[{"hash":"518031824782633770","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042594","count":3},{"id":"GO:0006189","count":3},{"id":"GO:0001889","count":3},{"id":"GO:0006552","count":3},{"id":"GO:0006541","count":2}]},{"hash":"2012985477674782801","title":"Ribosome biogenesis and translation with cell cycle","description":"This cluster centers on protein synthesis and ribosome assembly (translation GO:0006412; ribosome biogenesis GO:0042254; ribosomal small subunit biogenesis GO:0042274; tRNA modification GO:0006400) and includes cell division and cell cycle processes (GO:0051301; GO:0007049), indicating a cohesive module of ribosome biogenesis/translation closely linked to cell cycle progression. Minor stress-response-related terms are present but do not define the main function.","confidence":"High","size":29,"edges":33,"triangles":4,"max_degree":11,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0051301","count":7},{"id":"GO:0007049","count":7},{"id":"GO:1903833","count":6},{"id":"GO:0042274","count":6}]},{"hash":"1652068157462265773","title":"Mitotic cell cycle and kinetochore function","description":"The top GO terms point to core mitotic activities: DNA replication, DNA-templated transcription, mitotic cell cycle, and protein localization to the kinetochore (including attachment of meiotic spindle microtubules to kinetochores). While other terms like caveolin-mediated endocytosis, potassium transport, and glycogen catabolism appear, they are less central to the cluster\u2019s primary theme, which is chromosome replication/segregation and kinetochore dynamics. ","confidence":"High","size":29,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0006351","count":22},{"id":"GO:0000278","count":22},{"id":"GO:0034501","count":22},{"id":"GO:0006813","count":21}]},{"hash":"1966355880045284347","title":"Cell growth and division machinery","description":"The cluster is enriched for transcription, ribosome biogenesis, and cell division, with regulatory processes like GTPase activity and protein oligomerization that together reflect core growth and proliferation machinery; contextual terms such as liver regeneration and fatty-acid response suggest roles in tissue growth and metabolism.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0043547","count":4}]},{"hash":"1654473449646689061","title":"ER-to-Golgi Transport Proteins","description":"Mainly ER-to-Golgi vesicle transport and ER exit regulation, with ER membrane fusion as a core aspect; other annotations are minor or supporting but still related to the secretory pathway.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0055114","count":2},{"id":"GO:0035774","count":2},{"id":"GO:0010637","count":2},{"id":"GO:0000002","count":2}]},{"hash":"1866940584304603766","title":"Unknown","description":"These terms cover neural development, hepatocyte apoptosis, muscle stretch response, multiple signaling pathways (salicylic acid, vitamin D), protein ubiquitination, endothelial and prostate development, and hormone secretion. There is no single dominant function or pathway tying these terms together, and the network shows no edges, suggesting a heterogeneous set rather than a cohesive cluster. Therefore, label is Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021707","count":4},{"id":"GO:0097284","count":4},{"id":"GO:0035994","count":4},{"id":"GO:2000031","count":4},{"id":"GO:0033280","count":4}]},{"hash":"1323674623324640879","title":"DNA replication and chromatin organization","description":"The top GO terms are dominated by DNA replication and related licensing/elongation activities (DNA replication, DNA strand elongation, MCM complex assembly) along with chromatin-related processes (heterochromatin formation, subtelomeric heterochromatin formation). While there are ancillary terms for RNA processing and ribosome assembly, the core signal points to nuclear DNA replication and chromatin maintenance as the defining theme of this cluster.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0006397","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000902","count":2}]},{"hash":"1673777683701528699","title":"Cardiac morphogenesis and transcriptional regulation","description":"The cluster includes heart development terms (atrial septum development, endocardial cushion morphogenesis) suggesting a cardiac morphogenesis theme. It also features broader regulatory processes such as transcription elongation by RNA polymerase II and spliceosomal snRNP assembly, plus protein turnover/trafficking like ubiquitin-dependent endocytosis and autophagosome localization, indicating coordinated regulation of gene expression and protein handling during development. While not all terms point to a single pathway, the heart development signals combined with transcriptional/regulatory processes point to a cohesive, development- and regulation-focused group. Confidence is Medium due to the mix of general and tissue-specific terms and the absence of stronger, more specific clustering signals.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":2},{"id":"GO:0010923","count":2},{"id":"GO:0003283","count":1},{"id":"GO:0070086","count":1},{"id":"GO:0061753","count":1}]},{"hash":"850656617449334173","title":"Membrane transport and secretion proteins","description":"The Top Terms show a clear emphasis on transport and secretion processes (various substrate transports, phospholipid translocation, type I secretion, cytosol-to-ER transport, peptide export/antigen transport). Although DNA-templated transcription appears once, the dominant theme is transport/secretion across membranes, suggesting a coherent cluster of transporter and secretion-related proteins.","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:1900753","count":2},{"id":"GO:0031460","count":2},{"id":"GO:0045332","count":2},{"id":"GO:0030253","count":2}]},{"hash":"489408626777711659","title":"Endosome-Lysosome Trafficking","description":"This cluster is dominated by GO terms related to intracellular vesicle transport, especially endosome-to-lysosome and endosome maturation pathways (endosome to lysosome transport, early to late endosome transport, Cvt pathway to vacuole). This points to a cohesive vesicular trafficking function guiding cargo to lysosomal/vacuolar compartments. Some terms (e.g., mitotic cell cycle, hippocampus development) are broader or less directly related, appearing as background annotations rather than core drivers of the cluster\u2019s function. Overall, the vesicle trafficking theme best explains the observed term set.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008333","count":6},{"id":"GO:0050771","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0032258","count":4}]},{"hash":"1581064111911092011","title":"RNA splicing and ribosome biogenesis","description":"The top GO terms are dominated by spliceosome-related processes (alternative mRNA splicing; positive/negative regulation of mRNA splicing) and ribosome biogenesis, indicating a cluster centered on RNA processing and assembly of ribonucleoprotein complexes; other terms like nuclear envelope organization and mitochondrial electron transport are less representative but present as secondary associations.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0006998","count":2}]},{"hash":"5006887020594448","title":"Lipid Biosynthesis and Coenzyme Q/Tocopherol Metabolism","description":"The proteins show a cohesive theme around lipid metabolism, including ubiquinone (CoQ) biosynthesis, phosphatidylglycerol biosynthesis, and tocopherol regulation, as well as lipid homeostasis. A few neural development terms appear but are less represented, so the dominant signal is lipid-related metabolism.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1902171","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0001525","count":2},{"id":"GO:1901006","count":2}]},{"hash":"523586573372628853","title":"RNA and protein methylation","description":"The dominant GO terms point to methylation across RNA species (tRNA methylation, wobble uridine modification, rRNA modification, mRNA capping) and on proteins (peptidyl-arginine methylation, histone methylation, regulation of ubiquitination). A few outlier terms seem metabolic or developmental (cobalamin and vitamin E biosynthesis, nodulation), but the clear recurring theme is methylation-related modifications, justifying a cohesive label around RNA and protein methylation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0031397","count":2},{"id":"GO:0009236","count":1},{"id":"GO:0006370","count":1}]},{"hash":"1966679920887809567","title":"Metabolism and Stress Signaling","description":"The GO terms span various biosynthetic and metabolic processes (antibiotic, biotin, sterol biosynthesis; cellulose catabolic process) as well as defense and signaling activities (oxidant detoxification, lipopolysaccharide response, cytokinin-activated signaling, MAPKKK cascade). This suggests a broad set of proteins involved in general metabolism with roles in stress or environmental signaling, rather than a single cohesive pathway. ","confidence":"Low","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030245","count":7},{"id":"GO:0017000","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009736","count":4},{"id":"GO:0098869","count":3}]},{"hash":"314914456769919122","title":"Mitosis and Chromosome Segregation","description":"Predominant mitosis-related terms (cell division, mitotic spindle assembly, sister chromatid segregation, regulation of meiotic nuclear division) point to a cluster of proteins involved in mitosis and chromosome segregation. Additional terms about Okazaki fragment processing in mitotic DNA replication and cytoskeletal regulation (actin depolymerization, GTPase activity) reinforce a mitotic/cytoskeletal theme, with a few tissue-specific differentiation terms that do not override the core function. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:1903461","count":7},{"id":"GO:0070306","count":7},{"id":"GO:0000070","count":7},{"id":"GO:0043547","count":7}]},{"hash":"1550780674257456014","title":"DNA Damage Repair and Stress Response","description":"This cluster centers on genome maintenance activities (base-excision repair, DNA replication, error-prone translesion synthesis) and cell fate decisions (apoptotic process), with additional signals of cellular stress responses (response to xenobiotic stimulus, redox homeostasis). Together these terms suggest proteins involved in preserving genome integrity under stress rather than a single, narrow pathway. Obsolete GO terms are annotations artifacts and do not alter the overarching theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006486","count":4},{"id":"GO:0046354","count":4},{"id":"GO:0006284","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0006260","count":3}]},{"hash":"1368116817455856608","title":"Neural signaling and development","description":"Terms point to neural signaling and development (excitatory postsynaptic potentials, Schwann cell development, and cocaine response) with related calcium/NFAT and cyclic nucleotide signaling; a few cell-cycle related terms appear as incidental annotations, which keeps the neural theme as the main signal.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0009190","count":4},{"id":"GO:0014044","count":4},{"id":"GO:0051531","count":4},{"id":"GO:0042220","count":4}]},{"hash":"1408968214788467722","title":"Nuclear import and cell cycle regulation","description":"The cluster is dominated by GO terms related to nuclear import (NLS-bearing and ribosomal protein import into nucleus) and key cell cycle events (meiotic spindle elongation, female meiotic nuclear division, mitotic sister chromatid separation, and regulation of DNA replication). These together suggest a functional theme centered on transporting components into the nucleus and coordinating cell division processes, with some additional transcription and signaling annotations that are less central. Confidence: High","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0006607","count":6},{"id":"GO:0006610","count":6},{"id":"GO:0043547","count":5},{"id":"GO:2001241","count":5},{"id":"GO:0045945","count":5}]},{"hash":"1319896133867068685","title":"mRNA Splicing and Processing","description":"The terms show a clear emphasis on RNA maturation: spliceosome-mediated pre-mRNA splicing, splice site recognition, and small-subunit processome assembly, alongside regulation of poly(A) tail length and mRNA modification. Additional items like mRNA stability under stress and regulatory ncRNA-mediated silencing indicate broader post-transcriptional regulation of mRNA. A few translation-reinitiation terms are present, but the dominant theme is RNA processing and maturation. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0075525","count":3},{"id":"GO:0006376","count":3},{"id":"GO:0060211","count":3},{"id":"GO:1900363","count":3}]},{"hash":"1671594877845325593","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042594","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0006552","count":2},{"id":"GO:0006086","count":2},{"id":"GO:0006099","count":2}]},{"hash":"1509440413944029548","title":"Wnt/Hippo signaling and apoptosis regulation","description":"This cluster's top GO terms center on regulation of Wnt canonical signaling and Hippo signaling, with concurrent roles in growth control and apoptosis (e.g., positive Wnt signaling, negative regulation of cardiac muscle proliferation, and neuron apoptotic regulation). The presence of keratinocyte differentiation and DNA-templated transcription hints at developmental and differentiation programs. Taken together, these proteins appear to coordinate signaling-driven development with controlled apoptosis.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090263","count":7},{"id":"GO:0060044","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0030216","count":6},{"id":"GO:0035329","count":6}]},{"hash":"2129428494244876586","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":43,"triangles":45,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070417","count":12},{"id":"GO:0006260","count":12},{"id":"GO:0000716","count":11},{"id":"GO:0071042","count":11},{"id":"GO:0000466","count":11}]},{"hash":"224351612701949138","title":"Ribosome Biogenesis and Translation Initiation","description":"The most frequent GO terms are ribosome biogenesis, translation reinitiation, formation of translation preinitiation complex, and translation, indicating proteins primarily involved in assembling ribosomes and initiating protein synthesis. The presence of mitotic cell cycle and cell division terms suggests a broader link to cell proliferation, which is typically supported by active translation. The skeletal system development and conjugation with cellular fusion terms are outliers likely due to multifunctional annotations, but do not override the central theme of ribosome/translation machinery.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0001501","count":2}]},{"hash":"1402167364227507583","title":"RNA processing and transcription regulation cluster","description":"Top GO terms indicate a core focus on mRNA splicing and transcription initiation/regulation (Pol II/III), suggesting the proteins collectively participate in gene expression control. Supporting terms like cell cycle, SMAD signaling, actin assembly, and apoptosis reflect broader cellular context, but the dominant theme remains RNA processing and transcription regulation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0039702","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0051017","count":2}]},{"hash":"1720086028259654909","title":"Unknown","description":"Top terms span DNA replication, protein dephosphorylation, ER-to-Golgi vesicle transport, midbrain development, immune responses, neuromuscular control, and Rho signaling. With no observed interactions (edges 0, triangles 0, max degree 0), there is no single shared function tying these proteins together. Therefore I label this cluster Unknown.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0030901","count":2},{"id":"GO:0032496","count":2}]},{"hash":"2099938742888769915","title":"Unknown","description":"The proteins show a highly heterogeneous set of GO terms\u2014epoxygenase P450 pathway, stilbene catabolic process, various dephosphorylation steps, response to antibiotics and testosterone, lipopolysaccharide biosynthesis, serine biosynthesis, and zinc transport\u2014with no clear, shared biological function or process tying them together. This makes it difficult to assign a specific, representative label to the cluster.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0097755","count":5},{"id":"GO:0019373","count":5},{"id":"GO:0046272","count":5},{"id":"GO:0046839","count":5},{"id":"GO:0046677","count":5}]},{"hash":"204756786390565434","title":"Mitochondrial Transport and Membrane Potential","description":"Top GO terms are dominated by transmembrane transport into mitochondria (phosphate, thiosulfate, NAD, iron) and regulation of the mitochondrial membrane potential, pointing to a shared mitochondrial transport/metabolic function. Some terms like DNA-templated transcription and liver regeneration are broader or less directly connected, but the core signal supports mitochondrial transport and energy regulation as the cluster\u2019s theme.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035435","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051881","count":3},{"id":"GO:0097421","count":3},{"id":"GO:0097274","count":3}]},{"hash":"1032843605222662742","title":"Ubiquitin-Dependent Proteolysis","description":"The top terms are strongly dominated by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, ubiquitin-dependent ERAD pathway, autoubiquitination, K6-linked ubiquitination), indicating a cluster centered on ubiquitin-mediated protein degradation and quality control, with some related regulatory roles.