trafficking","description":"The terms cluster around two main themes: control of gene expression (DNA-templated transcription, mRNA transport, nuclear import) and intracellular signaling/transport (GTPase activity regulation, serine dephosphorylation, TORC1 signaling, ER-Golgi vesicle transport), with cell division as a related process. An outlier term about defense against Gram-positive bacteria is present but less central, so the label reflects a core of transcriptional and trafficking regulators that also tie into growth signaling. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0051028","count":4}]},{"hash":"308824580855618688","title":"Spliceosome-mediated RNA processing and export","description":"Based on the top GO terms, the proteins cluster around mRNA splicing (via spliceosome), mRNA export, and splicing regulation, indicating a shared role in RNA processing and maturation. Some terms like transcription or blastocyst formation are ancillary annotations, but the predominant signal is spliceosome-mediated RNA splicing and export.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0001825","count":2},{"id":"GO:1900363","count":2}]},{"hash":"2301425592025226356","title":"Ubiquitin-ERAD Proteostasis","description":"The set is enriched for GO terms tied to ubiquitin modification and ER-associated degradation, including deubiquitination, sumoylation, and ERAD-related processes, pointing to a protein quality-control/proteostasis module. While some terms appear outdated or peripheral (rRNA maturation, TNF signaling), the strongest signal centers on ubiquitin-dependent proteolysis and ER quality control.","confidence":"High","size":28,"edges":351,"triangles":2664,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":13},{"id":"GO:0016925","count":11},{"id":"GO:0030433","count":11},{"id":"GO:1904378","count":11},{"id":"GO:0014070","count":10}]},{"hash":"1916122441747537705","title":"RNA Processing and Translation Machinery under Cellular Stress","description":"This cluster centers on RNA processing and translation machinery (mRNA splicing, ribosome biogenesis, translation initiation/reinitiation, and protein homooligomerization) and includes stress- and development-related processes such as ER-stress\u2013induced apoptotic signaling, DNA damage checkpoint response, nutrient response, and brain development. The prominence of spliceosome and ribosome\u2013related terms, with supporting stress/apoptosis signals, suggests a cohesive module of gene expression machinery recruited during cellular stress, including neural development contexts.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":13},{"id":"GO:0042254","count":11},{"id":"GO:0001731","count":11},{"id":"GO:0007584","count":11},{"id":"GO:0002188","count":11}]},{"hash":"1559545945144003361","title":"Broad regulatory and developmental processes","description":"This cluster features terms tied to general cellular regulation (phosphorylation/dephosphorylation, translation) and developmental pathways (brain development, angiogenesis), with additional links to DNA repair and viral processes. The GO terms are diverse rather than pointing to a single cohesive pathway, suggesting a broad collection of proteins involved in regulation and development rather than a narrow function. Therefore a broad label that captures regulatory and developmental roles is appropriate.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016310","count":6},{"id":"GO:0016311","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0019310","count":3}]},{"hash":"1604061026529926339","title":"Carbohydrate Biosynthesis and DNA Repair","description":"The cluster shows strong signals for carbohydrate metabolism (glycogen/starch biosynthesis and sucrose metabolism) and several DNA metabolism/repair processes (DNA replication, nucleotide-excision and base-excision repair, RNA-templated DNA biosynthesis). This combination suggests proteins involved in both carbohydrate biosynthesis and genome maintenance, or a plant/chloroplast context where metabolic and DNA repair functions co-occur, hence the label. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0005978","count":5},{"id":"GO:0006260","count":3},{"id":"GO:0019252","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0070893","count":2}]},{"hash":"1759492060766463109","title":"Actin Cytoskeleton Remodeling in Oocyte Division","description":"The top terms cluster around actin-related processes and meiotic division, including actin nucleation, cleavage furrow formation, polar body extrusion, and oocyte karyosome formation. This suggests a primary theme of actin-driven cytoskeletal dynamics during oocyte meiosis and cell division, with some additional neuronal differentiation terms present but less central. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045010","count":2},{"id":"GO:0045671","count":2},{"id":"GO:0090116","count":1},{"id":"GO:0040038","count":1},{"id":"GO:0036089","count":1}]},{"hash":"1855514086537002797","title":"Cortical neuron development and synaptic maturation","description":"The top GO terms point to processes involved in cerebral cortex development, including layer formation, neuron migration, oligodendrocyte differentiation, and synaptic assembly/plasticity (long-term potentiation). Although angiogenesis terms appear, the strongest signal centers on neural development and synaptic maturation in the cortex, with estradiol responsiveness potentially modulating these processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0001525","count":2},{"id":"GO:2001223","count":2},{"id":"GO:0021819","count":2},{"id":"GO:0016525","count":2}]},{"hash":"1485501037689997661","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms are dominated by DNA-templated transcription, transcriptional regulation by RNA polymerase II, and chromatin-related processes (chromatin remodeling, nucleosome mobilization, meiosis chromosome pairing), suggesting the proteins in this cluster function mainly in controlling gene expression via chromatin state. A few terms (proteolysis, cell adhesion, sucrose catabolic process, apoptotic signaling, actin patch localization) are less directly related and may reflect diverse roles or annotation noise, but they do not override the central theme of transcription control and chromatin dynamics.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0007155","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0005987","count":2}]},{"hash":"1116131604033756431","title":"Ribosome Biogenesis and rRNA Maturation","description":"The top GO terms are dominated by maturation and processing steps for LSU- and SSU-rRNA (from tricistronic transcripts and ITS1), plus general ribosome biogenesis and a related RNA methylation step, indicating a cohesive cluster centered on ribosome production and rRNA maturation. A few terms related to TORC1 signaling, ERAD, and cell division may reflect ancillary regulatory connections but do not define the main function. This makes the label-specific to ribosome assembly processes.","confidence":"High","size":28,"edges":4,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":8},{"id":"GO:0000466","count":8},{"id":"GO:0042254","count":7},{"id":"GO:0000447","count":6},{"id":"GO:0036265","count":6}]},{"hash":"58902218888779432","title":"Unknown","description":"The top GO terms are very diverse, spanning insulin signaling, heart development, actin filament assembly, macrophage foam cell differentiation, chromatin organization, histone modification, and various developmental processes. Several terms are obsolete, and there is no single cohesive biological function linking the 28 proteins. Because of this heterogeneity, there isn\u2019t a clear, representative theme for the cluster. ","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0003281","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0035948","count":1},{"id":"GO:0010742","count":1}]},{"hash":"1765974958438213733","title":"Cell signaling and stress responses","description":"This cluster\u2019s top GO terms point to multiple signaling pathways (insulin, T cell receptor, PDGF) and cellular responses to diverse stimuli (nitric oxide, retinoic acid, UV damage), plus DNA replication/repair processes. The common thread is involvement in signal transduction and stress-response programs rather than a single pathway, justifying a label around cell signaling and stress responses. Confidence: Medium","confidence":"","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0008286","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0070914","count":3},{"id":"GO:0071300","count":3}]},{"hash":"1199094335960602313","title":"Neural development and signaling regulators","description":"This cluster shows GO terms tied to brain development, transcriptional control, cilium assembly, and signaling pathways (including GTPase regulation and GPCR signaling), as well as protein ubiquitination. Taken together, these features point to proteins involved in neural development and the regulation of cellular signaling, rather than a single narrow process. Therefore, labeling it as neural development and signaling regulators captures the most coherent shared theme among the terms.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000209","count":3},{"id":"GO:0060271","count":3}]},{"hash":"1237874719432259693","title":"Ribosome biogenesis and cytoplasmic translation","description":"This cluster is dominated by GO terms for translation initiation, cytoplasmic translation, and ribosome biogenesis, pointing to proteins involved in ribosome assembly and protein synthesis. While there are scattered terms related to actin cytoskeleton organization and cell shape, the translation-related terms are most prevalent, supporting a primary theme in ribosome function.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0008360","count":1},{"id":"GO:0090140","count":1}]},{"hash":"39835158561258021","title":"Transcription and Bacterial Biosynthesis","description":"The Top Terms show a strong emphasis on DNA-templated transcription along with multiple biosynthetic processes (lipopolysaccharide, antibiotic, poly-hydroxybutyrate), suggesting a cluster of proteins linked to gene expression and metabolite production in bacteria. Some obsolete or non-bacterial terms (Notch signaling regulation; histone demethylation) may reflect annotation noise rather than a core function. Confidence: Medium.","confidence":"","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0009103","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0042264","count":7},{"id":"GO:0017000","count":6}]},{"hash":"1127575775051828921","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000462","count":5},{"id":"GO:0000472","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0000466","count":5}]},{"hash":"2054495756908634056","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster\u2019s top GO terms point to ubiquitin-dependent proteolysis, including K48-linked ubiquitination, ERAD, autoubiquitination, and SCF-proteasomal pathways, indicating a core role in tagging proteins for proteasomal degradation. Peroxisomal import and X-chromosome inactivation-related terms appear less central, suggesting secondary or context-specific processes, but the dominant pattern is ubiquitin-proteasome\u2013mediated protein turnover.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0070936","count":8},{"id":"GO:0051865","count":7},{"id":"GO:0046621","count":6},{"id":"GO:0016558","count":6}]},{"hash":"239482423783706157","title":"Cardiac development and metabolic stress responses","description":"This cluster shows enrichment in heart development terms (in utero embryonic development; ventricular cardiac muscle tissue morphogenesis) alongside metabolism (glycolytic process; L-alanine catabolic process) and stress/ signaling responses (response to xenobiotic stimulus; cellular response to hyperoxia; cellular response to cAMP), suggesting proteins involved in cardiovascular development coupled with metabolic regulation and stress signaling. While there is some transcriptional activity represented, the dominant themes point to cardiac development intersecting with metabolic and signaling pathways.","confidence":"Medium","size":28,"edges":283,"triangles":1474,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0001701","count":6},{"id":"GO:0042853","count":6},{"id":"GO:0006096","count":5},{"id":"GO:0042493","count":5}]},{"hash":"1153624271505924912","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"Dominant GO terms are ubiquitin-dependent protein catabolic processes and polyubiquitination, SCF-dependent proteasomal degradation, and ERAD, indicating a cohesive role in tagging and degrading proteins, with some links to cell cycle and DNA damage regulation. ","confidence":"High","size":28,"edges":5,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":14},{"id":"GO:0031146","count":12},{"id":"GO:1902916","count":9},{"id":"GO:0031571","count":9},{"id":"GO:0000209","count":8}]},{"hash":"1010897951910379733","title":"Metabolic and Developmental Pathways","description":"The cluster features core energy metabolism terms (glycolytic process, pyruvate decarboxylation to acetyl-CoA, TCA cycle) alongside distinct developmental/morphogenesis terms (trophoblast giant cell differentiation, EMT in endocardial cushion formation, cartilage morphogenesis, pancreatic cell development). This mix suggests proteins involved in metabolism with links to differentiation programs, rather than a single unified pathway. Thus the label reflects a broad theme rather than a precise function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0043617","count":1},{"id":"GO:0006213","count":1},{"id":"GO:0033512","count":1},{"id":"GO:0006096","count":1}]},{"hash":"9081570167207416","title":"Unknown","description":"The top GO terms cover ubiquitination, cell proliferation, lens fiber differentiation, dendrite development, actin dynamics, meiotic division, intraciliary transport, aging, cytokinesis, and viral mRNA export. This mix spans diverse cellular processes (modification, growth, differentiation, cytoskeleton, transport, and host\u2013virus interactions) with no single cohesive function tying the proteins together. Therefore there is no clear shared theme to name the cluster more specifically.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070979","count":4},{"id":"GO:0008284","count":4},{"id":"GO:0070306","count":3},{"id":"GO:0050773","count":3},{"id":"GO:0030042","count":3}]},{"hash":"1573365575251281869","title":"Nuclear RNA and ribosomal subunit transport","description":"The top GO terms are dominated by nuclear import/export processes for RNAs and ribosomal subunits (ribosomal subunit export from the nucleus, RNA import/export, NLS-bearing protein import), indicating a cohesive function in transport of ribonucleoprotein complexes between nucleus and cytoplasm and involvement in ribosome biogenesis. Some secondary terms related to protein regulation appear but do not strongly redefine the main theme. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000056","count":4},{"id":"GO:0042176","count":4},{"id":"GO:0006607","count":3},{"id":"GO:0060188","count":3},{"id":"GO:0006656","count":3}]},{"hash":"1214080202777240466","title":"Splicing and mRNA decay machinery","description":"Top GO terms cluster around RNA processing and post-transcriptional control: spliceosome assembly and alternative splicing, plus decapping, deadenylation-independent decapping, translational repression, and granule formation (P-bodies, stress granules), indicating a core function in RNA splicing and mRNA turnover. A few terms reference innate immune signaling and germ-line feminization that are less central here.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":3},{"id":"GO:0000380","count":2},{"id":"GO:0010923","count":2},{"id":"GO:0040022","count":2},{"id":"GO:0045947","count":1}]},{"hash":"129768866713161704","title":"Viral Lifecycle and Host RNA Processing","description":"The dominant GO terms point to viral processes\u2014virion assembly, viral release from host, and proviral latency\u2014indicating components related to viral life cycles and virus-host interactions. The accompanying RNA processing terms (splicing, mRNA export, translational initiation regulation, and regulatory ncRNA-mediated silencing) suggest these proteins also interface with host RNA machinery\u2014often hijacked or modulated during viral infection. Together, they imply a cluster of factors involved in virus\u2013host dynamics rather than a single canonical host pathway.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":3},{"id":"GO:0019076","count":3},{"id":"GO:0030260","count":3},{"id":"GO:0075713","count":3},{"id":"GO:1900363","count":2}]},{"hash":"1751810609680181329","title":"Developmental growth and cell cycle regulation","description":"This cluster centers on processes tied to development and control of cell growth: root development, regulation of the cell cycle, cell migration, and negative regulation of cell proliferation, along with signals that modulate apoptosis and canonical pathways like Wnt. Additional hints from proton transmembrane transport and nuclear import suggest integrated membrane signaling and nuclear trafficking, all consistent with a developmental signaling module that governs growth, movement, and differentiation.","confidence":"High","size":27,"edges":179,"triangles":591,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015991","count":13},{"id":"GO:0006607","count":11},{"id":"GO:0043547","count":11},{"id":"GO:0048364","count":10},{"id":"GO:0007050","count":10}]},{"hash":"1238230633737108324","title":"Hippo-Wnt Growth and Differentiation Signaling","description":"This cluster is dominated by terms related to cell growth control and differentiation in epithelial contexts: Hippo signaling, positive regulation of canonical Wnt signaling, and contact inhibition. Keratinocyte differentiation and regulation of TGF-beta signaling further point to epithelial fate decisions, while apoptosis and transcriptional regulation indicate broader cellular state control.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006915","count":15},{"id":"GO:0035329","count":15},{"id":"GO:0090263","count":15},{"id":"GO:0030216","count":15},{"id":"GO:0060044","count":15}]},{"hash":"1911445480974744729","title":"Developmental differentiation and tissue morphogenesis","description":"Top terms indicate a developmental/differentiation focus: neuron differentiation, substantia nigra development, lung epithelial cell differentiation, branching involved in blood vessel morphogenesis, and cell-cell adhesion, all pointing to tissue morphogenesis. A few terms reflect general cellular processes (DNA replication, ER-Golgi transport, lipid A biosynthesis) that are less specific to the cluster\u2019s core function. Therefore, a label capturing development and morphogenesis is appropriate.","confidence":"High","size":27,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0009245","count":5},{"id":"GO:0001569","count":4},{"id":"GO:0098609","count":4}]},{"hash":"913395151894316483","title":"Cold-induced transcription and chromatin remodeling","description":"This cluster centers on cold response and regulation of gene expression, with GO terms for transcription, chromatin modification, and ubiquitination, plus cell growth/diversification signals; together these suggest coordinated transcriptional control and chromatin state changes in response to cold.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009409","count":6},{"id":"GO:0006351","count":4},{"id":"GO:0016049","count":4},{"id":"GO:0048709","count":4},{"id":"GO:0007049","count":4}]},{"hash":"978211042696834730","title":"Neural development and synaptic transmission","description":"The cluster centers on neural processes, with terms for brain development and both glutamatergic and GABAergic synaptic transmission, plus sensory perception of sound. Although there are accompanying terms related to transcription and ribosome biogenesis, the strongest and most frequent signals are neuronal development and synaptic signaling, suggesting proteins involved in forming and communicating neural networks.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0007605","count":2}]},{"hash":"1190695003392336849","title":"Meiosis and chromosome segregation","description":"This cluster is driven by meiosis-focused processes: synaptonemal complex assembly, meiosis I spindle assembly checkpoint signaling, regulation of homologous chromosome segregation, meiotic sister chromatid cohesion, and microsporogenesis. Ubiquitin-dependent protein catabolic process and related regulation also appear, suggesting proteostasis during meiosis. Together, these terms point to proteins involved in meiotic chromosome pairing and segregation and associated checkpoint control.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0007130","count":1},{"id":"GO:1905318","count":1},{"id":"GO:0060629","count":1},{"id":"GO:0009556","count":1}]},{"hash":"668330920409583979","title":"Mitochondrial gene expression and maintenance","description":"This cluster is dominated by GO terms linked to mitochondrial function: translation, DNA-templated transcription, and histidyl-tRNA aminoacylation within mitochondria, plus protein import into the mitochondrial matrix and respiration (electron transport chain). Additional signals for mitochondrial stress response (menadione) and DNA repair support a cohesive theme of mitochondrial gene expression and genome maintenance. Some terms are peripheral or broad (embryonic development, aging), but they can reflect mitochondrial roles in development and longevity, respectively.","confidence":"High","size":27,"edges":157,"triangles":295,"max_degree":19,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006281","count":3},{"id":"GO:0022904","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0030150","count":2}]},{"hash":"2105277597335226969","title":"Synaptic plasticity and vesicle transport","description":"The proteins appear to function in neuronal signaling and structural plasticity, with GO terms spanning long-term synaptic depression, neurotransmitter secretion, dendritic spine morphogenesis, and regulation of synapse structural plasticity, along with positive regulation of anterograde synaptic vesicle transport. Ubiquitination regulation (including K63-linked and autoubiquitination) suggests modulation of synaptic protein turnover, reinforcing a neural communication/plasticity theme. The vocalization term supports a neuronal context but is less specific than the core synaptic functions. Confidence in this cohesive theme is High.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060292","count":3},{"id":"GO:0071625","count":3},{"id":"GO:0051497","count":3},{"id":"GO:1902498","count":3},{"id":"GO:0007269","count":3}]},{"hash":"63666006961630288","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for ribosome biogenesis, ribosomal subunit biogenesis, and translation, with associated activity in mRNA export, which points to components of the protein synthesis machinery and its assembly. Additional terms on ER-to-Golgi transport and proteasome/ERAD-related processes suggest integrated protein quality control and trafficking linked to growth and proliferation. Together, these functions reflect a cohesive theme around ribosome production and the translation apparatus, with supportive roles in protein handling during cell growth.","confidence":"High","size":27,"edges":8,"triangles":1,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0051260","count":4}]},{"hash":"6637953738215693","title":"Antibiotic, lipid, and cofactor biosynthesis","description":"This cluster is dominated by biosynthetic process terms: antibiotic biosynthetic process, sterol biosynthesis, biotin biosynthesis, and phosphatidylcholine biosynthetic process, plus related methylation steps (N-terminal peptidyl methylation/trimethylation). These point to enzymes involved in diverse biosynthetic pathways for antibiotics, lipids, and cofactors, with a few outliers related to immune responses that may represent noise. Overall, the shared theme is biosynthesis of small molecules and lipids, sometimes accompanied by post-translational modifications of proteins in these pathways.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0016049","count":4},{"id":"GO:0016126","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0018013","count":4}]},{"hash":"153529435589033613","title":"DNA Damage Response and Chromatin Regulation","description":"The top GO terms cluster around genome maintenance and transcriptional control (DNA-templated transcription, DNA repair, chromatin organization, telomere maintenance) with associated cell-cycle and apoptosis processes (spindle assembly, apoptotic processes, neuron apoptosis). This suggests a cohesive module of proteins coordinating transcription, chromatin dynamics, and genome stability under stress, with downstream links to cell fate decisions. A few terms like hypoxia response and skeletal system development hint broader roles, but the core theme remains genome integrity and regulation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0071456","count":2}]},{"hash":"665020449411131075","title":"Neural development and vesicle trafficking","description":"Based on the top GO terms, the cluster is enriched for neural development processes (brain development, neural tube closure), suggesting a neural developmental role. Additional terms indicate involvement in intracellular logistics and regulation, including ER-to-Golgi vesicle transport, GTPase activity modulation, proteasomal ubiquitin-dependent protein turnover, and transcriptional control. Together, these point to a cohesive theme of neural development with emphasis on trafficking and regulatory processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0000132","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0031146","count":3}]},{"hash":"147960751763871854","title":"Peripheral nerve development and axon regeneration","description":"The terms cluster around Schwann cell development, axon extension/regeneration, and axon fasciculation, with supporting cell-ECM adhesion cues, indicating proteins involved in peripheral nerve growth and repair.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007160","count":4},{"id":"GO:0071372","count":3},{"id":"GO:0032495","count":3},{"id":"GO:0043113","count":3},{"id":"GO:2001274","count":3}]},{"hash":"2109692898554387499","title":"Unknown","description":"This cluster shows a highly heterogeneous set of functions, from antibiotic response and DNA integration to amino acid biosynthesis and various signaling/fate processes (cell cycle, migration, Wnt signaling, apoptosis). There isn\u2019t a clear, shared biological theme tying the proteins together, so a single coherent label isn\u2019t evident.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0015074","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0019284","count":2}]},{"hash":"348592382439475520","title":"Angiogenesis and organ development regulators","description":"The top terms cluster around regulation of blood vessel formation and VEGF signaling, alongside heart, eye, bone, muscle, and nervous system development, suggesting these proteins broadly modulate developmental pathways across multiple tissues, with vascular-related processes being prominent.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016525","count":3},{"id":"GO:1900748","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0070493","count":3},{"id":"GO:0042552","count":3}]},{"hash":"381124925803371503","title":"Dendritic Spine Morphogenesis and Cytoskeletal Signaling","description":"The cluster is enriched for processes related to dendritic spine morphogenesis, lamellipodium assembly, ephrin receptor signaling, and Wnt signaling, all of which center on actin-driven cytoskeletal remodeling during neural development and synapse formation. While some terms like apoptotic processes and blastocyst formation are present, the dominant theme ties to structural remodeling and signaling guiding neurite and synapse maturation.","confidence":"Medium","size":26,"edges":277,"triangles":1684,"max_degree":25,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0050798","count":4},{"id":"GO:0048013","count":4},{"id":"GO:0060997","count":4}]},{"hash":"7463853243373174","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":287,"triangles":1953,"max_degree":25,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0000472","count":6},{"id":"GO:0000480","count":6},{"id":"GO:0048568","count":5},{"id":"GO:0006289","count":5}]},{"hash":"1660350144797854934","title":"Hypoxia-regulated transcription in myogenesis and vasculogenesis","description":"The dominant GO terms point to transcriptional regulation (DNA-templated transcription, RNA Pol II regulation) with a specific link to hypoxia, plus development-related processes such as myoblast differentiation and vasculogenesis, and Notch signaling modulation. This suggests a cohesive theme where hypoxia-responsive transcriptional control governs muscle and blood vessel formation, with Notch as part of signaling interplay. Some terms appear obsolete or noisy (e.g., certain hydroxylations, LPS biosynthesis), but the core signal is transcriptional regulation in hypoxia-driven development.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0036138","count":5},{"id":"GO:0061428","count":5},{"id":"GO:0042264","count":5}]},{"hash":"837769586306152199","title":"Ubiquitin-mediated ERAD and Actin Dynamics","description":"This cluster is enriched for ubiquitination and ERAD-related terms (protein ubiquitination, polyubiquitination, ERAD pathway), suggesting a proteostasis/quality-control theme. It also includes several actin cytoskeleton remodeling terms (actin filament depolymerization, Arp2/3-mediated actin nucleation, actin filament bundle assembly), indicating dynamic cytoskeletal regulation. Some meiosis/mitosis-related terms hint at cell-division contexts, possibly linking proteostasis and cytoskeletal changes during division or stress responses. Overall, the label reflects both ubiquitin-dependent quality control and actin remodeling as core themes.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0000070","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0000209","count":2}]},{"hash":"1314819323072440689","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0000472","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0048568","count":5}]},{"hash":"565957353769554921","title":"DNA replication initiation and replication machinery","description":"The cluster is dominated by GO terms related to DNA replication initiation and progression (e.g., DNA replication initiation, DNA replication, mitotic DNA replication preinitiation complex assembly, DNA strand elongation in mitotic replication, and GINS complex assembly), pointing to a coherent set of proteins involved in starting and carrying out DNA replication during the cell cycle. A few spliceosomal assembly terms appear among the top terms, which may reflect annotation noise or multifunctional proteins, but the core signal centers on replication initiation/assembly. Confidence is High.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000387","count":1},{"id":"GO:0000245","count":1},{"id":"GO:1902977","count":1},{"id":"GO:1902983","count":1}]},{"hash":"1109833248008242959","title":"Wnt-regulated development and proliferation","description":"The top GO terms center on Wnt signaling regulation (positive regulation of canonical Wnt signaling), development and differentiation (keratinocyte differentiation, skeletal system development), and control of growth and apoptosis (apoptotic process, mitotic cell cycle, negative regulation of cell proliferation). Additional terms like receptor clustering and dendritic spine morphogenesis point to broader signaling and morphogenesis roles, suggesting a cluster of proteins involved in signaling-driven development and lineage/size regulation. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":7},{"id":"GO:0043113","count":7},{"id":"GO:0030216","count":7},{"id":"GO:0043065","count":6},{"id":"GO:0060997","count":6}]},{"hash":"1671094139690071617","title":"Neuronal transcription regulation and synaptic trafficking","description":"This cluster features GO terms for regulation of transcription (RNA polymerase II\u2013mediated) alongside neuronal/synaptic processes (glutamatergic synaptic transmission, receptor recycling, endosome size). The co-occurrence suggests proteins involved in activity-dependent gene expression and membrane trafficking at synapses, linking transcriptional control to synaptic signaling. Some terms are outdated or metabolic, but the dominant themes point to neuronal gene regulation coupled with receptor trafficking.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1613687285841330034","title":"Unknown","description":"The top terms span stress response, mitochondrial dynamics, organ development (heart, brain regions), vesicle transport, cell adhesion, and cell migration. There isn\u2019t a clear, unified biological function linking these terms, so a cohesive label isn\u2019t evident. ","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":3},{"id":"GO:0000266","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0070940","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2240739626282693541","title":"Mitotic division and microtubule regulation","description":"The top terms are dominated by cell division, metaphase/anaphase transition, and microtubule severing, which together indicate proteins involved in mitosis and spindle dynamics. Some entries are obsolete or peripheral (ERAD, chaperone refolding, chlorophyll, lead ion response) and likely reflect annotation noise rather than a distinct alternative function. Overall, the core theme is mitotic progression and microtubule regulation. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0030433","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0051013","count":5},{"id":"GO:1902325","count":4}]},{"hash":"1097647782441112668","title":"Mitochondrial ATP Synthesis and Respiration","description":"This cluster is dominated by mitochondrial energy metabolism signals: ATP synthesis coupled electron transport, proton motive force-driven ATP synthesis, and mitochondrial ATP synthase complex assembly, plus regulation of mitochondrial membrane potential and apoptotic changes, suggesting a cohesive theme of mitochondrial respiration and energy production. Some additional terms (iron-sulfur cluster assembly, tetrahydrofolate and formate metabolism) may reflect ancillary mitochondrial biosynthetic roles.","confidence":"High","size":26,"edges":324,"triangles":2576,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0008637","count":2},{"id":"GO:0046653","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0015942","count":2}]},{"hash":"1642705720000078453","title":"Vertebrate Development Transcription Regulators","description":"The top GO terms point to transcriptional regulation (DNA-templated transcription) and key vertebrate developmental processes (neural tube closure, forebrain development, skeletal system development, multicellular organism development). This suggests the cluster comprises proteins that regulate gene expression during vertebrate development. Peripheral terms like ER-stress\u2013related apoptosis and metal response appear less central to the core theme but may reflect pleiotropy or context-dependent regulation. ","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0050830","count":3}]},{"hash":"1394907564014626736","title":"Cell Signaling and Stimulus Response","description":"The cluster shows enrichment for signaling and responses to environmental cues, including GPCR signaling, cellular communication, detection of chemical and mechanical stimuli, sensory perception, and processes that regulate protein localization at the plasma membrane. While some terms are broad or obsolete, the recurring theme is how cells transmit and respond to signals across diverse contexts (signaling, stress responses, and differentiation).","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0061408","count":4},{"id":"GO:0070212","count":4},{"id":"GO:0097497","count":4},{"id":"GO:0045444","count":4}]},{"hash":"322197372787520174","title":"Embryonic Differentiation and ECM Adhesion","description":"The top GO terms suggest developmental processes such as endodermal differentiation and chondrocyte morphogenesis, paired with extracellular matrix and cell-adhesion pathways (hyaluronan metabolism, integrin signaling, heterotypic cell-cell adhesion). Immune components (T cell activation, complement) and coagulation appear as well, indicating roles in tissue remodeling during development where ECM interactions and cell adhesion guide morphogenesis. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":6},{"id":"GO:0070208","count":6},{"id":"GO:0003429","count":5},{"id":"GO:0007596","count":5},{"id":"GO:0002291","count":5}]},{"hash":"55363722004697732","title":"Cell cycle and transcriptional regulation cluster","description":"The cluster shows enrichment for GO terms related to cell cycle, DNA replication, intracellular signaling, and mRNA processing, indicating a core role in regulating cell division and gene expression. Additional terms touch on signaling and membrane processes, but the dominant signal is regulation of cell cycle and transcription.","confidence":"Medium","size":25,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1580366617988848704","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":82,"triangles":106,"max_degree":19,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006813","count":20},{"id":"GO:0071300","count":19},{"id":"GO:0007258","count":19},{"id":"GO:0031532","count":19},{"id":"GO:0002741","count":19}]},{"hash":"1016214456077840086","title":"Neural development and axon regeneration signaling","description":"The top GO terms cluster around neural development and regeneration\u2014cerebellar cortex formation, Bergmann glial differentiation, and regulation of axon regeneration\u2014together with signaling pathways (insulin receptor, MAPK/ERK) and their negative regulation. Although an immune signaling term appears, the predominant theme points to neural development and axon-regeneration signaling networks, with MAPK/ERK pathway modulation as a key component.","confidence":"High","size":25,"edges":16,"triangles":0,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048679","count":14},{"id":"GO:2001275","count":14},{"id":"GO:0050852","count":14},{"id":"GO:0008286","count":14},{"id":"GO:0021697","count":14}]},{"hash":"1359190948691838088","title":"Spliceosome-driven mRNA processing and regulation","description":"The cluster is enriched for spliceosome-mediated mRNA processing\u2014splicing, splice site recognition, and regulation of alternative splicing\u2014as well as regulation of polyadenylation and mRNA stability, with additional hints from ncRNA-mediated gene silencing. This cohesive pattern points to a core function in mRNA maturation and its regulation.","confidence":"High","size":25,"edges":252,"triangles":1398,"max_degree":24,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":15},{"id":"GO:0031047","count":13},{"id":"GO:0048026","count":13},{"id":"GO:0010610","count":12},{"id":"GO:0045292","count":11}]},{"hash":"2118833537180217896","title":"Redox and lipid metabolism with prostaglandins","description":"The cluster shows a cohesive set of GO terms centered on cellular redox homeostasis and oxidant detoxification (e.g., cellular redox homeostasis, cellular oxidant detoxification, response to hydrogen peroxide) alongside lipid metabolism processes (cholesterol catabolic process, fatty acid omega-oxidation) and prostaglandin biosynthesis. The presence of reproductive development terms (female gonad development, uterus development) aligns with prostaglandin signaling roles in reproduction, supporting a theme of redox-balanced lipid metabolism with reproductive signaling. Overall, the proteins appear tied to managing oxidative stress while engaging in lipid-derived signaling pathways.","confidence":"Medium","size":25,"edges":68,"triangles":89,"max_degree":16,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0046232","count":7},{"id":"GO:0045454","count":6},{"id":"GO:0008585","count":6},{"id":"GO:0001516","count":6}]},{"hash":"236986544442972349","title":"Steroidogenesis and lipid metabolism with ion transport","description":"The top terms cluster around steroid biosynthesis (cortisol and aldosterone) and P450-driven lipid oxidation (epoxygenase pathway, cholesterol catabolism, omega-oxidation), suggesting a lipid-metabolic, membrane-associated function. The inclusion of proton and potassium membrane transport and homeostasis hints at a coordinated role in maintaining membrane potential while processing lipids and steroids. The sparse edges and lack of many interaction triangles still support a cohesive theme around lipid metabolism and steroidogenesis tied to membrane transport processes.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034651","count":2},{"id":"GO:0032342","count":2},{"id":"GO:0019373","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0030322","count":2}]},{"hash":"1966819546973839403","title":"COPII trafficking and Rho/Rac GTPase signaling","description":"These proteins appear to form a module centered on ER-to-Golgi vesicle trafficking (COPII) with regulation of small GTPases, particularly Rho and Rac, which control cytoskeletal dynamics and vesicle dynamics. The presence of terms like COPII cargo loading, positive regulation of GTPase activity, and regulation of Rho/Rac signaling supports a cohesive theme around trafficking coupled to GTPase-driven signaling; other terms (e.g., transcription, apoptosis) may reflect broader network connections or pleiotropy rather than a core function of the cluster.","confidence":"Medium","size":25,"edges":24,"triangles":0,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0090110","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0090190","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035023","count":2}]},{"hash":"815808387793264708","title":"Diverse signaling and developmental responses","description":"This cluster shows a mix of GO terms centered on signal transduction and responses to stimuli across development and physiology (neural signaling, responses to cocaine, prostaglandins, GM-CSF, placental development, apoptosis, migration, and Rho signaling). The broad and heterogeneous functions suggest a general theme of signaling and developmental response rather than a single cohesive pathway, hence a broad label. ","confidence":"Low","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035249","count":4},{"id":"GO:0042220","count":3},{"id":"GO:0001893","count":3},{"id":"GO:0060709","count":3},{"id":"GO:0097194","count":3}]},{"hash":"2260368233741753209","title":"IFN-\u03b3\u2013driven innate immunity and antigen presentation","description":"The cluster is enriched for innate immune responses, including IFN-\u03b3 signaling (GO:0060335), TLR4 signaling, and dendritic cell antigen processing and presentation, indicating activation of innate immunity and antigen presentation pathways. It also includes terms for integrin signaling, keratinocyte migration, and membrane protein ectodomain proteolysis, suggesting coordinated cell adhesion and tissue remodeling during immune responses. A couple of terms related to subtelomeric heterochromatin formation and mitotic cell cycle may reflect proliferative or chromatin dynamics in immune/tissue cells.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060335","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007229","count":2}]},{"hash":"1814768029487237839","title":"Mitotic cell cycle and Golgi-ER transport proteins","description":"This cluster is dominated by GO terms related to the cell cycle, mitosis, and spindle assembly (cell cycle, cell division, mitotic cell cycle, mitotic spindle assembly), indicating proteins involved in mitotic progression. Alongside, there are several vesicle trafficking terms between the Golgi and ER (retrograde vesicle-mediated transport, Golgi to ER; ER to Golgi vesicle-mediated transport), suggesting concomitant roles in intracellular trafficking during cell division. A few neuronal development terms appear but are secondary to the core mitotic/trafficking theme. Overall, the cluster reflects coordination of mitosis and Golgi-ER transport processes. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007049","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0006890","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0071260","count":5}]},{"hash":"755682802736279434","title":"Rho-actin signaling and muscle development","description":"The top GO terms cluster around actin cytoskeleton organization, regulation of Rho protein signaling, GTPase activation, and skeletal muscle fiber development, with related calcium-response terms. This points to a set of proteins that coordinate cytoskeletal dynamics and calcium-dependent signaling during muscle differentiation and muscle cell function. A few terms such as sensory perception of sound or axis specification are less representative, but do not overwhelm the dominant muscle/cytoskeletal theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0048741","count":2}]},{"hash":"1389808604917176954","title":"Protein Dephosphorylation and Signaling Regulators","description":"The top GO terms point to regulation of signaling through dephosphorylation (protein dephosphorylation) and related pathways (Rho signaling, adenosine receptor signaling, inositol phosphate biosynthesis), suggesting a theme of modulating cellular signaling via phosphorylation status. However, several terms are more diverse (ECM biosynthesis, responses to phosphate starvation/anoxia), indicating a somewhat scattered set, so the label reflects the strongest cohesive theme without overcommitting.