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0030433","count":10},{"id":"GO:0051865","count":9},{"id":"GO:1901253","count":8},{"id":"GO:0033151","count":8}]},{"hash":"1764732722932258388","title":"Cell cycle and cytoskeletal regulation","description":"The dominant GO terms point to mitosis and cell division (cell division, mitotic spindle assembly, APC-dependent catabolic process) together with cytoskeletal organization (actin filament depolymerization, protein homooligomerization) and ubiquitin signaling (K11-linked ubiquitination). This suggests a cohesive module focused on cell-cycle control and cytoskeletal remodeling, with a few outliers related to neuron development and immune response that are less central. Overall, the label captures the core recurring theme, though some noise lowers certainty.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0031175","count":4},{"id":"GO:0050830","count":4}]},{"hash":"156069768374412305","title":"Transcription Regulation and Redox Response","description":"This cluster is enriched for transcription-related GO terms (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) and redox-related terms (cellular response to oxidative stress; cellular oxidant detoxification; redox homeostasis), suggesting proteins involved in regulating gene expression in response to redox changes. The presence of a proline hydroxylation term and an obsolete metabolism term may reflect broader regulatory roles or annotation artifacts, but the core pattern points to transcriptional control linked to oxidative stress. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0006662","count":2}]},{"hash":"894475563071187041","title":"Developmental and cell-cycle regulation","description":"This cluster\u2019s GO terms cluster around organism development (multicellular, skeletal muscle, neuron development) and cell cycle/mitosis (mitotic cell cycle, kinetochore localization), with related processes like apoptosis and proteasome regulation. The combination suggests proteins coordinating growth, differentiation, and division, with some estrogen response context.","confidence":"Medium","size":26,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0032435","count":2},{"id":"GO:0006915","count":2}]},{"hash":"2215829019520778065","title":"Unknown","description":"The top GO terms include mitochondrial complex IV assembly, Mg2+/Co2+ transport, sporopollenin biosynthesis, O antigen biosynthesis, sporulation, and GDP-mannose metabolism, spanning mitochondria, bacteria, and plants. The lack of a unifying function and the sparse connectivity (5 edges, 0 triangles) suggest no coherent cluster function, so Unknown with None confidence.","confidence":"","size":26,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0045016","count":2},{"id":"GO:0006824","count":2},{"id":"GO:1903830","count":2},{"id":"GO:0080110","count":1}]},{"hash":"2164964613187095091","title":"Amino acid metabolism and related biosynthesis","description":"The cluster is enriched with GO terms focused on amino acid biosynthesis and catabolism (notably L-serine, L-threonine, and L-proline), along with GABA and putrescine catabolism and transsulfuration. While there are also terms for biotin and protoporphyrinogen IX biosynthesis, the dominant theme is amino acid metabolism and its connected pathways, justifying a label centered on amino acid metabolism.","confidence":"High","size":26,"edges":299,"triangles":2060,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006565","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0009447","count":5},{"id":"GO:0006782","count":5}]},{"hash":"347137556222833939","title":"Transcription Regulation & Chromatin Remodeling","description":"Most of the top GO terms cluster around control of gene expression and chromatin state, including DNA-templated transcription, chromatin remodeling, and negative regulation of transcription by RNA polymerase II. There is also a term related to the centrosome cycle, suggesting a cell-cycle context for transcriptional regulation. A few terms about metabolism and development appear less central. Overall, the data suggest a cohesive theme of transcription regulation via chromatin remodeling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0007098","count":3},{"id":"GO:1903758","count":3}]},{"hash":"1273174049900112001","title":"Mitochondrial maintenance and metabolite transport","description":"The terms show a coherent focus on mitochondrial function, including membrane potential regulation, iron import into mitochondria, and NAD and thiosulfate transport, plus protein localization to mitochondrial membranes and ER unfolded protein response. Some entries are obsolete or peripheral (e.g., liver regeneration), suggesting annotation noise but not a shift in core function. Overall, the cluster appears to reflect mitochondrial homeostasis and transport of metabolites/ions. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":2},{"id":"GO:0030968","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0097274","count":1}]},{"hash":"1977574504174359246","title":"Negative Regulation of Signaling and Cytoskeletal Dynamics","description":"The cluster is enriched for GO terms describing negative regulation across diverse signaling and cytoskeletal processes (neutrophil degranulation, blood vessel remodeling, Rho/Ras signaling, inositol phosphate and fatty acid metabolism) as well as cytoskeletal/vesicle-related activities (filopodium assembly, synaptic vesicle priming, acrosome reaction, muscle contraction). This pattern suggests the proteins function broadly as negative regulators of signaling and cytoskeletal dynamics rather than a single pathway. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043314","count":10},{"id":"GO:0060313","count":10},{"id":"GO:0016082","count":10},{"id":"GO:0007340","count":10},{"id":"GO:0035023","count":10}]},{"hash":"1839387475790362029","title":"Mitotic division and centromere assembly proteins","description":"This cluster is dominated by GO terms tied to cell division, microtubule-based movement, and CENP-A\u2013containing chromatin assembly, which together point to mitotic spindle function and chromosome segregation. Some terms reference rRNA maturation and vesicle transport, but the core signal favors mitosis-related protein functions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0007018","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0071902","count":6},{"id":"GO:0031954","count":6}]},{"hash":"757170327731172991","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006284","count":2},{"id":"GO:0006297","count":2},{"id":"GO:0003413","count":2},{"id":"GO:0043044","count":2}]},{"hash":"384156092241027126","title":"Translation and mRNA turnover","description":"The cluster is dominated by translation-related terms (initiation, elongation, termination, and selenocysteine incorporation) and mRNA decay, indicating a core association with ribosome function and post-transcriptional RNA regulation. While terms like glial cell proliferation and response to antibiotic appear, they are less central to the cluster\u2019s primary theme. Confidence: High","confidence":"","size":25,"edges":69,"triangles":80,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0014009","count":3},{"id":"GO:0006413","count":3},{"id":"GO:2000767","count":3}]},{"hash":"68660575926359902","title":"Neurodevelopment and craniofacial morphogenesis","description":"The top GO terms center on neural lineage specification and differentiation (neuron development; Bergmann glial cell differentiation) with accompanying embryonic cranial skeleton morphogenesis, plus transcriptional activity and cell-cycle-related processes, suggesting a cluster of neural development tied to craniofacial formation. Metabolic signals like insulin signaling may also influence neural development in this set.","confidence":"Medium","size":25,"edges":8,"triangles":1,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0032435","count":13},{"id":"GO:0048666","count":13},{"id":"GO:0046826","count":12},{"id":"GO:0007100","count":11}]},{"hash":"91721795185865983","title":"Gene Expression and Growth Signaling","description":"The cluster\u2019s GO terms cluster around DNA-templated transcription, RNA guanine-N7 methylation, mRNA transport, and TORC1 signaling, pointing to transcriptional regulation and RNA processing intertwined with nutrient/growth control. The presence of cell division and apoptotic processes suggests links to cell-cycle regulation and survival signaling, with peptidyl-serine dephosphorylation and GTPase activity regulation further supporting signaling modulation. A peripheral term like glycine betaine transport is less central, but does not override the dominant theme of gene expression machinery and growth signaling. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0036265","count":4}]},{"hash":"431754470953577018","title":"RNA processing and translation initiation control","description":"This cluster centers on ribosome assembly and translation initiation (translation reinitiation, preinitiation complex formation, ribosome biogenesis) and also on RNA processing/splicing regulation (spliceosome-regulated splicing, ncRNA-mediated gene silencing, mRNA export), suggesting a cohesive module linking RNA processing with translation machinery.","confidence":"High","size":25,"edges":19,"triangles":11,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0048025","count":5},{"id":"GO:0031047","count":5}]},{"hash":"561960614948101011","title":"Amino acid catabolism and kynurenine pathway","description":"The top GO terms point to multiple amino acid catabolic processes (L-kynurenine, L-alanine, lysine-related steps, phenylalanine-related biosynthesis) and connected metabolic pathways (oxaloacetate, heme biosynthesis, kynurenic acid). Notch signaling and DNA-templated transcription appear, but the dominant theme is amino acid degradation and related metabolism, suggesting the cluster groups enzymes involved in amino acid catabolism and linked metabolic routes.","confidence":"Medium","size":25,"edges":292,"triangles":2123,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":19},{"id":"GO:0042853","count":19},{"id":"GO:0007219","count":19},{"id":"GO:0019878","count":13},{"id":"GO:0006351","count":13}]},{"hash":"1599706624942151936","title":"Intracellular Vesicle Trafficking","description":"The top GO terms are centered on vesicle movement within the cell, including ER\u2013Golgi transport, Golgi-to-ER and Golgi-to-vacuole trafficking, and endosome-to-melanosome transport, plus synaptic vesicle budding. Additional terms for filopodium assembly and dendrite extension suggest neuronal contexts where vesicle trafficking is critical for growth and signaling. Overall, the cluster seems defined by vesicle-mediated transport in the secretory/endocytic pathway. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0006896","count":3},{"id":"GO:0035646","count":3}]},{"hash":"2028893532699791192","title":"Biosynthesis and redox metabolism","description":"This cluster\u2019s top GO terms include several biosynthetic processes (biotin, menaquinone, antibiotic, glycogen) alongside redox- and stress-related terms (cellular oxidant detoxification, response to hypoxia, oxidation-reduction). The proteins appear involved in diverse metabolic pathways with a common theme of biosynthesis and redox responsiveness, rather than a single specific pathway. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0001666","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0009102","count":4}]},{"hash":"1097392516653483937","title":"Vitamin biosynthesis and lipid metabolism","description":"Top GO terms include biotin, cobalamin, and menaquinone biosynthesis, along with tRNA methylation and several lipid-catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine). The presence of xenobiotic response signals suggests broader metabolic/detoxification roles, but there isn\u2019t a single narrow function tying all terms together. Label reflects a general metabolic cluster focused on cofactor biosynthesis and lipid turnover rather than a specific pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":7},{"id":"GO:0009236","count":6},{"id":"GO:0030488","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0035690","count":4}]},{"hash":"1688524005076067470","title":"Plant Telomere Chromatin and Growth Regulation","description":"This cluster centers on telomere/heterochromatin maintenance (rDNA and subtelomeric heterochromatin formation, protection from NHEJ at telomere) and also includes plant growth and hormone response processes (jasmonic acid, gibberellin, seed growth, chlorophyll biosynthesis, leaf senescence), suggesting a theme of plant chromatin regulation linked to growth regulation.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0031848","count":4},{"id":"GO:0009753","count":4},{"id":"GO:0009739","count":4},{"id":"GO:0080113","count":4}]},{"hash":"2046914865115465460","title":"RNA Splicing and Processing Regulation","description":"The top GO terms cluster around spliceosome-mediated mRNA splicing, regulation of mRNA stability and poly(A) tail processing, and small-subunit processome assembly, indicating proteins focused on post-transcriptional RNA processing and splicing regulation. This cohesive theme justifies a concise label centered on RNA splicing and processing control.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":16},{"id":"GO:0048026","count":16},{"id":"GO:0010610","count":15},{"id":"GO:0006378","count":13},{"id":"GO:0045292","count":13}]},{"hash":"899957544657062399","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":266,"triangles":1823,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0007064","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0006406","count":3}]},{"hash":"1289622411108221428","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitination and ubiquitin-dependent degradation pathways: ubiquitin-dependent proteolysis, protein ubiquitination, autoubiquitination, and the ERAD pathway. A peroxisomal import term tied to ubiquitination also appears, consistent with ubiquitin signaling controlling peroxisome matrix protein import. A few terms (vitamin D response, TNF signaling) may reflect broader regulatory roles of ubiquitination. Overall, the cluster centers on ubiquitin-mediated protein turnover rather than a single direct substrate class.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0051865","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0016567","count":8},{"id":"GO:0016558","count":6}]},{"hash":"2013102397970927666","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0000455","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0039695","count":1},{"id":"GO:0006391","count":1}]},{"hash":"523712383143510471","title":"Chromatin methylation and transcription regulation","description":"The cluster is enriched for chromatin-related activities: rDNA heterochromatin formation, RNA polymerase II\u2013mediated transcription, and multiple lysine methylation events (peptidyl-lysine dimethylation/trimethylation) as well as rRNA methylation. This pattern points to enzymes that modify chromatin or transcription machinery and influence gene expression. A couple of developmental GO terms may reflect broader roles of chromatin modifiers in embryo and tissue differentiation.","confidence":"High","size":24,"edges":270,"triangles":1899,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":4},{"id":"GO:0006366","count":4},{"id":"GO:0018013","count":3},{"id":"GO:0018023","count":3},{"id":"GO:0031167","count":3}]},{"hash":"838659319124932145","title":"RNA and Protein Methylation","description":"This cluster is dominated by GO terms related to various methylation and RNA modification processes (mRNA capping, rRNA and tRNA modification, peptidyl-arginine methylation, histone methylation) and related post-translational modifications. While a few terms touch on metabolic processes, the strongest recurring theme is methylation/modification, spanning RNA and protein contexts. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0009236","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0030488","count":1}]},{"hash":"1009347046420503229","title":"RNA processing and ribosome biogenesis","description":"These proteins are largely annotated with RNA metabolism functions: mRNA splicing via the spliceosome, mRNA export, ribosomal large subunit biogenesis, and regulation of translation initiation, plus ncRNA-mediated gene silencing. These together point to a core theme of RNA processing and ribosome assembly, with a few vesicle- trafficking terms that may reflect broader annotations rather than the main function of the cluster.","confidence":"High","size":24,"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:0042273","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1137827693779971141","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0006783","count":1},{"id":"GO:1902001","count":1},{"id":"GO:0070453","count":1}]},{"hash":"284657706310227953","title":"Intracellular Signaling and Endocytosis","description":"The cluster centers on intracellular signal transduction, endocytosis-related processes (pinocytosis and endosomal vesicle fusion), and regulation of Rho signaling, with accompanying ubiquitination\u2014together suggesting a coherent theme of signaling linked to vesicle trafficking. Some terms appear more peripheral (brain development, hepatocyte apoptosis, vitamin D and salicylic acid signaling) and may reflect broader GO annotations rather than core cluster function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0034058","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0021707","count":2}]},{"hash":"942654528014966425","title":"MAPK signaling and immune-related gene expression","description":"The cluster is dominated by terms tied to MAPK pathways (ERK1/ERK2 cascade, p38MAPK cascade), PMA and GM-CSF\u2013related signaling, and calcium release, pointing to signaling events that regulate immune responses and downstream gene expression. The presence of cytoplasmic translation and mRNA processing suggests coordinated transcriptional/post-transcriptional regulation following MAPK signaling. Some terms like cholesterol biosynthesis and muscle stretch are peripheral, but the core theme centers on MAPK-driven signaling leading to gene expression changes in an immune context.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0006695","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0043029","count":2},{"id":"GO:1904628","count":2}]},{"hash":"549248622629077527","title":"Neuronal development and dendritic spine morphogenesis","description":"The cluster is dominated by neuron-centric GO terms, especially dendritic spine morphogenesis and neuron development, with supporting terms like regulation of protein stability and potassium ion transport that relate to neuronal signaling and synaptic remodeling. While a few terms (e.g., Fc receptor signaling, kinetochore localization) are less central, the strongest signal points to neuronal development and synapse formation. ","confidence":"High","size":23,"edges":40,"triangles":21,"max_degree":10,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0032435","count":21},{"id":"GO:0060997","count":21},{"id":"GO:0031647","count":21},{"id":"GO:0045736","count":21},{"id":"GO:0048666","count":21}]},{"hash":"1477132060784298727","title":"Unknown","description":"The top GO terms are broad and span several unrelated processes (mitotic cell cycle, invasive growth under nutrient limitation, GTPase signaling, rRNA processing, ion transport, organismal development, immunity, neural development, imprinting regulation, and transcription). This spread does not point to a single cohesive function or pathway for the cluster, so a specific, representative label cannot be confidently assigned.","confidence":"","size":23,"edges":12,"triangles":0,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0006813","count":2}]},{"hash":"1084627639103108487","title":"Bacterial Metabolism and Sporulation","description":"Top GO terms indicate bacterial-centered metabolism and development: redox processes, serine biosynthesis, alanine catabolism, formate catabolism, menaquinone biosynthesis, and responses to hypoxia and nutrients, along with sporulation and photosynthetic carbon pathways. This combination strongly points to a cluster of bacterial metabolic pathways and sporulation-related processes, rather than a single eukaryotic function.","confidence":"Medium","size":23,"edges":14,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0006564","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0030435","count":5},{"id":"GO:0009234","count":4}]},{"hash":"1191049628546328213","title":"Mitotic checkpoints and RNA splicing machinery","description":"This cluster shows strong enrichment for mitotic cell-cycle terms (mitotic cell cycle, mitotic G1 DNA damage checkpoint signaling) and RNA processing/splicing components (spliceosomal tri-snRNP complex assembly, cytosolic ribosome assembly, negative regulation of mRNA splicing), suggesting a core theme of cell-cycle control coupled with RNA processing. Additional terms related to innate immune and stress signaling appear, but they are less central to the main pattern, supporting a label focused on mitosis and gene-expression machinery.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0031571","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0006397","count":2}]},{"hash":"45974816562527903","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":248,"triangles":1670,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0001682","count":1}]},{"hash":"2295029603655074655","title":"Mitochondrial translation and respiration machinery","description":"The cluster is dominated by mitochondrial-associated terms: mitochondrial ribosome assembly, mitochondrial electron transport (NADH to ubiquinone), and assembly of the mitochondrial respiratory chain complex II, suggesting a shared function in mitochondrial protein synthesis linked to respiration. Additional signals for ribosome biogenesis and tRNA modification align with a broader role in ribosome production, but the strongest signal centers on mitochondrial gene expression feeding into electron transport.","confidence":"High","size":23,"edges":176,"triangles":612,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0061668","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0034553","count":2},{"id":"GO:0000747","count":1}]},{"hash":"1613239645997354157","title":"Oxidative Stress Response and Detoxification","description":"The proteins show enrichment for detoxification of cellular oxidants, hypoxia response, and toxin/metal stress terms, plus mitochondrial respiration-related assembly and antioxidant responses, suggesting a cohesive role in managing oxidative and metabolic stress.","confidence":"Medium","size":23,"edges":23,"triangles":5,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0033617","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0051092","count":2}]},{"hash":"1206568715716399747","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0032728","count":1}]},{"hash":"168377745809260299","title":"Splicing and translation initiation regulation","description":"The cluster is enriched for mRNA processing terms (mRNA splicing via spliceosome, splice site recognition, polyadenylation) as well as translation initiation/reinitiation steps (formation of translation preinitiation complex, translation reinitiation), suggesting a cohesive role in RNA processing coupled to regulation of protein synthesis. A regulatory ncRNA-mediated gene silencing term further supports broader RNA-centric regulation. ","confidence":"High","size":23,"edges":33,"triangles":2,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":12},{"id":"GO:0045292","count":12},{"id":"GO:0002188","count":11},{"id":"GO:0001731","count":11},{"id":"GO:1901407","count":11}]},{"hash":"1064640950751997398","title":"Ubiquitin-Dependent Protein Degradation & DNA Repair","description":"Enrichment is dominated by ubiquitin-dependent protein catabolic processes, with supporting DNA damage response/repair terms, suggesting these proteins function in ubiquitin-mediated turnover linked to genome maintenance; a few RNA processing/transcription terms may reflect broader regulatory roles.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0042769","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0006369","count":2},{"id":"GO:0060325","count":1}]},{"hash":"1375208390850189350","title":"Mitotic Spindle and Chromosome Segregation","description":"The top terms cluster around mitosis and cell division, especially mitotic spindle assembly, sister chromatid segregation, and regulation of nuclear division, with supporting cytoskeletal changes (actin filament depolymerization). Some terms (mRNA splicing, ERAD) are less directly connected and may reflect housekeeping functions, but the predominant signal is mitotic machinery.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":8},{"id":"GO:0000398","count":7},{"id":"GO:1903461","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0070306","count":7}]},{"hash":"910068621894841918","title":"Xenobiotic and Plant Metabolite Catabolism","description":"The GO terms point to a broad set of catabolic and metabolic processes affecting diverse small molecules, including xenobiotics (response to toxic substance, cocaine catabolic process, endocannabinoid signaling regulation) and plant-derived metabolites (alkaloid metabolism, strigolactone biosynthesis), along with general metabolism (proteolysis, menaquinone biosynthesis, nitrogen utilization). This suggests a cluster centered on breaking down a variety of metabolites rather than a single specific pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":1},{"id":"GO:0009820","count":1},{"id":"GO:0019380","count":1},{"id":"GO:0006660","count":1},{"id":"GO:1901601","count":1}]},{"hash":"31128447284384815","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":21,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0042594","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0006207","count":3},{"id":"GO:0006107","count":2}]},{"hash":"1110124773647182234","title":"Developmental transcription and mitotic cell cycle","description":"Top GO terms indicate a core theme of DNA-templated transcription and developmental processes, particularly linkage to the mitotic cell cycle. While additional terms suggest auxiliary roles in stress signaling and other pathways, the dominant pattern centers on developmental gene expression and cell proliferation, justifying the proposed label.