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000670","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0050650","count":1}]},{"hash":"1080798147026777393","title":"Developmental morphogenesis across neural, renal, and bone","description":"The top GO terms include nervous system development, metanephric tubule morphogenesis, and ossification in bone, along with related morphogenesis and cell adhesion processes. This pattern suggests proteins involved in tissue development and differentiation across multiple organs, especially neural and renal tissues, with broader involvement in bone formation and morphogenesis.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0071392","count":2},{"id":"GO:0048714","count":2},{"id":"GO:0046627","count":2}]},{"hash":"2232813657132965532","title":"Pain and Temperature Sensing with Inflammation","description":"The top GO terms cluster around nociception and thermoception (detection of chemical/mechanical/temperature stimuli, detection of temperature, pain response) along with inflammatory signaling (production of macrophage inflammatory protein 1 alpha) and related vascular/endothelial context. Despite no reported interactions among the proteins, the dominant theme ties nociceptive and inflammatory responses together, with some vascular/ion signaling hints. This supports a coherent label centered on pain/temperature sensing and inflammatory signaling.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097497","count":8},{"id":"GO:0050968","count":8},{"id":"GO:0071651","count":8},{"id":"GO:1903444","count":8},{"id":"GO:0050966","count":8}]},{"hash":"1963935084898688163","title":"Neural signaling and adherens junction dynamics","description":"Based on the GO terms, the cluster centers on neural communication (glutamate secretion; long-term synaptic depression; vocalization behavior) and cell\u2013cell junction regulation (protein localization to adherens junction; zonula adherens assembly; regulation of Rho protein signal transduction). While there are also terms related to barrier function and transport, the strongest shared theme is the coupling of neuronal signaling with adherens junction dynamics.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0048549","count":2},{"id":"GO:0090557","count":2},{"id":"GO:0014047","count":2},{"id":"GO:0060292","count":2}]},{"hash":"1962504562774863796","title":"Redox Homeostasis and Oxidative Stress Response","description":"This cluster is dominated by GO terms related to oxidation-reduction processes, cellular redox homeostasis, NADPH regeneration, cellular oxidant detoxification, and cellular response to oxidative stress, which together point to a shared function in maintaining redox balance and defending against oxidative damage. Some amino acid biosynthesis and transcription/transport terms appear less central, likely peripheral or organism-specific, but the redox-focused terms strongly define the cluster's theme.","confidence":"High","size":25,"edges":23,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0045454","count":3},{"id":"GO:0006571","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0006740","count":3}]},{"hash":"808253123382383106","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by ubiquitin-related processes: ubiquitin-dependent protein catabolic processes, protein polyubiquitination, and SCF-dependent proteasomal degradation, indicating a cohesive role in tagging proteins for degradation. Some terms also touch on stress responses and meiotic/oocyte maturation, suggesting broader regulation by ubiquitin signaling in stress and cell-cycle contexts.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0000209","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0071276","count":6},{"id":"GO:1903378","count":5}]},{"hash":"1307988217766722537","title":"Post-translational modifications and signaling regulation","description":"The cluster is enriched for post-translational modification processes (ubiquitination, poly-ADP-ribosylation, auto-ADP-ribosylation) and signaling/trafficking regulators (calcium release into cytosol, SNARE complex regulation, proteasome assembly). This suggests a cohesive theme centered on how protein modifications govern signaling pathways and vesicle trafficking, rather than a single linear pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051209","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0035544","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0000083","count":3}]},{"hash":"695447158880798437","title":"Neuroinflammation and Pain Signaling","description":"The cluster connects immune/inflammatory processes (innate immune response, cytokine signaling, interferon production) with neural-related functions (synapse assembly, corpus callosum development) and pain responses (mechanical stimulus response, formalin-induced pain behavior). This pattern suggests proteins involved in neuroimmune interactions that modulate pain signaling rather than a single, isolated pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051965","count":5},{"id":"GO:0071260","count":4},{"id":"GO:0006954","count":4},{"id":"GO:0006469","count":4},{"id":"GO:0014068","count":4}]},{"hash":"1886235146241047207","title":"Antiviral innate immune signaling","description":"The cluster\u2019s top GO terms center on innate immunity and antiviral responses, including innate immune response, cellular response to dsRNA, and cellular response to type I interferon, suggesting involvement in antiviral sensing and signaling. Some terms appear as outliers (plant hormone signaling and photoreceptor organization), which may reflect annotation noise or multifunctional proteins, but the dominant theme is antiviral innate immunity.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009938","count":9},{"id":"GO:0050689","count":9},{"id":"GO:0071360","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0071357","count":9}]},{"hash":"241164016828228672","title":"Developmental growth and protein turnover","description":"These proteins show a broad developmental signature (brain development, multicellular organism development, neural tube closure, skin development) together with core growth-related processes (mitotic cell cycle, ribosome biogenesis, rRNA maturation). The presence of proteostasis-related terms (SCF-dependent ubiquitin-proteasomal degradation, ER-stress\u2013induced apoptotic signaling) indicates coupling of development with protein turnover and stress responses. Overall, the cluster seems to reflect a general developmental program linked to growth and protein quality control rather than a single pathway.","confidence":"High","size":24,"edges":24,"triangles":1,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1993360754419953477","title":"Chromatin Regulation and Developmental Morphogenesis","description":"The top GO terms show chromatin-level control (heterochromatin formation, negative regulation of transcription by RNA Pol II) alongside multiple morphogenesis terms (pericardium, cardiac atrium, midbrain), suggesting a theme of transcriptional regulation in developmental processes. Some terms, like vitellogenesis and pro-B cell differentiation, broaden this to general development, while ribosomal subunit assembly appears as a minor, non-defining note. Overall, the cluster seems to center on chromatin-mediated regulation with developmental morphogenesis.","confidence":"Medium","size":24,"edges":14,"triangles":3,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030466","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0006348","count":5},{"id":"GO:0007296","count":4},{"id":"GO:2000973","count":4}]},{"hash":"210774949461571962","title":"ER proteostasis and unfolded protein response","description":"The top GO terms point to endoplasmic reticulum\u2013associated proteostasis: proteolysis, ubiquitin-dependent ERAD, protein folding in the ER, response to unfolded protein, and translation initiation regulation during ER stress. While there are outlier terms like DNA replication and mesoderm formation, the strongest signal is ER-quality control and the unfolded protein response.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006508","count":6},{"id":"GO:1901621","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006986","count":3}]},{"hash":"2259931554818385774","title":"Mitochondrial Translation and Ribosome Assembly","description":"Reason: The clearest shared theme is mitochondrial protein synthesis \u2014 evidenced by mitochondrial translation and ribosome assembly terms, plus general translation. Other terms are diverse and don't form a tight alternative theme, so label centers on mitochondrial translation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001246","count":2},{"id":"GO:2001247","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070131","count":1}]},{"hash":"113857745105976578","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":7},{"id":"GO:0000472","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0042273","count":5}]},{"hash":"747123848188259549","title":"Transcriptional Regulation in Development","description":"Top GO terms indicate broad involvement in transcription regulation (DNA-templated transcription, RNA polymerase II activity) and widespread developmental and immune-related processes (pancreas development, megakaryocyte differentiation, lens proliferation, MHC II biosynthesis, IL-4 response). The common thread is that these proteins likely act as transcriptional regulators that influence multiple downstream developmental and immune pathways, rather than a single pathway.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0031017","count":2},{"id":"GO:0045348","count":2},{"id":"GO:0035470","count":2},{"id":"GO:0071353","count":2}]},{"hash":"1622049802655711255","title":"Telomere maintenance and PARP activity","description":"This cluster is driven by telomere-focused terms (telomere maintenance via telomerase, telomere capping, localization to the telomeric region) and ADP-ribosylation (poly- and auto-ADP-ribosylation), pointing to PARP-related regulation of telomere biology. A spindle assembly term appears but is less central, so the telomere-PARP connection best represents the group.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":2},{"id":"GO:0051225","count":2},{"id":"GO:1904743","count":2},{"id":"GO:0032212","count":2},{"id":"GO:1904357","count":2}]},{"hash":"1351658883374549003","title":"Unknown","description":"The top GO terms are diverse, with several translation-related terms (glutamyl-tRNA aminoacylation, glutaminyl-tRNAGln biosynthesis via transamidation, regulation of translational fidelity, mitochondrial translation) but also terms for distal tubule morphogenesis, spindle midzone localization, ubiquitination, and B cell receptor signaling, making it unclear to assign a single cohesive function to the entire cluster.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006424","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0072156","count":1}]},{"hash":"1936296847209699004","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms cluster around ubiquitination steps (ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, polyubiquitination, autoubiquitination), indicating proteins primarily involved in tagging substrates for proteasomal degradation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0070936","count":8},{"id":"GO:0000209","count":7},{"id":"GO:0090073","count":7},{"id":"GO:0051865","count":7}]},{"hash":"861839316273845663","title":"Female reproductive development and prostaglandin biosynthesis","description":"The top GO terms are dominated by uterus development, female gonad development, and maternal processes in parturition, with a strong emphasis on prostaglandin biosynthesis, all pointing to female reproductive development and labor signaling. Some metabolic terms are present, but they do not outweigh the central reproductive theme.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":4},{"id":"GO:0008585","count":4},{"id":"GO:0001516","count":4},{"id":"GO:0006412","count":4},{"id":"GO:1901536","count":3}]},{"hash":"113579968434547941","title":"NO-sGC-cGMP signaling and vascular relaxation","description":"The cluster is enriched for GO terms such as receptor guanylyl cyclase signaling, cGMP biosynthesis, and relaxation of vascular smooth muscle, with supportive signals for hypoxia/CO2 sensing and inflammatory responses. This points to proteins involved in NO-mediated signaling that modulates vascular tone and related chemosensory/inflammatory pathways.","confidence":"Medium","size":24,"edges":126,"triangles":184,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0032026","count":13},{"id":"GO:0006355","count":11},{"id":"GO:0060087","count":10},{"id":"GO:0006171","count":10},{"id":"GO:0003031","count":10}]},{"hash":"1607187173852632924","title":"Ubiquitin-ERAD protein quality control","description":"The top GO terms center on ubiquitin-dependent ERAD, negative regulation of deubiquitinases, and ER-associated protein catabolic processes, suggesting a cohesive module of ubiquitin-mediated protein quality control and degradation. Some terms like protein deglycosylation and nucleotide excision repair may reflect broader roles for ubiquitination or annotation artifacts, and several entries are obsolete. Overall, the cluster likely represents components of the ubiquitin-ERAD proteostasis network.","confidence":"Medium","size":24,"edges":17,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:2000157","count":4},{"id":"GO:1903094","count":4},{"id":"GO:0055114","count":4},{"id":"GO:1901340","count":3}]},{"hash":"166450647504331171","title":"Sterol and ether lipid biosynthesis","description":"The cluster is dominated by GO terms for cholesterol and ergosterol biosynthesis and ether lipid metabolic processes, pointing to lipid/sterol biosynthesis as the core theme. A few ergothioneine-related terms appear, but they are less representative of the overall function. This grouping best captures the shared biochemical activity across the proteins.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903255","count":1},{"id":"GO:1903257","count":1},{"id":"GO:0052707","count":1},{"id":"GO:0052704","count":1},{"id":"GO:1903253","count":1}]},{"hash":"2119320038833162167","title":"Growth Factor Signaling and Development","description":"GO terms point to cellular responses to epidermal growth factor and insulin-like growth factor receptor signaling, plus regulation of cell growth and development processes such as heart and germ cell development. The presence of Rho signaling regulation and filopodium assembly suggests accompanying cytoskeletal remodeling essential for morphogenesis. Taken together, the proteins appear to form a cluster centered on growth factor\u2013driven signaling that promotes cell growth and developmental processes, with supporting cytoskeletal changes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":3},{"id":"GO:0045725","count":2},{"id":"GO:0048009","count":2},{"id":"GO:0014065","count":2},{"id":"GO:0030307","count":2}]},{"hash":"1877556252955118801","title":"Rap GTPase Signaling and Secretory Vesicle Trafficking","description":"The cluster is dominated by GO terms related to Rap/Ras-like GTPase signaling (activation of GTPase activity, Rap protein signal transduction) and vesicle trafficking in the secretory pathway (COPII cargo loading, endosome-to-Golgi and retrograde transport), suggesting a cohesive theme of small GTPase\u2013driven regulation of cargo trafficking. Some terms about lens morphogenesis or viral genome replication appear as less central associations, but the core signal is around trafficking and GTPase activity.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0032486","count":3},{"id":"GO:0048009","count":3},{"id":"GO:0090110","count":2},{"id":"GO:0070309","count":2}]},{"hash":"663871524925378296","title":"Retrotransposon activity and RNA Pol II transcription","description":"This cluster is dominated by terms linking transcription by RNA polymerase II with DNA integration and retrotransposition, pointing to retroelement activity and its transcriptional regulation as the central theme. Some additional terms (e.g., mRNA export, proteasome assembly) may reflect connected processes or noise, while a few others (prostate development, xenobiotic response) are less directly related. Overall, the core connection is genome mobility and transcriptional control.","confidence":"Medium","size":23,"edges":74,"triangles":62,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0032197","count":4},{"id":"GO:0060743","count":2},{"id":"GO:0070682","count":2}]},{"hash":"1116659706625138057","title":"DNA Repair and Genome Maintenance","description":"The cluster is dominated by DNA repair processes (base-excision repair, nucleotide-excision repair) and DNA recombination, with somatic hypermutation linking to DNA modification during immune diversification. The presence of transcription-related GO terms and stress responses (response to xenobiotic stimulus, ethanol) supports a cohesive theme of genome maintenance and damage response rather than unrelated metabolic functions.","confidence":"High","size":23,"edges":101,"triangles":209,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006284","count":5},{"id":"GO:0007568","count":4},{"id":"GO:0045471","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006289","count":3}]},{"hash":"2205845151053425740","title":"Nucleic acid modification and transposition","description":"This cluster centers on nucleic acid dynamics, with terms like retrotransposition and DNA integration suggesting mobile element activity, along with RNA modification processes (rRNA/tRNA methylation) and chromatin-related regulation (histone demethylation). Some terms (e.g., nodulation, osteoblast differentiation) appear less connected and may reflect broader annotation contexts, but the core theme is nucleic acid modification and genome dynamics.","confidence":"Medium","size":23,"edges":13,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032197","count":7},{"id":"GO:0015074","count":7},{"id":"GO:0030961","count":3},{"id":"GO:0000447","count":2},{"id":"GO:0031167","count":2}]},{"hash":"613700647661780859","title":"Nuclear import and ciliogenesis proteins","description":"The GO terms cluster around nucleocytoplasmic transport (NLS-bearing and ribosomal protein import into the nucleus, nuclear pore complex assembly) and intraciliary transport/docking, with related regulatory processes. This points to a cohesive group of proteins involved in nuclear import and ciliogenesis/centrosomal transport.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006607","count":7},{"id":"GO:0060188","count":7},{"id":"GO:0035735","count":7},{"id":"GO:0042176","count":7},{"id":"GO:0006610","count":7}]},{"hash":"833215959671852275","title":"Transcription Regulation and Chromatin Remodeling under Stress","description":"This cluster is dominated by GO terms for DNA-templated transcription, chromatin remodeling, and regulation of transcription by RNA polymerase II, with accompanying stress-response signals (abscisic acid signaling, PERK-mediated unfolded protein response). While a few terms point to immune or viral contexts, the shared theme is transcriptional control and chromatin dynamics in response to cellular stress.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0043044","count":5},{"id":"GO:0036091","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0009737","count":4}]},{"hash":"432288504079552179","title":"Mitochondrial respiration and RNA modification","description":"This cluster's strongest signals are mitochondrial respiratory chain assembly (Complex II/III) and aerobic respiration, indicating a focus on energy metabolism and mitochondrial function. The accompanying RNA modification terms (tRNA methylation, rRNA modification) suggest involvement in mitochondrial translation or RNA processing, which often co-occur with respiration. Some biosynthetic terms (biotin/menaquinone) may reflect broader bacterial ancestry or annotation artifacts, but they do not outweigh the mitochondrial energy and RNA-processing theme. Confidence: Medium","confidence":"","size":23,"edges":245,"triangles":1608,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0030488","count":3}]},{"hash":"604797385735372415","title":"Unknown","description":"The top GO terms are highly heterogeneous and include diverse processes such as negative regulation of protein modification, peptidyl-tyrosine sulfation, photoreceptor organization, histone methylation regulation (obsolete terms), unfolded protein response, centrosome maintenance, and even virus-defense regulation. The lack of a unifying pathway or cellular context, plus the presence of obsolete terms, suggests there is no coherent function tying these 23 proteins together. Confidence in a specific, representative label is therefore None.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031400","count":23},{"id":"GO:0006478","count":23},{"id":"GO:0035845","count":23},{"id":"GO:2001162","count":23},{"id":"GO:0009938","count":23}]},{"hash":"1477156592209011951","title":"Telomere recombination and DNA repair","description":"Reasoning: the GO terms are dominated by telomere-related processes (telomeric D-loop disassembly, t-circle formation, regulation of telomere maintenance) along with DNA repair and DNA recombination and their regulation. This points to a cluster of proteins involved in telomere maintenance via recombination and DNA damage response pathways (potential ALT-like mechanisms).","confidence":"High","size":23,"edges":55,"triangles":11,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0072429","count":1},{"id":"GO:0061820","count":1},{"id":"GO:0090656","count":1},{"id":"GO:1905261","count":1}]},{"hash":"2173906312578795051","title":"Lung development and retinoic acid signaling","description":"The cluster is enriched for lung development and retinoic acid/retinal metabolism terms, with supporting biosynthetic and transcription-regulation processes that are known to coordinate during fetal lung maturation. While there are some peripheral metabolic terms (e.g., mycolic acid and androgens), the strongest signals point to developmental signaling and retinoic acid\u2013related metabolism as a cohesive theme.","confidence":"Medium","size":23,"edges":144,"triangles":387,"max_degree":21,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":20},{"id":"GO:0030324","count":18},{"id":"GO:0006704","count":18},{"id":"GO:0055114","count":18},{"id":"GO:0002138","count":18}]},{"hash":"247833355240102945","title":"Unknown","description":"The GO terms are highly heterogeneous, covering redox/detoxification, lipid remodeling, various catabolic processes, and signaling regulation, with several terms marked obsolete. There is no single unifying function that clearly ties the 23 proteins together, so Unknown with no confidence is appropriate.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0098869","count":4},{"id":"GO:0009086","count":3},{"id":"GO:1990577","count":3},{"id":"GO:0046839","count":3}]},{"hash":"238137796008475124","title":"Ribosome and Translation Machinery","description":"The top GO terms are dominated by various aspects of protein synthesis\u2014cytoplasmic and mitochondrial translation, translational initiation and termination, and ribosome disassembly\u2014indicating a cluster centered on the ribosome and translational machinery. Some secondary terms like antibiotic response may reflect indirect links to translation inhibitors, but the overarching theme is translation-related processes.","confidence":"High","size":23,"edges":248,"triangles":1673,"max_degree":22,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":19},{"id":"GO:0046677","count":6},{"id":"GO:0006413","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0070125","count":3}]},{"hash":"1839314542515531709","title":"Telomere maintenance regulation","description":"The top GO terms are dominated by telomere-focused processes: positive and negative regulation of telomere maintenance via telomerase, telomere capping, and regulation of telomere maintenance, plus a link to telomeric cohesion. PARP-related protein ADP-ribosylation also ties into chromatin/DNA repair aspects of telomere biology. Some terms about synaptic signaling and GPCR pathways appear, but the strongest, most coherent signal across the cluster centers on telomere maintenance regulation, with additional chromatin modification context. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900383","count":4},{"id":"GO:1901187","count":4},{"id":"GO:0070212","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1995098795712904665","title":"Cardiac Calcium Handling and Secretory Targeting","description":"This cluster is dominated by GO terms tied to calcium release from the sarcoplasmic reticulum and regulation of ryanodine receptors, highlighting a cardiac calcium signaling theme. It also includes GO terms for secretory pathway processes (SRP-dependent targeting to membranes) and protein modification/repair, suggesting involvement of proteins in membrane-associated and post-translational processing pathways. A cardiac morphogenesis term also appears, supporting a cardiac context, though the calcium signaling and secretory-targeting themes are most consistent across the terms. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:0061179","count":2},{"id":"GO:0055010","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0060315","count":2}]},{"hash":"414273805740150963","title":"Epigenetic Regulation and Cell Cycle Control","description":"The top GO terms point to chromatin-level regulation (histone modification and heterochromatin-related processes) together with centrosome cycle and negative regulation of cellular proliferation, suggesting a cohesive role in coordinating epigenetic state with cell-cycle control. The presence of obsolete histone modification terms indicates historical annotations but supports the overall theme of chromatin regulation linked to cell division and transcriptional control.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0097536","count":2}]},{"hash":"1328814288960573254","title":"Myogenesis and cell cycle regulation","description":"This cluster centers on genes involved in muscle development and differentiation (myoblast fusion, multicellular organism development) and tightly linked cell cycle control (G2/M transition, mitotic cell cycle, CDK activity regulation), which is characteristic of myogenesis where cells proliferate before fusing into muscle fibers and exiting the cell cycle. The presence of apoptotic regulation and kinetochore localization further supports a theme of coordinated proliferation, differentiation, and cell fate, with some neural signaling terms showing broader shared cellular signaling roles. ","confidence":"Medium","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":13},{"id":"GO:0034501","count":13},{"id":"GO:0014850","count":12},{"id":"GO:0007275","count":12},{"id":"GO:0007520","count":11}]},{"hash":"1161988030600140678","title":"Unknown","description":"The top GO terms cover a wide range of distinct processes, including spindle assembly and mitotic cohesion (cell division), transcriptional activity, metabolic biosynthesis of vitamins (biotin and cobalamin), lipid remodeling, and various signaling and differentiation cues. There isn\u2019t a clear, single functional theme connecting these terms, suggesting the cluster may be compositionally diverse rather than representing one cohesive biological module.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0009409","count":2},{"id":"GO:1904908","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0032869","count":2}]},{"hash":"648395420170691597","title":"Mitotic progression and cell division","description":"The cluster\u2019s top GO terms are dominated by cell division and mitotic transitions (e.g., GO:0051301, GO:0007091, GO:0045842), suggesting these proteins mainly function in mitosis and cell-cycle control. The presence of prostate development and steroid hormone receptor assembly terms may reflect tissue-specific roles or pleiotropy, but the clear signal is mitotic regulation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0006463","count":5},{"id":"GO:0030850","count":5},{"id":"GO:0046661","count":5},{"id":"GO:0035457","count":4}]},{"hash":"1591297991039298733","title":"Protein Modification and Chromatin Regulation","description":"The top GO terms are dominated by post-translational modifications (peptidyl-tyrosine sulfation; negative regulation of protein modification) and chromatin-related processes (histone methylation and histone dephosphorylation). Although a few terms relate to immune or stress responses, the core signal points to PTMs and histone/epigenetic regulation.","confidence":"Medium","size":22,"edges":9,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043278","count":15},{"id":"GO:0031400","count":14},{"id":"GO:0006478","count":14},{"id":"GO:2001162","count":14},{"id":"GO:0009938","count":14}]},{"hash":"631645694862747412","title":"Cytoskeletal dynamics and cell migration","description":"This cluster shows enrichment for actin filament bundle assembly, Rho signal transduction regulation, cell migration, and polarity-establishing processes (including epithelial and barrier-related terms) along with related signaling like Wnt, indicating a shared role in cytoskeletal control, movement, and cell polarity.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0016477","count":2},{"id":"GO:0048265","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051017","count":2}]},{"hash":"1779643236873222002","title":"Developmental morphogenesis and organogenesis","description":"This cluster is enriched for GO terms spanning heart morphogenesis (outflow tract, endocardial cushion EMT), left-right patterning, cartilage morphogenesis, pancreatic endocrine development, placenta/trophoblast differentiation, and endocrine system development, all pointing to broad developmental and organ formation processes. The 5S rRNA transcription term is ancillary but does not negate the overarching theme of developmental morphogenesis across tissues. Overall, the proteins likely participate in diverse developmental programs rather than a single tissue-specific function.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003151","count":2},{"id":"GO:1990441","count":2},{"id":"GO:0003198","count":1},{"id":"GO:0060707","count":1},{"id":"GO:0003323","count":1}]},{"hash":"551133417316917531","title":"Mitochondrial membrane transport and dynamics","description":"This cluster shows strong enrichment for mitochondrial-focused terms: transport across mitochondrial membranes (e.g., alpha-ketoglutarate, ATP), regulation of membrane permeability and membrane potential, and mitochondrial membrane fission. These collectively point to a coherent theme of mitochondrial membrane function and energy metabolism, despite the lack of observed edges in this specific dataset.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":7},{"id":"GO:0015742","count":7},{"id":"GO:0090149","count":7},{"id":"GO:1990314","count":7},{"id":"GO:0046902","count":7}]},{"hash":"1217397101376110601","title":"Skeletal development and ECM adhesion","description":"This cluster centers on developmental differentiation and cell\u2013matrix interactions, with GO terms like endodermal differentiation, chondrocyte morphogenesis in growth plates, and multiple adhesion/ECM remodeling processes (calcium-independent adhesion, substrate\u2011dependent migration, heterotypic adhesion, negative regulation of ECM assembly). A few terms touch on immunity and coagulation, but the predominant pattern links tissue morphogenesis and ECM\u2013mediated adhesion, consistent with skeletal development and general developmental differentiation.","confidence":"Medium","size":22,"edges":62,"triangles":73,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":5},{"id":"GO:0003429","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0007596","count":2},{"id":"GO:0007161","count":2}]},{"hash":"1685525919208614094","title":"Glycine, Glyoxylate, and Serine Metabolism with Fe-S Cluster Assembly","description":"This cluster is dominated by GO terms related to amino acid metabolism, especially glycine and glyoxylate catabolic pathways and serine biosynthesis, along with pyruvate biosynthesis and cysteine catabolism. The presence of an Fe-S cluster assembly term ([2Fe-2S] cluster) strongly links these metabolic processes to iron-sulfur biogenesis, suggesting a cohesive function in amino acid turnover coupled with Fe-S protein maturation. The combination of these related metabolic steps plus Fe-S cluster formation provides a coherent, specific theme for the cluster.","confidence":"High","size":22,"edges":149,"triangles":402,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006546","count":6},{"id":"GO:0051591","count":6},{"id":"GO:0042866","count":6},{"id":"GO:0051384","count":6},{"id":"GO:0018283","count":6}]},{"hash":"539993851376090598","title":"Neural signaling and sensory function","description":"The top GO terms are dominated by neural/sensory processes\u2014long-term synaptic depression; sensory perception of sound; auditory receptor cell stereocilium organization; vocalization and social behavior\u2014suggesting a cluster centered on neuronal signaling and sensory roles. Some terms (epithelial polarity, barrier formation, Rho signaling) are broader cellular processes that can intersect with neural development, but the strongest signal is neural and sensory function. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0090557","count":3},{"id":"GO:0060292","count":3},{"id":"GO:0071625","count":3},{"id":"GO:0032782","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1661246297583076895","title":"Notch-linked metabolism","description":"The top terms show a notable Notch signaling term alongside several core metabolic processes (pyruvate/TCA cycle, amino acid catabolism). This suggests a cluster centered on metabolism with some signaling regulation, hence a Notch-linked metabolic theme.","confidence":"Medium","size":22,"edges":227,"triangles":1464,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":10},{"id":"GO:0097053","count":10},{"id":"GO:0042853","count":10},{"id":"GO:0042866","count":9},{"id":"GO:0019878","count":8}]},{"hash":"1764217641297900416","title":"Centromere and spindle assembly proteins","description":"The top GO terms point to centromere-associated chromatin (CENP-A), microtubule severing, mitotic spindle assembly, and general cell division, suggesting the proteins function together in chromosome segregation and spindle dynamics. Some terms (e.g., skin development, ER-Golgi transport) seem less directly related and may reflect pleiotropy, but the core signal aligns with centromere and spindle machinery.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0061641","count":2}]},{"hash":"299497329306607930","title":"ECM remodeling during branching morphogenesis","description":"Top GO terms point to proteolysis of extracellular matrix components (collagen catabolic process, basement membrane disassembly) and processes like bone resorption, reflecting matrix remodeling. Additionally, epithelial tube branching in lung morphogenesis indicates developmental morphogenesis dependent on ECM remodeling. The presence of bradykinin and neuropeptide catabolic processes supports a proteolytic, peptide turnover theme. Taken together, these terms suggest a cluster of proteins involved in remodeling the extracellular matrix during tissue morphogenesis, especially branching events in development.","confidence":"High","size":22,"edges":67,"triangles":101,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":11},{"id":"GO:0051603","count":9},{"id":"GO:0030574","count":9},{"id":"GO:0097067","count":9},{"id":"GO:0035593","count":9}]},{"hash":"883218703589786492","title":"Developmental Regulation and PTM Modulators","description":"The cluster centers on multicellular development (including heart development) and transcriptional control, with supporting signals from cell-cycle processes and post-translational modification regulators (deubiquitination, lysine dimethylation, serine phosphorylation). This points to a theme of developmental gene regulation modulated by PTMs, despite some dispersion among specific terms.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0045060","count":2},{"id":"GO:0071285","count":2}]},{"hash":"1593276964493075311","title":"Secretory pathway and membrane trafficking","description":"This cluster\u2019s terms center on vesicle transport between the ER and Golgi, retrograde transport, and localization to the plasma membrane, along with integrin signaling and phagolysosome assembly. These point to a group of proteins enriched for secretory/vesicular trafficking and membrane-associated functions. Translation is present but less defining, and lens fiber differentiation reflects tissue context rather than core function. Overall, the dominant theme is proteins involved in the secretory pathway and membrane trafficking.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0042493","count":2}]},{"hash":"26895519521862725","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002047","count":2},{"id":"GO:0008615","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042823","count":2},{"id":"GO:0009443","count":2}]},{"hash":"2387430529020440","title":"Embryonic Neural and Germline Development","description":"This cluster emphasizes developmental processes, with entries for peripheral nervous system development and nerve myelination, plus embryonic/germline events like germ-band shortening and germ-line stem cell division. Hormone response and regulatory processes (estradiol signaling, transcription/miRNA regulation, glycogen biosynthesis) suggest broader developmental regulation. Overall, the dominant theme is embryonic development with neural and germline emphasis, plus supportive regulatory context.","confidence":"Medium","size":21,"edges":32,"triangles":10,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007422","count":2},{"id":"GO:2000252","count":2},{"id":"GO:0071392","count":2},{"id":"GO:0048932","count":2},{"id":"GO:0048132","count":2}]},{"hash":"1457723405835407112","title":"DNA Damage Response and Cell Cycle Control","description":"The cluster is enriched for apoptosis, DNA recombination, and base-excision repair, along with oxidative stress response and signals that influence G1/S progression. These collectively point to a DNA damage response network that coordinates repair, stress signaling, and cell-cycle decisions. ","confidence":"High","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006915","count":6},{"id":"GO:0006310","count":6},{"id":"GO:2000327","count":5},{"id":"GO:0071320","count":5},{"id":"GO:1903507","count":5}]},{"hash":"980881848588799793","title":"Unknown","description":"The terms are heterogeneous, with Notch signaling alongside various amino acid metabolism and biosynthesis processes. No single cohesive theme emerges, so I label this cluster Unknown.","confidence":"","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":8},{"id":"GO:0097053","count":8},{"id":"GO:0042853","count":8},{"id":"GO:0019878","count":6},{"id":"GO:0033512","count":6}]},{"hash":"1395641697611873412","title":"Focal Adhesion and Mechanotransduction Signaling","description":"The top GO terms cluster around regulation of focal adhesion assembly, ephrin receptor signaling, response to mechanical stimulus, and cell migration, which together point to a module governing how cells sense and respond to mechanical cues and move. While other terms like fat cell differentiation and telomere maintenance appear, the core signal transduction themes are adhesion, mechanotransduction, and motility.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051893","count":4},{"id":"GO:0048013","count":4},{"id":"GO:0046330","count":4},{"id":"GO:0033138","count":4},{"id":"GO:0045444","count":3}]},{"hash":"680641213418605587","title":"Telomere maintenance and DNA damage response","description":"This cluster is dominated by GO terms related to telomere maintenance (telomerase regulation, telomere capping, telomere protection at telomeres) and DNA damage response (G2/M checkpoint signaling, DNA replication, PARP-related protein modification). These features suggest a cohesive theme of genomic stability and telomere protection, with a few auxiliary terms (such as cortical development and morphogenesis) likely reflecting broader roles of individual proteins rather than a core function of the cluster.","confidence":"High","size":21,"edges":35,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":3},{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0007095","count":2},{"id":"GO:0021987","count":2}]},{"hash":"1721496095678616637","title":"Membrane Trafficking and Signaling","description":"The cluster spans GO terms centered on intracellular signaling and membrane dynamics, including GTPase/Rho regulation, autophagy-related lysosome exocytosis, and ER membrane organization, plus dendrite growth and other signaling processes; this suggests a coherent theme of membrane trafficking and signal transduction across diverse systems.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0009789","count":2},{"id":"GO:1990927","count":2},{"id":"GO:0061736","count":2},{"id":"GO:0045945","count":2}]},{"hash":"927823363211095659","title":"Ribosome Biogenesis and Translation Machinery","description":"Dominant GO terms are translation-related: translation, translational initiation/termination, and cytoplasmic translation, with supporting terms for ribosome biogenesis and export of the large subunit, plus selenocysteine incorporation. This pattern points to proteins involved in the protein-synthesis machinery and ribosome assembly, indicating a cohesive cluster centered on translation.","confidence":"High","size":21,"edges":186,"triangles":954,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0046677","count":5},{"id":"GO:0006415","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0006450","count":3}]},{"hash":"174942426826676957","title":"Unknown","description":"The listed GO terms span transcription, extracellular matrix remodeling, immune signaling, neuronal dopamine response, development, and mechanical stimulus detection, with no single unifying function. The absence of a cohesive theme and the lack of edges imply this set does not form a coherent functional cluster.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030199","count":3},{"id":"GO:0097350","count":3},{"id":"GO:0031018","count":3},{"id":"GO:0045356","count":2}]},{"hash":"1838985220203007568","title":"Cardiac development and angiogenesis","description":"The proteins show strong enrichment for heart development processes, notably atrioventricular canal development and endocardial cushion EMT, plus angiogenesis, which together indicate a cardiac/vascular development theme. Some terms like keratinocyte differentiation, ubiquitination, phagocytosis, and Th1 differentiation appear, possibly reflecting shared regulatory pathways or annotation noise, but the core signal points to heart development and vascular formation.","confidence":"Medium","size":21,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":2},{"id":"GO:0036302","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0003198","count":2}]},{"hash":"1546299026783077800","title":"Ribosome Biogenesis and Mitotic Progression","description":"This cluster is dominated by terms for ribosome biogenesis and rRNA maturation, plus strong signals for mitotic processes (mitotic cell cycle, sister chromatid cohesion, anaphase-promoting complex\u2013dependent catabolic process) and growth signaling (TORC1). While there are also RNA and histone methylation terms, the co-occurrence of ribosome assembly with cell-cycle machinery suggests a shared theme of coordinating growth with division. Neural tube closure appears incidental. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0000278","count":8},{"id":"GO:0036265","count":7},{"id":"GO:2001162","count":6}]},{"hash":"1802746920296639357","title":"DNA Replication and Cell Cycle Cluster","description":"The proteins largely share functions in DNA replication, transcription, repair, and mitosis (DNA-templated transcription, DNA repair, mitotic cell cycle, and replication initiation regulation). A few terms touch signaling and endocytosis (JUN phosphorylation, caveolin-mediated endocytosis, p53 mediator regulation), suggesting links between genome maintenance and cell-cycle control. Overall, the dominant theme is genome replication and cell-cycle coordination, hence the chosen label.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":21},{"id":"GO:0006351","count":21},{"id":"GO:0006281","count":21},{"id":"GO:0000278","count":21},{"id":"GO:0032298","count":20}]},{"hash":"1406622211330500147","title":"Mitotic progression and ubiquitin-mediated regulation","description":"The top terms cluster around mitosis and cell-cycle control (mitotic cell cycle, APC-dependent catabolic process) with concomitant ubiquitin-related regulation (K11-linked ubiquitination, ERAD pathway) and growth signaling (TORC1). Some growth/development terms (spinal cord development, multicellular organism growth) appear but are less central, suggesting a core theme of coordinating cell division with ubiquitin-mediated regulation and growth signals. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0021510","count":2}]},{"hash":"2212143179441378908","title":"ER stress\u2013linked apoptosis and proteostasis","description":"The cluster is dominated by GO terms tied to apoptosis triggered by endoplasmic reticulum stress and to protein quality control mechanisms (ubiquitination and ERAD), indicating a focus on ER-stress\u2013driven cell death and proteostasis. While a few terms relate to ribosome biogenesis, cytoskeletal remodeling, or lens differentiation, the strongest signals point to stress-induced apoptotic signaling and protein homeostasis pathways.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070059","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0042254","count":6},{"id":"GO:0070306","count":6},{"id":"GO:0072432","count":6}]},{"hash":"471508168323163884","title":"T and B cell receptor signaling","description":"The cluster is dominated by GO terms for adaptive immune signaling, including activated T cell proliferation, T cell receptor signaling, and B cell receptor signaling, indicating an immune signaling module. While neural development terms appear, the strongest and most representative signal is T/B cell receptor signaling pathways.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050798","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0021697","count":4},{"id":"GO:0060020","count":4}]},{"hash":"870569433453920274","title":"Vesicle trafficking and cell polarity","description":"The cluster is driven by GO terms for ER-Golgi vesicle transport and vesicle docking, along with processes for cell adhesion, polarity establishment, and cytoskeletal organization. Additional signals related to development and immune signaling (ROBO, TCR) fit within broader themes of cellular organization, trafficking, and shape regulation, including mitotic division. This combination points to a cohesive theme around intracellular transport and the orchestration of cell polarity and architecture.","confidence":"Medium","size":21,"edges":20,"triangles":2,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0035385","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0007399","count":4}]},{"hash":"1406641277095081968","title":"Neural development and growth signaling","description":"This cluster is driven by neural-theme terms (brain development, neuron projection development) but also shows strong growth and protein-handling signals (cell division, mitotic cell cycle, TORC1 signaling, ribosome biogenesis, ER-Golgi transport, ER stress\u2013related apoptosis). The combination suggests a context where neural development proceeds alongside cellular growth and stress-response pathways, rather than a single narrowly defined process.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":4},{"id":"GO:1904263","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0031532","count":2}]},{"hash":"1971996691034025466","title":"Mitochondrial apoptosis regulation and calcium transport","description":"The top GO terms cluster around apoptosis signaling (extrinsic and regulation of intrinsic pathways) and mitochondrial inner membrane processes, with calcium ion transmembrane transport and ROS metabolism supporting a stress/apoptosis context. While interferon-beta and retinoic acid responses appear, the core theme is mitochondria-associated apoptosis and calcium handling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070588","count":2},{"id":"GO:0097191","count":1},{"id":"GO:0035458","count":1},{"id":"GO:0071300","count":1},{"id":"GO:0072593","count":1}]},{"hash":"1371434978590472124","title":"Nucleolar ribosome biogenesis and proteostasis","description":"The top GO terms cluster around ribosome assembly and rRNA processing, including ubiquitin-proteasome\u2013dependent protein degradation, ERAD, transcription, and histone methylation. This combination suggests a nucleolar/nucleus-centric program coordinating ribosome production with proteostasis and chromatin regulation, hence the chosen label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1239904797713467848","title":"Nuclear gene expression and ribosome biogenesis","description":"The GO terms center on nuclear processes: rRNA processing (endonuclolytic cleavage in ITS1 for separating rRNA components) and regulation of transcription, plus nuclear transport and DNA topology changes, suggesting a coherent theme of nuclear gene expression control and ribosome assembly. Some terms appear less directly related (otolith tethering, tetrapyrrole linkage), likely reflecting annotation noise or multifunctional proteins. Overall, the cluster seems to represent nuclear regulation of gene expression with a focus on ribosome biogenesis.","confidence":"Medium","size":20,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0006265","count":1},{"id":"GO:0009386","count":1},{"id":"GO:0033160","count":1},{"id":"GO:0006355","count":1}]},{"hash":"986985512069388763","title":"Neural development and cytoskeletal division dynamics","description":"The top GO terms point to neural development (neuron differentiation, neuron migration) together with cytoskeletal and cell-division processes (microtubule organization, cell division/cytokinesis, septum assembly, protein polymerization). Translation regulation also ties into broad cellular growth, supporting a theme where neural differentiation proceeds alongside cytoskeleton-driven morphogenesis and division. A non-central term related to interleukin-4 response is present but does not define the cluster.","confidence":"Medium","size":20,"edges":10,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":5},{"id":"GO:0051301","count":4},{"id":"GO:1905789","count":4},{"id":"GO:2000767","count":4},{"id":"GO:0090529","count":4}]},{"hash":"510555048935582315","title":"RNA Polymerase II Transcription Regulation","description":"The cluster is dominated by GO terms related to transcription by RNA polymerase II and its regulation (DNA-templated transcription, negative regulation of RNAP II transcription, RNAP II\u2013dependent transcription), with additional terms pointing to stress- and xenobiotic-responsive transcription and some developmental processes. The common thread is transcriptional control by RNAP II across contexts, suggesting a cohesive regulatory function.","confidence":"High","size":20,"edges":94,"triangles":234,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":6},{"id":"GO:0035690","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0000117","count":4},{"id":"GO:0006351","count":4}]},{"hash":"1322236064948461606","title":"Wnt/Hippo signaling in developmental growth","description":"The top GO terms point to growth control and cell fate decisions across tissues: canonical Wnt signaling and Hippo pathway regulation, mitotic cell cycle, apoptosis, and differentiation (keratinocytes and muscle lineages), plus related processes like myoblast fusion and synaptic plasticity modulation. The inclusion of visual perception (retinal development) alongside cardiac proliferation regulation further suggests a broad developmental program governed by Wnt/Hippo signaling, shaping proliferation, differentiation, and survival across tissues. Confidence in this theme is High.","confidence":"","size":20,"edges":80,"triangles":151,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":16},{"id":"GO:0007601","count":16},{"id":"GO:0090263","count":15},{"id":"GO:0060044","count":15},{"id":"GO:0006915","count":15}]},{"hash":"244222838648849723","title":"Neural Development and Synaptic Regulation","description":"GO terms point to neural development and synaptic regulation (forebrain development, negative regulation of synaptic plasticity), with related processes in glial/apoptotic signaling, receptor clustering, and mRNA processing, suggesting roles in neuron\u2013glia interaction and synapse maintenance.","confidence":"Medium","size":20,"edges":30,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0034351","count":3},{"id":"GO:0043113","count":3}]},{"hash":"1034895896978238136","title":"RNA processing and post-transcriptional regulation","description":"The cluster is dominated by GO terms related to post-transcriptional control: splicing via the spliceosome, mRNA export, mRNA stability and regulatory control of translation initiation, plus ncRNA-mediated gene silencing. While there is one transcription/axis specification term, the overall pattern points to RNA processing and regulation after transcription.","confidence":"High","size":20,"edges":30,"triangles":14,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1506009595245483231","title":"Immune receptor signaling and cell adhesion","description":"This cluster centers on immune signaling pathways (T cell receptor and Fc receptor signaling) and integrin-mediated adhesion/spreading, suggesting a coherent theme of immune cell communication and interaction with the extracellular matrix. While some terms touch broader signaling contexts (retinoic acid, nitric oxide, neurotrophin pathways), the strongest shared signals relate to immune receptor signaling and adhesion processes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071300","count":3},{"id":"GO:0007229","count":3},{"id":"GO:0050798","count":3},{"id":"GO:0042997","count":3},{"id":"GO:0048011","count":3}]},{"hash":"1831219389105773959","title":"Neuronal development and synaptic plasticity","description":"The top GO terms cluster around CNS development and synaptic regulation, with emphasis on synapse-associated processes such as regulation of synaptic plasticity by receptor localization to the synapse, ephrin signaling, and glutamate secretion, all central to neural connectivity. Protein ubiquitination also fits with synaptic protein turnover, while some terms like angiogenesis and lipoprotein clearance are peripheral noise. Overall, the strongest signal points to neural development and synaptic signaling/plasticity.","confidence":"Medium","size":20,"edges":19,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:1900383","count":3},{"id":"GO:1901187","count":3},{"id":"GO:0007417","count":3},{"id":"GO:0071260","count":2},{"id":"GO:0071651","count":2}]},{"hash":"33410032729963543","title":"Retinal Neuron Development and Axonogenesis","description":"The top GO terms cluster around retinal/optic nerve development and neural wiring\u2014optic nerve morphogenesis, retinal ganglion cell axon guidance, CNS projection neuron axonogenesis, and synapse assembly\u2014with retinoic acid signaling supporting developmental processes. Immune-related terms appear less cohesively but do not override the neural-development theme. Overall, the dominant pattern reflects retinal neuron development and axon guidance.","confidence":"High","size":20,"edges":15,"triangles":1,"max_degree":6,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071300","count":4},{"id":"GO:0002741","count":4},{"id":"GO:0050798","count":4},{"id":"GO:0042535","count":4},{"id":"GO:0051092","count":4}]},{"hash":"2155267028484368199","title":"Actin Cytoskeleton Remodeling and Cell Polarity","description":"This cluster is dominated by GO terms tied to actin dynamics and cellular polarity, such as actin filament bundle assembly, cell migration, establishment of epithelial cell polarity, and centrosome localization. These point to coordinated cytoskeletal remodeling and polarity establishment as the core theme. While a few terms (e.g., mRNA export, synaptic depression, ADP-ribosylation) are more peripheral or broader signaling processes, the predominant signal is actin-driven movement and polarity. Confidence: Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0060292","count":2}]},{"hash":"1799226965376876723","title":"Fatty acid elongation and sphingolipid biosynthesis","description":"The Top Terms show a strong emphasis on fatty acid biosynthesis and elongation (long-chain, saturated, unsaturated, very long-chain) plus a sphingolipid biosynthetic process, pointing to a lipid metabolism-focused cluster. A single post-Golgi vesicle transport term adds a note of lipid trafficking, while the tissue development terms likely reflect context-specific roles rather than a separate function. Overall, the core theme is lipid biosynthesis and remodeling.","confidence":"High","size":20,"edges":25,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0043403","count":2},{"id":"GO:0042759","count":1},{"id":"GO:0048794","count":1},{"id":"GO:0006892","count":1},{"id":"GO:0034625","count":1}]},{"hash":"1198482256719168754","title":"Ribosome biogenesis and translation with cell cycle","description":"This cluster is dominated by GO terms for translation and ribosome biogenesis (translation, cytoplasmic translation, ribosome biogenesis, ribosomal subunit biogenesis, ribosomal large subunit export from nucleus). The presence of cell cycle and cell division terms (cell cycle, cell division, cell septum assembly) suggests coordination between ribosome production/translation and cell cycle progression. A few terms about antibiotic response and conjugation are present but seem secondary to the core ribosome/translation theme.","confidence":"High","size":20,"edges":63,"triangles":33,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0042274","count":4},{"id":"GO:0007049","count":4}]},{"hash":"132687741657202257","title":"Fatty acid biosynthesis and lipid transport","description":"Most terms cluster around fatty acid metabolism and transport (fatty acid biosynthesis; long-chain fatty acid metabolism and import; medium-chain fatty acid transport) with supportive catabolic pathways (malonate and phenylacetate) and related biosynthetic processes (nonribosomal peptide and antibiotic biosynthesis). This suggests a cohesive module centered on fatty acid production and handling, with some secondary metabolite biosynthesis context and potential plant seed lipid biology.","confidence":"High","size":20,"edges":100,"triangles":181,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0010214","count":4},{"id":"GO:0001579","count":4},{"id":"GO:0043041","count":4}]},{"hash":"106782730439702294","title":"Rho/Rac GTPase signaling and cytoskeleton regulation","description":"This cluster is dominated by GO terms for regulation of Rho and Rac GTPase signaling and processes affecting the cytoskeleton (e.g., stress fiber assembly), with supporting signals from Wnt and various immune-related pathways (T cell proliferation, dendritic cell apoptosis) and exocytosis. The central thread appears to be signaling control that governs cytoskeletal dynamics and cell behavior, particularly in immune contexts.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0051497","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0050798","count":2}]},{"hash":"1211790382870454699","title":"Neural development and synaptic function","description":"The cluster shows enrichment for neural-related GO terms: regulation of long-term synaptic potentiation, memory, and cell adhesion, which collectively point to neuronal connectivity and synaptic plasticity. While there are also terms tied to broader development (endodermal differentiation) and other processes (digestion, protein autoprocessing), the recurring neural signaling and adhesion themes provide a coherent functional thread for this group.","confidence":"Medium","size":20,"edges":46,"triangles":10,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":2},{"id":"GO:1900271","count":2},{"id":"GO:0035987","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0007586","count":2}]},{"hash":"1043938803568383306","title":"Actin cytoskeleton remodeling and cell migration","description":"These proteins are enriched for GO terms related to actin filament organization and assembly, small GTPase\u2013mediated signaling (Rho pathways), cell migration, and related membrane remodeling processes such as endocytosis and plasma membrane tubulation, indicating a common function in cytoskeletal dynamics and motility. The presence of these actin- and motility-related terms across the cluster supports labeling it as components of actin cytoskeleton remodeling and cell migration pathways.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007015","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0007264","count":2}]},{"hash":"1048078875116182431","title":"Regulation of gene expression and signaling","description":"The prominent GO terms center on regulation of gene expression (mRNA stability, transcription) and protein modification (ubiquitination), with supporting signals related to cell behavior (cell migration) and signaling pathways (GPCR), suggesting a cluster describing how cells regulate expression in response to signaling cues.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007205","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0016477","count":2},{"id":"GO:2001275","count":2}]},{"hash":"1203998987642066501","title":"Developmental transcriptional and epigenetic regulation","description":"This cluster centers on developmental processes across tissues (heart, glands, myotube) and regulators of gene expression and chromatin state (DNA-templated transcription, DNA methylation, histone modification, and p53 signaling), suggesting a shared theme of developmental gene regulation and epigenetic control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:1903699","count":2},{"id":"GO:0097676","count":2},{"id":"GO:0032635","count":2},{"id":"GO:1903709","count":2}]},{"hash":"437214340843071396","title":"Actin Cytoskeleton Remodeling and Signaling","description":"Dominant terms point to actin cytoskeleton organization and cell migration, suggesting cytoskeletal remodeling as a core function. Additional terms involving ubiquitination and PARylation indicate regulation of protein modification during remodeling, while ceramide transport hints at membrane trafficking linked to signaling and cytoskeletal dynamics. Despite some obsolete terms, the recurring theme centers on cytoskeletal dynamics with associated signaling and modification processes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0050966","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0016477","count":3},{"id":"GO:2001275","count":3}]},{"hash":"290986641198921832","title":"Endosome dynamics and innate immune signaling","description":"The top GO terms point to endosomal regulation and receptor trafficking (regulation of endosome size, receptor recycling) with supporting roles in transcription and signaling; additionally, there are immune-related terms such as TLR4 signaling, dsRNA response, and dendritic cell antigen processing. The combination suggests a cluster of proteins involved in vesicle trafficking that modulates immune sensing and antigen presentation, with some links to synaptic receptor trafficking. Therefore, a label focusing on endosome dynamics linked to immune signaling best fits the data.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006355","count":2}]},{"hash":"693041679758727602","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is characterized by strong enrichment for ribosome-related GO terms: ribosome biogenesis, large subunit export from the nucleus, and tRNA processing. Together they point to nucleolar/nuclear factors involved in assembling ribosomes and processing rRNA/tRNA, i.e., ribosome production machinery. The additional terms (e.g., transcription regulation, protein folding/STK regulation) may reflect broader nuclear housekeeping roles or annotations in diverse nuclear processes, but the core signal remains ribosome biogenesis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0000161","count":1}]},{"hash":"394140556682420406","title":"Sterol Biosynthesis and Lipid Metabolism in Fungi","description":"The top GO terms cluster around ergosterol and sterol biosynthesis, sterol metabolic processes, and long-chain fatty-acyl-CoA metabolism, pointing to membrane lipid production typical of fungi. While there are related terms for ER-Golgi transport and mitochondrial respiration, the lipid/sterol biosynthesis signals are most prominent, justifying this label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0035336","count":1},{"id":"GO:0001081","count":1}]},{"hash":"1693626312978315202","title":"TLR-Mediated Antiviral Immune Signaling","description":"These terms cluster around Toll-like receptor signaling (both MyD88-dependent and -independent), TLR9, and responses to dsRNA, with related antiviral defense and cytokine production in dendritic cells (including IL-18 and chemokines) and interferon-alpha, indicating a cohesive theme of innate antiviral signaling via TLRs in dendritic cells.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045356","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0002755","count":2},{"id":"GO:0034162","count":2},{"id":"GO:0043330","count":2}]},{"hash":"222838212474921065","title":"Sterol and Fatty Acid Lipid Biosynthesis","description":"The top terms are dominated by lipid biosynthetic processes: cholesterol biosynthesis via lathosterol, ergosterol biosynthesis, fatty acid biosynthesis, ether lipid metabolism, and sphingolipid metabolism. Related terms touch on lipid-rich tissues and membranes, such as CNS myelin maintenance and sebaceous gland differentiation, which supports a cohesive theme around lipid production and remodeling. Some terms (e.g., B cell chemotaxis) are less directly linked and a bacterial PHB biosynthesis term appears, but the prevailing signal points to sterol and fatty acid lipid biosynthesis. Confidence: Medium","confidence":"","size":19,"edges":33,"triangles":12,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0035754","count":5},{"id":"GO:0042619","count":4},{"id":"GO:0033490","count":3},{"id":"GO:0001949","count":3}]},{"hash":"1341652528003723021","title":"Fatty acid biosynthesis and elongation","description":"The cluster is dominated by GO terms for fatty acid biosynthesis and elongation across various lipid types (long-chain, very long-chain, saturated, monounsaturated, polyunsaturated) and includes sphingolipid biosynthesis, indicating a cohesive lipid metabolism function. A couple of organismal terms (swim bladder development, courtship behavior) are present but do not override the lipid-centric pattern. Overall, the proteins are best characterized by lipid/fatty acid biosynthesis activity.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042759","count":2},{"id":"GO:0048794","count":2},{"id":"GO:0006892","count":2},{"id":"GO:0034625","count":2},{"id":"GO:0030148","count":2}]},{"hash":"2192275481323980448","title":"Multisubstrate Membrane Transporters","description":"The cluster shows strong enrichment for multiple transmembrane transport terms across diverse substrates (galactose, arabinose, nitrite, nitrate, phosphate, xenobiotics), indicating a common function as transport proteins with broad substrate specificity. Some terms related to oligomerization and mitosis are present but appear less central to the dominant theme of membrane transport.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0035435","count":3}]},{"hash":"828574743228923507","title":"Retrotransposition and DNA integration","description":"Dominant GO terms are retrotransposition (GO:0032197) and DNA integration (GO:0015074), each with six proteins, pointing to elements involved in genome mobility and insertion events. Additional terms such as 7-methylguanosine mRNA capping and rRNA modification appear at low frequency, suggesting some RNA processing involvement but not as prominent. Overall, the cluster is best described as related to retrotransposon activity and genome integration rather than a single canonical pathway.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032197","count":6},{"id":"GO:0015074","count":6},{"id":"GO:0006370","count":2},{"id":"GO:0070555","count":1},{"id":"GO:0031167","count":1}]},{"hash":"284874403446314351","title":"Protein quality control and stress response","description":"This cluster is dominated by GO terms tied to protein folding, processing, and turnover (ER unfolded protein response, stress granule disassembly, proteasome regulatory particle assembly, glycosylation), indicating a core theme of proteostasis and cellular stress management. Additional terms relate to energy metabolism and ciliary motion, but the strongest signal is maintenance of protein homeostasis.","confidence":"Medium","size":19,"edges":170,"triangles":952,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0009060","count":2},{"id":"GO:0003341","count":2},{"id":"GO:0030968","count":2}]},{"hash":"665619508550274651","title":"Immune signaling and lymphocyte regulation","description":"The proteins cluster around immune-related functions: integrin-mediated signaling, response to lipopolysaccharide, B cell differentiation and its regulation, and thymic T cell selection, with ancillary links to NF-kappaB signaling. While there are some general cellular processes (DNA replication, mRNA decay) present, the dominant theme is immune system signaling and lymphocyte regulation. ","confidence":"High","size":19,"edges":64,"triangles":72,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0007229","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0045060","count":4},{"id":"GO:0045647","count":4}]},{"hash":"485250967032543963","title":"Actin Remodeling and Cell Migration","description":"This cluster is dominated by GO terms tied to actin-driven protrusions (filopodium and lamellipodium assembly), GTPase activation, and adhesion-dependent cell spreading, all hallmark features of cytoskeleton remodeling and cell movement. The presence of GPCR-mediated signaling (acetylcholine receptor pathway) often modulates cytoskeletal dynamics and motility, reinforcing this theme. Additional terms related to vascular remodeling, neutrophil activity, and morphogenesis reflect broader developmental and immune contexts where cytoskeletal control of migration is key, including midbrain morphogenesis and vascular smooth muscle differentiation. Taken together, the proteins likely participate in actin dynamics that drive cell migration and spreading in development and immune/vascular settings.","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007213","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0043314","count":2}]},{"hash":"666950693060375032","title":"Gene expression and actin dynamics regulators","description":"The top GO terms span transcription regulation, mRNA stability, and translation initiation, together with actin filament assembly, cell migration, and Rho signaling, indicating a cohesive theme where signaling modulates both gene expression and cytoskeletal dynamics.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0043488","count":2},{"id":"GO:1903679","count":2},{"id":"GO:0060972","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1463722393355481151","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006452","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0097428","count":1}]},{"hash":"1386297540768789341","title":"Membrane remodeling and endocytic trafficking","description":"The top GO terms point to membrane dynamics and vesicle handling\u2014endosome transport regulation, pinocytosis, plasma membrane tubulation, and GTPase activity regulation\u2014along with related cell polarity and cytokinesis terms. This suggests a cohesive theme of membrane remodeling and vesicular trafficking, rather than a single narrow function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006986","count":2},{"id":"GO:2000769","count":2},{"id":"GO:0000281","count":2},{"id":"GO:0048310","count":2}]},{"hash":"936672885201824294","title":"Cell growth and protein synthesis machinery","description":"The top GO terms point to core cellular processes: cell division and cell cycle, translation and ribosome biogenesis, and protein quality control. Additional terms touch on peroxisome import and stress responses, suggesting a broad set of essential housekeeping functions tied to growth and protein production. The lack of edges could reflect dispersed functional roles among the proteins, but the common theme remains fundamental biosynthesis and cell proliferation activities.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006515","count":3},{"id":"GO:0016558","count":3}]},{"hash":"211832746985370629","title":"COPI-Mediated Golgi-ER Vesicle Trafficking","description":"The top GO terms cluster around COPI coating and vesicle budding, ER-to-Golgi transport, and Golgi ribbon formation, which together indicate COPI-dependent trafficking within the secretory pathway between the ER and Golgi. While some developmental terms appear, the strongest signal is vesicle transport and Golgi organization, justifying a label focused on COPI-mediated Golgi-ER trafficking.","confidence":"High","size":19,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048205","count":2},{"id":"GO:0048042","count":2},{"id":"GO:0090161","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0035964","count":2}]},{"hash":"1648977279829372174","title":"ER proteostasis and redox stress response","description":"This cluster centers on maintaining proteostasis in the endoplasmic reticulum while managing oxidative stress. Key terms include ER protein folding, ER stress response, cellular redox homeostasis, and cellular oxidant detoxification, indicating proteins that fold and detoxify under oxidative challenges, with transcriptional regulation as a secondary facet.","confidence":"High","size":19,"edges":86,"triangles":185,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":14},{"id":"GO:0034975","count":12},{"id":"GO:0098869","count":11},{"id":"GO:0006351","count":9},{"id":"GO:0034599","count":9}]},{"hash":"87488135560196190","title":"Unknown","description":"The GO terms are highly diverse with no single dominant function linking the proteins (telomere maintenance regulation, cell cycle/regulation, respiration signaling, pain/thermoception, adipocyte differentiation, endothelial delamination, proteasome assembly, and ADP-ribosylation), making a cohesive label inappropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904357","count":6},{"id":"GO:0000083","count":5},{"id":"GO:1903759","count":5},{"id":"GO:0048265","count":5},{"id":"GO:0070682","count":5}]},{"hash":"11679564892475662","title":"Developmental signaling and cell cycle control","description":"Top GO terms indicate developmental processes (skin and spinal cord development, multicellular organism development) alongside signaling regulation (serine/threonine kinase activity regulation, autophosphorylation, GTPase activity) and cell cycle activity (mitotic cell cycle), with supplementary roles in mRNA transport and ribosome biogenesis. This suggests a broad theme of developmental signaling coupled with growth/division control, though the data show diversity and no interaction edges. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":8},{"id":"GO:0043588","count":8},{"id":"GO:0071456","count":8},{"id":"GO:0031954","count":8},{"id":"GO:0021510","count":8}]},{"hash":"265429093265781568","title":"Genome Mobility and DNA Integration","description":"The cluster prominently features GO terms tied to genome dynamics, especially retrotransposition and DNA integration, with supporting hints from mRNA decay and repair regulation. Although some terms relate to development and signaling, the strongest shared theme is genome mobility/integration, suggesting roles in transposon activity or genome maintenance.","confidence":"Low","size":19,"edges":24,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":2},{"id":"GO:0051571","count":2},{"id":"GO:0032197","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0032423","count":1}]},{"hash":"40688068169915834","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018120","count":1},{"id":"GO:0071660","count":1},{"id":"GO:0019677","count":1},{"id":"GO:0080188","count":1},{"id":"GO:0000467","count":1}]},{"hash":"1249169031897883805","title":"Signaling and developmental regulation","description":"This cluster shows dominance of GO terms involving negative regulation of signaling pathways (protein kinase activity, insulin receptor signaling, PI3K/AKT) and growth-related processes (angiogenesis, embryonic digit morphogenesis). Some proteins are linked to spliceosomal assembly and glutamate secretion, indicating potential multi-functional roles. Overall, the shared thread is modulation of signaling that impacts cell proliferation and development rather than a single pathway.","confidence":"Low","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0000245","count":1},{"id":"GO:0046627","count":1},{"id":"GO:0046325","count":1}]},{"hash":"1610603249672334563","title":"Glycan biosynthesis and embryonic development","description":"This cluster appears driven by glycan biosynthesis terms (xyloglucan, fucose, heparan sulfate proteoglycans) and developmental processes (endoderm development, embryonic fin morphogenesis, BMP signaling). The mix of plant cell wall biosynthesis and animal development terms suggests a shared theme around extracellular matrix\u2013related glycan production and signaling involved in embryogenesis across species. Confidence: Medium.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009969","count":2},{"id":"GO:0042353","count":2},{"id":"GO:0015014","count":2},{"id":"GO:0007492","count":2},{"id":"GO:0072498","count":2}]},{"hash":"290848679807226038","title":"Unknown","description":"GO terms are heterogeneous (calcium signaling, muscle regulation, metabolism, development, cytoskeleton transport, etc.), with no single dominant function, so there is no cohesive theme to name this cluster.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099509","count":3},{"id":"GO:1901077","count":3},{"id":"GO:0035774","count":3},{"id":"GO:0019749","count":3},{"id":"GO:0035191","count":3}]},{"hash":"1046219598556567815","title":"Lymphocyte signaling and development","description":"The top GO terms cluster around immune signaling and lymphocyte differentiation, with multiple terms for NK T cell differentiation, IL-7 response, IL-4 production, and B cell maturation, plus integrin signaling and cell migration that underpin immune cell trafficking. While there are also broad developmental terms (telencephalon, heart), the recurrent theme is signaling pathways guiding lymphocyte development and function. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0098761","count":3},{"id":"GO:0001865","count":3}]},{"hash":"1742861169981429763","title":"Melanocyte Differentiation and Pigment Granule Transport","description":"This cluster centers on melanocyte/pigment biology: eye pigment granule organization, pigment cell differentiation, and endosome-to-lysosome transport, with vesicle trafficking driven by GTPases. The terms point to melanosome biogenesis and pigment granule maintenance, supporting the label; a few outliers (e.g., NK cell activation) do not define the main theme.","confidence":"High","size":18,"edges":16,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0008057","count":1},{"id":"GO:0032816","count":1}]},{"hash":"2205705583180575047","title":"Calcium signaling in heart and neurons","description":"The cluster is dominated by GO terms tied to calcium ion dynamics (calcium transport, cellular response to calcium, intracellular signaling) and excitability-related processes (SA node action potential regulation, heart development, long-term potentiation, memory, neuronal signaling). This points to a shared function of calcium-dependent signaling in excitable tissues, particularly cardiac and neuronal contexts, with a minor link to membrane lipid remodeling. ","confidence":"High","size":18,"edges":17,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0035994","count":3}]},{"hash":"2249191183614860022","title":"Cardiac Muscle Contraction and Calcium Handling","description":"The top GO terms reference ventricular cardiac muscle morphogenesis, heart development, and cardiac muscle contraction, plus calcium signaling via release of Ca2+ from the sarcoplasmic reticulum and regulation of ryanodine-sensitive Ca2+ channels. This points to cardiomyocyte function and calcium-dependent contraction as the cluster\u2019s common theme.","confidence":"High","size":18,"edges":26,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032925","count":2},{"id":"GO:0055010","count":2},{"id":"GO:0022417","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0060315","count":2}]},{"hash":"555790780469450379","title":"Membrane signaling and lipid metabolism","description":"This cluster shows terms tied to membrane-associated signaling and trafficking (Rho signaling regulation, cell migration, pinocytosis) and lipid-related processes (sterol biosynthesis, lipid glycosylation, myelin assembly), with supporting notes on protein modification (poly-ADP-ribosylation) and oligomerization (protein tetramerization). The mixture suggests a theme around membrane dynamics and lipid metabolism rather than a single enzymatic pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0016477","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0048549","count":2}]},{"hash":"1241523891310813828","title":"Ribosome biogenesis and translation","description":"The cluster is centered on translation and ribosome biology: translation, ribosome biogenesis, translational initiation and termination, and positive regulation of translation, plus selenocysteine incorporation. Deadenylation-dependent decay links mRNA turnover to translation, suggesting coordinated control of protein synthesis. A couple of terms (response to antibiotic, glial cell proliferation) are less central and may reflect broader regulatory connections or annotation spillover. Overall, the set represents the translation machinery and its regulation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":6},{"id":"GO:0006413","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0001514","count":4}]},{"hash":"167016481569696809","title":"Cell Cycle and Mitochondrial Energy Production","description":"Based on GO terms, the cluster centers on core cell cycle processes (cell division, DNA replication, microtubule dynamics) while also emphasizing mitochondrial energy production (complex III assembly, oxidative phosphorylation, aerobic respiration) and supporting pathways (ER-Golgi transport, protein quality control). This combination suggests a coordinated role in fueling cell growth and division via mitochondrial metabolism, with associated protein handling and trafficking.","confidence":"High","size":18,"edges":109,"triangles":353,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":10},{"id":"GO:0051260","count":9},{"id":"GO:0034551","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0071218","count":8}]},{"hash":"1805002178922925679","title":"DNA replication and SOS response","description":"This cluster is dominated by GO terms tied to DNA replication and associated processes (DNA replication, DNA unwinding, primer synthesis, DNA topological changes) plus the SOS response, indicating proteins involved in genome replication and DNA damage response. Additional terms like methylation, UV protection, and hypoxia response seem to reflect broader cellular stress regulation rather than a distinct separate pathway, but do not outweigh the core replication/repair theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006268","count":6},{"id":"GO:0009432","count":6},{"id":"GO:0006269","count":5},{"id":"GO:0000184","count":5}]},{"hash":"707916522301419597","title":"DNA replication and repair","description":"This cluster is dominated by DNA-centric terms: DNA replication, DNA recombination, and double-strand break repair via homologous recombination, pointing to a nucleus-associated DNA maintenance function. Nuclear pore localization also fits a nuclear role. While there are neural development and immune signaling terms present, they are less frequent, suggesting they are ancillary annotations rather than core functions of the cluster. Overall, the label reflects the strongest and most coherent theme in the top terms.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0031175","count":2}]},{"hash":"399598972410566285","title":"Neural development and synaptic signaling","description":"The top GO terms center on neural plasticity (long-term potentiation, dendritic spine morphogenesis) with supporting signaling pathways (Wnt, insulin receptor signaling) and developmental contexts, plus some apoptotic and nitric oxide responses. This suggests a cluster of proteins involved in signaling processes underlying neural development and synaptic modulation, rather than a single narrow function. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0097011","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0071732","count":3},{"id":"GO:0008286","count":3}]},{"hash":"1903973385595089026","title":"Ribosome biogenesis and RNA modification","description":"The cluster shows strong enrichment for RNA processing and ribosome-related functions, notably RNA (guanine-N7)-methylation and rRNA modification, which are essential steps in ribosome assembly. Additional terms for DNA-templated transcription, cell division, and regulation of the cell cycle suggest a growth/proliferation context where ribosome production is upregulated. Magnesium ion response and sterol biosynthesis further support cellular growth and membrane biosynthesis accompanying proliferation. Immune-related responses appear present but are secondary to the dominant ribosome biogenesis and RNA modification signal.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036265","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0032026","count":3},{"id":"GO:0071157","count":3}]},{"hash":"1355256745806215397","title":"Telomere maintenance and PARP activity","description":"The cluster's top GO terms cluster around telomere biology\u2014regulation of telomere maintenance, telomerase activity, telomere capping, and localization to telomeric regions\u2014coupled with poly-ADP-ribosylation (PARP) and auto-ADP-ribosylation. The presence of spindle assembly also hints at coordination with mitosis. Together, these terms suggest a cohesive role in telomere protection/regulation linked to PARP activity during the cell cycle.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":4},{"id":"GO:0051225","count":4},{"id":"GO:1904743","count":4},{"id":"GO:0032212","count":4},{"id":"GO:1904355","count":4}]},{"hash":"1982334551531779453","title":"Neuronal vesicle trafficking and dendrite morphogenesis","description":"The cluster shows strong enrichment for ER\u2013Golgi and retrograde vesicle transport, along with regulation of synaptic vesicle exocytosis, and neural development terms such as brain development and dendrite morphogenesis. This points to a cohesive role in neuronal vesicle trafficking and shaping dendritic architecture, with some cell-cycle terms likely reflecting shared cellular machinery rather than a primary function.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0006890","count":6},{"id":"GO:1904263","count":5}]},{"hash":"2253557142698825496","title":"Protein homeostasis: translation initiation and proteasome assembly","description":"Most prominent terms relate to initiation of translation (formation of translation preinitiation complex, regulation of translational initiation) and protein turnover (protein deneddylation, proteasome assembly). A trafficking term (Golgi to plasma membrane transport) also appears, reinforcing a broader theme of protein processing and turnover. Although a few terms are cell-cycle or signaling-related, the dominant pattern centers on coordinating protein synthesis, modification, and degradation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000338","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0043248","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0006893","count":2}]},{"hash":"1750355407764421247","title":"Redox Detoxification and DNA Repair","description":"The GO terms show a strong emphasis on cellular oxidant detoxification, glutathione and redox balance, and toxin catabolic processes, along with nucleotide-excision repair, indicating a cluster of proteins involved in protecting cells from oxidative stress and maintaining genome integrity. A couple of terms related to calcium signaling and muscle contraction appear peripheral and may reflect annotation noise rather than core function.