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0051260","count":2}]},{"hash":"2034700468367266350","title":"RNA Processing and mRNA Stability Regulation","description":"These proteins cluster around post-transcriptional RNA handling: polyadenylation and tail shortening, splicing, mRNA modification, and regulation of mRNA stability in stress, with some hints of translation reinitiation and regulatory ncRNA\u2013mediated silencing. The common thread is RNA maturation and turnover rather than transcriptional control, pointing to RNA processing and post-transcriptional regulation as the cluster\u2019s theme.","confidence":"High","size":22,"edges":6,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0075525","count":3},{"id":"GO:0006376","count":3},{"id":"GO:0060211","count":3},{"id":"GO:1900363","count":3}]},{"hash":"78329688373924682","title":"Ribosome biogenesis and RNA modification","description":"This cluster is enriched for GO terms related to nuclear RNA processing and ribosome assembly, including mRNA export, ribosomal subunit export, ribosome biogenesis, and RNA modification activities (pseudouridine synthesis in rRNA and tRNA). While a few terms reference other cellular processes (Golgi retention, GTPase regulation, mitotic movement), the dominant signal points to ribosome biogenesis and RNA maturation pathways, justifying this label.","confidence":"High","size":22,"edges":45,"triangles":18,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0000056","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0000455","count":2},{"id":"GO:0031119","count":2}]},{"hash":"507273372352166481","title":"Unknown","description":"The GO terms are scattered across proteolysis, antibiotic biosynthesis, growth, transcription regulation, detoxification, DNA repair, RNA processing, vitamin biosynthesis, and cellulose metabolism, with no clear, shared function uniting the cluster. The lack of edges/triangles and diverse annotations suggest the proteins do not represent a single cohesive pathway, so a specific functional label isn\u2019t supported.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0009636","count":2}]},{"hash":"866756398856475733","title":"ER Stress and ERAD","description":"The top GO terms point to endoplasmic reticulum organization, ER overload response, and ubiquitin-dependent ERAD, suggesting proteins in ER quality control and stress signaling. A few biosynthetic and differentiation terms appear unrelated, implying annotation noise or multifunctionality but with a prominent ER-centered core.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0006983","count":1},{"id":"GO:0006780","count":1}]},{"hash":"968426027283061826","title":"Rho-driven cytoskeleton remodeling and endomembrane trafficking","description":"This cluster is dominated by GO terms tied to Rho GTPase signaling, actin-based protrusion (filopodium) assembly, cell migration, and endomembrane organization/transport, pointing to a cohesive theme of cytoskeletal remodeling coupled with vesicular trafficking. Some scattered terms (e.g., behavioral fear response, cellulose catabolic process) appear unrelated and may reflect annotation noise, but the core signals align with actin dynamics and membrane dynamics.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0046847","count":3},{"id":"GO:0016197","count":3},{"id":"GO:0001662","count":2},{"id":"GO:0030245","count":2}]},{"hash":"1005402068820286075","title":"Synaptic assembly and neuronal signaling","description":"The top GO terms center on neural processes such as presynapse assembly, receptor recycling, visual perception, and neuronal signaling responses, with supporting hints from GTPase regulation and axon guidance. Some terms (e.g., mitotic cell cycle, obsolete histidine metabolism) seem unrelated and may reflect annotation noise, but the dominant themes are neuronal and synaptic. Therefore, the label reflects the main cluster function, with moderate confidence due to some conflicting terms.","confidence":"Medium","size":21,"edges":196,"triangles":1103,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":11},{"id":"GO:0007601","count":11},{"id":"GO:0043547","count":10},{"id":"GO:1905490","count":10},{"id":"GO:0006547","count":10}]},{"hash":"1626317751471923211","title":"Epithelial proliferation and fate signaling","description":"The top GO terms point to transcriptional regulation (DNA-templated transcription), cell-cycle processes (mitotic cycle, DNA replication), and apoptosis, complemented by key growth-regulating pathways (Hippo, Wnt) and keratinocyte differentiation, suggesting a cohesive theme of transcriptional control and signaling that governs epithelial cell proliferation and differentiation.","confidence":"High","size":21,"edges":99,"triangles":152,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0006915","count":9},{"id":"GO:0060044","count":9},{"id":"GO:0030216","count":9},{"id":"GO:0035329","count":9}]},{"hash":"310754995102064131","title":"DNA replication and repair processes","description":"The top GO terms are dominated by DNA replication, DNA repair, recombination, and related genome maintenance activities (with supporting terms like mitotic cell cycle, SOS response, and DNA-templated transcription), indicating a cluster of proteins involved in DNA metabolism and genome maintenance. While a few terms touch development and signaling, the prevailing theme is DNA maintenance and expression.","confidence":"High","size":21,"edges":78,"triangles":164,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":21},{"id":"GO:0048701","count":20},{"id":"GO:0006351","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0006281","count":11}]},{"hash":"1588386766406152468","title":"Neural development and synaptic signaling","description":"The dominant terms point to neural development and synaptic communication, including regulation of synaptic vesicle exocytosis, brain development, and GABAergic synaptic transmission, with ephrin receptor signaling supporting neural patterning. Less central terms such as mitotic cell cycle, cell division, heart contraction, and mitochondrion inheritance may reflect shared components or annotation artifacts. Overall, the cluster appears to group proteins involved in neural development and synaptic signaling.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0010796","count":3}]},{"hash":"784788932670600304","title":"Translation Machinery and Translational Regulation","description":"Most of the top GO terms are centered on various aspects of protein synthesis and translation, including translation itself, initiation, elongation, termination, mitochondrial translation, and selenocysteine incorporation. Additional terms involve mRNA turnover and upregulation of translation, suggesting a cohesive theme around the cellular translation machinery and its regulation. A few terms are less directly connected (e.g., glial cell proliferation, response to antibiotic) and may reflect secondary associations in the data.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0014009","count":5},{"id":"GO:0006413","count":5},{"id":"GO:0000288","count":5},{"id":"GO:0002184","count":5}]},{"hash":"972015782569210552","title":"Ribosome biogenesis and translation","description":"Cluster centers on ribosome production and protein synthesis. The presence of GO terms for ribosome biogenesis, ribosomal small subunit biogenesis, cytoplasmic translation, and tRNA modification points to a core function in assembling and operating the protein synthesis machinery, with secondary signals of growth/division that align with increased biosynthetic activity. Other terms reflect broader regulation rather than changing the main theme.","confidence":"High","size":21,"edges":39,"triangles":25,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:1990126","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0000747","count":1}]},{"hash":"2068943858277409274","title":"Cell wall polysaccharide degradation and defense","description":"This cluster is dominated by GO terms for catabolic breakdown of plant/fungal cell wall components (cellulose, xylan, chitin, and other cell wall macromolecules) and includes defense-related terms (defense response, killing of cells of another organism). These converge on enzymes or pathways involved in breaking down cell wall polysaccharides as a defense strategy. A few biosynthetic terms appear, but the prominent theme is cell wall degradation linked to defense.","confidence":"Medium","size":21,"edges":22,"triangles":2,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0080028","count":2},{"id":"GO:0017186","count":1},{"id":"GO:0031640","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0072722","count":1}]},{"hash":"2070659592397859618","title":"Cell Cycle and Stress\u2013Immune Response","description":"This cluster combines terms tied to cell proliferation (mitotic cell cycle, cell division, morphogenesis) with broad stress and immune-related functions (ubiquitin-dependent proteolysis, protein folding, cadmium response, innate immune response, defense against virus). The proteins likely participate in both cell-cycle regulation and general stress/immune signaling, suggesting a mixed but coherent theme rather than a single pathway. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0045087","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0000413","count":3}]},{"hash":"1778697997473326267","title":"Unknown","description":"These GO terms are highly diverse and include ubiquitination (K48 and K6 linkages), TNF signaling, Wnt receptor catabolism, mitotic spindle orientation checkpoint signaling, X chromosome inactivation, histone methylation, and regulation of intracellular transport of viral material, with several entries marked obsolete. There is no clear, single function tying these proteins together, so a concise label cannot be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":1},{"id":"GO:1902364","count":1},{"id":"GO:0031578","count":1},{"id":"GO:0070512","count":1},{"id":"GO:0085020","count":1}]},{"hash":"1971300840248631701","title":"RNA and protein methylation","description":"The top GO terms are dominated by methylation-related processes, including rRNA and tRNA methylation, RNA guanine-N7 methylation, peptidyl-arginine methylation, and histone methylation, pointing to a cohesive theme of methyltransferase activities modifying RNA and proteins. A few unrelated terms (cobalamin/vitamin E biosynthesis, nodulation) are minor outliers, but do not disrupt the core methylation signal. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0010189","count":1}]},{"hash":"1665461615633000617","title":"Transcription, Cell Cycle and Developmental Regulation","description":"Top GO terms center on DNA-templated transcription and transcriptional regulation, cell division and meiosis, and multiple developmental processes across tissues. While redox/detoxification terms are present, they are not dominant. This suggests a cluster of proteins involved in nuclear gene regulation with links to cell cycle and development, rather than a single cohesive pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":4}]},{"hash":"135785988495910389","title":"Microtubule-driven transport and neuronal development","description":"The top GO terms cluster around microtubule-based movement and intracellular transport (microtubule-dependent transport), vesicle trafficking between ER and Golgi, and cytoskeleton regulation, plus neuron-focused processes like neuron projection morphogenesis and nervous system development. Regulation of GTPase activity further ties to cytoskeleton dynamics. While some terms touch broader developmental contexts (e.g., intestinal epithelial or spermatid development), the dominant signal is cytoskeleton-dependent transport and neuronal development, justifying a cohesive label.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060628","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0008340","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0051493","count":1}]},{"hash":"746856834080258194","title":"Cell cycle and DNA replication machinery","description":"This cluster is dominated by GO terms for DNA replication, centrosome cycle, and regulation of the nuclear cell cycle, such as positive regulation of nuclear cell cycle DNA replication, DNA replication, centrosome cycle, and DNA-templated transcription. While there are also developmental and signaling terms (embryonic cranial skeleton morphogenesis, Wnt signaling, dendritic spine morphogenesis, GM-CSF response) and apoptosis, the strongest, most recurrent themes are cell-cycle control and DNA synthesis, suggesting proteins in this cluster mainly participate in replication and cell division processes with related regulation.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":10},{"id":"GO:0048701","count":10},{"id":"GO:0007098","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0006351","count":9}]},{"hash":"1576502931557197204","title":"Cerebellar neurodevelopment and signaling","description":"This cluster is dominated by cerebellar-specific terms such as cerebellar cortex formation and Bergmann glial cell differentiation, with additional related neural development signals like axon regeneration and insulin signaling. The combination suggests a cohesive theme around cerebellar development and neural signaling pathways, despite some general signaling terms present. ","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":11},{"id":"GO:0035335","count":11},{"id":"GO:0045736","count":10},{"id":"GO:2001275","count":9},{"id":"GO:0060020","count":9}]},{"hash":"86775571517221208","title":"Bacterial membrane transport and secretion","description":"This cluster is dominated by GO terms related to transport across membranes and export/secretion, including antibiotic/drug transport (doxorubicin/daunorubicin), amino acid transport (glycine betaine, branched-chain), lipid translocation (phospholipid, ceramide), and secretion/export systems such as Type I secretion and peptide pheromone export. The convergence on diverse transport and secretion processes, especially bacterial secretion pathways, suggests a cohesive functional theme of membrane transport and secretion.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:1900753","count":3},{"id":"GO:0031460","count":3},{"id":"GO:0045332","count":3},{"id":"GO:0030253","count":3}]},{"hash":"2045569354553842798","title":"Autophagy\u2013Lysosome Degradation","description":"The top GO terms cluster around lysosomal function and autophagy: ubiquitin-dependent proteolysis, autophagy, lysosome organization, secretion of lysosomal enzymes, ER-to-Golgi vesicle transport feeding lysosomes, and N-glycan processing to lysosome. Additional terms on cellular detoxification and TNF signaling may reflect stress-related regulation of autophagy. Overall, the proteins likely participate in the autophagy-lysosome system and lysosome-mediated protein turnover.","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1937281282958859814","title":"Ribosome Biogenesis and Cell Division","description":"The top GO terms cluster around ribosome biogenesis (small and large subunit biogenesis), ribosomal export from the nucleus, tRNA modification, and cytoplasmic translation, indicating a group focused on ribosome assembly and protein synthesis. The inclusion of cell division and septum assembly suggests coupling of ribosome production with cell cycle progression and cytokinesis. Taken together, the theme is ribosome biogenesis and function linked to cell division, hence the chosen label.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0000747","count":3},{"id":"GO:0002181","count":3},{"id":"GO:1903833","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006400","count":3}]},{"hash":"557365596626008360","title":"Ubiquitin-Dependent Immune Signaling","description":"This cluster is dominated by GO terms related to ubiquitination and ubiquitin-mediated protein turnover (ubiquitin-dependent proteolysis, autoubiquitination, various ubiquitin linkages, ERAD) alongside immune signaling processes (adaptive immune response, RIG-I signaling regulation, NF-kappaB activation, JNK pathway regulation). The common theme appears to be ubiquitin-modulated proteostasis coupled with modulation of innate/adaptive immune signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0051865","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0002250","count":7},{"id":"GO:0039536","count":7}]},{"hash":"1915894042094574857","title":"Vesicle trafficking and autophagy","description":"This cluster is dominated by GO terms describing intracellular transport between endomembrane compartments (endosome\u2013lysosome, endosome\u2013Golgi, plasma membrane\u2013endosome) and the cytoplasm-to-vacuole targeting pathway, which together point to vesicle trafficking and autophagy-related processes. A few terms (photosynthesis, NF-kappaB signaling) are more context-specific or incidental, but the strongest signal is endomembrane transport and cargo sorting.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0008333","count":2}]},{"hash":"552718189017785504","title":"Xenobiotic metabolism and lipid mediator biosynthesis","description":"These proteins are enriched for xenobiotic detoxification processes (insecticide and alkaloid catabolic, xenobiotic catabolic) and for lipid mediator pathways (prostaglandin biosynthesis) as well as related retinoid metabolism and environmental response terms. The common thread seems to be processing foreign compounds and generating lipid-based signals, with some broader metabolic connections. However, the cluster appears not highly cohesive (low triangle/edge connectivity), so the label is plausible but with moderate confidence.