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":13},{"id":"GO:0009072","count":9},{"id":"GO:0006749","count":8},{"id":"GO:0006289","count":8},{"id":"GO:0060316","count":8}]},{"hash":"2032909843923658319","title":"Mitotic spindle assembly and microtubule dynamics","description":"The cluster is strongly characterized by GO terms centered on mitosis and microtubule organization (spindle midzone assembly, metaphase chromosome alignment, centrosome separation, spindle assembly, and microtubule regulation/depolymerization). These themes point to a cohesive role in mitotic processes and cytoskeletal dynamics, with a few outliers likely representing broader cytoplasmic RNA granule contexts. ","confidence":"High","size":18,"edges":21,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051255","count":15},{"id":"GO:0035617","count":15},{"id":"GO:0007080","count":15},{"id":"GO:0032487","count":15},{"id":"GO:0032886","count":15}]},{"hash":"1648840721323851652","title":"Embryogenesis and Epigenetic Regulation","description":"This cluster is dominated by GO terms related to epigenetic regulation (DNA methylation in gamete generation; histone H3-K4 methylation/demethylation) and embryonic development (in utero embryonic development; regulation of primitive erythrocyte differentiation). The recurring theme is chromatin modification guiding gene expression during early development, despite some obsolete or metabolic terms present. ","confidence":"High","size":18,"edges":53,"triangles":64,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0043046","count":12},{"id":"GO:0009228","count":12},{"id":"GO:0045454","count":11},{"id":"GO:0010725","count":10}]},{"hash":"597521630255905111","title":"Ribosome biogenesis and translation","description":"GO terms in this cluster center on ribosome biogenesis (large and small subunits), cytoplasmic translation, and ribosomal subunit export from the nucleus, with accompanying cell cycle and cell division terms. This strongly suggests a set of proteins involved in ribosome assembly and protein synthesis that support cell growth, with some links to division processes. ","confidence":"High","size":18,"edges":39,"triangles":0,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0000055","count":6},{"id":"GO:0000002","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0042274","count":5}]},{"hash":"1967258561517829440","title":"Muscle and heart development with transcription regulation","description":"The top GO terms cluster around mesoderm-derived tissue development, especially skeletal muscle development and heart development, along with multiple transcription regulation terms (DNA-templated transcription and RNA polymerase II regulation). This suggests the proteins collectively participate in developmental programs governing muscle and cardiac tissues, with a common emphasis on transcription control. Some immune signaling and nervous system development terms are present but appear less central to the core theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0035914","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0007519","count":3},{"id":"GO:0048741","count":3}]},{"hash":"1158060318237642375","title":"Mitochondrial Transport and Dynamics","description":"The cluster centers on mitochondrial function: changes in membrane permeability and potential, mitochondrial fission, and transport of key metabolites (alpha-ketoglutarate, ATP) and lipids, plus responses to growth-factor signaling and fatty acids. Together these GO terms indicate a cohesive mitochondrial energy/metabolism and dynamics theme, justifying the label.","confidence":"High","size":18,"edges":22,"triangles":12,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":13},{"id":"GO:0008637","count":12},{"id":"GO:0015742","count":12},{"id":"GO:0090149","count":12},{"id":"GO:1990314","count":12}]},{"hash":"2024893908742687740","title":"Transcription regulation and heterochromatin formation","description":"The dominant GO terms point to nuclear functions: DNA-templated transcription, RNA polymerase II transcription preinitiation complex assembly, and transcription elongation are central, along with multiple forms of heterochromatin formation (including pericentric and silent mating-type cassette contexts). This suggests a cluster of proteins involved in chromatin organization and transcription control. A few terms (negative regulation of apoptotic process, MyD88-dependent toll-like receptor signaling pathway, collagen catabolic process) are present but less representative of the core theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":2},{"id":"GO:0002755","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0035551","count":1}]},{"hash":"2272087445919918515","title":"Cytoskeletal remodeling and vesicle trafficking","description":"The top GO terms cluster around actin dynamics (depolymerization, crosslinking) and Rho signaling, along with exocytosis and spindle assembly, plus fungal developmental processes (karyogamy, ascospore formation). This suggests a cohesive module coordinating cytoskeleton-driven cell shape/movement with membrane trafficking during division and morphogenesis, especially in fungi.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0030042","count":3},{"id":"GO:0051764","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0006887","count":3}]},{"hash":"1836829362287175272","title":"Cell-cycle regulators and innate immune signaling","description":"The cluster centers on regulation of mitosis and kinase activity alongside innate immune signaling pathways (cytokine signaling, interferon production, lipopeptide detection), suggesting proteins that coordinate cell division with immune responses. Some terms are less tightly connected (polarity maintenance, liver regeneration, sensory perception of sound), but the core theme remains regulatory signaling affecting proliferation and defense.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0045842","count":3},{"id":"GO:0007605","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0097421","count":2}]},{"hash":"1157588119946155132","title":"Unknown","description":"The top GO terms cover a wide and unrelated spectrum, including signaling, transcription under heat stress (obsolete), poly-ADP-ribosylation, endothelial delamination, fat cell differentiation, mechanosensing, spindle assembly, nociception, protein localization, and electrical coupling\u2014plus no edges to imply a shared pathway. This lack of a cohesive theme and network support makes a clear, representative cluster label inappropriate.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0061408","count":1},{"id":"GO:0070212","count":1},{"id":"GO:0097497","count":1},{"id":"GO:0045444","count":1}]},{"hash":"1163761164096852597","title":"Cytoskeletal dynamics in B cell signaling","description":"Top GO terms emphasize actin cytoskeleton reorganization, lamellipodium assembly, Rho signaling, and responses to mechanical stimuli, along with B cell receptor signaling; these together point to a module where cytoskeletal remodeling interfaces with immune receptor\u2013mediated signaling. This supports naming the cluster as Cytoskeletal dynamics in B cell signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0043536","count":2}]},{"hash":"418561805223346059","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":125,"triangles":541,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0071300","count":3},{"id":"GO:0007258","count":3}]},{"hash":"1383697766579145225","title":"Core gene expression and cell cycle machinery","description":"The cluster centers on fundamental cellular processes: mRNA processing, formation of translation preinitiation complex, DNA-templated transcription, DNA replication, and the mitotic cell cycle, indicating core gene expression and genome duplication machinery. Additional terms reflect protein quality control and stress responses (proteasomal degradation, ER stress\u2013induced apoptosis) and developmental contexts, which can share components with these core processes. Overall, the dominant theme is central gene expression and cell cycle regulation with related stress responses.","confidence":"High","size":17,"edges":57,"triangles":81,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006397","count":5},{"id":"GO:0032436","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0001843","count":4}]},{"hash":"1030707849522665917","title":"Developmental signaling and morphogenesis","description":"This cluster\u2019s GO terms cluster around developmental processes and signaling pathways (fat cell differentiation, neural tube closure, Wnt signaling) as well as cell movement (cell migration) and cytoskeletal-associated activities (mitotic contractile ring actin filament bundle assembly) that are key to morphogenesis. Some terms (telomere maintenance, pinocytosis) are more general but can be linked to cellular dynamics during development. Overall, the dominant theme is developmental signaling guiding morphogenesis and cell behavior.","confidence":"Medium","size":17,"edges":20,"triangles":5,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":2},{"id":"GO:0016477","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0035994","count":2}]},{"hash":"361666927987895976","title":"Rho/Rac-driven actin cytoskeleton remodeling","description":"These proteins are enriched for GO terms centered on Rho and Rac GTPase signaling, small GTPase-mediated signal transduction, and actin cytoskeleton organization, including the formation of filopodia and lamellipodia and cell migration. The convergence on actin dynamics and adhesion-dependent spreading suggests a module controlling cytoskeletal remodeling downstream of Rho family GTPases.","confidence":"High","size":17,"edges":10,"triangles":1,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":9},{"id":"GO:0032287","count":9},{"id":"GO:0016477","count":9},{"id":"GO:0007264","count":9},{"id":"GO:1900026","count":9}]},{"hash":"72830587064769044","title":"Multi-system signaling regulation","description":"The GO terms span immune signaling (NFAT, TNF production, B cell differentiation), neural changes (dendritic spine modification), vascular processes (permeability, sprouting angiogenesis), Golgi localization, and GH receptor signaling. There isn\u2019t a single cohesive pathway, but a general theme of regulation of signaling across diverse cell types and systems, so a multi-system signaling regulation label is appropriate.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051531","count":1},{"id":"GO:0035021","count":1},{"id":"GO:0043114","count":1},{"id":"GO:0098886","count":1},{"id":"GO:0051683","count":1}]},{"hash":"207265065691977677","title":"B cell maturation and signaling","description":"The standout GO terms are isotype switching and somatic hypermutation, which are hallmark processes of B cell maturation, supported by PI3K/AKT signaling and activation-induced cell death reflecting immune cell signaling. Some terms (dendritic spine development, regulation of myelination) are neuronal or broad, possibly annotation noise, but do not override the immune-centric signals. Overall, the cluster most plausibly represents B cell maturation and signaling, with some less specific terms present.","confidence":"Medium","size":17,"edges":13,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045190","count":2},{"id":"GO:0016446","count":2},{"id":"GO:0055085","count":2},{"id":"GO:0060996","count":2},{"id":"GO:0031641","count":2}]},{"hash":"1894291895130505022","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":25,"triangles":9,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0010742","count":2},{"id":"GO:0070935","count":2},{"id":"GO:0021537","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0007160","count":2}]},{"hash":"1795418193771051980","title":"Unknown","description":"The GO terms are highly diverse, ranging from apoptosis regulation and transcription to bone resorption, immune signaling, protein targeting, organ system development, stress response, and cell migration. This spread suggests no single coherent function ties the proteins together, so a generic Unknown label is appropriate. ","confidence":"","size":17,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":3},{"id":"GO:0045893","count":2},{"id":"GO:0045779","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0006616","count":1}]},{"hash":"2185327688830276398","title":"Ubiquitin-Dependent Proteolysis in Mitosis","description":"The highlighted GO terms cluster around ubiquitin-mediated degradation machinery (SCF and APC/C), proteasome activity, and mitotic progression (G2/M transition, anaphase-promoting complex\u2013dependent catabolic processes, exit from mitosis) with supporting roles from neddylation and K11-linked ubiquitination. This points to coordinated regulation of mitosis via targeted protein degradation. Some terms like viral process are less central and may reflect broader associations, not core to the cluster\u2019s function.","confidence":"High","size":17,"edges":130,"triangles":597,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0016032","count":13},{"id":"GO:0070911","count":13},{"id":"GO:0070979","count":13},{"id":"GO:0051301","count":12}]},{"hash":"1073326318415461507","title":"Multi-system signaling and stimulus response","description":"The GO terms point to proteins involved in various signaling pathways and cellular responses to diverse stimuli\u2014LPS, GM-CSF, cadmium, TCR signaling, and Rho regulation\u2014as well as processes in neural (glutamatergic transmission) and reproductive (acrosome, testosterone secretion) systems. The cluster thus appears to group broad signal transduction roles across multiple cell types rather than a single pathway, justifying a multi-system signaling and stimulus-response label.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0019933","count":2},{"id":"GO:0071276","count":2}]},{"hash":"894411972053763075","title":"Rho-regulated neural junctions and signaling","description":"Top terms cluster around Rho signaling, adherens junction assembly, and neuronal functions (glutamate secretion, long-term synaptic depression, vocalization), plus barrier-related terms (endothelial/zonula junctions). This points to a theme of Rho-driven junctional organization and signaling impacting neural communication and barrier integrity.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:2000009","count":3},{"id":"GO:0090557","count":2},{"id":"GO:0014047","count":2},{"id":"GO:0060292","count":2}]},{"hash":"1065961594005378278","title":"Actin Cytoskeleton Remodeling and Podosome/Microspike Formation","description":"The proteins show enrichment for actin-related processes (microspike and podosome assembly, actin cortical patch localization, sarcomere organization) and regulation of Rho signaling, pointing to coordinated actin cytoskeleton remodeling and assembly of actin-rich structures; other signaling terms (IL-2/IGF) are likely secondary. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902951","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0030035","count":3},{"id":"GO:1900042","count":3},{"id":"GO:1990314","count":2}]},{"hash":"492814651787641482","title":"Developmental signaling and morphogenesis","description":"This cluster is dominated by terms related to development and morphogenesis, including neural migration, renal tubule morphogenesis, and regulation of signaling pathways (Rho signaling and kinase activity). Although a couple of plant-specific terms appear, the common thread is developmental processes governed by signaling regulation, suggesting a general theme of how cells coordinate growth and tissue formation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022028","count":2},{"id":"GO:0048833","count":2},{"id":"GO:0071374","count":2},{"id":"GO:2001013","count":2},{"id":"GO:0035023","count":2}]},{"hash":"171837528545280438","title":"Golgi-ER trafficking and SNARE-mediated synaptic exocytosis","description":"The top GO terms cluster around vesicle transport between the ER and Golgi, Golgi ribbon formation, SNARE complex assembly, and synaptic vesicle docking/exocytosis, including neurotransmitter receptor insertion and synaptic plasticity (LTP). This points to a cohesive function in vesicle trafficking through the Golgi-ER axis and exocytosis at the synapse, with SNAREs as central components.","confidence":"High","size":17,"edges":34,"triangles":27,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":7},{"id":"GO:0006891","count":7},{"id":"GO:0090161","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0035493","count":6}]},{"hash":"63394971123065192","title":"Proteasome-mediated ubiquitination and cell cycle control","description":"This cluster centers on ubiquitination and proteasomal degradation (polyubiquitination; SCF-dependent degradation) with clear links to cell cycle and division (cell cycle, cell division). Additional signals point to stress and signaling contexts (cadmium response, NF-kB-related regulation), but the predominant theme is coordinated proteostasis governing cell cycle progression.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0007049","count":3}]},{"hash":"537253584592236716","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":93,"triangles":249,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0006607","count":4},{"id":"GO:0060188","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0006351","count":4}]},{"hash":"1935965085394489534","title":"Placental development and immune signaling","description":"The leading GO terms center on placenta formation (maternal and embryonic glycogen cell differentiation) and associated extracellular matrix remodeling (hyaluronan metabolism), with supporting signals for cell migration and immune regulation (fibroblast migration, prostaglandin response, IL-4 production). Some terms touch on apoptosis and hematopoiesis, which can occur in developing placental tissue. Overall, the cluster reflects placental development with remodeling and immune-related cues.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":3},{"id":"GO:0060709","count":3},{"id":"GO:0071380","count":3},{"id":"GO:0030212","count":3},{"id":"GO:0010763","count":3}]},{"hash":"1449536502824497235","title":"Unknown","description":"The cluster lists highly diverse GO terms (ribosome biogenesis, lens differentiation, DNA damage response, dendrite development, phagolysosome assembly, ubiquitination, actin depolymerization, apoptotic signaling, RNA and histone methylation) with no evident shared function, and there are no edges connecting members. This suggests there isn\u2019t a coherent single theme to label; thus Unknown is appropriate.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0072432","count":2},{"id":"GO:0050773","count":2},{"id":"GO:0001845","count":2}]},{"hash":"1383751293462191666","title":"Cardiac lipid metabolism and development","description":"This cluster centers on lipid metabolism with links to heart and liver development, as shown by beta-oxidation, fatty-acyl-CoA biosynthesis, and cardiac muscle differentiation/heart development terms; it may reflect proteins involved in cardiometabolic processes and energy production.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006915","count":2},{"id":"GO:0006663","count":2},{"id":"GO:0009791","count":2},{"id":"GO:0046949","count":2}]},{"hash":"91330436535409303","title":"Eye development and lens differentiation","description":"The top GO terms include retina development in camera-type eye and lens fiber cell differentiation, which strongly point to eye tissue development. Additional terms reflect general cellular processes (ribosome biogenesis, RNA methylation, ubiquitination) and stress/damage responses (DNA damage checkpoint signaling, apoptosis), suggesting the cluster centers on proteins involved in eye development with linked cellular regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0072432","count":2},{"id":"GO:0001845","count":2}]},{"hash":"997295535703510470","title":"Skin development and pigmentation signaling","description":"Top GO terms highlight skin development, pigmentation, and multicellular development, paired with kinase signaling and actin remodeling (Arp2/3). This suggests a developmental, skin- and pigment-related signaling module with cytoskeletal dynamics, supporting a label focused on skin development and pigmentation signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":4},{"id":"GO:0043588","count":4},{"id":"GO:0071456","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0008284","count":4}]},{"hash":"1568598724428473739","title":"Nuclear transport and telomere maintenance","description":"The top GO terms are dominated by nuclear-related processes: nuclear pore localization, nuclear pore complex assembly, tRNA export from nucleus, mitotic nuclear membrane disassembly, and telomere tethering at the nuclear periphery, plus chromatin silencing at telomeres. This suggests a core theme around nuclear transport/architecture and genome maintenance. The other terms (proteolysis, chemokine production regulation) appear peripheral and do not define the cluster\u2019s main function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0071651","count":2},{"id":"GO:2000340","count":2},{"id":"GO:0031081","count":1},{"id":"GO:0034398","count":1}]},{"hash":"879760772308107771","title":"Rap GTPase Signaling and Differentiation","description":"This cluster is anchored by GO terms describing Rap protein signal transduction and activation of GTPase activity, with additional representation of cerebellar granule cell differentiation and other differentiation-related processes. The repeated emphasis on Rap/GTPase signaling suggests a cohesive theme of signaling pathways governing cellular differentiation across tissues, despite some outliers related to cell cycle or mechanical stimuli. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021707","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0032486","count":3},{"id":"GO:0061408","count":2},{"id":"GO:0070212","count":2}]},{"hash":"158188017523459911","title":"Unknown","description":"The GO terms are highly diverse (signaling, transcription, DNA repair, metabolism, lipid modification, redox detoxification, endocannabinoid signaling) with no clear shared function or connectivity, so a coherent, specific label cannot be assigned. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0006360","count":1},{"id":"GO:0070816","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0009086","count":1}]},{"hash":"491653315104123637","title":"Rho GTPase Signaling and Cell Migration","description":"The top GO terms are centered on small GTPase signaling, especially Rho-regulated pathways, with evident links to cell migration and downstream trafficking or growth factor signaling. This points to a module where GTPase-driven signaling controls cytoskeleton dynamics and movement, potentially coordinating endosomal trafficking with growth signals. Therefore, a Rho/Small GTPase\u2013mediated migration signaling label fits best.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0000077","count":3},{"id":"GO:0045792","count":2},{"id":"GO:0007205","count":2}]},{"hash":"427117026521547476","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0042797","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000472","count":2}]},{"hash":"2276428503505042309","title":"Unknown","description":"The 17 proteins are annotated with a broad and disparate set of GO terms, including xenobiotic transport, heart development, insulin regulation, immune signaling, retinoic acid response, gut hormone response, neutrophil degranulation, osteoclast development, and actin cytoskeleton dynamics, with no edges or coherent shared process linking them. This lack of a unifying function leads to an Unknown label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0036302","count":1},{"id":"GO:0046676","count":1},{"id":"GO:0045356","count":1},{"id":"GO:0071300","count":1}]},{"hash":"1490293328701135197","title":"Cerebellar development and synaptic signaling","description":"The cluster shows strong representation of cerebellar cortex formation, Bergmann glial cell differentiation, and Schwann cell development, plus long-term synaptic potentiation and axon regeneration terms, indicating a neural development and synaptic function theme. Insulin receptor signaling also appears, suggesting metabolic signaling integration in neural contexts. A few terms (e.g., some immune-related) are less central.","confidence":"High","size":16,"edges":31,"triangles":1,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030948","count":9},{"id":"GO:0048679","count":9},{"id":"GO:2001275","count":9},{"id":"GO:0050852","count":9},{"id":"GO:0008286","count":9}]},{"hash":"1783113909422786166","title":"Apoptosis and Embryonic Development","description":"This cluster centers on programmed cell death events (apoptotic process; execution phase of apoptosis) and embryonic tissue development (placenta and cerebral cortex), with related differentiation processes and hematopoiesis. While there are a few immune or reproductive terms, the dominant pattern links apoptosis to developmental contexts across multiple tissues.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0045793","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0048240","count":2}]},{"hash":"1461602165757560698","title":"TCR signaling and cell cycle regulation","description":"The top GO terms are dominated by T cell receptor signaling (GO:0050852) and mitotic cell cycle/division (GO:0051301, GO:0000278), with additional notes on negative regulation of ERK signaling and protein stability. While there are some neuronal development terms that appear as weaker signals, the strongest pattern ties immune signaling to cell proliferation control, justifying a label that centers on TCR signaling and cell cycle regulation.","confidence":"Medium","size":16,"edges":13,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":11},{"id":"GO:0051301","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0031647","count":7},{"id":"GO:0000200","count":6}]},{"hash":"32369999230868934","title":"Cell-cycle Regulation and Developmental Signaling","description":"The cluster shows strong representation of DNA replication and cell-cycle terms (DNA replication, nuclear DNA replication, centrosome cycle) alongside signaling and development terms (Wnt signaling, Hippo signaling, morphogenesis, differentiation). This suggests a module coordinating cell proliferation with developmental patterning and organogenesis, rather than a single pathway.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0090263","count":10},{"id":"GO:0048701","count":10},{"id":"GO:0060044","count":10},{"id":"GO:0006915","count":10}]},{"hash":"553882386621909333","title":"Transmembrane Solute Transporters","description":"The cluster is strongly enriched for GO terms describing transport across membranes for a wide range of substrates (nitrate, xenobiotics, various ions, and sugars like galactose and arabinose, as well as related metabolic processes). This pattern points to a group of membrane transporter proteins with broad substrate specificity rather than enzymes or other functions. Confidence: High","confidence":"","size":16,"edges":21,"triangles":19,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":7},{"id":"GO:0006855","count":6},{"id":"GO:0035725","count":6},{"id":"GO:0042128","count":6},{"id":"GO:0015757","count":6}]},{"hash":"948415860422326781","title":"Lariciresinol/pinoresinol lignan metabolism","description":"The top GO terms include multiple entries for lariciresinol and pinoresinol biosynthesis and catabolism, indicating a shared function in lignan metabolism. Other associations (DNA-templated transcription, GTPase regulation, heart development, nitrogen-regulated transcription, and amino acid metabolism) appear peripheral and do not form a single cohesive theme, so the core signal is lignan biosynthesis/catabolism.","confidence":"Medium","size":16,"edges":15,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0001081","count":2},{"id":"GO:1902129","count":2}]},{"hash":"1322331057965297564","title":"Vestibular morphogenesis and somite development","description":"The cluster includes terms tied to vestibular system formation (semicircular canal morphogenesis, vestibular reflex) and axial development (somite development, multicellular organism growth), suggesting a vertebrate developmental theme. However, several other terms (e.g., immune and obsolete processes) dilute the coherence, so the connection is noticeable but not strong.","confidence":"Medium","size":16,"edges":31,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:1900625","count":1},{"id":"GO:0048752","count":1},{"id":"GO:0009444","count":1},{"id":"GO:0032765","count":1},{"id":"GO:0060005","count":1}]},{"hash":"241191276388402445","title":"Developmental morphogenesis and BMP signaling","description":"The terms are dominated by development- and morphogenesis-related processes across multiple tissues (hair follicle, spinal cord, hair cell differentiation, lymph vessels, placenta) with BMP signaling also present, suggesting a coherent theme around developmental morphogenesis and signaling. Some outlier terms (ER retention, plant cell wall biogenesis) likely reflect annotation noise.","confidence":"Medium","size":16,"edges":14,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0031069","count":2},{"id":"GO:0006621","count":2},{"id":"GO:0042353","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0048903","count":1}]},{"hash":"1482185605079319908","title":"Actin Cytoskeleton Remodeling and Signaling","description":"The top GO terms cluster around actin cytoskeleton organization and filopodium assembly, suggesting a core theme of cytoskeletal remodeling. Additional terms point to signaling pathways (Ras, GPCR) and processes tied to cell structure and movement (synapse plasticity, neutrophil regulation, blood vessel remodeling), indicating a broader but connected cytoskeleton-signaling network. Some terms are less directly related (ossification, mitotic cycle), but the predominant signal is cytoskeleton dynamics coupled with signaling.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":2},{"id":"GO:0051835","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0046847","count":2}]},{"hash":"631957406504988579","title":"Unknown","description":"The top terms span immune response, Rho signaling, neural development and synaptic function, plant ABA signaling, muscle development, apoptosis, and cell proliferation, with no single biological process dominating. This lack of a cohesive theme suggests the proteins in this cluster do not share a common function label.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0031914","count":2},{"id":"GO:0060291","count":2}]},{"hash":"368592469761852318","title":"Neural Development and Synaptic Regulation","description":"These proteins show a clear emphasis on nervous system development and synaptic function. Terms like oligodendrocyte differentiation and CNS morphogenesis indicate CNS developmental roles, while regulation of synaptic plasticity by receptor localization to the synapse and ephrin signaling point to synaptic regulation. Transcription and mRNA processing terms suggest coordinated neuronal gene expression, and deubiquitination terms imply post-translational control of neuronal proteins. A behavioral fear response term aligns with CNS-related phenotypes. Overall, the cluster appears to represent neural development and synaptic regulation, with some supportive but less CNS-specific processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0048709","count":2},{"id":"GO:1900383","count":2},{"id":"GO:1901187","count":2}]},{"hash":"504379599787335071","title":"Neurodevelopment and Immune Signaling","description":"This cluster shows a theme around brain development (positive regulation of synapse assembly, corpus callosum development) coupled with immune signaling (cytokine-mediated signaling, IFN-\u03b1 production) and some post-transcriptional regulation (mRNA stabilization, translation initiation). The mix suggests proteins involved in neural development with accompanying immune and translational control roles, rather than a single narrowly defined pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":3},{"id":"GO:0022038","count":3},{"id":"GO:0016525","count":3},{"id":"GO:0048255","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1053062646632678055","title":"Mitochondrial Translation and Respiratory Complex Assembly","description":"This cluster is dominated by terms for mitochondrial translation and the assembly of respiratory chain complexes I and IV, as well as mitochondrial electron transport, pointing to a coherent theme of mitochondrial protein synthesis and energy production. The developmental terms likely reflect tissue-specific roles or downstream effects, but the core signal centers on mitochondria.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006123","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0007420","count":2}]},{"hash":"651714076469130429","title":"Membrane signaling and mechanosensing","description":"This cluster's GO terms center on sensing and responding to mechanical cues, signaling at the plasma membrane, and regulation of cell communication, with additional links to differentiation and cell cycle processes (spindle assembly). The common thread appears to be membrane-associated signaling and mechanotransduction integrated with developmental contexts, justifying the name. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":6},{"id":"GO:0061408","count":5},{"id":"GO:0070212","count":5},{"id":"GO:0097497","count":5},{"id":"GO:0045444","count":5}]},{"hash":"903558394032536686","title":"Mitochondrial dynamics and energy metabolism","description":"The top GO terms cluster around mitochondria: membrane fission, regulation of membrane permeability and potential, and transmembrane transport of ATP, alpha-ketoglutarate, and phosphate ions, plus related apoptotic changes. Although a few terms like learning and IGF stimulus are less central, the dominant signals point to mitochondrial morphology and energy metabolism. Overall, the proteins likely function in mitochondrial dynamics and metabolite/energy transport.","confidence":"High","size":16,"edges":18,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007612","count":4},{"id":"GO:0008637","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0090149","count":4},{"id":"GO:1990314","count":4}]},{"hash":"1252054802285952741","title":"RNA Pol II transcription regulation and chromatin remodeling","description":"The Top Terms are dominated by transcriptional control related to RNA Pol II (regulation and preinitiation complex assembly, negative regulation) and chromatin state (histone acetylation, nucleosome mobilization). Although a few terms touch other processes, the overall signal points to nuclear transcription regulation and chromatin modification as the cluster's theme. Some terms are obsolete, contributing noise, but the core alignment remains clear.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000436","count":1},{"id":"GO:0061408","count":1},{"id":"GO:2000306","count":1},{"id":"GO:0043457","count":1},{"id":"GO:0043966","count":1}]},{"hash":"147871071166579234","title":"Organogenesis and branching morphogenesis signaling","description":"This cluster centers on organ and tissue morphogenesis with multiple terms about branching (lung, blood vessel) and organ development (thalamus, prostate, oligodendrocyte differentiation), plus hedgehog signaling involvement, suggesting a shared developmental signaling/morphogenesis theme.","confidence":"High","size":16,"edges":68,"triangles":180,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0016540","count":3},{"id":"GO:0035224","count":2},{"id":"GO:2000063","count":2},{"id":"GO:0060463","count":2},{"id":"GO:0021794","count":2}]},{"hash":"2221748886657171231","title":"Iron transport and protein turnover","description":"Reasoning: Several terms point to iron handling (intracellular iron ion homeostasis, iron import across the plasma membrane, transferrin transport) and to protein turnover/quality control (protein catabolic processes in the vacuole, ERAD-related glycoprotein processing, C-terminal protein deglutamylation). A plant-specific term (stomatal complex morphogenesis) seems incidental. Overall, the cluster centers on iron metabolism with linked proteostasis processes.","confidence":"Medium","size":16,"edges":21,"triangles":6,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042135","count":1},{"id":"GO:0006879","count":1},{"id":"GO:0035609","count":1},{"id":"GO:0010103","count":1},{"id":"GO:0006898","count":1}]},{"hash":"1906286324792439072","title":"Stimulus-responsive growth and differentiation","description":"The terms point to broad growth and differentiation processes (cell growth; fat cell differentiation; spindle assembly) and transcriptional control (DNA-templated transcription; heat-stress transcription regulation). They also reflect responses to various stimuli (insulin/glucose signaling; mechanical stimulus; chemical stimuli related to pain) and tissue remodeling events (endothelial delamination; adipogenesis). This suggests a cohesive theme of coordinating growth and differentiation programs in response to diverse environmental cues, rather than a single specific pathway. ","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0061408","count":1},{"id":"GO:0070212","count":1}]},{"hash":"1313910255952960097","title":"DNA Integration and Recombination","description":"Proteins in this cluster are annotated with DNA-related processes: DNA integration, DNA recombination, retrotransposition, and negative regulation of DNA amplification, suggesting a core role in genome rearrangement or mobility. The scattered metabolic terms (nicotinate salvage, nicotinamide metabolism, creatinine catabolic, phenazine biosynthesis) appear incidental and do not define a shared pathway beyond DNA dynamics.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0006486","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0032197","count":1},{"id":"GO:0001302","count":1}]},{"hash":"1591538561507194094","title":"GPCR Signaling and Endocytic Trafficking","description":"The top terms cluster around G protein-coupled receptor signaling, receptor internalization, and endocytic trafficking (endosome transport, endocytic recycling), with supporting phosphorylation events and GPCR-related pathways (acetylcholine and tachykinin receptors). Some heart-related terms (cardiac muscle contraction, heart development) align with GPCR roles in cardiac signaling, suggesting a cohesive theme of GPCR signaling coupled with receptor trafficking, despite an outlier fungal-related term. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002031","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0031914","count":2},{"id":"GO:0007213","count":2},{"id":"GO:0060048","count":2}]},{"hash":"967994333285674413","title":"MyD88-Dependent TLR Signaling and Innate Immunity","description":"The top GO terms cluster strongly around MyD88-dependent toll-like receptor signaling, LPS-mediated signaling, innate immune response, and xenophagy, pointing to a cohesive set of proteins involved in pathogen recognition and antimicrobial autophagy. Some terms (e.g., dopamine response, Wnt regulation) are less central, but the prevailing signal is innate immune sensing and response.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":6},{"id":"GO:1903351","count":6},{"id":"GO:0043330","count":6},{"id":"GO:0046827","count":6},{"id":"GO:0031663","count":6}]},{"hash":"2225829390904246523","title":"Mitochondrial Translation and Respiratory Chain Assembly","description":"GO terms cluster around mitochondrial protein synthesis and the assembly of respiratory chain components (notably Complex IV and cytochrome complexes), with copper transport supporting Complex IV assembly and redox-related terms fitting mitochondrial function. Some peripheral terms exist, but the dominant pattern points to mitochondrial translation and respiration machinery.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006120","count":2},{"id":"GO:0008535","count":1},{"id":"GO:0007308","count":1},{"id":"GO:0017004","count":1}]},{"hash":"2265888808611962791","title":"Lipid Mobilization and Phospholipid Remodeling","description":"The top GO terms are dominated by triglyceride catabolic/mobilization processes and phospholipid catabolic/remodeling activities, indicating a cluster of proteins involved in lipid breakdown and turnover of membrane lipids such as phosphatidylethanolamine and phosphatidylcholine. A minor regulatory term (negative regulation of PKA activity) is present but does not outweigh the lipid-centric pattern, supporting a cohesive lipid metabolism theme.","confidence":"High","size":15,"edges":18,"triangles":3,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0006642","count":2},{"id":"GO:0010898","count":2},{"id":"GO:0046338","count":2},{"id":"GO:2000480","count":2}]},{"hash":"1346281556599594929","title":"Apoptosis and necroptosis signaling","description":"The cluster is dominated by terms related to programmed cell death, including necroptotic signaling, extrinsic apoptotic signaling, and various apoptotic regulatory processes, with some influence on PKC signaling and oligodendrocyte fate. A few outliers (circadian temperature homeostasis, lateral root formation) suggest some noise, but the core theme is apoptosis and cell death signaling.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010467","count":2},{"id":"GO:0097252","count":1},{"id":"GO:0048713","count":1},{"id":"GO:0097527","count":1},{"id":"GO:0090037","count":1}]},{"hash":"919594835816502275","title":"Fungal cell division and polarity signaling","description":"The top GO terms point to regulation of GTPase activity, phosphatidylinositol-mediated signaling, and processes tied to cell polarity, mitotic division, and cytokinesis, along with sporulation-related membrane formation and some membrane trafficking. This pattern suggests a cohesive role in coordinating cytoskeletal dynamics, membrane organization, and cell division in fungi, with occasional related processes like mating/conjugation and endosome transport regulation contributing to the broader signaling context. Therefore, the name reflects the core theme of fungal cell division and polarity signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0048015","count":3},{"id":"GO:0032120","count":3},{"id":"GO:0000278","count":3},{"id":"GO:2000769","count":2}]},{"hash":"95615419247456430","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060972","count":4},{"id":"GO:0060743","count":3},{"id":"GO:0035470","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0097150","count":3}]},{"hash":"181197520020820682","title":"Cell cycle control and neuronal development","description":"The cluster centers on cell cycle regulation (DNA replication; G2/M transition; mitotic G2 DNA damage checkpoint signaling; meiotic cell cycle) and development, with neuronal-related processes (dendritic spine morphogenesis; receptor clustering) and proteostasis activities (ubiquitin-dependent protein catabolic process; protein folding in endoplasmic reticulum) that together suggest coordinated regulation of cell division and neuronal development, including proliferation control.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0034975","count":2}]},{"hash":"817786059122011360","title":"Immune signaling and lymphovascular development","description":"The terms show a pattern of immune activation (leukocyte tethering, complement activation, Fc-gamma receptor signaling) alongside vascular/lymphatic remodeling (platelet activation, lymph vessel morphogenesis). A few development terms (cartilage condensation, kidney development) indicate broader morphogenesis contexts. Taken together, the cluster most reasonably reflects immune signaling intertwined with vascular/lymphatic development.","confidence":"Medium","size":15,"edges":47,"triangles":57,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0050901","count":3},{"id":"GO:0001867","count":3},{"id":"GO:0010572","count":3},{"id":"GO:0036303","count":2},{"id":"GO:0090403","count":2}]},{"hash":"1586909878790782445","title":"Neural and sensory organ development","description":"The terms converge on development of neural and sensory tissues\u2014ear (middle and inner ear) and retina (retinal rod cells), plus cerebellar Purkinje cell layer development and related locomotor rhythms\u2014suggesting a shared theme of neural/sensory tissue formation and function. Supporting terms like lysosome organization and ubiquitination may reflect broader cellular housekeeping during development, but the primary signal is neural and sensory organ development.","confidence":"Medium","size":15,"edges":20,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042474","count":1},{"id":"GO:0046548","count":1},{"id":"GO:0060119","count":1},{"id":"GO:0007040","count":1},{"id":"GO:0005975","count":1}]},{"hash":"1458581120434903097","title":"Retroviral integration and latency","description":"This cluster\u2019s top GO terms point to retroviral life-cycle processes: entry into the host (including symbiont entry into host cell and viral penetration into the nucleus), reverse transcription (RNA-templated DNA synthesis; DNA-templated transcription), DNA replication and recombination, DNA integration, and establishment of integrated proviral latency. The prominent emphasis on proviral latency and integration strongly supports a retroviral mechanism rather than general host- or bacterial-symbiont activity.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0075732","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0006278","count":2},{"id":"GO:1903704","count":2}]},{"hash":"1665004971417393119","title":"Embryogenesis and circulatory-hematopoietic development","description":"The top terms point to early developmental processes (axial mesoderm development, somitogenesis) and later blood/vascular formation (thrombocyte differentiation, circulatory system development), with Notch signaling as a regulatory layer and chromatin remodeling as a mechanism for controlling these programs. A rhabdomere development term appears, likely reflecting species-specific eye development rather than core hematovascular themes, but the overall pattern fits embryogenesis and hematovascular differentiation. Overall, the cluster appears to capture developmental programs shaping tissues and the blood/vasculature.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002574","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0048318","count":1},{"id":"GO:0033577","count":1},{"id":"GO:0045747","count":1}]},{"hash":"988820593172190720","title":"Neural development and immune signaling components","description":"The top GO terms cluster around neural development features (mesoderm formation; dorsal/ventral neural tube patterning via Smoothened signaling; synapse assembly) and signaling responses relevant to neural, endocrine, and immune contexts (dopamine response, parathyroid hormone response, lipopolysaccharide and dsRNA responses, defense against Gram-positive bacteria). DNA replication and protein kinase activity regulation appear but do not define a single cohesive function, suggesting the proteins contribute to multiple signaling and developmental roles rather than one tight pathway. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:1901621","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0006469","count":2}]},{"hash":"944265244970342206","title":"Cilium Biogenesis and Centrosome Dynamics","description":"These proteins map to centrioles, centrosomes, and cilium assembly processes, including centriole replication and elongation, centrosome separation, astral microtubule nucleation, and microtubule polymerization. The presence of both non-motile and motile cilium assembly terms, along with the Smoothened signaling pathway, strongly points to ciliogenesis and related centrosome/microtubule organization functions.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902857","count":1},{"id":"GO:0046599","count":1},{"id":"GO:0007099","count":1},{"id":"GO:0030954","count":1},{"id":"GO:0046785","count":1}]},{"hash":"899182774898259839","title":"Neuronal development signaling and endocytosis","description":"The top terms cluster around neural development and signaling: neuron projection morphogenesis, cellular retinoic acid response, and integrin-mediated signaling, plus PDGF receptor signaling and caveolin-mediated endocytosis. JUN phosphorylation suggests transcriptional responses tied to these signaling events, with apoptotic processes indicating cell fate choices during development. The mix points to a cohesive theme of neuronal development paired with membrane signaling and endocytic regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0048008","count":3},{"id":"GO:0061847","count":3},{"id":"GO:0072584","count":3},{"id":"GO:0071300","count":3},{"id":"GO:0048812","count":3}]},{"hash":"848669830736644022","title":"Unknown","description":"The top GO terms are highly diverse, including post-translational modification, plastid and mitochondrial transcription/modification, stress responses, centrosome maintenance, and plant-specific developmental signals (GA signaling, seed dormancy). There isn\u2019t a single coherent functional theme tying these proteins together, so a specific, intuitive label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006478","count":15},{"id":"GO:0031400","count":15},{"id":"GO:0035845","count":15},{"id":"GO:2001162","count":15},{"id":"GO:0042793","count":15}]},{"hash":"1102617176414529258","title":"Developmental Differentiation and Cellular Regulation","description":"Top GO terms indicate involvement in multiple developmental pathways (brain, thymus, uterus) and cell differentiation (Bergmann glial cells), complemented by general cellular processes like ubiquitination and pinocytosis. This points to a broad role in developmental differentiation and broader cellular regulation rather than a single pathway, matching the diverse functions observed. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0071260","count":2},{"id":"GO:2001275","count":2}]},{"hash":"1790105026529494650","title":"Neural development and neuron migration","description":"This cluster is strongly tied to brain development and neuronal positioning, with GO terms for neuron migration and development of substantia nigra and cerebral cortex, suggesting a cohesive theme of neural development and regional specification. Other terms (insulin response, Golgi localization, protein interactions) are peripheral or supporting, but do not override the brain development signal.","confidence":"High","size":15,"edges":13,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":3},{"id":"GO:0030307","count":2},{"id":"GO:0001764","count":2},{"id":"GO:0006977","count":2},{"id":"GO:1902309","count":2}]},{"hash":"2204251086846852013","title":"Unknown","description":"These proteins show a dispersed set of GO terms including insulin receptor signaling, cell migration, spindle assembly, telomere maintenance regulation, and protein poly-ADP-ribosylation, with some terms labeled obsolete. There is no clear, cohesive biological theme tying all terms together, suggesting annotation noise or multiple unrelated roles within the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0016477","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0070212","count":2}]},{"hash":"107711215413845441","title":"Cytoskeletal remodeling and signaling","description":"Based on the prominent GO terms Rho protein signal transduction and lamellipodium assembly, both indicators of actin cytoskeleton remodeling and cell motility, the cluster most plausibly groups proteins involved in cytoskeletal dynamics and related signaling. Other terms span diverse developmental and signaling processes, which may reflect broad annotations rather than a single cohesive pathway; the shared thread appears to be actin remodeling and its regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0007375","count":2}]},{"hash":"355780978376527826","title":"Neural Development and Signaling","description":"These proteins show strong enrichment for nervous system-related terms (spinal cord development, amygdala development, eye morphogenesis) and neurotransmission (gamma-aminobutyric acid secretion). Signaling-related GO terms (regulation of Rho/Rac, adenylate cyclase activity) further support a neural development and signaling theme. A few terms (platelet activation, obsolete glycosylation) seem less connected and may reflect noise or multifunctionality, but the core cluster centers on neural development and synaptic signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0010572","count":2},{"id":"GO:0006486","count":2},{"id":"GO:0098597","count":1}]},{"hash":"2271551778654237678","title":"Cytoskeletal dynamics and polarity establishment","description":"The cluster\u2019s top GO terms cluster around actin filament dynamics (depolymerization, cytoskeleton reorganization), microtubule localization (plus/minus ends), and establishment of cell polarity (bipolar cell polarity). These point to a shared role in cytoskeletal remodeling and polarity, with a few outliers like DNA repair or nutrient absorption that likely reflect separate functions in a mixed set. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0043087","count":1},{"id":"GO:1904825","count":1},{"id":"GO:0061171","count":1},{"id":"GO:0030042","count":1}]},{"hash":"1816224908075562466","title":"Cardiac and neuronal signaling regulators","description":"The cluster shows enrichment in heart development and cardiac muscle contraction, alongside neuronal signaling and plasticity (long-term potentiation) as well as signaling pathway terms (GPCR-related). Additional terms point to transcriptional regulation and nuclear import, suggesting a set of proteins that act as signaling and gene-expression regulators affecting both cardiac and neural functions, with some involvement in cell migration and apoptosis. Overall, it points to regulators that coordinate signaling, transcription, and cellular transport in heart and brain contexts.","confidence":"Medium","size":14,"edges":15,"triangles":2,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006607","count":2}]},{"hash":"1120314260224629668","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":79,"triangles":239,"max_degree":13,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071300","count":14},{"id":"GO:0007258","count":14},{"id":"GO:0031532","count":14},{"id":"GO:0002741","count":14},{"id":"GO:0070935","count":14}]},{"hash":"457397164839742640","title":"Spliceosome-Mediated mRNA Splicing and Processing","description":"The top GO terms cluster around spliceosome-driven mRNA processing: mRNA splicing, regulation of splicing (including alternative splicing), splice-site recognition, and mRNA stabilization. This points to a cohesive group focused on post-transcriptional RNA maturation rather than transcriptional control, with only a minor outlier related to IRES-dependent translation initiation. ","confidence":"High","size":14,"edges":15,"triangles":2,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0001825","count":1},{"id":"GO:1900363","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0075522","count":1},{"id":"GO:0006376","count":1}]},{"hash":"2019528843994654460","title":"Diverse Metabolic Processes","description":"The Top Terms show retinal and retinol metabolism, cholesterol catabolism, norepinephrine metabolism, xenobiotic and plant-hormone related metabolism, and other metabolic or redox-related processes, indicating proteins linked to various metabolic pathways rather than a single cohesive function.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":10},{"id":"GO:0042572","count":10},{"id":"GO:0006707","count":9},{"id":"GO:0071395","count":9},{"id":"GO:0042415","count":9}]},{"hash":"1942481621678282028","title":"RNA Transcription and Processing","description":"Dominant GO terms point to RNA-based gene expression: transcription initiation (Pol II and Pol III), transcription by RNA polymerase II, RNA-templated transcription, and mRNA processing, indicating a cluster of proteins involved in RNA synthesis and processing. Positive regulation of translational initiation appears once, aligning with potential links between transcription and translation control. A few stress-related terms (response to exogenous dsRNA, hydroperoxide) are present but less represented. Overall, the core theme centers on RNA transcription and processing.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071360","count":2},{"id":"GO:1902083","count":1},{"id":"GO:1903204","count":1},{"id":"GO:0071447","count":1},{"id":"GO:0006397","count":1}]},{"hash":"873975140459370516","title":"Integrin-mediated adhesion and platelet activation","description":"The top GO terms point to regulation of integrin activation and positive regulation of platelet activation, suggesting a module focused on cell adhesion and platelet/immune signaling (integrin-driven adhesion and related T cell activation/death). Some unrelated terms (snoRNP assembly, histidine biosynthesis, cuticle development, auditory stereocilium organization) likely reflect noise or multi-species annotations, but the core signal supports an integrin/adhesion\u2013platelet function theme.","confidence":"Medium","size":14,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033623","count":2},{"id":"GO:0006924","count":2},{"id":"GO:0010572","count":2},{"id":"GO:0060088","count":1},{"id":"GO:0050910","count":1}]},{"hash":"2238985147342296650","title":"Mitotic spindle assembly and microtubule regulation","description":"The cluster is dominated by GO terms related to mitosis and microtubule dynamics\u2014spindle midzone assembly, metaphase chromosome alignment, centrosome separation, spindle assembly, and microtubule depolymerization\u2014suggesting proteins function primarily in mitotic spindle processes. A few listed terms (stress granule disassembly, development-related terms) are less central but do not override the core mitotic theme.","confidence":"High","size":14,"edges":82,"triangles":274,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051255","count":6},{"id":"GO:0035617","count":6},{"id":"GO:0007080","count":6},{"id":"GO:0032487","count":6},{"id":"GO:0032886","count":6}]},{"hash":"1835578315375475635","title":"Ribosome Biogenesis and RNA Modification","description":"The cluster shows strong signals for nucleolus organization, rRNA processing, and multiple RNA modification pathways (tRNA methylation, wybutosine biosynthesis, mitochondrial tRNA methylation), which together point to roles in ribosome assembly and RNA maturation. While there are also general transcription and histone methylation terms present, the core theme centers on RNA processing and modification in nucleolar and mitochondrial contexts.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007000","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0002939","count":1},{"id":"GO:0043985","count":1},{"id":"GO:0090398","count":1}]},{"hash":"492310271480820683","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0006384","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1279187817881094488","title":"TLR-MyD88 signaling and chemokine production","description":"Top GO terms point to innate immune signaling via the MyD88-dependent toll-like receptor pathway and to upregulation of chemokines such as CCL5 and CXCL1. Although a few terms are obsolete and the network has no edges, the common theme among the annotations is activation of inflammatory signaling and chemokine production, with some oxidative detoxification processes that can accompany inflammation. This suggests a cluster of proteins involved in initiating and modulating innate immune responses.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0002755","count":2},{"id":"GO:0071651","count":2},{"id":"GO:2000340","count":2}]},{"hash":"1922362252297294069","title":"Metabolic and xenobiotic response proteins","description":"The cluster\u2019s top GO terms center on responses to external compounds ( xenobiotic stimulus, glucocorticoid, antibiotics) and on lipid/metabolic processes (diacylglycerol catabolism, cholesterol ester hydrolysis, antibiotic biosynthesis), suggesting a general theme of metabolism and detoxification/hormonal signaling. While there are diverse terms (including plant-specific signaling), the common thread appears to be proteins involved in processing external stimuli and regulating metabolic pathways.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0042136","count":3},{"id":"GO:0046340","count":3},{"id":"GO:0014912","count":2}]},{"hash":"2173035778925208337","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by ribosome biogenesis (GO:0042254), translation (GO:0006412), and related processes such as ribosomal subunit export from the nucleus and cytoplasmic translation, indicating a core theme of ribosome assembly and protein synthesis. Supporting terms include cell division and cell cycle, suggesting growth-translation coordination, with a few stress-related terms (antibiotic response, amino acid starvation) that connect translation to cellular stress.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0007049","count":2}]},{"hash":"2048746011284524487","title":"General cellular maintenance and stress responses","description":"These terms cover ribosome biogenesis, RNA methylation, protein ubiquitination, actin filament dynamics, phagolysosome assembly, apoptotic signaling, DNA damage response, and developmental processes like dendrite and lens fiber differentiation. The set does not point to a single pathway or process, but rather a collection of core cellular maintenance and stress-response activities across different cellular contexts. Therefore a broad label like \"General cellular maintenance and stress responses\" best captures the shared theme while remaining concise.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0070306","count":1},{"id":"GO:0072432","count":1},{"id":"GO:0050773","count":1},{"id":"GO:0001845","count":1}]},{"hash":"1176591405205052439","title":"Vesicle transport and organelle dynamics","description":"This cluster centers on membrane trafficking and organelle remodeling: ER-Golgi and Golgi-ER transport, endocytosis, and protein targeting to vacuole indicate vesicle-mediated movement within the secretory and endomembrane systems; plus tubulin complex assembly and mitochondrial fission point to cytoskeletal dynamics and organelle fission that often accompany trafficking. A few terms about neuronal development and xenobiotic response appear, but do not overshadow the core trafficking theme.","confidence":"Medium","size":14,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0006890","count":4},{"id":"GO:0006897","count":4},{"id":"GO:0006623","count":4},{"id":"GO:0060079","count":3}]},{"hash":"670223141606325315","title":"Unknown","description":"The GO annotations for this cluster are highly diverse, spanning lipid metabolism (sphingomyelin and sphingolipid processes), signaling (JNK regulation, GPCR pathway), development (dorsal/ventral identity, prostate epithelial differentiation), and respiration, with no clear shared function or tissue context that ties all proteins together. The absence of a coherent unifying biological theme makes a specific label unreliable.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000016","count":1},{"id":"GO:0048264","count":1},{"id":"GO:0043508","count":1},{"id":"GO:0043496","count":1},{"id":"GO:0006685","count":1}]},{"hash":"477256634600051559","title":"Golgi trafficking and organization","description":"The top GO terms point to Golgi apparatus functions, notably Golgi organization (GO:0007030) and retrograde transport within the Golgi (GO:0000301), suggesting a theme of Golgi-mediated vesicle trafficking. Other terms refer to development or chromatin-related processes and include some obsolete entries, which weakens but does not overturn the central Golgi-focused signal. Overall, there is a coherent but not exclusive link to Golgi trafficking. ","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":1},{"id":"GO:0030961","count":1},{"id":"GO:0070544","count":1},{"id":"GO:0034720","count":1},{"id":"GO:0035775","count":1}]},{"hash":"2118910670138012525","title":"Embryonic Development and Organ Morphogenesis","description":"The GO terms point to broad embryonic development and tissue/morphogenesis processes, including epithelial-to-mesenchymal transition in heart cushion formation, cartilage morphogenesis, left-right patterning, and endocrine system development. A few terms relate to cellular trafficking, but the dominant theme is developmental differentiation and organ formation across tissues.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003198","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060536","count":2},{"id":"GO:0035270","count":2}]},{"hash":"1276563774404397821","title":"Unknown","description":"The top GO terms span apoptotic signaling, neural and forebrain development, skeletal and multicellular development, transcription, DNA repair, cadmium and Gram-positive defense responses. This mix shows no single coherent function or pathway tying the proteins together, and the cluster has no edges or hubs, so a precise, representative label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1083819434431459206","title":"Chromosome maintenance and cell cycle regulation","description":"This cluster centers on processes tied to genome integrity and chromosome dynamics, including double-strand break repair (meiotic recombination and NHEJ), kinetochore-microtubule attachment, and transcription-related phosphatase activity, suggesting combined roles in DNA repair and cell-cycle progression. Some terms appear unrelated (angiogenesis/cardiac stress signals) and likely reflect broad annotations not core to the cluster\u2019s theme.","confidence":"Medium","size":13,"edges":65,"triangles":177,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030846","count":9},{"id":"GO:1990918","count":9},{"id":"GO:0070940","count":9},{"id":"GO:0001569","count":9},{"id":"GO:0070262","count":9}]},{"hash":"2035131802171658622","title":"Cofactor and metabolite biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for cofactors and metabolites (biotin, protoporphyrinogen IX, cobalamin, and fatty acids), with oxaloacetate metabolism also appearing, suggesting a cluster of proteins involved in biosynthesis and central metabolism. A few terms like DNA-templated transcription and xenobiotic response are present but less central, so the core theme is biosynthesis and metabolic production rather than a single specialized pathway. This labeling captures the shared functional focus without over-specificity.","confidence":"Medium","size":13,"edges":76,"triangles":264,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019518","count":5},{"id":"GO:0009102","count":4},{"id":"GO:0006782","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0019878","count":4}]},{"hash":"118653885620325862","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902004","count":1},{"id":"GO:0001302","count":1},{"id":"GO:1903469","count":1},{"id":"GO:0090267","count":1},{"id":"GO:0045190","count":1}]},{"hash":"1823983136052930210","title":"GTPase-Regulated Neurite Outgrowth and Spine Dynamics","description":"This cluster is driven by small GTPase\u2013mediated signaling that governs cytoskeletal remodeling underlying filopodium assembly, neurite extension, and dendritic spine development, and it links to GABAergic synaptic transmission. While a few terms touch on broader processes such as cell spreading, the core theme is GTPase-regulated neuronal morphology and synaptic signaling.","confidence":"Medium","size":13,"edges":16,"triangles":4,"max_degree":10,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000266","count":9},{"id":"GO:0046847","count":9},{"id":"GO:0007264","count":9},{"id":"GO:0051932","count":9},{"id":"GO:0045792","count":9}]},{"hash":"16166900208128423","title":"Cardiac Potassium Transport and Action Potential Regulation","description":"The top GO terms cluster around cardiac electrical activity and potassium handling\u2014potassium ion transport, membrane potential stabilization and resting potential, and cardiac action potentials (including atrial and bundle of His), as well as heart rate regulation by conduction\u2014pointing to a cohesive role in cardiac electrophysiology and potassium homeostasis.","confidence":"High","size":13,"edges":10,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":4},{"id":"GO:0098914","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0086091","count":3},{"id":"GO:0030322","count":3}]},{"hash":"941998981761277326","title":"Developmental signaling and cytoskeletal regulation","description":"The GO terms point to development (heart development, hemopoiesis), signaling pathways (thrombin-activated receptor signaling), transcriptional control, protein turnover, and cytoskeletal/transport processes (filopodium assembly, GTPase regulation, pigment granule transport), suggesting a cohesive theme around developmental signaling coordinating cytoskeletal dynamics and gene regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051489","count":2},{"id":"GO:0070493","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0006351","count":2}]},{"hash":"549785127912701814","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016973","count":1},{"id":"GO:0071028","count":1},{"id":"GO:0000467","count":1},{"id":"GO:0071039","count":1},{"id":"GO:0071051","count":1}]},{"hash":"301241364459386473","title":"Chromatin modification and remodeling","description":"The top GO terms are dominated by histone modifications (H3K27 trimethylation, H3K4 methylation/demethylation, histone acetylation) and chromatin remodeling, with additional related processes like transcriptional regulation and centrosome/spindle-associated mitotic roles, indicating a cluster of proteins involved in chromatin state control and cell-cycle regulation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098532","count":4},{"id":"GO:0034720","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0007098","count":3}]},{"hash":"1616337338302157400","title":"Hypoxia-linked Growth and Differentiation Signaling","description":"The Top Terms show cellular response to hypoxia, positive regulation of cell proliferation and the mitotic cell cycle, TORC1 signaling, and development-related processes such as heart contraction regulation, blood vessel morphogenesis, and retinal neuron differentiation. This combination suggests a theme where hypoxic conditions affect growth and differentiation programs, coordinating cell cycle and growth signaling with organ development, especially in cardiovascular and neural contexts. Some terms (mRNA transport, nuclear import) are broad, but the overall pattern supports a growth/differentiation signaling theme under hypoxia.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1904263","count":2}]},{"hash":"1073062826116034302","title":"RNA Splicing Regulation and ncRNA Silencing","description":"The dominant GO terms show spliceosome-mediated mRNA processing (splicing, splice site recognition, alternative splicing regulation) and regulatory ncRNA\u2013mediated gene silencing, with related hints of mRNA stability control in stress. Together, these point to a cohesive module focused on post-transcriptional mRNA regulation via splicing and ncRNA-guided silencing.","confidence":"High","size":13,"edges":58,"triangles":166,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":9},{"id":"GO:0048026","count":9},{"id":"GO:0006378","count":7},{"id":"GO:0010610","count":7},{"id":"GO:0000398","count":6}]},{"hash":"2371399005929195","title":"Ribosome biogenesis and cell proliferation","description":"The cluster is dominated by GO terms for ribosome biogenesis (including both large and small subunit biogenesis) and cell division/proliferation, pointing to a group of proteins involved in ribosome assembly and growth-related processes. Additional terms about kinase activity regulation suggest a signaling layer that may modulate these growth-related functions, though the core theme is ribosome production and cell growth. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0000747","count":6},{"id":"GO:0042273","count":5},{"id":"GO:0042274","count":4}]},{"hash":"1860596327200993295","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0000184","count":8},{"id":"GO:0000467","count":7},{"id":"GO:0071051","count":7},{"id":"GO:0006265","count":7}]},{"hash":"1594461311551207690","title":"Rho/Rac signaling and lamellipodium assembly","description":"The cluster is dominated by GO terms for regulation and mediation of Rho family GTPases (Rho, Rac, Ras) and lamellipodium assembly, pointing to a cohesive module of small GTPase\u2013driven cytoskeletal remodeling. The presence of immune-related terms (IL-7 response, NKT differentiation, IL-4 production, B cell maturation) suggests these signaling components may also influence immune cell signaling and differentiation, but the core theme remains actin dynamics regulated by Rho family GTPases. Overall, it appears to be a set of proteins coordinating cytoskeletal rearrangements via small GTPase pathways. ","confidence":"Medium","size":13,"edges":28,"triangles":3,"max_degree":8,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":13},{"id":"GO:0007264","count":13},{"id":"GO:0035020","count":13},{"id":"GO:0030032","count":13},{"id":"GO:0098761","count":13}]},{"hash":"462131305230296035","title":"Actin Cytoskeleton Dynamics and Cell Motility","description":"The top GO terms cluster around actin-related processes: regulation of actin nucleation, actin-based transport, membrane repair, and cell migration, spanning muscle contraction and immune cell polarity, organelle inheritance, and yeast mating projection. This points to a unifying theme of actin cytoskeleton remodeling driving diverse cellular movements and trafficking.","confidence":"High","size":13,"edges":53,"triangles":100,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":4},{"id":"GO:0051904","count":3},{"id":"GO:1904601","count":3},{"id":"GO:0003009","count":3},{"id":"GO:0009826","count":3}]},{"hash":"2168381268775880680","title":"Unknown","description":"The GO terms span plant development (leaf morphogenesis, flower development), signaling (Notch), immune differentiation, and broad metabolic processes, with no clear single function or pathway tying all proteins together. This suggests the cluster lacks a cohesive, specific biological theme to name confidently.","confidence":"","size":13,"edges":27,"triangles":17,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0009965","count":2},{"id":"GO:0045019","count":2},{"id":"GO:0009911","count":2},{"id":"GO:0046477","count":2},{"id":"GO:0005975","count":2}]},{"hash":"1276977081921736434","title":"Hedgehog signaling in neural and kidney development","description":"The top GO terms cluster around Hedgehog signaling (Smoothened) and developmental processes for the nervous system and kidney morphogenesis, including neurogenesis and axonogenesis, suggesting these proteins function together in Hedgehog-mediated coordination of neural and nephric development.","confidence":"High","size":13,"edges":69,"triangles":200,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":3},{"id":"GO:0001822","count":3},{"id":"GO:0050772","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0007601","count":2}]},{"hash":"2067808165802512599","title":"Ubiquitin-Proteasome\u2013Mediated Immune Signaling","description":"The cluster shows enrichment for ubiquitin-dependent protein degradation (SCF proteasomal pathways, ERAD) and innate immune signaling (defense against Gram-positive bacteria, NF-kappaB regulation, NOD2 signaling), suggesting a core theme around ubiquitin-proteasome\u2013driven regulation of immune pathways, with additional cell-cycle and cytoskeletal processes likely reflecting broader housekeeping roles.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0045444","count":2}]},{"hash":"194805032774523413","title":"Unknown","description":"The GO terms are highly disparate, including viral DNA integration and proviral latency alongside various unrelated cellular processes (differentiation, spindle assembly, mechanical response, etc.). There is no clear single function tying these proteins together, so a concise, representative label can\u2019t be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0061408","count":1}]},{"hash":"851879698224724809","title":"Unknown","description":"The Top Terms span neural (glutamatergic synaptic transmission, neuroblast polarity) and plant (root meristem growth, cytokinin signaling) processes, plus generic signaling and stress-related pathways, with no clear shared function or interaction pattern linking the proteins. Because the terms are diverse and there are no edges or cohesive theme, a single meaningful label is not apparent.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":2},{"id":"GO:0045201","count":1},{"id":"GO:1900037","count":1},{"id":"GO:2000299","count":1},{"id":"GO:0010449","count":1}]},{"hash":"1808652541383081850","title":"Immune signaling and apoptosis regulation","description":"This cluster\u2019s top GO terms cluster around immune-related processes (adaptive immune response; dendritic cell apoptosis regulation) and protein turnover (ubiquitination), with supporting signaling and development cues (Rho signaling, TGF-beta response, forebrain development). The absence of network edges suggests a functional theme across diverse proteins rather than a single interaction module, making \u201cimmune signaling and apoptosis regulation\u201d a concise, representative label.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0071260","count":5},{"id":"GO:2001275","count":4},{"id":"GO:0071560","count":3},{"id":"GO:0030900","count":3}]},{"hash":"1970389577695395502","title":"Cartilage Matrix and Chondrocyte Development","description":"This cluster is dominated by cartilage-related biology, highlighted by chondroitin sulfate biosynthetic process and chondrocyte development terms. The presence of GPI-anchor attachment and proteolysis hints at membrane-associated or secreted proteins involved in extracellular matrix remodeling, which can align with cartilage ECM biology and related tissue development. While there are some diverse terms (renal system process, complement regulation, ERBB signaling), the strongest signal centers on cartilage matrix formation and chondrocyte maturation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030206","count":2},{"id":"GO:0002063","count":2},{"id":"GO:0010765","count":1},{"id":"GO:0001869","count":1},{"id":"GO:0045959","count":1}]},{"hash":"1087716793318908583","title":"Central Carbon Metabolism","description":"The dominant GO terms point to core energy and carbon-flow pathways: glycolysis, TCA cycle, acetyl-CoA biosynthesis, thiamine biosynthesis, and branched-chain amino acid catabolism. Some other terms (e.g., DNA damage response, isotype switching, meiotic repair) appear ancillary or noisy, but the metabolism-related terms clearly define the cluster\u2019s theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061732","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0010510","count":2},{"id":"GO:0009083","count":2},{"id":"GO:0006096","count":2}]},{"hash":"1322404284654571509","title":"Spliceosome-Mediated mRNA Processing and Translation","description":"The top GO terms show a clear focus on mRNA splicing via the spliceosome, including regulation of alternative splicing, splice site recognition, and general mRNA splicing via the spliceosome, complemented by a translation term. This combination points to a cluster of proteins involved in post-transcriptional mRNA processing and the initiation/etablishment of translation, rather than a single metabolic or signaling pathway. The presence of a few obsolete terms likely reflects historical annotations but does not undermine the core theme.","confidence":"High","size":12,"edges":51,"triangles":110,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0001825","count":2},{"id":"GO:1900363","count":2}]},{"hash":"1769037132530921290","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009051","count":2},{"id":"GO:0019262","count":2},{"id":"GO:0006043","count":2},{"id":"GO:0006046","count":2},{"id":"GO:0005975","count":2}]},{"hash":"574045461969756223","title":"Meiotic DNA repair and chromosome segregation","description":"The top terms point to meiotic double-strand break repair and repair via nonhomologous end joining, plus attachment of spindle microtubules to kinetochores, all highlighting DNA maintenance and chromosome segregation during meiosis/mitosis. There are also phosphatase-related terms affecting transcription and cell-cycle regulation, which can tie into broader control of these processes. Overall, the cluster seems centered on DNA repair and chromosome dynamics rather than a single metabolic pathway.","confidence":"Medium","size":12,"edges":59,"triangles":162,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030846","count":5},{"id":"GO:1990918","count":5},{"id":"GO:0070940","count":5},{"id":"GO:0001569","count":5},{"id":"GO:0070262","count":5}]},{"hash":"277114815812290512","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000453","count":1},{"id":"GO:0050843","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0017183","count":1},{"id":"GO:0009236","count":1}]},{"hash":"840914658014170730","title":"Golgi vesicle trafficking and acrosome-related processes","description":"This cluster is dominated by GO terms tied to Golgi organization and vesicle fusion (with Golgi and vacuole) and includes the acrosome reaction, which is tightly linked to Golgi-derived acrosomal vesicles. The presence of PI3K/AKT signaling and membrane trafficking-related processes (glucose transport, sphingolipid metabolism) supports a broader membrane trafficking theme, with some terms (mitochondrial assembly, myelination, T cell death) being peripheral. Overall, a coherent focus on Golgi dynamics and vesicle trafficking, including acrosome-related functions, is most consistent.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903358","count":2},{"id":"GO:0007340","count":2},{"id":"GO:0031641","count":2},{"id":"GO:0043491","count":2},{"id":"GO:0015758","count":2}]},{"hash":"1853704141132592013","title":"Vesicle trafficking and synaptic modulation","description":"The terms converge on vesicle dynamics (vacuole fusion, Golgi fusion, receptor recycling, membrane targeting) and neuronal signaling (long-term potentiation, potassium channel regulation), suggesting a cluster of proteins involved in membrane trafficking and modulation of synaptic activity; peripheral terms like hindgut contraction and mucus secretion may reflect broader secretory roles but do not override the main theme.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1903070","count":2},{"id":"GO:1902259","count":1}]},{"hash":"1153666050966345444","title":"Transcription-coupled DNA repair and redox homeostasis","description":"The top GO terms point to transcription regulation and transcription-coupled nucleotide-excision repair, linking transcription with DNA repair. Additional terms emphasize oxidative stress response and redox balance, plus protein repair and a proline hydroxylation modification, suggesting a cohesive module that coordinates transcription/repair with cellular redox state and protein maintenance. This combination supports a label focused on DNA repair in the context of transcription and oxidative stress.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0030091","count":1}]},{"hash":"1683739584808917982","title":"Unknown","description":"The GO terms span diverse processes across different tissues and systems (nuclear import, indole-3-methanol response, oviduct/lung/renal development, centriole cohesion regulation, heart rate conduction, and host-symbiont responses), with no single coherent function or pathway tying all proteins together. This lack of a shared theme supports labeling Unknown.","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":8},{"id":"GO:0071681","count":8},{"id":"GO:0060066","count":8},{"id":"GO:0030997","count":8},{"id":"GO:0060492","count":8}]},{"hash":"1834204392190975075","title":"Multi-tissue developmental differentiation","description":"GO terms span neural, cardiac, gonadal differentiation across tissues, plus immune regulation and hormonal response; together they point to broad tissue development rather than a single pathway. This broad theme justifies naming the cluster Multi-tissue developmental differentiation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021526","count":1},{"id":"GO:0046013","count":1},{"id":"GO:0035195","count":1},{"id":"GO:0055011","count":1},{"id":"GO:0070527","count":1}]},{"hash":"1308414724140300288","title":"Thermosensation and Pain Perception","description":"GO terms strongly point to sensing temperature and pain (thermoception, detection of temperature stimulus, response to cold, sensory perception of pain, chemical nociception), suggesting proteins involved in nociception and thermosensation. A couple of outlier terms (cartilage condensation, vasopressin secretion) appear infrequently and are less representative. Overall, the cluster seems to group temperature- and pain-sensing proteins.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001502","count":2},{"id":"GO:0071226","count":2},{"id":"GO:0050968","count":2},{"id":"GO:0050960","count":2},{"id":"GO:1903759","count":2}]},{"hash":"332961246522977801","title":"Neural development and deubiquitination regulation","description":"This cluster centers on protein deubiquitination (K11, K6, K63 linkages) and transcriptional regulation (DNA-templated transcription, regulation of transcription), with neural development signals (central nervous system morphogenesis, behavioral fear response) and chaperone-mediated protein complex assembly. The combination suggests proteins coordinating neural gene expression programs via deubiquitinases, relevant to CNS development and associated behaviors.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035871","count":1},{"id":"GO:0070537","count":1},{"id":"GO:0021551","count":1},{"id":"GO:0090035","count":1},{"id":"GO:0044313","count":1}]},{"hash":"83136834343818002","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":3},{"id":"GO:0006094","count":2},{"id":"GO:0006147","count":2},{"id":"GO:0007411","count":2},{"id":"GO:0006207","count":2}]},{"hash":"1300832255279837670","title":"Rho/Rac-Driven Actin Remodeling and Cell Migration","description":"This cluster is dominated by terms related to actin cytoskeleton dynamics, filopodium assembly, and cell migration, along with small GTPase\u2013mediated signaling (notably Rac and Ras pathways) and regulation of Rac signaling. These points together suggest a cohesive theme of actin remodeling controlled by Rho/Rac GTPases to drive cell movement, with a few peripheral terms that may reflect broader pleiotropy. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046847","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0032633","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0007205","count":2}]},{"hash":"1245255652211669198","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0071300","count":11},{"id":"GO:0007258","count":11},{"id":"GO:0031532","count":11}]},{"hash":"198951998186552335","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002107","count":2},{"id":"GO:0000467","count":2},{"id":"GO:0034415","count":2},{"id":"GO:0000289","count":2},{"id":"GO:0010606","count":2}]},{"hash":"605203686581921815","title":"Synaptic Assembly and APP Metabolism","description":"The cluster\u2019s top GO terms point to synaptic function (presynaptic membrane assembly; protein localization to synapse) and amyloid precursor protein metabolic processing, with additional neuronal-related terms such as circadian regulation and glucocorticoid response, alongside some ion transport terms typical of neuronal signaling. This suggests a cohesive theme around neuronal synaptic organization and APP processing, despite a few outlier terms. ","confidence":"High","size":12,"edges":15,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0009939","count":1},{"id":"GO:0097105","count":1}]},{"hash":"1565697318240093220","title":"Cerebral Cortex Neurovascular Development","description":"The top GO terms point to cortical layer formation, synapse assembly, and neuronal response pathways, alongside angiogenesis and endothelial proliferation. Rho signaling, Wnt pathway regulation, and TORC1 signaling connect cytoskeletal dynamics and growth with neuronal connectivity and vascular development. Together, these terms suggest a cluster focused on coordinated brain development involving neurons and blood vessels in the cerebral cortex.","confidence":"High","size":12,"edges":23,"triangles":0,"max_degree":6,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0042220","count":7},{"id":"GO:0001525","count":7},{"id":"GO:0007266","count":7},{"id":"GO:0021819","count":7},{"id":"GO:0051965","count":7}]},{"hash":"2118634750730226436","title":"DNA Replication Machinery","description":"The top GO terms are dominated by DNA replication and initiation (GO:0006260, GO:0006270, GO:0032508), strongly suggesting the proteins cluster around DNA replication processes. The remaining single-occurrence terms appear as secondary annotations or multifunctional roles, but do not outweigh the replication signal. Thus, labeling this cluster as DNA Replication Machinery is representative of the main function.","confidence":"High","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006270","count":2},{"id":"GO:0032508","count":2},{"id":"GO:0034551","count":1},{"id":"GO:0071392","count":1}]},{"hash":"453269244358186223","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":51,"triangles":116,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":5},{"id":"GO:0051084","count":2},{"id":"GO:0022417","count":2},{"id":"GO:0045041","count":2},{"id":"GO:0032543","count":2}]},{"hash":"632959241331292346","title":"Synaptic Transmission and Plasticity Regulation","description":"The top GO terms are dominated by neural functions: synaptic transmission (glutamatergic), long-term potentiation, and regulation of synaptic plasticity, with supporting terms for transcription, apoptosis, and development signaling (e.g., Wnt). While some terms touch on muscle development and broader signaling, the core signal centers on neuronal communication and plasticity regulation.","confidence":"Medium","size":11,"edges":26,"triangles":22,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031914","count":6},{"id":"GO:0007520","count":6},{"id":"GO:0050852","count":6},{"id":"GO:0043065","count":6},{"id":"GO:0090263","count":6}]},{"hash":"2109227773233183627","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by ribosome- and translation-related GO terms: translation (GO:0006412) appears most strongly (6 proteins), with supporting terms in ribosome biogenesis (GO:0042254, GO:0042274), maturation of SSU-rRNA (GO:0000462), ribosomal small subunit assembly (GO:0000028), and rRNA methylation (GO:0031167). Together, these indicate a cohesive role in ribosome production and protein synthesis. A few non-ribosome terms (G1/S transition, T cell proliferation, oogenesis, and apoptotic regulation) are present but likely peripheral noise. ","confidence":"High","size":11,"edges":49,"triangles":120,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0000082","count":1}]},{"hash":"673716324416885902","title":"Cytoskeleton Remodeling and Mitotic Cell Cycle Regulation","description":"The top GO terms cluster around cytoskeletal dynamics (actin cytoskeleton reorganization, cell spreading), mitochondrial fission, and progression through the cell cycle (cell division, mitotic cell cycle), with signaling links via TORC2 and adhesion-related processes. Some terms pertain to neuronal structure and apoptosis, which can relate to cytoskeletal remodeling in neurons, supporting a unifying theme of structural dynamics coordinating growth, division, and signaling. Overall, the data point to a cohesive theme of cytoskeleton-driven regulation of mitosis and related signaling pathways.","confidence":"Medium","size":11,"edges":29,"triangles":31,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0033144","count":10},{"id":"GO:1900026","count":10},{"id":"GO:0000266","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0000278","count":9}]},{"hash":"2266692255960823195","title":"Rho Rac GTPase signaling and lamellipodium assembly in immune cells","description":"This cluster is dominated by small GTPase signaling terms (Rho and Rac) and lamellipodium assembly, indicating actin-driven cytoskeletal remodeling. The presence of immune-related terms (hemopoiesis, NK T cell differentiation, IL-7 response) suggests a role in immune cell signaling and migration, where Rho/Rac pathways regulate lamellipodia formation and movement. Some insulin signaling terms appear but do not redefine the primary theme; the core theme is cytoskeletal dynamics linked to immune cell function.","confidence":"High","size":11,"edges":26,"triangles":31,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":8},{"id":"GO:0030097","count":7},{"id":"GO:0007264","count":7},{"id":"GO:0048009","count":7},{"id":"GO:2001275","count":7}]},{"hash":"295789820084224823","title":"RNA and protein methylation enzymes","description":"This cluster is dominated by RNA methylation and RNA modification terms, along with multiple protein methylation terms (lysine, arginine, N-terminal methylation). Together, these GO terms suggest a group of methyltransferases acting on RNA and various proteins, with additional signals from biosynthetic methylation processes (cobalamin and antibiotic biosynthesis) that support a broader methylation-centric function.","confidence":"High","size":11,"edges":51,"triangles":133,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":3},{"id":"GO:0018027","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0018012","count":2}]},{"hash":"1107515143777354360","title":"Cardiovascular Development Signaling","description":"The top GO terms cluster around heart contraction regulation, branching morphogenesis of blood vessels, VEGF receptor signaling regulation, Wnt/calcium signaling, and guanylate cyclase activity, all pointing to cardiovascular development and vascular signaling. Though a couple terms touch on nuclear import or retinal neuron differentiation, the dominant theme is heart and blood vessel development and related signaling pathways, justifying this label.","confidence":"High","size":11,"edges":20,"triangles":9,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0030948","count":5},{"id":"GO:0006607","count":4},{"id":"GO:0006919","count":4},{"id":"GO:0060040","count":4}]},{"hash":"1329439691089489195","title":"Bone development and osteoclast podosome dynamics","description":"This cluster centers on bone biology signals: cranial skeletal system development, bone development, and osteoblast fate commitment, complemented by podosome assembly and regulation of Rho signaling\u2014key aspects of cytoskeletal remodeling in bone-resorbing cells. Translation and ribosome biogenesis terms appear as background cellular processes rather than defining features. Overall, the dominant theme points to skeletal development with cytoskeletal dynamics. ","confidence":"Medium","size":11,"edges":16,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:1904179","count":2},{"id":"GO:1904888","count":2},{"id":"GO:0060348","count":2}]},{"hash":"1874089498865102745","title":"TLR-mediated inflammatory and interferon signaling","description":"The top GO terms cluster around innate immune sensing and inflammatory pathways: TLR8 signaling, detection of diacyl lipopeptides, LPS response, cytokine signaling, and interferon production. A couple terms point to neural development and dopamine response, but the dominant theme is pattern-recognition\u2013driven inflammatory signaling, suggesting these proteins function mainly in innate immune responses with a potential secondary link to neuroimmune interactions.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":3},{"id":"GO:0045356","count":2},{"id":"GO:0019221","count":2},{"id":"GO:0042496","count":2},{"id":"GO:1904027","count":2}]},{"hash":"549600397134837678","title":"Meiosis Chromosome Cohesion and Synaptonemal Complex","description":"Several terms point to meiotic chromosome dynamics: synaptonemal complex assembly, meiotic chromosome condensation, meiotic sister chromatid cohesion (centromeric and general), and spindle attachment during meiosis I, along with telomere tethering to the nuclear envelope and oocyte maturation. The convergence on meiotic processes suggests this cluster represents proteins involved in meiotic chromosome organization and segregation, especially cohesion and synaptonemal complex formation. Thus, the label captures the common theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007130","count":1},{"id":"GO:0003187","count":1},{"id":"GO:0051455","count":1},{"id":"GO:0034087","count":1},{"id":"GO:0001556","count":1}]},{"hash":"798411125590901393","title":"Actin Cytoskeleton Dynamics","description":"This cluster is defined by strong representation of Arp2/3 complex-mediated actin nucleation and actin cortical patch assembly, pointing to roles in actin remodeling and cytoskeleton organization. Other listed terms (RNA splicing, inheritance, sumoylation) appear sporadic or ancillary, not forming a cohesive alternative theme, so actin dynamics is the most plausible unifying function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007369","count":1},{"id":"GO:0007095","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0034314","count":1},{"id":"GO:0000147","count":1}]},{"hash":"761429218085353089","title":"Sterol and lipid biosynthesis","description":"The top GO terms are dominated by sterol biosynthetic processes (cholesterol via lathosterol; ergosterol) and broader lipid metabolism (fatty acid, ether lipid, sphingolipid/metabolic processes, including MIPC). This points to a cohesive cluster centered on lipid and sterol biosynthesis across systems. Occasional terms related to lipid-rich tissues (sebaceous gland differentiation, myelin maintenance) further support the lipid theme, while a lone immune chemotaxis term appears incidental. ","confidence":"High","size":11,"edges":26,"triangles":25,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0071432","count":3},{"id":"GO:0033490","count":2}]},{"hash":"566801975332346317","title":"Ethylene- and hormone-regulated fruit ripening","description":"The terms point to plant hormone signaling and fruit maturation (ethylene and gibberellin-related processes, fruit ripening, salicylic acid turnover) along with secondary metabolism (proanthocyanidin biosynthesis) and stress responses (hydrogen peroxide\u2013driven PCD). This pattern suggests a cluster of proteins involved in coordinating ripening and defense through hormonal regulation and related metabolism, rather than a single linear pathway.","confidence":"Medium","size":11,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0010023","count":1},{"id":"GO:0045487","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0009693","count":1}]},{"hash":"365232945646512654","title":"Mitochondrial energetics and dynamics","description":"These 11 proteins cluster around mitochondrial functions: transport of key metabolites (alpha-ketoglutarate, phosphate) across mitochondrial membranes, ATP transmembrane transport, regulation of membrane potential and permeability, mitochondrial membrane fission, and apoptotic mitochondrial changes. The IGF stimulus term suggests broader metabolic signaling linked to growth, and the pregnancy term likely reflects tissue-specific energy metabolism in reproductive contexts. Overall, the dominant theme is mitochondrial energy production coupled with structural remodeling, justifying the label.","confidence":"High","size":11,"edges":27,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":9},{"id":"GO:0008637","count":8},{"id":"GO:0015742","count":8},{"id":"GO:0090149","count":8},{"id":"GO:1990314","count":8}]},{"hash":"2059468522694276311","title":"Methylation and RNA/Chromatin Modification","description":"The top GO terms are dominated by methylation-related processes: peptidyl-arginine methylation (asymmetric dimethyl arginine), rRNA methylation/modification, and histone H4-R3 methylation, suggesting a cluster centered on methylation-based regulation of RNA and chromatin. Other terms (cell growth, cellular senescence, response to IL-1, cobalamin biosynthesis, and metal/tumor responses) appear ancillary, not defining the core function, but do not negate the methylation-centric theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":4},{"id":"GO:0009236","count":3},{"id":"GO:0043985","count":3},{"id":"GO:0019919","count":3},{"id":"GO:0046690","count":3}]},{"hash":"2040511855230154103","title":"Amino acid biosynthesis and catabolism","description":"The top GO terms are dominated by amino acid biosynthesis and catabolic processes (threonine, serine, tryptophan, and homocysteine), along with related intermediates like 2-oxobutyrate and general amine catabolism, indicating a cluster of proteins functioning in amino acid metabolism.","confidence":"High","size":11,"edges":38,"triangles":64,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0070689","count":3},{"id":"GO:0009310","count":3},{"id":"GO:0046360","count":3},{"id":"GO:0000162","count":3},{"id":"GO:0043418","count":3}]},{"hash":"2023927132588959490","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007175","count":1},{"id":"GO:1902570","count":1},{"id":"GO:0000390","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0051096","count":1}]},{"hash":"1424315517108079882","title":"N-terminal acetylation and propionylation","description":"The cluster shows a strong representation of N-terminal post-translational modification terms, including N-terminal protein amino acid propionylation and N-terminal acetylation (GO:0061606, GO:0018002, GO:0017198). This points to a coherent theme around N-terminal modifications, which is the most specific common function among the terms. The presence of other diverse processes (glucosamine metabolism, melatonin biosynthesis, angiogenesis, leaf formation, ectoine biosynthesis) suggests broad or cross-species annotations, but the PTM signal is the clearest link. ","confidence":"Medium","size":11,"edges":49,"triangles":117,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":10},{"id":"GO:0061606","count":10},{"id":"GO:0046208","count":10},{"id":"GO:0006041","count":10},{"id":"GO:0018002","count":10}]},{"hash":"5801573559419545","title":"Endosomal trafficking and phagosome maturation","description":"This cluster is dominated by GO terms for endosome-to-lysosome/melanosome transport, phagosome acidification, and regulation of secretory pathways, pointing to vesicle trafficking and phagosome maturation as the core function. Some terms related to mitochondrial assembly and signaling are present but appear as peripheral themes. ","confidence":"Medium","size":11,"edges":13,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035646","count":2},{"id":"GO:0008333","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0038027","count":1},{"id":"GO:0001667","count":1}]},{"hash":"1115228934438161439","title":"Nuclear Transport and Meiotic Regulation","description":"The top GO terms point to nuclear-centered processes (NLS-bearing protein import into nucleus, mRNA transport, transcription by RNA polymerase III) and meiosis-related functions (meiotic spindle elongation, regulation of meiotic cell cycle in oocytes), with additional signals for post-translational regulation and signaling. Together, they suggest a cluster of proteins coordinating nuclear transport and meiotic progression, with supporting roles in regulation and signaling.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":2},{"id":"GO:0006607","count":1},{"id":"GO:0060188","count":1},{"id":"GO:0097711","count":1},{"id":"GO:0051232","count":1}]},{"hash":"1644257671065938371","title":"Cardiac Muscle Development and Heart Contraction","description":"Most terms center on cardiac and muscle development (cardiac muscle tissue/cell development, muscle organ development) and heart contraction, with vascular smooth muscle involvement and a swim bladder inflation note in fishes. This points to proteins participating in cardiac muscle differentiation and contractile function, making Cardiac Muscle Development and Heart Contraction a coherent label. The non-muscle terms (UV response, retinoic acid, DNA damage signaling) appear incidental.","confidence":"High","size":11,"edges":12,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007517","count":1},{"id":"GO:0048738","count":1},{"id":"GO:0060047","count":1},{"id":"GO:0048747","count":1},{"id":"GO:0048798","count":1}]},{"hash":"1818319342782746137","title":"Cardiac Calcium Signaling and Contraction Regulation","description":"The set repeatedly points to calcium-dependent control of cardiac function, including regulation of cardiac muscle contraction via release of sequestered calcium, AV node action potential regulation, and epinephrine-responsive signaling. Calcium transporter activity and heart development terms (outflow tract morphogenesis) reinforce a cardiac/calcium theme, while skin development and ossification may be incidental annotations. Altogether, the proteins appear linked to calcium-mediated contraction and adrenergic modulation in the heart.","confidence":"High","size":10,"edges":15,"triangles":4,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0014850","count":4},{"id":"GO:0097050","count":4},{"id":"GO:1901896","count":4},{"id":"GO:0098735","count":4},{"id":"GO:0003151","count":4}]},{"hash":"1880183308595541674","title":"Ribosome biogenesis and secretory vesicle trafficking","description":"Top GO terms show cytoplasmic translation and SSU-rRNA maturation, indicating ribosome biogenesis, while several terms point to vesicle trafficking and secretion (Golgi-related transport, vesicle fusion, and secretion events), suggesting a cluster linking protein synthesis with the secretory pathway.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0000462","count":2},{"id":"GO:1902259","count":1},{"id":"GO:0001921","count":1},{"id":"GO:0048280","count":1}]},{"hash":"590406962734792440","title":"Lipoprotein remodeling and oxidative stress response","description":"The proteins are tied to lipoprotein metabolism and remodeling (HDL remodeling, LDL clearance, cholesterol catabolism) and to oxidative stress pathways (superoxide regulation, hydroperoxide response) with macrophage foam cell differentiation and nitric oxide signaling, suggesting lipid-associated inflammatory/vascular functions. A transcription regulation term is less clearly connected, but the lipid/oxidative stress theme best fits the cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006707","count":1},{"id":"GO:2000334","count":1},{"id":"GO:2000121","count":1},{"id":"GO:0034375","count":1}]},{"hash":"11946138408131487","title":"Splicing Regulation and mRNA Stability","description":"Most terms describe spliceosome-mediated mRNA processing (splice site recognition, cis splicing, and regulation of splicing) and mRNA stability/polyadenylation, with one term touching IRES-driven translation. This suggests a function cluster around RNA processing and transcript stability rather than protein interactions.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":7},{"id":"GO:0010610","count":7},{"id":"GO:0001825","count":6},{"id":"GO:1900363","count":6},{"id":"GO:0006378","count":6}]},{"hash":"1855496557450475569","title":"Protein transport and intracellular signaling","description":"The cluster highlights intracellular protein transport and localization (intracellular protein transport; maintenance of protein location in plasma membrane) with supporting roles in signaling and structural organization (cell communication by electrical coupling; cellular response to mechanical stimulus; spindle assembly). Some differentiation/remodeling processes (fat cell differentiation; endothelial delamination) appear, suggesting a group of proteins involved in transport/ localization and coordinated signaling during cell organization and function.","confidence":"Medium","size":10,"edges":11,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0070212","count":2},{"id":"GO:0097497","count":2},{"id":"GO:0045444","count":2}]},{"hash":"525439841942797060","title":"RNA processing and chromatin regulation","description":"The top GO terms cluster around RNA metabolism (spliceosome assembly, rRNA maturation, transcription termination, mRNA decapping/deadenylation, histone mRNA metabolism, P-body assembly) and chromatin organization (pericentric heterochromatin formation), suggesting a coherent theme of RNA processing and chromatin state regulation, with a couple of potential noise terms such as hair cycle or water deprivation response.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":8},{"id":"GO:0042633","count":8},{"id":"GO:0070317","count":8},{"id":"GO:0033962","count":8},{"id":"GO:1990141","count":8}]},{"hash":"2213201417312640874","title":"Ubiquitination-Driven Protein Degradation and Signaling","description":"The cluster is dominated by terms related to ubiquitination and ubiquitin-dependent degradation (protein ubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process), along with ERAD, histone ubiquitination, and regulatory influences on TNF signaling and necroptosis, indicating a cohesive theme around ubiquitin-mediated protein turnover and signaling modulation.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:1903265","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0060546","count":4}]},{"hash":"46364265768815205","title":"ER Stress and Redox Protein Quality Control","description":"These proteins appear linked to cellular stress management, especially ER stress response and redox regulation. Non-obsolete terms point to detoxification of oxidants, protein repair and deglutathionylation, and regulation of nuclear export, suggesting a coordinated response to oxidative stress and maintenance of protein integrity during stress, with transcriptional regulation likely coordinating these processes.","confidence":"Medium","size":10,"edges":18,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903206","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034976","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0098869","count":1}]},{"hash":"2100515823908315021","title":"Membrane Proteolysis and Calcium-Dependent Signaling","description":"The cluster's GO terms emphasize membrane protein proteolysis (ectodomain and intracellular), retrograde proteolysis from ER to cytosol, and positive regulation of the calcineurin-NFAT signaling cascade, along with calcium-regulated lysosome exocytosis and autophagosome engulfment. Together, these point to proteins involved in regulated membrane proteolysis linked to calcium-dependent signaling and vesicle trafficking, with a secondary tie to immune modulation. ","confidence":"Medium","size":10,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006509","count":1},{"id":"GO:0050776","count":1},{"id":"GO:0031293","count":1},{"id":"GO:0070886","count":1},{"id":"GO:1904211","count":1}]},{"hash":"496914944496334863","title":"Glutamatergic synapse signaling and spine morphogenesis","description":"The top GO terms cluster around neuronal synaptic activity (glutamate secretion, chemical synaptic transmission) and structural remodeling of synapses (dendritic spine morphogenesis, Rho signaling, phosphorylation-related regulation), suggesting a functional theme of synaptic communication and spine development. While a few terms are more pleiotropic (e.g., fibroblast migration), the dominant signals point to glutamatergic signaling and spine dynamics as the core function of this cluster.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014047","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0007268","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0060997","count":2}]},{"hash":"1189089571991442484","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster shows strong enrichment for ubiquitin-related processes: ubiquitin-dependent ERAD, autoubiquitination, K48-linked ubiquitination, and ubiquitin-dependent protein catabolic processes, indicating a common function in tagging and degrading proteins. A few terms (e.g., dosage compensation and peroxisomal import) are peripheral to this core theme. Overall, the dominant signal is ubiquitin-mediated protein turnover.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0070936","count":3},{"id":"GO:0060816","count":3},{"id":"GO:0038018","count":3}]},{"hash":"57736963710515903","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0098532","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0021592","count":2}]},{"hash":"1977553480381626907","title":"Lipid Biosynthesis and Retinoid/Steroid Metabolism","description":"Top GO terms indicate a strong emphasis on lipid metabolism: polyhydroxybutyrate biosynthesis, mycolic acid biosynthesis, retinol/retinal/retinoic acid biosynthesis, and glucocorticoid biosynthesis. This suggests the cluster comprises proteins involved in lipid biosynthetic pathways and lipid-derived molecule production. Some terms like sporulation or lung development appear unrelated or context-dependent, likely reflecting annotation noise or multifunctionality. Overall, a lipid metabolism-related theme best explains the cluster.","confidence":"Medium","size":10,"edges":39,"triangles":81,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0030435","count":4},{"id":"GO:0042574","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0042572","count":3}]},{"hash":"1181234594861608967","title":"Ubiquitin-Dependent Regulation of Translation and Cell Growth","description":"The top GO terms point to ubiquitin-related processes (polyubiquitination, ERAD) and translation initiation/reinitiation, alongside cell division/proliferation and broad developmental terms (forebrain development, multicellular growth, TGF-beta response). This suggests a coherent theme where ubiquitin signaling intersects with translation control to regulate growth and development, justifying the label, even though the proteins show no detected interactions in this network. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008283","count":2}]},{"hash":"2011483014879546845","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:0044206","count":2},{"id":"GO:0044205","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0007584","count":2}]},{"hash":"1002291911593716592","title":"Unknown","description":"The top GO terms are highly diverse and span phototransduction, neutrophil homeostasis, vascular permeability regulation, signaling pathways (TGF-beta, dopamine, epinephrine), pH response, and even a fungal development term, showing no clear shared function. Therefore no coherent theme; label Unknown.","confidence":"","size":10,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007603","count":3},{"id":"GO:0001780","count":3},{"id":"GO:0043116","count":3},{"id":"GO:0019934","count":3},{"id":"GO:1903206","count":3}]},{"hash":"863003944823268872","title":"Heart and neural development","description":"Top GO terms point to developmental programs spanning heart formation, vascularization, and nervous system growth (heart development, angiogenesis, axonogenesis, synaptic potentiation). Additional signals related to transcriptional control and signaling via phosphorylation, along with cell cycle and apoptosis regulation, fit typical developmental cascades. Taken together, these terms suggest a cluster of proteins involved in coordinating cardiovascular and neural development and maturation, rather than a single linear pathway. The lack of observed interactions does not negate a shared developmental theme, given the broad nature of these processes.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0060291","count":2}]},{"hash":"611917657523155237","title":"Unknown","description":"The terms cover transcription regulation, development, and a mix of hormone and metabolite biosynthetic processes, as well as unrelated bacterial biosynthesis terms, with no clear shared function across the cluster. The lack of edges further suggests no cohesive functional theme.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0030324","count":2},{"id":"GO:0006704","count":2},{"id":"GO:0002138","count":2}]},{"hash":"1346787448700770935","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071300","count":2},{"id":"GO:0007258","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0002741","count":2},{"id":"GO:0070935","count":2}]},{"hash":"1518367159354099207","title":"Embryonic organogenesis and cytoskeleton","description":"The cluster is dominated by developmental morphogenesis terms (limb joint morphogenesis, hair placode formation, oviduct development, renal vesicle formation) alongside cytoskeletal and cell division processes (intermediate filament bundle assembly, mitotic cytokinesis) and even a nuclear import term, suggesting a cohesive theme around embryonic organ formation and the cellular machinery that supports morphogenesis. Confidence: Medium","confidence":"","size":10,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":7},{"id":"GO:0036023","count":7},{"id":"GO:0045110","count":7},{"id":"GO:0060789","count":7},{"id":"GO:0000281","count":7}]},{"hash":"30164989729744591","title":"Central carbon metabolism and energy production","description":"The terms point to core carbon flux pathways (glycolysis, TCA cycle) and gluconeogenesis, plus 2-oxoglutarate metabolism and amino acid catabolism (leucine, lysine), thiamine biosynthesis, and fatty acid biosynthesis\u2014together signaling central energy generation and carbon flow.","confidence":"High","size":10,"edges":39,"triangles":78,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0006096","count":5},{"id":"GO:0006103","count":4},{"id":"GO:0006552","count":3},{"id":"GO:0033512","count":3}]},{"hash":"2231122741206712559","title":"Neddylation and Ubiquitination Regulation","description":"The GO terms show a clear focus on protein neddylation, including positive and negative regulation of neddylation, and related control of ubiquitin-protein transferase activity, alongside protein catabolic processes. UV-C and gamma radiation responses are present but appear ancillary to the central theme of neddylation/ubiquitination control and protein turnover, suggesting the cluster centers on regulation of these post-translational modifications rather than a single damage-response pathway.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045116","count":1},{"id":"GO:0010225","count":1},{"id":"GO:0010332","count":1},{"id":"GO:2000435","count":1},{"id":"GO:0044254","count":1}]},{"hash":"2094647167308950205","title":"Neuronal development and signaling","description":"The cluster is dominated by terms related to neural processes and signaling, such as neurotransmitter secretion, brain development, and Wnt signaling. While there are also terms tied to general cellular processes (cell division, ubiquitination) and stress responses (cadmium ion), the most representative theme centers on neuronal development and intercellular communication. This label captures the strongest signal among the GO terms observed.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007269","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0007091","count":2}]},{"hash":"1386073609618112855","title":"Cell cycle progression and apoptosis signaling","description":"This cluster is dominated by GO terms tied to DNA replication, mitotic and meiotic cell cycle transitions, and kinetochore localization, plus apoptotic signaling (including ER-stress\u2013related pathways). While a few terms touch neural or hormonal contexts, the central theme appears to be cell-cycle regulation paired with apoptosis, making this label representative of the cluster\u2019s function.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0060079","count":2}]},{"hash":"1848494209227383474","title":"Regulated Signaling and Developmental Processes","description":"The top GO terms point to diverse regulatory roles in signaling pathways (insulin receptor, MET/HGF, MAPK), barrier and vascular-related processes (endothelial barrier establishment, regulation of vascular permeability), and developmental events (atrioventricular canal development, dendritic spine development, postsynaptic density assembly), plus immune signaling (interferon-beta production) and cell cycle regulation. This suggests the cluster is comprised of proteins that regulate multiple signaling and developmental pathways rather than a single, cohesive pathway, hence a label emphasizing broader regulation of signaling across development and barrier-related contexts.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090557","count":2},{"id":"GO:0008286","count":2},{"id":"GO:1903753","count":2},{"id":"GO:0097107","count":2},{"id":"GO:0061000","count":1}]},{"hash":"1599997657320283569","title":"Neural development and transcription","description":"The cluster is dominated by GO terms related to neural development (nervous system, cerebellar cortex, hippocampus, and heart development) and DNA-templated transcription, suggesting proteins that regulate gene expression during neural development. While there are some stress-related responses (hydrogen peroxide, glucose stimulus), these appear secondary to the core theme of transcriptional control in neural contexts. Overall, the functions point to a coherent theme of transcriptional regulation guiding neural development.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0070301","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0007399","count":2}]},{"hash":"1800069359913617585","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048366","count":1},{"id":"GO:0048451","count":1},{"id":"GO:0043630","count":1},{"id":"GO:0051607","count":1},{"id":"GO:0006955","count":1}]},{"hash":"644085724981073325","title":"Signaling and trafficking regulators","description":"The GO terms point to a mix of signaling pathways (integrin signaling, Rho regulation, T cell activation, interferon signaling) alongside membrane trafficking processes (caveolin-mediated endocytosis, Golgi to plasma membrane transport) and developmental/morphogen cues (retinoic acid response, anterior/posterior pattern specification). This suggests the proteins collectively participate in coordinating signaling with vesicle trafficking rather than a single, narrow function, hence the label \u201cSignaling and trafficking regulators.\u201d ","confidence":"Medium","size":9,"edges":11,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071300","count":8},{"id":"GO:0061847","count":8},{"id":"GO:0045953","count":8},{"id":"GO:0007229","count":8},{"id":"GO:0050798","count":8}]},{"hash":"453348050882167793","title":"Fungal cell wall biosynthesis and protein targeting","description":"This cluster combines fungal-specific processes like beta-glucan biosynthesis (cell wall) with membrane-associated protein targeting (SRP-dependent and post-translational translocation), plus components of cell morphogenesis and related metabolic processes, suggesting a coherent theme around fungal cell growth and protein trafficking to membranes.","confidence":"Medium","size":9,"edges":21,"triangles":26,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":6},{"id":"GO:0006880","count":6},{"id":"GO:0070880","count":6},{"id":"GO:0006616","count":6},{"id":"GO:0070389","count":6}]},{"hash":"549685328962254568","title":"Immune signaling and cytoskeletal remodeling","description":"Top GO terms indicate strong enrichment for immune signaling (T cell receptor signaling, TLR2 signaling, mast cell proliferation, B cell differentiation) and cytoskeletal dynamics (lamellipodium morphogenesis, microspike assembly, substrate adhesion-dependent cell spreading). Other terms like cellular response to retinoic acid and nitric oxide are present but appear ancillary. Overall, the cluster likely represents proteins coordinating immune cell activation with cytoskeletal rearrangements.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0071300","count":8},{"id":"GO:0051902","count":8},{"id":"GO:2000394","count":8},{"id":"GO:0050852","count":8},{"id":"GO:0071732","count":8}]},{"hash":"1948727542793102680","title":"T and B cell signaling and maturation","description":"The terms include T cell receptor signaling, B cell receptor signaling, NK T cell differentiation, B cell affinity maturation, IL-4 production, and hemopoiesis, pointing to adaptive immune cell activation, signaling, and development. Additional terms about responses to GM-CSF and fungal origin reflect broader immune responsiveness. Together they describe a cohesive cluster of lymphocyte signaling and maturation processes.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0071226","count":3},{"id":"GO:0032633","count":3},{"id":"GO:0030097","count":3}]},{"hash":"1256779576385024347","title":"Bacterial cell wall biosynthesis and morphogenesis","description":"Most top GO terms point to biosynthesis and organization of the cell wall (O antigen, lipid A, peptidoglycan) and cell shape/morphogenesis, suggesting an envelope biogenesis theme for this cluster. A few RNA processing terms appear, but they seem incidental to the dominant cell envelope biology.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":1},{"id":"GO:0010204","count":1},{"id":"GO:0009870","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0008360","count":1}]},{"hash":"1374729998362581084","title":"Neuronal morphogenesis and actin remodeling","description":"Based on the predominance of neural development and neurite morphogenesis terms (hippocampus development, dendrite morphogenesis, axon extension) and actin cytoskeleton remodeling (lamellipodium assembly), the cluster appears to group proteins involved in shaping neuronal processes via cytoskeletal dynamics. The presence of Wnt signaling and cell cycle terms suggests broader developmental signaling contexts; the T cell receptor signaling term seems an outlier due to shared signaling components. Overall, the core theme is neuronal morphogenesis tied to actin remodeling.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021766","count":5},{"id":"GO:0031532","count":4},{"id":"GO:0050771","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0048813","count":4}]},{"hash":"1064745693386603095","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":1},{"id":"GO:0071031","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0039702","count":1},{"id":"GO:0006508","count":1}]},{"hash":"755589878148714132","title":"Mitochondrial energy production and catabolic pathways","description":"This cluster is dominated by GO terms related to mitochondrial electron transport and ATP synthesis, plus ferredoxin metabolic and other catabolic processes, pointing to a core theme of energy metabolism. The other terms (sodium transport, nitrogen fixation, and vascular/endothelial regulation) appear more peripheral or context-specific, contributing noise rather than defining the main function.","confidence":"Medium","size":9,"edges":23,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:0006124","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0009115","count":1}]},{"hash":"1879772072748521753","title":"Microtubule-guided vesicle transport","description":"The top GO terms are dominated by microtubule-related processes (microtubule nucleation regulation, plus-end-directed vesicle transport, retrograde vesicle transport, tubulin folding) along with membrane trafficking and biogenesis, indicating a cluster of proteins involved in microtubule-dependent transport and membrane trafficking.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090063","count":1},{"id":"GO:0048491","count":1},{"id":"GO:0007023","count":1},{"id":"GO:0044861","count":1},{"id":"GO:0045577","count":1}]},{"hash":"1586436450390332147","title":"Energy metabolism and proteostasis","description":"The terms point to cellular energy production (mitochondrial respiratory chain assembly, oxidative phosphorylation, aerobic respiration, photosynthesis, bacteriochlorophyll biosynthesis) and protein quality control (response to misfolded protein) together with vesicle trafficking (ER to Golgi transport). While there are outliers like DNA replication and viral genome replication, the dominant theme is energy/metabolism intertwined with proteostasis and trafficking, suggesting a cluster focused on metabolic energy and protein homeostasis. Medium","confidence":"Medium","size":9,"edges":10,"triangles":2,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0034551","count":2},{"id":"GO:0071218","count":2},{"id":"GO:0031117","count":2},{"id":"GO:0019079","count":2}]},{"hash":"326332301401022254","title":"Chromatin organization and transcriptional regulation","description":"This cluster centers on chromatin dynamics and transcription control, with GO terms for heterochromatin formation, replication-dependent chromatin assembly, and chromatin remodeling, plus negative regulation of transcription by RNA Pol II and transcription initiation\u2013coupled remodeling. The presence of protein heterotetramerization aligns with multi-subunit chromatin factors. A couple of terms (defense response, vitellogenesis) appear less connected, but the dominant signal is chromatin-based regulation.","confidence":"High","size":9,"edges":32,"triangles":62,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0051290","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006335","count":3},{"id":"GO:0045815","count":3}]},{"hash":"146486608178603528","title":"Proteasome- and immune-signaling cluster","description":"This cluster prominently groups proteasome- and ubiquitin-related processes (protein deubiquitination; proteasomal ubiquitin-independent protein catabolic process; proteasome core complex assembly) with immune signaling and antigen processing pathways (non-canonical NF-kappaB signaling; T cell receptor signaling; Fc-epsilon receptor signaling; antigen processing and presentation via MHC class I, TAP-dependent). It also includes cell-cycle regulation (negative regulation of G2/M transition) and metabolic regulation (regulation of amino acid metabolic process), plus a salt-stress response term. The combination suggests a module where proteasome and deubiquitination activities control immune signaling and antigen presentation, potentially coordinated with cell-cycle control during immune activation.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":9},{"id":"GO:0010499","count":9},{"id":"GO:0038061","count":9},{"id":"GO:0010972","count":9},{"id":"GO:0006521","count":9}]},{"hash":"1558489095652774859","title":"Neuroimmune signaling and neural development","description":"The terms show a mix of innate immune responses (LPS, dsRNA, Gram-positive defense, interferon-beta production) and neural development processes (axonogenesis, corpus callosum development), along with signaling responses to hormones and dopamine. This pattern suggests proteins involved in signaling coordination between the nervous and immune systems, i.e., a neuroimmune development-focused cluster.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071372","count":4},{"id":"GO:1903351","count":4},{"id":"GO:0043330","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0007409","count":4}]},{"hash":"1502575800962798471","title":"Chaperone-assisted folding and microtubule assembly","description":"This cluster is driven by GO terms centered on protein folding and chaperone activity (protein folding; chaperone-mediated protein complex assembly; cytoplasmic protein quality control by the ubiquitin-proteasome system) together with microtubule-related processes (tubulin complex assembly; cortical microtubule organization). These together suggest a coherent module where chaperones support correct folding and turnover while guiding cytoskeletal assembly and organization. Some terms (endodermal differentiation, angiogenesis, egg activation, glutamate signaling) appear as single, potentially incidental annotations rather than core functions of the cluster.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0043622","count":1}]},{"hash":"843732373945371022","title":"Actin regulation and vesicle trafficking during cell division","description":"The cluster centers on actin cytoskeleton remodeling, including positive regulation of actin polymerization and formin-nucleated cables, and regulatory GTPases, alongside vesicle trafficking processes (ER to Golgi transport, endocytosis) and division-related activities (mitotic cell cycle, cell polarity). This suggests a cohesive module where actin dynamics coordinate membrane trafficking and cytoskeletal organization during division and polarity establishment.","confidence":"High","size":9,"edges":21,"triangles":16,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006897","count":3},{"id":"GO:0031532","count":2},{"id":"GO:0090338","count":2},{"id":"GO:0006888","count":2}]},{"hash":"985965044598149530","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":15,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0071392","count":1},{"id":"GO:0045719","count":1},{"id":"GO:0031953","count":1}]},{"hash":"395007171434376960","title":"Ubiquitin-dependent proteolysis in mitosis and DNA repair","description":"The terms point strongly to ubiquitin-mediated protein degradation (SCF, APC/C, K11-linked ubiquitination, ERAD) coupled with mitotic processes (APC/C-dependent catabolic activity, mitotic cell cycle, chromatin organization) and DNA repair (homologous recombination), suggesting a cohesive role in cell cycle control and genome maintenance through controlled proteolysis.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0031497","count":4}]},{"hash":"327582316997588841","title":"Proteolysis and ECM remodeling","description":"These proteins are enriched for bone resorption, collagen catabolic, and various peptide/protease catabolic processes (neuropeptides, bradykinin), as well as regulation of catalytic activity, pointing to proteolytic remodeling of the extracellular matrix and turnover of signaling peptides. Some terms like decidualization or thyroid hormone response are ancillary contexts but do not define the core theme. ","confidence":"High","size":9,"edges":11,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":3},{"id":"GO:0050790","count":2},{"id":"GO:2000179","count":2},{"id":"GO:0051603","count":2},{"id":"GO:0030574","count":2}]},{"hash":"1484291626955328104","title":"Porphyrin and sphingolipid biosynthesis in plants","description":"The top GO terms point to core biosynthetic pathways, notably heme/porphyrin (heme biosynthetic process, protoporphyrinogen IX biosynthetic process) and sphinganine biosynthesis (sphingolipid). There are also related amino acid biosynthesis terms and plant-specific processes (fruit ripening, salicylic acid\u2013mediated defense), suggesting a plant metabolic cluster with emphasis on porphyrin and sphingolipid production. This supports a label focused on these key biosynthetic activities.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006783","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0046511","count":1},{"id":"GO:0000105","count":1},{"id":"GO:0009862","count":1}]},{"hash":"476860490302317381","title":"Ribosome biogenesis and cell division","description":"The GO terms are dominated by ribosome-related processes (ribosome biogenesis, cytoplasmic translation, ribosomal small subunit biogenesis) and by division-related processes (cell septum assembly, cell cycle), with intracellular protein transport also aligning with cellular organization during growth. This suggests a cluster of proteins involved in assembling the protein synthesis machinery and coordinating bacterial cell division, rather than unrelated processes. Peripheral terms like conjugation and stress response appear less central to the core theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0042274","count":1}]},{"hash":"2092726832141979516","title":"GTPase-regulated cytoskeleton remodeling and vesicle trafficking","description":"The cluster\u2019s top GO terms cluster around small GTPase signaling (Rho/small GTPases), actin cytoskeleton organization, and vesicle-related processes (acrosome reaction, synaptic vesicle priming, intracellular transport). This points to a theme of GTPase-driven cytoskeletal dynamics coordinating vesicle trafficking and exocytosis, with supporting roles from IGF signaling and remodeling processes.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007340","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0048009","count":2}]},{"hash":"894242936068447345","title":"Neuronal cytoskeleton dynamics and development","description":"The cluster centers on actin cytoskeleton remodeling (formin-nucleated actin cable assembly, actin reorganization) and mitochondrial fission, with neuronal-development terms such as hippocampus development and learning, suggesting a theme of neuronal growth and function governed by cytoskeletal dynamics and organelle trafficking, rather than a generic housekeeping process. The presence of ER-Golgi transport and spindle-microtubule regulation also fits into coordinated cytoskeletal and vesicular dynamics important for neurons.","confidence":"Medium","size":8,"edges":13,"triangles":8,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000266","count":8},{"id":"GO:0031532","count":8},{"id":"GO:1904515","count":8},{"id":"GO:0050771","count":8},{"id":"GO:0090338","count":8}]},{"hash":"385760616286519447","title":"RNA Splicing and Polyadenylation Regulation","description":"Top GO terms center on mRNA processing, especially splicing and regulation via the spliceosome, plus related polyadenylation elements. This points to a shared role in RNA processing rather than a single signaling or developmental function, despite a few outlier terms that may reflect annotation noise. Confidence in this label is Medium.","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":3},{"id":"GO:0070588","count":2},{"id":"GO:0009651","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0001825","count":2}]},{"hash":"1318225443112680530","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006909","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0002250","count":2},{"id":"GO:1903679","count":2},{"id":"GO:0045199","count":2}]},{"hash":"1039917901037340785","title":"Rho-GTPase and GPCR signaling with calcium exocytosis","description":"The top terms cluster around Rho-family and GPCR signaling, plus calcium-dependent exocytosis, which points to a signaling-and-vesicle-release function. Mitochondrial fission and developmental terms appear as ancillary associations or cross-species annotations, with one outlier (pseudohyphal growth).","confidence":"Medium","size":8,"edges":14,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000266","count":3},{"id":"GO:0007124","count":3},{"id":"GO:0007213","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0045956","count":3}]},{"hash":"1090805883760283765","title":"Mitochondrial-immune signaling and remodeling","description":"The cluster combines mitochondrial stress response terms (stress-induced fusion; mitochondrial membrane potential) with innate and adaptive immune signaling (TLR3 signaling; T cell polarity), plus membrane/lipid signaling (SREBP; membrane raft localization) and ECM remodeling (extracellular matrix disassembly), suggesting a module where mitochondria interface with signaling and remodeling processes.","confidence":"Medium","size":8,"edges":12,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1990046","count":3},{"id":"GO:0034141","count":3},{"id":"GO:1901585","count":3},{"id":"GO:0072249","count":3},{"id":"GO:1903044","count":3}]},{"hash":"1274239422868815223","title":"Cardiac and vascular calcium signaling","description":"The top GO terms center on calcium handling (calcium ion transmembrane transport; calcium-modulating pathways), heart function (positive regulation of heart contraction; cardiac muscle hypertrophy in response to stress), and vascular development (branching in blood vessel morphogenesis), with supporting cytoskeletal remodeling (actin crosslink formation) and related signaling (Wnt/calcium modulation). Although a couple of terms are obsolete, the overall pattern points to calcium-regulated cardiac and vascular development and contractile function.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006919","count":2},{"id":"GO:0031284","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0007223","count":2},{"id":"GO:0001569","count":2}]},{"hash":"750484401907878308","title":"Unknown","description":"The terms mix animal TGF-beta/BMP signaling regulation with plant-specific processes (meristem identity, photosystem adjustments) and vacuole fusion, showing no single shared function for the cluster. This lack of a cohesive theme justifies an Unknown label.","confidence":"","size":8,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0046827","count":1},{"id":"GO:0010991","count":1},{"id":"GO:0030514","count":1},{"id":"GO:0061191","count":1}]},{"hash":"1753069622339580399","title":"Ribosome biogenesis and translation regulation","description":"Dominant terms are translation, ribosomal large subunit assembly, rRNA maturation, and regulation of translation initiation, pointing to a cluster of proteins involved in ribosome biogenesis and translation control. Secondary signals include ubiquitin-mediated proteostasis and stress-response pathways, but the core theme centers on assembly and function of the protein synthesis machinery.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0050821","count":2},{"id":"GO:2000059","count":2},{"id":"GO:1904667","count":2},{"id":"GO:0000027","count":2}]},{"hash":"623657915913119954","title":"Mitochondrial Cristae Formation and Ca2+ Homeostasis","description":"The dominant GO terms point to mitochondrial biology\u2014cristae formation, mitochondrial calcium ion homeostasis, and import into the mitochondrial intermembrane space\u2014indicating a cohesive theme around mitochondrial structure and function. The presence of a few nuclear transcription and meiotic DNA repair terms is likely secondary or due to multifunctional proteins, so the core signal remains mitochondrial. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042407","count":1},{"id":"GO:0051560","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0030846","count":1},{"id":"GO:1990918","count":1}]},{"hash":"383561564063756074","title":"Organelle Protein Import and Mitochondrial Respiratory Complex Assembly","description":"The cluster\u2019s top GO terms point to targeting and import of proteins into organelles (chloroplast stroma, mitochondrial matrix, and nucleus) and to assembly processes of mitochondrial respiratory complexes (respirasome and complex IV). This combination suggests proteins involved in directing proteins to organelles and integrating mitochondrial respiratory machinery, with some peripheral terms; the core signal centers on organelle protein targeting and mitochondrial complex assembly.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045037","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0032094","count":1}]},{"hash":"852869878718715822","title":"Multi-Tissue Development","description":"The top GO terms point to developmental processes across several tissues (CNS, kidney, cartilage, reproductive tissues) and related structural processes, suggesting a general role in organogenesis rather than a single pathway. Some terms appear as noise (e.g., lipoteichoic acid biosynthetic process) or outliers, but the overall theme favors broad developmental roles.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030200","count":1},{"id":"GO:0061580","count":1},{"id":"GO:0032836","count":1},{"id":"GO:0070395","count":1},{"id":"GO:0042425","count":1}]},{"hash":"1516470091189418836","title":"Unknown","description":"The GO terms are too diverse to infer a single function for the cluster; they include protein tetramerization, regulation of proliferation, learning, GPCR signaling, sprouting regulation, LPS signaling, glucocorticoid response, and cholesterol metabolism, with a plant hormone pathway term appearing, suggesting no coherent shared role among the proteins.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0007612","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0048671","count":2}]},{"hash":"773873512431210666","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009242","count":1},{"id":"GO:0042351","count":1},{"id":"GO:0009243","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006012","count":1}]},{"hash":"1036095373784944144","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for ribosome biogenesis and translation (GO:0042254, GO:0002181, GO:0000027), plus SRP-dependent cotranslational targeting to membrane (GO:0006614), indicating proteins involved in ribosome assembly and cotranslational protein trafficking. A subset includes activation of protein kinase activity, suggesting regulatory signaling of these processes. Other terms are less represented but touch on cell cycle and migration regulation, but the strongest signal is ribosome/translation.","confidence":"High","size":8,"edges":14,"triangles":7,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0032147","count":4},{"id":"GO:0002181","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0071353","count":1}]},{"hash":"10509716039021664","title":"Adaptive immune regulation and antibody isotype switching","description":"These proteins cluster around immune signal modulation: negative regulation of T cell proliferation, IL-4 production, and type 2 immune responses, along with regulation of canonical NF-kappaB signaling and protein ubiquitination, plus regulation of IgG and IgE isotype switching and vacuolar transport. The common theme is regulation of adaptive immunity, especially T/B cell\u2013mediated responses and antibody class switching.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051224","count":1},{"id":"GO:0002761","count":1},{"id":"GO:0007034","count":1},{"id":"GO:0042130","count":1},{"id":"GO:0043123","count":1}]},{"hash":"1588864242943252957","title":"Mitochondrial and Nuclear Stress Response","description":"The cluster includes terms spanning mitochondrial dynamics and respiration, nuclear DNA repair and transcription regulation, and immune signaling/ubiquitination, all of which point to a broad cellular stress response coordinating energy production, genome maintenance, and signaling across compartments.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000266","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0006303","count":1},{"id":"GO:0051103","count":1},{"id":"GO:0006368","count":1}]},{"hash":"371573755630286780","title":"RNA processing and transcription regulation","description":"Proteins here cluster around RNA metabolism and transcription control: spliceosome assembly, rRNA maturation, RNAP II termination, mRNA decay via deadenylation and decapping, P-body assembly, and histone mRNA metabolism; several terms also touch chromatin dynamics and cell-cycle regulation, suggesting a broader link between RNA processing and gene expression control.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":5},{"id":"GO:0042633","count":5},{"id":"GO:0070317","count":5},{"id":"GO:0033962","count":5},{"id":"GO:1990141","count":5}]},{"hash":"1248882562475686320","title":"Unknown","description":"The top terms span immune signaling (B cell differentiation, BCR signaling, transcytosis), vascular/endothelial functions, and neural development (substantia nigra development, sensory perception of sound), with no clear single functional theme and no edges connecting proteins. This lack of cohesive biological signal suggests the cluster cannot be reliably labeled with a specific function.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001766","count":1},{"id":"GO:0021762","count":1},{"id":"GO:0061028","count":1},{"id":"GO:0035208","count":1},{"id":"GO:0007605","count":1}]},{"hash":"1719621146932838233","title":"Unknown","description":"The cluster shows a highly heterogeneous set of terms spanning RNA modification, transcription regulation under heat stress, protein PARylation, endothelial remodeling, adipogenesis, mechanosensing, spindle assembly, pain detection, membrane protein localization, and electrical cell coupling. Because there isn't a coherent shared function or pathway across most proteins, it's not possible to assign a meaningful high-level label beyond Unknown.","confidence":"","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031120","count":2},{"id":"GO:0061408","count":1},{"id":"GO:0070212","count":1},{"id":"GO:0097497","count":1},{"id":"GO:0045444","count":1}]},{"hash":"583616183938317585","title":"Retroviral integration and transposon activity","description":"Top GO terms strongly point to retroelement mobility and host-virus interactions, including DNA transposition, DNA integration, retrotransposition, viral entry into the host nucleus, and proviral latency. The cluster thus appears to group proteins involved in transposable element activity and proviral integration, with a few minor outlier terms contributing less to the overall theme.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":3},{"id":"GO:0075732","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0039651","count":3}]},{"hash":"651590629995154180","title":"Lung Epithelial Differentiation and Innate Immunity","description":"Two of the strongest signals are lung epithelial cell differentiation and innate immune response, suggesting the proteins may participate in airway epithelial development and host defense. A related term points to autophagy-related processes (engulfment by autophagosome), which can intersect with immune functions, while a few other terms are obsolete or less coherent with the main theme. Overall, the cluster appears to center on epithelial differentiation with an innate immune/autophagy component.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060487","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0010768","count":1},{"id":"GO:0060242","count":1}]},{"hash":"279592264479793718","title":"Ubiquitin-regulated chromatin and immune signaling","description":"The terms cluster around ubiquitin-dependent protein catabolism and histone modifications (ubiquitination, histone catabolic/acetylation), coupled with innate and adaptive immune pathways (TNF signaling, RIG-I regulation, V(D)J recombination), suggesting a shared theme of ubiquitin- and chromatin-mediated control of immune gene expression.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:1903762","count":5},{"id":"GO:0036205","count":5},{"id":"GO:1901253","count":5},{"id":"GO:0070535","count":5}]},{"hash":"1168264246749581520","title":"Ribosome biogenesis and rRNA maturation","description":"This cluster is dominated by GO terms related to ribosome biogenesis and maturation of LSU- and 5.8S rRNA, suggesting a core function in ribosome assembly. The other terms (viral mRNA export, lens differentiation, DNA damage checkpoint signaling, dendrite regulation, phagolysosome assembly, ubiquitination, actin depolymerization) are diverse and less represented, likely annotation noise around the same protein set. Overall, the strongest signal points to ribosome biogenesis and rRNA maturation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0046784","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0070306","count":2}]},{"hash":"91660613292909172","title":"N-terminal and peptidyl acetylation","description":"The cluster\u2019s top GO terms are dominated by acetylation-related processes: peptidyl-lysine N6-acetylation (GO:0018003), N-terminal peptidyl-glutamic acid acetylation (GO:0018002), and N-terminal protein amino acid propionylation (GO:0061606). This points to a cohesive theme around protein acetylation (and related modifications) as a common function among the proteins, even though several other diverse terms appear and may reflect broader, cross-species annotations. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":4},{"id":"GO:0018003","count":4},{"id":"GO:0061606","count":3},{"id":"GO:0046208","count":3},{"id":"GO:0006041","count":3}]},{"hash":"452092298387403401","title":"Glycolysis and TCA with amino acid metabolism","description":"Most terms point to central carbon metabolism: glycolysis, glucose metabolic process, and the TCA cycle dominate the term list. Additional entries relate to amino acid catabolism and biosynthesis (threonine, tryptophan, homocysteine), suggesting a cohesive cluster of proteins involved in energy generation and amino acid turnover. ","confidence":"High","size":8,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006006","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0070689","count":2}]},{"hash":"702891947287873779","title":"Retroviral life cycle and latency","description":"This cluster centers on processes of proviral latency, uncoating, and virion assembly, along with host-mediated activation of viral genome replication, which together define a retroviral life cycle. Additional GO terms referencing ribosome biogenesis and rRNA maturation reflect the virus\u2019s reliance on host translation machinery, and transcriptional/chromatin regulation (RNA Pol II, histone methylation) aligns with mechanisms that control proviral latency. Overall, a cohesive theme of retroviral replication and latency emerges.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1014507357735640270","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0071300","count":6},{"id":"GO:0007258","count":6},{"id":"GO:0031532","count":6}]},{"hash":"687302798514953821","title":"Developmental and Immune Differentiation","description":"These proteins show GO terms spanning broad developmental processes (cerebral cortex development, multicellular organism development, ovulation cycle, sperm capacitation) and immune cell differentiation (natural killer cell differentiation, T cell receptor signaling). Additional terms for apoptosis, response to toxic substances, and cell adhesion/size regulation point to general regulation of cell fate, survival, and interactions during development and immune maturation. There isn\u2019t a single tight pathway, but a unifying theme around development and differentiation across tissues, including immune lineages.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0045793","count":3},{"id":"GO:0021987","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0048240","count":3}]},{"hash":"143327125063061481","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA metabolism and the assembly/ regulation of the translation machinery: mRNA splicing, formation of the translation preinitiation complex, translation reinitiation, and regulation of mRNA stability in response to stress, along with ribosome biogenesis. These points suggest a cohesive theme of RNA processing coupled to ribosome production and translation control. Some additional terms (lens differentiation, phagolysosome, actin depolymerization, ubiquitination, DNA damage signaling) appear peripheral and do not define the main function of the cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0042254","count":1}]},{"hash":"970953395133928860","title":"Eye Development and Lens Differentiation","description":"The top GO terms are dominated by retina development in a camera-type eye and lens fiber cell differentiation, indicating that the cluster centers on eye development. The other terms reflect general cellular processes that may occur in eye tissues but do not override the primary eye-related signal. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060041","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0070306","count":3},{"id":"GO:0072432","count":3},{"id":"GO:0001845","count":3}]},{"hash":"1028572671833115667","title":"Unknown","description":"The top GO terms show a mix of cell junction/adherens junction assembly and barrier-related processes alongside neuronal signaling, metabolism, and immune-related terms, with no single predominant function tying them together. This makes a cohesive, intuitive label difficult to justify.","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":1},{"id":"GO:0090557","count":1},{"id":"GO:0014047","count":1},{"id":"GO:0060292","count":1},{"id":"GO:0071896","count":1}]},{"hash":"635005012834383380","title":"Plant cell wall biosynthesis and pollen exine formation","description":"The top GO terms cluster around plant cell wall construction and pollen wall formation: glucuronoxylan biosynthesis, plant-type secondary cell wall biogenesis, and cell wall organization, along with pollen exine formation. A few terms about proteoglycan biosynthesis and ion transport are present but less central, so the core theme is plant cell wall biosynthesis with involvement in pollen wall processes.","confidence":"High","size":8,"edges":10,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030204","count":1},{"id":"GO:0010584","count":1},{"id":"GO:0050650","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0009834","count":1}]},{"hash":"1194023358741464875","title":"Meiosis and germ cell development","description":"The cluster\u2019s GO terms are dominated by germ cell and embryonic development, meiotic recombination, and cell cycle regulation, with supporting terms for microtubule-based movement and DNA repair pathways (e.g., NHEJ). While there are a couple of immunology-related terms (isotype switching, somatic hypermutation), the overall pattern points to developmental progression and meiotic genome maintenance. Thus, a label focusing on meiosis and germ cell development best captures the shared function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007281","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0042771","count":1},{"id":"GO:0045190","count":1}]},{"hash":"288535328523352411","title":"Plant gravitropism and amyloplast organization","description":"The top GO terms are dominated by gravity-related processes: detection of gravity, negative gravitropism, and amyloplast organization, plus cellular response to mechanical stimulus. This points to a cohesive theme of plant gravity sensing and plastid-based statolith function. While other terms (e.g., Wnt signaling, mitochondrial fission, lipid metabolism) appear, they are less central to the cluster\u2019s core signal. Thus, a label centered on plant gravitropism and amyloplast organization best captures the shared function of these proteins.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090141","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0032197","count":1},{"id":"GO:0015074","count":1}]},{"hash":"308499511177837016","title":"Vertebrate Organogenesis and Patterning","description":"The top GO terms point to embryonic development of multiple organs (pancreas, ureter) and developmental processes (neural crest, bilateral symmetry) and include retinoic acid responsiveness and cAMP signaling, which are key in patterning and organogenesis in vertebrates. The cluster therefore appears to represent genes/proteins involved in embryonic development rather than a single metabolic or signaling pathway.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010133","count":6},{"id":"GO:0019544","count":6},{"id":"GO:0031016","count":6},{"id":"GO:0071300","count":6},{"id":"GO:0019545","count":6}]},{"hash":"1018139245651723374","title":"Endosomal sorting and vacuolar targeting","description":"This cluster centers on vesicle trafficking within the endomembrane system, with GO terms pointing to Golgi-to-endosome transport, endocytosis, multivesicular body sorting, and endosome-to-Golgi and vacuolar targeting pathways. Together, these terms describe proteins involved in sorting and delivering cargo through endosomes to the vacuole/lysosome, i.e., endosomal sorting machinery. Some terms are peripheral (e.g., development-related terms) and may reflect broader annotations or species-specific roles, but the core signals a cohesive endosomal/vacuolar trafficking theme.","confidence":"High","size":7,"edges":13,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0007565","count":1},{"id":"GO:0071985","count":1},{"id":"GO:0006897","count":1}]},{"hash":"25159432998088686","title":"Unknown","description":"The top GO terms cover a broad, unrelated mix: regulation of glucose metabolism, phagocytosis, platelet aggregation, cytokinesis, skeletal muscle filament assembly, fungal spore wall assembly, vacuole inheritance, DNA unwinding, and retina/homeostasis. There is no single biological process or pathway unifying these terms, and the proteins do not appear to share a coherent function that would define a specific cluster label. As a result, there isn't a reliable, narrowly defined function to assign; hence the label Unknown.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0033132","count":2},{"id":"GO:0090526","count":2},{"id":"GO:0006909","count":2},{"id":"GO:0070527","count":2},{"id":"GO:0000281","count":2}]},{"hash":"2062684732512578242","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0000472","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1}]},{"hash":"311768270681072673","title":"Calcium-mediated neural and muscle signaling","description":"This cluster shows terms tied to signaling pathways that are modulated by calcium, including Wnt calcium signaling, regulation of heart contraction, and response to muscle activity, plus neural differentiation (retinal bipolar neurons). Together with general signaling regulators and a nuclear import term, the common thread is calcium-dependent signaling in neural and muscular contexts.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0006607","count":3},{"id":"GO:0006919","count":3},{"id":"GO:0060040","count":3},{"id":"GO:0031284","count":3}]},{"hash":"317869412447365611","title":"Inflammation signaling and endothelial angiogenesis regulation","description":"The cluster is enriched for inflammatory-related terms (inflammatory response, response to lipopolysaccharide) and NF-kappaB signaling (positive regulation of canonical NF-kappaB signaling), plus a specific connection to endothelial cell proliferation and sprouting angiogenesis (negative regulation of endothelial proliferation in sprouting angiogenesis). This pattern suggests proteins that link inflammatory signaling to vascular remodeling, potentially modulated by mechanotransduction and cell shape changes. Despite some broad terms and obsolete GO entries, the core theme centers on inflammatory signaling interfacing with angiogenesis in endothelial contexts. Confidence: Medium","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0006919","count":3},{"id":"GO:0043123","count":3},{"id":"GO:1903588","count":3},{"id":"GO:0032496","count":3}]},{"hash":"629241066091179489","title":"Developmental signaling and environmental responses","description":"The cluster includes terms tied to development (osteoclast development, branching morphogenesis of a nerve, regulation of kidney size) and varied stimulus responses (dopamine, mechanical stimulus, manganese), with a notable enrichment for small GTPase\u2013mediated signal transduction, suggesting a role in signaling during development and adaptation to environmental cues.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903206","count":5},{"id":"GO:1902902","count":5},{"id":"GO:0036035","count":5},{"id":"GO:1903351","count":5},{"id":"GO:0071260","count":5}]},{"hash":"1671258657343342185","title":"Meiotic Chromatin Regulation and Ubiquitination","description":"This cluster centers on meiosis-specific chromosomal events (chiasma assembly, synaptonemal complex organization) and chromatin regulation, with strong signals of ubiquitin-mediated control (free ubiquitin chain polymerization, polyubiquitination). Additional terms point to heterochromatin formation, DNA repair, and transcription regulation linked to chromatin dynamics during meiosis, suggesting a cohesive theme of meiosis-associated chromatin remodeling governed by ubiquitin signaling.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010994","count":7},{"id":"GO:1902916","count":7},{"id":"GO:0051026","count":7},{"id":"GO:0070193","count":7},{"id":"GO:0006915","count":7}]},{"hash":"1579982009083017749","title":"Translation Machinery and mRNA Decay","description":"The majority of the top GO terms pertain to protein synthesis: translation in general, initiation, elongation, and termination, as well as positive regulation of cytoplasmic translation and selenocysteine incorporation, indicating a core theme around the translational apparatus. Also represented is deadenylation-dependent mRNA decay, signaling associated mRNA turnover. A couple of terms like glial cell proliferation and response to antibiotic are less directly connected but do not overshadow the central translation/translation regulation signal. Overall, the cluster appears to group proteins involved in the translation machinery and related mRNA processing/turnover.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":1},{"id":"GO:0006415","count":1},{"id":"GO:0014009","count":1},{"id":"GO:0001514","count":1}]},{"hash":"581808732227891802","title":"Unknown","description":"The top GO terms are broad and conflicting (neural development, vasculature morphogenesis, autophagy, GTPase signaling, transcription and catabolic regulation) with several obsolete annotations, showing no single cohesive function tying all proteins together.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0001843","count":2},{"id":"GO:0010768","count":2},{"id":"GO:0060242","count":2},{"id":"GO:0060977","count":2}]},{"hash":"1621522799000113799","title":"Unknown","description":"The GO terms span metabolism, neuronal signaling, immunity, development, and trafficking, with no single unifying function for the cluster.","confidence":"","size":7,"edges":12,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0044381","count":1},{"id":"GO:0050884","count":1},{"id":"GO:0035455","count":1},{"id":"GO:0035456","count":1},{"id":"GO:0009607","count":1}]},{"hash":"2209496914292678569","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":11,"triangles":10,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032781","count":4},{"id":"GO:0097428","count":4},{"id":"GO:0046825","count":4},{"id":"GO:0051259","count":4},{"id":"GO:0006452","count":3}]},{"hash":"242805860079678263","title":"Proteostasis and mitotic machinery","description":"The cluster centers on protein quality control and trafficking, with several GO terms related to proteostasis (ubiquitin-dependent ERAD, chaperone-assisted refolding, aggresome assembly, ER-to-Golgi transport) and protein handling. In addition, there are terms tied to microtubule dynamics and chromatin assembly (microtubule severing, CENP-A chromatin assembly) that connect to cell division, suggesting a link between proteostasis and mitotic processes. While a few items are development- or methylation-related, the strongest cohesive theme is maintenance of protein homeostasis alongside mitotic machinery.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0051013","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070389","count":2}]},{"hash":"227266948839818796","title":"RNA processing and methylation","description":"This cluster centers on methylation-related processes across RNA (rRNA/tRNA, including mitochondrial tRNA methylation) and proteins (histone and peptidyl-arginine methylation), with an additional tie to DNA-templated transcription and growth/senescence. The common theme is methylation-driven regulation of RNA maturation and chromatin/protein modification, suggesting a cohesive functional module around methylation.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0002939","count":1},{"id":"GO:0043985","count":1}]},{"hash":"1810342457799503640","title":"Calcineurin-NFAT signaling in muscle and neural development","description":"The cluster centers on the calcineurin-NFAT signaling cascade with both positive and negative regulation terms, plus associations with cardiac muscle hypertrophy, slow/fast muscle fiber transitions, and brain development (substantia nigra) and peripheral myelination. This suggests a cohesive theme around calcium-driven transcriptional signaling influencing muscle and neural development and function. Some terms like blood vessel branching and miRNA processing indicate broader regulatory roles, but the core signal appears to be calcium/NFAT\u2013mediated developmental regulation in muscle and nervous system contexts.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":4},{"id":"GO:0032516","count":4},{"id":"GO:0014898","count":4},{"id":"GO:0014883","count":4},{"id":"GO:0033173","count":4}]},{"hash":"761028240128993261","title":"Xenobiotic detoxification and oxidative stress response","description":"The top GO terms cluster around responses to xenobiotics, metals like cadmium, vitamin-related antioxidant responses, and oxidant detoxification, indicating a cohesive theme of detoxification and protection against oxidative stress among these proteins.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0046686","count":2},{"id":"GO:0033197","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0033189","count":2}]},{"hash":"1074267128863027288","title":"Neurodevelopmental Signaling","description":"This cluster is enriched for nervous system development, neurogenesis, dendrite development, and axon guidance terms (e.g., Smoothened/Hedgehog and Roundabout/ROBO signaling). While kidney development and some immune-related terms appear, the dominant theme ties to neural development and its signaling pathways.","confidence":"Medium","size":7,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":7},{"id":"GO:0001822","count":7},{"id":"GO:0050852","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0035385","count":7}]},{"hash":"673432711775341966","title":"Cytoskeletal remodeling and developmental signaling","description":"The cluster\u2019s GO terms include actin cytoskeleton dynamics (lamellipodium assembly; actin filament depolymerization) alongside diverse developmental and signaling roles (neuron and forebrain differentiation, cardiac muscle differentiation, growth hormone signaling, immune signaling). This suggests a broad, multi-functional set of proteins that link cytoskeletal remodeling to signaling across tissues, rather than a single cohesive pathway. Confidence in a tight, unique function is limited given the term diversity and lack of edges.","confidence":"Low","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050859","count":2},{"id":"GO:0060396","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0021526","count":1},{"id":"GO:0046013","count":1}]},{"hash":"172880834802748230","title":"Growth Factor Signaling and Development","description":"This cluster is dominated by GO terms for growth hormone receptor signaling and regulation of insulin receptor signaling, both endocrine signaling pathways, along with thymus and placenta development. The combination suggests a main theme around growth-factor\u2013mediated signaling and developmental processes, with other signaling regulation terms supporting this context.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060396","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0048538","count":2},{"id":"GO:0000187","count":2}]},{"hash":"221026310484348535","title":"Notch-regulated Developmental Differentiation","description":"Top terms point to Notch signaling regulation (positive regulation; obsolete negative regulation) alongside diverse developmental processes (hypochord, ovarian follicle, intestinal epithelial development, pattern specification, marginal zone B cell differentiation). This suggests a cluster enriched for proteins involved in Notch-mediated developmental differentiation across tissues.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032092","count":4},{"id":"GO:0045747","count":3},{"id":"GO:0002315","count":3},{"id":"GO:0055016","count":3},{"id":"GO:1902367","count":3}]},{"hash":"1653090745576785555","title":"Unknown","description":"The terms cover heat response, cardiac action potential regulation, retina development, nuclear import, GTPase regulation, synaptic vesicle endocytosis, and protein modification, with no consistent function across proteins; thus a single coherent label cannot be inferred.","confidence":"","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0043547","count":2}]},{"hash":"181449379614496032","title":"Intracellular trafficking and cytoskeleton dynamics","description":"The Top Terms cluster around vesicle trafficking and organelle transport (Golgi localization, synaptic vesicle budding, constitutive secretory pathway regulation) and cytoskeleton-associated processes (actin remodeling, phagosome acidification, mitochondrial fission, cell migration). Although some terms relate to development or signaling, the common theme is intracellular transport and cytoskeletal dynamics that coordinate vesicle trafficking and organelle function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038027","count":1},{"id":"GO:0070142","count":1},{"id":"GO:0000042","count":1},{"id":"GO:0001667","count":1},{"id":"GO:0002093","count":1}]},{"hash":"117539975947220258","title":"ER stress response and protein quality control","description":"The top GO terms cluster around unfolded protein response, ER-associated degradation (ERAD), chaperone-assisted refolding, and translation regulation under ER stress, indicating a cohesive module of ER protein folding and degradation pathways. A few terms (mRNA processing, DNA replication) are broader cellular processes and less directly linked, but the strongest signals support ER stress and protein quality control as the core theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0032781","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1076892355825650242","title":"Sumoylation and Deubiquitination in DNA Damage Response","description":"The cluster shows prominent post-translational modification processes (protein sumoylation and deubiquitination), with associations to transcription factor regulation, PML body organization, and DNA-related repair processes (nucleotide-excision repair, DNA-binding regulation). The presence of mitophagy and immune signaling hints (TLR pathway) suggests broader cellular stress responses, but the unifying theme centers on regulation of protein function and genome maintenance under stress. Hence, a label focused on PTMs linked to DNA damage response best captures the common function of these proteins.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0034126","count":4},{"id":"GO:0043433","count":4},{"id":"GO:0000423","count":4},{"id":"GO:0014070","count":4}]},{"hash":"1076797987839053184","title":"Unknown","description":"The GO terms are highly heterogeneous, ranging from maltose transport to various nuclear processes and meiotic/immunoglobulin-related events, with no shared function and no interactions among proteins. This suggests no coherent functional theme for a specific label.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015768","count":1},{"id":"GO:1904751","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0045190","count":1}]},{"hash":"1638712643937184650","title":"Neuronal development and synaptic signaling","description":"The terms point to brain development and synaptic structure: Rho signaling, dendritic spine morphogenesis, cerebral cortex development, and receptor clustering suggest roles in neuronal growth and synapse formation/plasticity. A few entries refer to DNA replication and mitotic checkpoints, which are less connected to neural differentiation, possibly reflecting gene roles in progenitors or annotation noise. Overall, the dominant theme is neuronal development and synaptic signaling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0007118","count":2}]},{"hash":"551727676874081301","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045071","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0090141","count":2},{"id":"GO:0045356","count":1}]},{"hash":"512537224473919414","title":"Transcription Regulation and Chromatin Modification","description":"The proteins in this cluster are tied to gene expression control, with GO terms pointing to DNA-templated transcription and transcriptional regulation from RNA Pol II promoters, plus chromatin-related processes such as histone demethylation. There are also terms indicating post-translational modifications like peptidyl-arginine and peptidyl-histidine hydroxylation, suggesting regulation of protein function that can influence transcriptional machinery. While some terms are historical/obsolete, the dominant signal is transcriptional regulation and chromatin modification.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904780","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0030961","count":1},{"id":"GO:0036138","count":1},{"id":"GO:0061428","count":1}]},{"hash":"1052395773619972960","title":"DNA Endoreduplication and Damage Response","description":"Most top GO terms cluster around DNA endoreduplication and stress signaling (DNA endoreduplication; cell cycle comprising mitosis without cytokinesis; positive regulation of DNA endoreduplication; intrinsic apoptotic signaling in response to DNA damage). This points to a core theme of regulating atypical DNA replication cycles under stress. A few terms (glucosinolate metabolism, chorionic trophoblast differentiation, axis specification, transcription, and mRNA stabilization) appear less connected and may reflect context-specific annotations or noise rather than the cluster\u2019s primary function.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008630","count":2},{"id":"GO:0008069","count":1},{"id":"GO:0019760","count":1},{"id":"GO:0033301","count":1},{"id":"GO:0032877","count":1}]},{"hash":"1093318302016159723","title":"Unknown","description":"There are no GO terms to define a shared function for this 6-protein cluster, so a specific label cannot be inferred.","confidence":"","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"519944381963172744","title":"Meiosis Chromosome Organization and Ubiquitin Regulation","description":"The cluster centers on meiosis-related chromatin events (synaptonemal complex organization, chiasma assembly, silent mating-type cassette heterochromatin formation) and ubiquitin-dependent regulation (free ubiquitin chain polymerization, positive regulation of polyubiquitination), with links to DNA repair and apoptosis, suggesting a coherent role in meiosis-specific chromosome dynamics and ubiquitin-mediated genome maintenance.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010994","count":6},{"id":"GO:1902916","count":6},{"id":"GO:0051026","count":6},{"id":"GO:0070193","count":6},{"id":"GO:0006915","count":6}]},{"hash":"1404063753941451979","title":"Mitochondrial protein import and mitophagy","description":"Based on the GO terms, the cluster centers on mitochondrial functions: import of proteins into the mitochondrial matrix, calcium import into mitochondria, regulation of mitophagy, and control of ROS. While neuronal terms (learning, synaptic transmission, fear) appear, they likely reflect mitochondrial roles in neurons rather than a separate pathway. Thus the prevalent theme is mitochondrial import and quality control.","confidence":"High","size":6,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0036444","count":2},{"id":"GO:0006506","count":2},{"id":"GO:2000378","count":1},{"id":"GO:1903146","count":1},{"id":"GO:0007612","count":1}]},{"hash":"929582671922340186","title":"Autophagy and phagophore targeting","description":"Based on the top GO terms, notably protein localization to the phagophore assembly site, cytoplasm-to-vacuole targeting by the Cvt pathway, and autophagy of peroxisome, the cluster appears to group proteins involved in autophagy and related vesicle targeting to the vacuole. The presence of several unrelated terms (nitrate assimilation, lignin/cellulose catabolic processes, sporulation, arsenate transport) suggests annotation noise, but the core theme is autophagy machinery and phagophore/vacuolar targeting.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034497","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0030245","count":1}]},{"hash":"452767304334496941","title":"Lipid catabolism and acyl-chain remodeling","description":"This cluster is enriched with triglyceride and phospholipid catabolic processes (triglyceride catabolic process, triglyceride mobilization, phosphatidylethanolamine/phosphatidylcholine catabolic processes) and with acyl-chain remodeling terms, indicating involvement in lipid breakdown and remodeling of lipid substrates. A few terms relate to regulatory pathways like PKA and endocannabinoid signaling, but the dominant pattern centers on lipid catabolism and acyl-chain remodeling. The proteins likely function in triglyceride turnover and membrane lipid remodeling.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0006642","count":3},{"id":"GO:0010898","count":3},{"id":"GO:0046338","count":3},{"id":"GO:2000480","count":3}]},{"hash":"927105948318598755","title":"RNA Processing and Gene Expression Regulation","description":"This cluster is dominated by RNA processing terms (mRNA processing, tRNA processing, and related gene expression regulation), with additional developmental/morphogenesis signals (mitotic cell cycle, cell morphogenesis, terminal fate specification, larval behavior) that may reflect broader development-related transcriptional control. Some cytokinin-related terms likely represent annotation noise or cross-species effects. Overall, RNA maturation and regulation appear to be the core theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0034265","count":1},{"id":"GO:0009691","count":1}]},{"hash":"2297553091570825464","title":"Plant metabolism and vitamin biosynthesis","description":"This cluster centers on biosynthetic and metabolic pathways, including pentose phosphate shunt, gluconeogenesis, arginine biosynthesis, and biosynthesis of vitamins (thiamine and pyridoxine), with evidence of chlorophyll metabolism and UV-B response\u2014suggesting plant-associated metabolism and stress-related modulation. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006098","count":2},{"id":"GO:0006526","count":2},{"id":"GO:0009229","count":1},{"id":"GO:0006094","count":1}]},{"hash":"811960997256628398","title":"Unknown","description":"These proteins carry a highly diverse set of GO terms, including stem cell proliferation, erythrocyte differentiation, pituitary development, cAMP response, histone methylation regulation (obsolete), thiamine biosynthesis, and mitochondrial electron transport. The lack of a single cohesive biological process or pathway among these terms makes it unclear what common function defines the cluster.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":3},{"id":"GO:0071320","count":2},{"id":"GO:0051572","count":2},{"id":"GO:0045648","count":2},{"id":"GO:0009228","count":2}]},{"hash":"120510083996932447","title":"Unknown","description":"The top GO terms include several CNS myelination-related processes, but they are mixed with a wide range of unrelated regulatory and cellular processes (transcription regulation, stalk cell differentiation, root meristem growth, osmotic stress response, meiotic recombination, telomere localization). The cluster lacks a coherent, single functional theme and has no interactions, so no meaningful collective function label can be assigned beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031643","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0022010","count":1},{"id":"GO:0031285","count":1},{"id":"GO:0006355","count":1}]},{"hash":"742409427858300421","title":"Androgen signaling and male reproductive development","description":"The cluster\u2019s top GO terms cluster around steroid hormone receptor complex assembly, prostate gland development, and male sex differentiation, indicating involvement in androgen-driven hormonal signaling and male reproductive development. While heart morphogenesis is also listed, the strongest and most representative signals are in male reproductive development and steroid receptor\u2013mediated processes, justifying a label centered on androgen signaling. ","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006463","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0003007","count":2},{"id":"GO:1902325","count":1}]},{"hash":"50181443222765148","title":"Unknown","description":"The GO terms span disparate processes (capsule biosynthesis, thiamine biosynthesis, glycolysis, cellular response to cAMP, apoptosis, and regulatory histone methylation) with no evident shared pathway or function, and there are no edges linking the proteins, so a cohesive, specific label cannot be drawn.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045227","count":3},{"id":"GO:0009229","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0006915","count":2}]},{"hash":"251131033923480510","title":"Rho/Ras Signaling, Cytoskeleton\u2013Vesicle Regulation","description":"The cluster includes GO terms for Rho and Ras signaling, actin cytoskeleton remodeling, vesicle fusion and regulation of exocytosis, and phosphorylation control, with additional terms pointing to development (brain development, mating projection). This suggests a unifying theme of signaling pathways that coordinate cytoskeletal dynamics and vesicle trafficking, across contexts. The presence of both plant and animal/development-related terms indicates a broad but cohesive role in signaling-coupled cytoskeletal and vesicle processes.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":3},{"id":"GO:0009789","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0007420","count":2}]},{"hash":"2035179420655738745","title":"Embryonic development and morphogenesis","description":"These terms point to developmental processes and tissue morphogenesis, including gastrulation-related cell migration, convergent extension in axis elongation, organogenesis, and specific organ development (pancreas, prostate). There are also general transcription regulation terms (positive regulation of RNA polymerase III transcription, regulation of DNA-templated transcription) that often accompany developmental programs. Taken together, the cluster seems to group proteins involved in embryonic development and morphogenesis rather than housekeeping functions or signaling alone.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045945","count":2},{"id":"GO:0031016","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0014812","count":1},{"id":"GO:0006355","count":1}]},{"hash":"496751494192713284","title":"Cellular stress response regulation","description":"These proteins collectively show GO terms spanning regulation of cell cycle, immune signaling (TNF production, LPS response), mitochondrial function, and responses to environmental stresses (manganese, herbicide, ethanol) and aging processes (cellular senescence). The common thread is modulation of diverse stress and metabolic responses rather than a single specific pathway, suggesting a broad regulatory role in cellular stress responses.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051726","count":2},{"id":"GO:0032720","count":2},{"id":"GO:1905804","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0071222","count":2}]},{"hash":"1772905598993036098","title":"Splicing and RNA processing machinery","description":"This cluster is dominated by GO terms related to mRNA splicing via the spliceosome, spliceosomal complex assembly, and alternative splicing, with additional ties to RNA metabolism (P-body assembly and rRNA maturation). The common thread is RNA processing/splicing machinery, possibly including factors involved in RNA storage/decay and ribosome biogenesis, suggesting a cohesive RNA-processing cluster.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0042386","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0042633","count":1}]},{"hash":"559421829594905202","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006452","count":4},{"id":"GO:0032781","count":4},{"id":"GO:0006458","count":4},{"id":"GO:0070843","count":4}]},{"hash":"350556359292912597","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1544853589376697467","title":"Diverse Transmembrane Transport","description":"These proteins are linked to transmembrane transport of xenobiotics, vitamins, lipids (ceramide, glycerophosphodiesters), and amino acids (methionine), indicating a primary role in membrane transport of diverse substrates. Other GO terms (cytochrome complex assembly, MHC I antigen processing) appear as ancillary annotations and do not define the cluster.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0099040","count":3},{"id":"GO:0099133","count":3},{"id":"GO:0017004","count":3}]},{"hash":"1778737782282017128","title":"Unknown","description":"The top GO terms are very diverse (ribosome biogenesis, lens fiber cell differentiation, DNA damage response, phagolysosome assembly, ubiquitination, actin depolymerization, apoptosis, various methylation processes, and SREBP signaling) with no clear shared function or pathway, and the cluster shows no interactions (edges/triangles = 0). This suggests there is no coherent biological theme tying these proteins together.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0070306","count":3},{"id":"GO:0072432","count":3},{"id":"GO:0001845","count":3},{"id":"GO:0000209","count":3}]},{"hash":"1505916965340393596","title":"Vacuolar amino acid transporters","description":"GO terms repeatedly show transmembrane import into the vacuole for diverse amino acids (tyrosine, arginine, proline, lysine, histidine, serine, alanine, etc.), plus related transport terms, pointing to proteins that function as vacuolar membrane transporters responsible for amino acid uptake.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090452","count":1},{"id":"GO:0090514","count":1},{"id":"GO:0090518","count":1},{"id":"GO:0015824","count":1},{"id":"GO:0061402","count":1}]},{"hash":"2103422057971222991","title":"Polyamine biosynthesis and transport","description":"This cluster\u2019s top GO terms center on polyamine metabolism: putrescine biosynthesis from arginine via ornithine, spermidine biosynthesis, and polyamine transmembrane transport. These recurring themes suggest a cohesive function around polyamine production and movement, with other terms (e.g., trafficking or development) likely representing annotation noise or broader cellular context. ","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:1902269","count":1},{"id":"GO:0033387","count":1},{"id":"GO:0006527","count":1},{"id":"GO:0009089","count":1}]},{"hash":"344172380064051980","title":"Endocytosis and vesicle trafficking","description":"The top GO terms cluster around membrane remodeling and vesicle trafficking: endosome transport, intralumenal vesicle formation, pinocytosis, plasma membrane tubulation, and related processes. A few terms touch on cell polarity, cytokinesis, and mast cell histamine secretion, which are also connected to membrane dynamics and vesicle trafficking during cell division and secretion. Taken together, these proteins likely participate in endocytosis, vesicle formation, and trafficking between endosomal compartments and the plasma membrane, rather than a single specialized process.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000769","count":1},{"id":"GO:0000281","count":1},{"id":"GO:0048310","count":1},{"id":"GO:0031139","count":1},{"id":"GO:1904179","count":1}]},{"hash":"2233816856612311090","title":"Ubiquitin-dependent proteolysis in neural development","description":"The cluster is dominated by ubiquitin-related terms (ubiquitin-dependent protein catabolic process; positive regulation of protein polyubiquitination) alongside neural development signals (initiation of neural tube closure; establishment/maintenance of imaginal disc polarity) and neuronal functional terms (negative regulation of excitatory postsynaptic potential, oxidative stress\u2013induced neuronal signaling). This suggests proteins involved in ubiquitin-mediated proteostasis that intersect with neural development and stress responses. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":2},{"id":"GO:0042787","count":2},{"id":"GO:1903378","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0016336","count":1}]},{"hash":"21440709668505274","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000467","count":5},{"id":"GO:0071051","count":5},{"id":"GO:0071038","count":5},{"id":"GO:0034475","count":5},{"id":"GO:0071042","count":5}]},{"hash":"778453353248167542","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0010501","count":2},{"id":"GO:0071038","count":2},{"id":"GO:0070417","count":2},{"id":"GO:0031124","count":2}]},{"hash":"1464175438671740293","title":"Fungal lipid and sterol metabolism","description":"The top terms cluster around ergosterol biosynthesis regulation, sphingolipid metabolism (mannosyl-inositol phosphorylceramide), and unsaturated fatty acid biosynthesis\u2014collectively core components of fungal membrane lipid and sterol pathways. Some terms appear unrelated (e.g., nitrate assimilation, CNS myelin maintenance) likely due to annotation noise, but the dominant theme points to fungal lipid/sterol metabolism. ","confidence":"Medium","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0000001","count":5},{"id":"GO:0006809","count":5},{"id":"GO:0032286","count":5}]},{"hash":"546075064285400864","title":"Unknown","description":"GO terms span neural and tissue development (forebrain regionalization; medial motor column neuron differentiation; atrial cardiac muscle cell differentiation; female gonad development), immune regulation, miRNA-mediated post-transcriptional silencing, actin filament depolymerization, thyroid hormone response, and platelet aggregation, with no clear shared function tying the proteins together; the cluster appears heterogeneous rather than representing a single cohesive pathway.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021526","count":1},{"id":"GO:0046013","count":1},{"id":"GO:0035195","count":1},{"id":"GO:0055011","count":1},{"id":"GO:0070527","count":1}]},{"hash":"429813957128202587","title":"Unknown","description":"The terms are too disparate to form a cohesive function for the cluster (immune-related processes like B cell differentiation and immunoglobulin production; glycosylation; Notch signaling; development terms; plus plant-specific xylan catabolism), suggesting no single representative theme.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009312","count":1},{"id":"GO:0018279","count":1},{"id":"GO:0045747","count":1},{"id":"GO:0002315","count":1},{"id":"GO:0002378","count":1}]},{"hash":"1319903626286295041","title":"Caveolin-Mediated Endocytosis and Signaling","description":"This cluster is best described by caveolae/caveolin-associated functions, given terms for caveolin-mediated endocytosis and caveola assembly, plus related signaling steps such as PI3K/AKT regulation and calcium transport modulation. A few terms touch on other developmental or host interaction processes, but the dominant theme centers on membrane microdomain\u2013mediated endocytosis and signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071455","count":2},{"id":"GO:0051896","count":1},{"id":"GO:0072584","count":1},{"id":"GO:0051926","count":1},{"id":"GO:0033138","count":1}]},{"hash":"1661423792132757271","title":"Unknown","description":"The terms span disparate processes (translation, RNA splicing regulation, mRNA decay, EJC dynamics, nuclear export, microtubule localization, Wnt signaling, development, and lipid metabolism) with no evident shared pathway or strong protein\u2013protein connectivity (Edges: 0). This suggests no coherent functional theme tying the proteins together, so Unknown is appropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0033119","count":1},{"id":"GO:0006407","count":1},{"id":"GO:1902897","count":1},{"id":"GO:0035372","count":1}]},{"hash":"663656644117142480","title":"Unknown","description":"The top GO terms are split between cell migration and GTPase regulation (2 instances each) and several DNA replication/repair processes (mostly 1 instance each). There is no clear, unified function that ties all terms together, so a single, representative label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0001711","count":2},{"id":"GO:1903459","count":1},{"id":"GO:0006260","count":1}]},{"hash":"581089667803656248","title":"Neural Development and Differentiation","description":"This cluster is dominated by neural development terms such as spinal cord development, neural tube closure, lens fiber cell differentiation, and regulation of dendrite development, suggesting a core theme around neurodevelopment and neuronal differentiation. The presence of RNA processing and ribosome biogenesis terms likely reflects general gene-expression roles in these processes, but the neural development signals appear most representative of the cluster\u2019s function.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0042254","count":2}]},{"hash":"919099829547226779","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071300","count":3},{"id":"GO:0007258","count":3},{"id":"GO:0031532","count":3},{"id":"GO:0002741","count":3},{"id":"GO:0070935","count":3}]},{"hash":"1799338349704410214","title":"RNA and protein methylation","description":"Based on the GO terms, methylation-related functions dominate the cluster: rRNA methylation, rRNA modification, general methylation, peptidyl-lysine dimethylation, and N-terminal peptidyl-alanine trimethylation. While there are outliers like brain development and immune response terms, the strongest recurring signal is RNA and protein methylation/modification, suggesting a cluster centered on methylation activities.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0031167","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0070555","count":1},{"id":"GO:0018027","count":1}]},{"hash":"1485462399911924579","title":"Unknown","description":"This cluster's top GO terms are scattered across apoptosis, cerebral cortex development, cell size regulation, metabolism, hormone and neurotransmitter signaling (corticosterone, dopamine, cAMP), and chromatin modification, with no obvious shared pathway. There are no edges among the proteins, so there isn't a cohesive function to label with confidence.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0009229","count":1},{"id":"GO:0010725","count":1}]},{"hash":"2245168841901605037","title":"Unknown","description":"There is no clear shared function linking these five proteins; the GO terms cover a highly diverse set of processes (RNA polymerase II transcription initiation and CTD regulation, mitochondrial tRNA modification, proteolysis, telomere recombination, blue light response, chaeta development, and cyclin-dependent kinase regulation), indicating no single representative theme for this cluster.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":1},{"id":"GO:0046944","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0072670","count":1},{"id":"GO:0045944","count":1}]},{"hash":"38833994225344433","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning metabolism (glucose starvation response, gluconeogenesis, GTP biosynthesis), cell cycle regulation, immune signaling (IL-4 response, lymphocyte proliferation), development (retina development), and amino acid catabolism. With no single unifying function dominating the cluster, there isn\u2019t a coherent label to assign beyond Unknown. ","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042149","count":5},{"id":"GO:0006183","count":5},{"id":"GO:0060041","count":5},{"id":"GO:0043418","count":5}]},{"hash":"110844692726064658","title":"Bacterial quinone and antibiotic biosynthesis","description":"The top GO terms indicate strong involvement in quinone biosynthesis (menaquinone and phylloquinone) and antibiotic biosynthetic processes, suggesting a bacterial module tied to cofactor production and secondary metabolite synthesis. Other terms mention cell wall components and fatty acid metabolism, which are common in metabolically active bacteria but are less central to the main theme. Overall, the strongest, coherent signal is quinone and antibiotic biosynthesis.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0010124","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0006574","count":3},{"id":"GO:0042372","count":3}]},{"hash":"123485063287091652","title":"Unknown","description":"The top GO terms span angiogenesis, sporulation, leaf formation, melatonin biosynthesis, and multiple metabolic and protein modification processes, across varied organisms. This diversity shows no single cohesive function or pathway linking the proteins, so a confident, specific label cannot be assigned.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":5},{"id":"GO:0061606","count":5},{"id":"GO:0046208","count":5},{"id":"GO:0006041","count":5},{"id":"GO:0018002","count":5}]},{"hash":"2188948870180460079","title":"TLR-MyD88 innate immune signaling and cytokine production","description":"The proteins show enrichment for TLR8 signaling and MyD88-dependent TLR pathways, plus regulation of interferon and cytokine production (including IL-8), which points to an innate immune signaling module. While some GO terms like dopamine response and nerve morphogenesis are present, they are less consistent with the core immune theme, making the TLR/interferon/cytokine axis the most representative explanation.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045356","count":1},{"id":"GO:0051638","count":1},{"id":"GO:1903351","count":1},{"id":"GO:0034158","count":1},{"id":"GO:2000172","count":1}]},{"hash":"556475209211890387","title":"Mitotic Cell Cycle and Ubiquitin-Mediated Proteolysis","description":"Based on the strongest signals being cell division, mitotic cell cycle, APC-dependent catabolic process, and K11-linked ubiquitination, the cluster appears centered on mitotic regulation and ubiquitin-driven protein degradation. The other terms (cadmium response, defense to virus, histone modification, ribosome biogenesis, lens differentiation) are less represented and likely context-specific or incidental. Confidence in this theme is high.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001162","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0070979","count":2}]},{"hash":"795186828166978094","title":"Nervous system development and axonogenesis","description":"Based on the top GO terms, the cluster centers on nervous system development, particularly peripheral nervous system development, regulation of axonogenesis, and myelination of nerve axons. The presence of hormone-related responses (estradiol and FSH) may reflect modulatory signaling in neural contexts, but the dominant signal is neural growth and maturation. Some terms (placental development, TLR signaling, germ-line division) appear as outliers, likely reflecting broader signaling roles rather than core function of this group.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007422","count":2},{"id":"GO:2000252","count":2},{"id":"GO:0045356","count":2},{"id":"GO:0071392","count":2},{"id":"GO:0050770","count":2}]},{"hash":"2114750839139702389","title":"Unknown","description":"The GO terms are highly diverse, touching endocrine signaling (thyroid hormone receptor regulation), metabolism (energy homeostasis), immune activation (T cell activation and costimulation), tissue remodeling (angiogenesis in wound healing and ECM regulation), pigment cell biology (melanocyte proliferation), detoxification, and even plant-specific processes (cellulose catabolic process). With only five proteins and no clear single functional thread linking these terms, there isn\u2019t a coherent, specific theme to name a meaningful cluster\u2014thus Unknown.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002155","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0097009","count":2},{"id":"GO:0060055","count":2},{"id":"GO:0042110","count":2}]},{"hash":"358277425136980860","title":"Secretory Trafficking and Autophagy Regulation","description":"These proteins cluster around processes that control vesicle trafficking, lysosome exocytosis, and autophagy, including regulation of GTPase activity (key for vesicle movement), lysosome exocytosis, autophagosome engulfment, ER membrane organization (part of the secretory pathway), and secretory events like insulin release. While some GO terms appear less related (e.g., bitter taste, ABA signaling), the shared theme is intracellular trafficking and secretion with autophagic regulation. Confidence: Medium","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":1},{"id":"GO:0009789","count":1},{"id":"GO:0050913","count":1},{"id":"GO:1990927","count":1},{"id":"GO:0061736","count":1}]},{"hash":"409647622480887723","title":"Actin cytoskeleton remodeling and cell morphogenesis","description":"Reason: multiple terms point to actin-based structures (filopodium/lamellipodium assembly), adhesion-dependent spreading, and GTPase activation driving cytoskeletal remodeling and morphogenesis; autophagy-related terms are less central.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0043314","count":2},{"id":"GO:1904693","count":2}]},{"hash":"996813588961183618","title":"Ion and metal ion transport","description":"GO terms indicate a clear emphasis on transmembrane transport of ions and metals (e.g., copper ion transport, arsenate ion transmembrane transport, monoatomic anion transmembrane transport) with calcium-response as a related signal. While a couple of terms are less directly related (ceramide translocation, nitrate assimilation), the dominant pattern points to ion and metal transport and homeostasis. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051592","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0099040","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0099133","count":1}]},{"hash":"563582317813254652","title":"Unknown","description":"The GO terms are highly diverse, spanning immune processes (isotype switching, B cell cytokine production, T cell\u2013mediated responses), virion assembly, reproduction (sperm binding to zona pellucida), general cell division, protein stabilization, and nuclear localization to telomeres and Cajal bodies. There is no clear, single biological theme tying these functions together, so a concise, cohesive label cannot be confidently assigned.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048291","count":4},{"id":"GO:0002842","count":4},{"id":"GO:0007339","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0002368","count":4}]},{"hash":"1058339071545662440","title":"Heterochromatin maintenance and transcriptional regulation","description":"The top GO terms point to chromatin-based control of gene expression: DNA-templated transcription, rDNA heterochromatin formation/maintenance, and peptidyl-lysine deacetylation, all suggesting histone modification and silent chromatin. Additional terms about negative regulation of transcription and differentiation reinforce a theme of transcriptional repression via chromatin state. This aligns well with a function in chromatin silencing and transcriptional regulation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060303","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0006344","count":3},{"id":"GO:0045820","count":3}]},{"hash":"2093640653559475423","title":"Mitophagy and mitochondrial stress response","description":"This cluster centers on mitochondrial quality control and redox balance, evidenced by terms for mitophagy (autophagy of mitochondrion), cellular oxidant detoxification, positive regulation of SOD activity, and regulation of oxidative phosphorylation. Additional terms for L-glutamine metabolism and proteolysis suggest metabolic remodeling during stress, with a contextual hint of stress-related dormancy in host-associated symbionts. Confidence: High","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0006950","count":2},{"id":"GO:0085014","count":2},{"id":"GO:0018323","count":1}]},{"hash":"559585040849087773","title":"Mitochondrial inner membrane protein import","description":"The GO terms point to proteins involved in targeting to mitochondria and inserting proteins into the mitochondrial inner membrane, indicating a coherent set of mitochondrial import/assembly factors. The presence of obsolete terms does not obscure the underlying theme of inner-membrane import.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072321","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0006626","count":1}]},{"hash":"916913478274256673","title":"Ketone Body and Acetyl-CoA Metabolism","description":"The top GO terms cluster around ketone body biosynthesis and catabolism, acetyl-CoA catabolic processes, and propionyl-CoA biosynthesis, indicating a common theme of mitochondrial acetyl-CoA and ketone body metabolism. A related term about mitochondrial membrane permeability in apoptosis fits the energy/mitochondrial context, while several developmental terms are more peripheral. Overall, the dominant signal is ketone/acetyl-CoA metabolic pathways.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0014070","count":3},{"id":"GO:0046951","count":3},{"id":"GO:0046356","count":3},{"id":"GO:1902109","count":3},{"id":"GO:1902860","count":3}]},{"hash":"1989229443600412657","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to protein synthesis and ribosome assembly, including translation, ribosome biogenesis, small subunit (SSU) assembly, and SSU-rRNA maturation, indicating a cohesive group of proteins involved in ribosome construction and function. A few additional terms like transcription antitermination and UV response appear as secondary associations, but the primary signal clearly points to ribosome biogenesis and translation machinery.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0006407","count":2},{"id":"GO:0000028","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1901943347520838280","title":"Intracellular signaling regulators (dephosphorylation, cGMP)","description":"Proteins in this cluster are tied to signaling regulation, notably dephosphorylation and regulation of guanylate cyclase (cGMP) signaling, with additional hints from nuclear import and muscle/heart activity terms. Although several annotations are obsolete, the recurring theme points to modulation of intracellular signaling and localization. The cluster is small with limited connectivity, suggesting a broad signaling-related grouping rather than a specific pathway.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0042994","count":2},{"id":"GO:0072205","count":2},{"id":"GO:0006607","count":1},{"id":"GO:0006919","count":1}]},{"hash":"2213256493551426594","title":"Nuclear RNA methylation and capping","description":"The terms are dominated by RNA modification and maturation in the nucleus: rRNA and tRNA methylation, 7-methylguanosine cap formation/hypermethylation, and related ribonucleoprotein complex import or nucleologenesis. This points to nuclear RNA processing rather than other metabolic processes. Some noise terms (cobalamin biosynthesis, blastocyst formation) likely reflect annotation artifacts, but the primary signal supports a nuclear RNA modification/maturation theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":1},{"id":"GO:0017126","count":1},{"id":"GO:0071167","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0036261","count":1}]},{"hash":"2281641249824853307","title":"Ras signaling regulation with innate immune defense","description":"This cluster centers on small GTPase\u2013mediated signaling and regulation of Ras pathways, plus innate antiviral defense terms, suggesting a cohesive theme around Ras pathway modulation in immune responses. Additional terms related to transcription, cell cycle, and mitochondria distribution may reflect broader cellular context rather than core function, but do not override the Ras-immune signaling focus.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007264","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0045842","count":3}]},{"hash":"2198663986791084861","title":"Ribosome Biogenesis and Translation Regulation","description":"The top GO terms cluster around translation and ribosome-related processes (translation, ribosomal large subunit biogenesis, maturation of SSU-rRNA, and regulation of translation), suggesting these proteins participate in ribosome assembly and control of protein synthesis. Supporting terms like RNA splicing and antibiotic response appear as ancillary functions but do not override the dominant ribosome/translation theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0000372","count":1},{"id":"GO:0033120","count":1},{"id":"GO:0034337","count":1}]},{"hash":"227062400483871880","title":"Actin Cytoskeleton Remodeling","description":"Top terms are dominated by actin-related processes (actin filament/bundle assembly, cytokinesis, skeletal muscle thin filament assembly) with supporting roles in phagocytosis, calcium response, and vesicle trafficking, pointing to a shared theme of actin cytoskeleton remodeling driving division and cellular movement.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006909","count":4},{"id":"GO:0070527","count":4},{"id":"GO:0000281","count":4},{"id":"GO:0030240","count":4},{"id":"GO:0030476","count":4}]},{"hash":"455410575510874508","title":"Mitosis and Microtubule Organization","description":"The top GO terms cluster around mitosis and microtubule functions\u2014metaphase chromosome alignment, sister chromatid separation, spindle disassembly, cytoplasmic microtubule organization, nuclear membrane reassembly, and DNA replication\u2014indicating a cohesive theme of cell division and cytoskeletal dynamics. Some terms (mitochondrial complex III assembly, telomerase regulation) are less central but do not override the dominant signal.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034551","count":1},{"id":"GO:0007080","count":1},{"id":"GO:0010569","count":1},{"id":"GO:2000331","count":1},{"id":"GO:0051974","count":1}]},{"hash":"534053740274172642","title":"Fungal cytokinesis and septum formation","description":"The GO terms with the strongest ties are about cell wall organization, division septum site selection, and actomyosin contractile ring contraction, all core components of cytokinesis and septum formation in fungi. While a few terms appear unrelated, the common theme centers on fungal cell division machinery and septum biogenesis.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":1},{"id":"GO:0000920","count":1},{"id":"GO:0000918","count":1},{"id":"GO:0000916","count":1},{"id":"GO:0034217","count":1}]},{"hash":"589910082803474970","title":"Vesicle trafficking and exocytosis regulation","description":"This cluster is dominated by GO terms related to membrane trafficking and secretion, including COPI Golgi vesicle coating, calcium-dependent exocytosis, and secretory processes like VLDL assembly and cytokinesis-associated vesicle dynamics, suggesting a cohesive role in vesicle trafficking and exocytosis regulation across contexts.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048205","count":1},{"id":"GO:0061000","count":1},{"id":"GO:1902307","count":1},{"id":"GO:0035021","count":1},{"id":"GO:0045956","count":1}]},{"hash":"609784609201315954","title":"Mitochondrial respiration and calcium signaling","description":"The set centers on energy production (mitochondrial respiratory chain complex IV assembly and aerobic respiration) and calcium-mediated signaling pathways (calcium ion transport and Wnt calcium signaling), with links to cytoskeletal dynamics and angiogenesis (tubulin assembly and branching in blood vessel morphogenesis). This suggests a theme where mitochondrial function and calcium signaling coordinate cellular energy use with cytoskeletal remodeling.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":1},{"id":"GO:0007023","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0006919","count":1}]},{"hash":"293120869194418526","title":"Cholesterol and fatty acid biosynthesis regulation","description":"The top GO terms cluster around lipid metabolism, especially cholesterol and fatty acid biosynthesis and their regulation (e.g., HMG-CoA reductase regulation, cholesterol biosynthetic process). Some terms about ER-Golgi transport or morphogenesis seem less connected and may reflect broader cell-context associations, but the lipid biosynthesis regulation signal is strongest and representative of the group.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0060363","count":1}]},{"hash":"1096800520627470713","title":"Embryonic neural tube and axis patterning","description":"GO terms center on neural tube formation, ventricle development, somite patterning, and Notch signaling control\u2014key embryogenesis processes; despite some obsolete annotations, the core theme is early developmental patterning.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021993","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0060763","count":1},{"id":"GO:0036138","count":1},{"id":"GO:0070544","count":1}]},{"hash":"507331260141995430","title":"Developmental signaling and secretory transport","description":"The top GO terms cluster around signaling pathways involved in development (TGF-beta response, retinoic acid response, forebrain and heart development) and a secretory pathway component (ER-to-Golgi vesicle transport). This combination suggests proteins participating in developmental regulation with extracellular signaling and trafficking, rather than a single, narrow molecular function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0035264","count":2},{"id":"GO:2000270","count":1}]},{"hash":"1534403898285986460","title":"Unknown","description":"Top terms span heart development, insulin secretion regulation, retinoic acid response, cholecystokinin signaling, neutrophil degranulation regulation, osteoclast development, immune tolerance, T-helper 1 lineage commitment, and mechanical stimulus response. This broad, multidisciplinary mix provides no single cohesive function to assign a specific label, especially given the small cluster size, so Unknown is the most appropriate name.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036302","count":1},{"id":"GO:0046676","count":1},{"id":"GO:0071300","count":1},{"id":"GO:0061847","count":1},{"id":"GO:0043313","count":1}]},{"hash":"1154868392686545954","title":"Humoral and cellular immune activation","description":"Based on the Top Terms, the cluster is enriched for immune-related processes, especially B cell\u2013driven humoral responses (isotype switching to IgG; B cell cytokine production) and T cell\u2013mediated anti-tumor responses. A few other terms (virion assembly, sperm binding to zona pellucida, protein localization to telomere/Cajal bodies) appear as outliers, possibly reflecting multifunctional proteins or annotation noise. The dominant theme is immune activation, so the name emphasizes both humoral and cellular immune functions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048291","count":3},{"id":"GO:0002842","count":3},{"id":"GO:0007339","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0002368","count":3}]},{"hash":"2280162014749614723","title":"Developmental signaling in muscle, heart, and nervous system","description":"This cluster centers on developmental processes across tissues: myoblast fusion (muscle development), angiogenesis and heart development (cardiovascular development), and axonogenesis plus synaptic activity (neural development and function). The presence of cell-cycle and apoptotic terms is compatible with developmental regulation. Overall, the common theme is multi-tissue developmental signaling and maturation, especially in muscle, heart, and nervous system.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007520","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0060079","count":3}]},{"hash":"1799517199296272027","title":"Nuclear transport and pore organization","description":"The favored terms point to processes in and around the nucleus: tRNA export from the nucleus, import of NLS-bearing proteins, nuclear pore organization, and mitotic nuclear membrane disassembly, all indicating a cohesive theme of nuclear transport and pore dynamics, with some oligomerization terms accompanying protein complexes involved in these processes.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006409","count":3},{"id":"GO:0006607","count":2},{"id":"GO:0036228","count":2},{"id":"GO:0006999","count":2},{"id":"GO:0070208","count":2}]},{"hash":"357922224342458975","title":"Sphingolipid and phospholipid metabolism","description":"Based on the GO terms, the proteins in this cluster are enriched for lipid-related processes, especially sphingosine/sphingolipid metabolism and various phospholipid biosynthetic/degradative steps (phospholipid catabolic/dephosphorylation, phosphatidylglycerol biosynthesis). While a few terms touch on other, less coherent processes (e.g., Wnt-related or germ cell signals), the dominant theme is lipid metabolism and signaling, justifying a lipid-metabolism\u2013centered label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":1},{"id":"GO:0044329","count":1},{"id":"GO:0006670","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0035233","count":1}]},{"hash":"1168842894394903282","title":"Unknown","description":"The three proteins have only loosely related GO terms: two about protein glycosylation (O-linked mannose and O-GlcNAc), and one about larval cuticle development, offering no cohesive functional theme for a specific label.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035269","count":1},{"id":"GO:0097370","count":1},{"id":"GO:0008363","count":1}]},{"hash":"2015340212657760189","title":"Nutrient Transport and Osmotic Stress Response","description":"The GO terms cluster around membrane transport activities (selenite, organic anions, phosphate, trehalose) and cellular responses to nutrient limitation and osmotic stress (glucose starvation, osmotic stress), suggesting a coherent theme of transport-driven nutrient uptake and stress adaptation. Some terms (replicative senescence, intestinal epithelial structure maintenance) are less directly linked to transport, appearing as weaker or peripheral annotations rather than core features of this cluster.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097080","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0043252","count":1},{"id":"GO:0042149","count":1}]},{"hash":"2086344113971967198","title":"Neuronal Synaptic Transmission and Plasticity","description":"This cluster centers on neuronal signaling and vesicle-mediated secretion, with terms for neurotransmitter transport, neurotransmitter secretion, dendritic spine maintenance, and actin remodeling (Arp2/3). The presence of dense core granule maturation and long-term synaptic depression further points to synaptic transmission and plasticity regulation in neurons. Overall, the proteins seem to participate in synaptic function and vesicle trafficking rather than a non-neuronal process.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060292","count":1},{"id":"GO:0034316","count":1},{"id":"GO:0015844","count":1},{"id":"GO:0050796","count":1},{"id":"GO:0046928","count":1}]},{"hash":"1478628826797740899","title":"Unknown","description":"There are no GO terms or interaction signals to tie these proteins to a shared function, and with zero edges and an empty term list, a coherent label cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"750872579230022533","title":"Pro-angiogenic PI3K/AKT-MAPK signaling","description":"This cluster is driven by GO terms indicating positive regulation of PI3K signaling, PI3K/AKT signaling, MAPK cascade, endothelial cell proliferation, and angiogenesis, suggesting a shared role in promoting angiogenesis via these pathways.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014068","count":1},{"id":"GO:0001938","count":1},{"id":"GO:0051897","count":1},{"id":"GO:0045766","count":1},{"id":"GO:0043410","count":1}]},{"hash":"1533772831267042925","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by cytoplasmic translation, ribosomal large subunit assembly, preribosome assembly, and ribosomal large subunit biogenesis, indicating a shared function in ribosome production and protein synthesis. Some other terms (retinal development, T cell differentiation) appear incidental and do not reflect the core function of these proteins in the cluster.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0046632","count":1},{"id":"GO:0060041","count":1},{"id":"GO:0021554","count":1}]},{"hash":"383427843200731579","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001825","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0006376","count":2}]},{"hash":"963100954580096132","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034414","count":1},{"id":"GO:1903999","count":1},{"id":"GO:0098789","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0030420","count":1}]},{"hash":"1038721199469000463","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990577","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0021871","count":1},{"id":"GO:0098869","count":1}]},{"hash":"1536370424807445003","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080182","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0010768","count":1}]},{"hash":"709969652708682783","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060539","count":1},{"id":"GO:0006665","count":1},{"id":"GO:0021794","count":1},{"id":"GO:0060603","count":1},{"id":"GO:0060644","count":1}]},{"hash":"775198522825246859","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050773","count":3},{"id":"GO:0007422","count":3},{"id":"GO:0022008","count":3},{"id":"GO:0071372","count":3},{"id":"GO:0072178","count":3}]},{"hash":"919633532719111106","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060982","count":1},{"id":"GO:0035774","count":1},{"id":"GO:0021696","count":1},{"id":"GO:0021516","count":1},{"id":"GO:0006337","count":1}]},{"hash":"475655285382670302","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902181","count":1},{"id":"GO:0001561","count":1},{"id":"GO:0019491","count":1},{"id":"GO:0097089","count":1},{"id":"GO:0042400","count":1}]},{"hash":"449019508880429651","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036129","count":1},{"id":"GO:1902376","count":1},{"id":"GO:0045454","count":1}]},{"hash":"770355558395112969","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1860637973089498217","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071915","count":2},{"id":"GO:0002101","count":2},{"id":"GO:0010833","count":2},{"id":"GO:0070146","count":2},{"id":"GO:0070200","count":2}]},{"hash":"2268805000043331976","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090529","count":2}]},{"hash":"523914392725289725","title":"Neuronal morphogenesis and synaptic plasticity","description":"The cluster\u2019s terms predominantly point to neuron projection morphogenesis, positive regulation of synaptic plasticity, and cytoskeletal remodeling (actin filament debranching, focal adhesion assembly), which together indicate neuronal growth and synaptic remodeling. While there are related immune signals (e.g., defense response to fungus, TNF signaling), the strongest cohesive theme is neuronal development and synaptic adaptability.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030307","count":1},{"id":"GO:0071356","count":1},{"id":"GO:0014070","count":1},{"id":"GO:1990314","count":1},{"id":"GO:0048812","count":1}]},{"hash":"1700125304378920418","title":"Unknown","description":"Top GO terms are extremely diverse (epithelial migration, glomerular development and filtration, CNS development, innervation, chondrocyte development, lipoteichoic acid and choline biosynthesis, FGFR signaling regulation). With no shared pathway or clear functional theme and no edges connecting the proteins, there is no coherent function to assign.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061580","count":1},{"id":"GO:0032836","count":1},{"id":"GO:0070395","count":1},{"id":"GO:0042425","count":1},{"id":"GO:0060384","count":1}]}]