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":6},{"id":"GO:0017143","count":5},{"id":"GO:0042904","count":5},{"id":"GO:0042738","count":5},{"id":"GO:0010193","count":5}]},{"hash":"1877693770782113253","title":"Developmental transcription and cell cycle regulation","description":"The cluster is enriched for DNA-templated transcription and development-related terms (multicellular organism development, neural tube closure, skeletal system development) along with mitotic cell cycle, suggesting proteins that regulate gene expression during vertebrate development and cell division. Immune/toxin-response terms appear less central to the core function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0042220","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0050830","count":4}]},{"hash":"1071310078165694527","title":"Unknown","description":"The GO terms show a mix of intracellular trafficking (endosome organization, transferrin transport, Golgi retention) and nuclear RNA processing/chromatin assembly, plus some unrelated terms like sensory perception of sound and interferon response, making it hard to identify a single cohesive function for the cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0007032","count":2},{"id":"GO:0033572","count":2},{"id":"GO:0035455","count":2},{"id":"GO:0007605","count":2}]},{"hash":"2228141715859154380","title":"RNA processing and translation initiation","description":"The GO terms are dominated by RNA metabolism and translation-related processes: translation reinitiation, formation of translation preinitiation complex, ribosomal large subunit export from the nucleus, and mRNA export from the nucleus. There is also regulation of alternative mRNA splicing, linking to RNA processing. A few terms touch on cell division and development (follicle cell development, mitotic cohesion), suggesting these proteins may function in RNA/translation control during cell proliferation. Overall, the cluster appears to represent RNA processing and translation machinery with possible cell-cycle or developmental context.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0000381","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0007064","count":3}]},{"hash":"864137689323592605","title":"Unknown","description":"The top GO terms span diverse processes (lung development, meiosis, cell cycle transitions, ER-Golgi trafficking, unfolded protein response, adhesion, DNA replication, GPI anchor biosynthesis, and meiosis-specific cytokinesis), with no single shared function uniting the cluster. This heterogeneity makes a cohesive functional label unlikely, so Unknown with no confidence.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":2},{"id":"GO:0010032","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006986","count":2}]},{"hash":"1134091585147861291","title":"Wnt signaling and differentiation programs","description":"The top GO terms are dominated by Wnt signaling (GO:0016055) and multiple differentiation-related terms across tissues (cerebellar granule cell differentiation, venous endothelial cell differentiation, epithelial cell maturation in the prostate). Additional terms point to regulatory processes such as ubiquitination and responses to hormones or stimuli (vitamin D, salicylic acid, muscle stretch) and apoptosis, suggesting broader developmental regulation. The core theme appears to be signaling-driven differentiation across cell types, anchored by Wnt pathway activity.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":4},{"id":"GO:0021707","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0035994","count":3},{"id":"GO:2000031","count":3}]},{"hash":"2274905732161926347","title":"DNA Repair and Stress Response","description":"The cluster shows enrichment for DNA repair activities (double-strand and single-strand break repair, telomere maintenance regulation) and stress-related responses (xenobiotic stimulus, heat-shock-related chromatin changes, cocaine response), suggesting a role in maintaining genome integrity under stress.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0060236","count":1},{"id":"GO:0006302","count":1},{"id":"GO:0008210","count":1}]},{"hash":"814637149317104484","title":"Gene Expression Regulation (Transcription & Translation)","description":"The top GO terms cluster around regulation and execution of gene expression at both transcriptional (DNA-templated transcription, regulation of transcription) and translational (translation initiation, preinitiation complex formation, IRES-dependent initiation) levels, with phosphorylation-related modulation. Although developmental terms appear, the strongest common theme is control of gene expression across transcription and translation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0075522","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0001825","count":2},{"id":"GO:0006446","count":2}]},{"hash":"389602349853694236","title":"Dopamine and Serotonin Metabolism and Regulation","description":"Top GO terms cluster around dopamine metabolism/catabolism and regulation of serotonin secretion, along with stress-related responses (ethanol and corticosterone). This pattern suggests proteins involved in dopaminergic/serotonergic signaling and metabolic regulation, with redox and metal ion stress context. While a thiamine biosynthetic process term appears, it seems less central to the core theme. Overall, the cluster seems to capture dopamine/serotonin metabolic regulation and associated stress-response pathways.","confidence":"Medium","size":19,"edges":41,"triangles":35,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":9},{"id":"GO:0043046","count":9},{"id":"GO:0014063","count":8},{"id":"GO:0042420","count":8},{"id":"GO:0045471","count":8}]},{"hash":"1335490079975224110","title":"Ribosome biogenesis and translation machinery","description":"The top GO terms cluster around translation, ribosome biogenesis, and RNA processing (translation, formation of translation preinitiation complex, SSU-rRNA maturation, RNA methylation), indicating proteins primarily involved in ribosome assembly and translation initiation, with some ancillary RNA processing roles.","confidence":"High","size":19,"edges":168,"triangles":921,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0036265","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0000462","count":3}]},{"hash":"703854841914890762","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015969","count":1},{"id":"GO:0010139","count":1},{"id":"GO:0006402","count":1},{"id":"GO:0001680","count":1},{"id":"GO:0006808","count":1}]},{"hash":"53698657572096320","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":20,"triangles":0,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007030","count":9},{"id":"GO:1903434","count":8},{"id":"GO:0032707","count":8},{"id":"GO:0071985","count":8},{"id":"GO:0071963","count":8}]},{"hash":"808193288139485169","title":"Methylation enzymes and chromatin regulation","description":"The top terms show a clear enrichment for various methylation activities (rRNA methylation, peptidyl-lysine dimethylation/trimethylation, N-terminal methylation) and rDNA heterochromatin formation, which points to roles in RNA/protein modification and chromatin dynamics. Some related terms about transcription regulation under stress and cell growth align with broader gene-expression control, while an outlier term related to MHC class II biosynthesis likely reflects annotation noise. Overall, these proteins likely cluster around methyltransferase functions that influence chromatin state and RNA/protein modification.","confidence":"Medium","size":19,"edges":158,"triangles":784,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":6},{"id":"GO:0031167","count":5},{"id":"GO:0016049","count":5},{"id":"GO:0018027","count":5},{"id":"GO:0045348","count":5}]},{"hash":"152271834051950935","title":"RNA Processing and Ubiquitin-Dependent Trafficking","description":"This cluster is dominated by RNA biogenesis terms (rRNA processing regulation, tRNA processing regulation, mRNA capping, ribosomal large subunit export from nucleus) and ubiquitin-related processes (ubiquitin-dependent protein catabolic process, endocytosis, and free ubiquitin polymerization) with some autophagy-related localization. The combination suggests a cohesive theme around RNA processing coupled with ubiquitin-mediated protein turnover and trafficking, despite a few outlier terms such as a developmental pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000232","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0006370","count":2},{"id":"GO:0050847","count":2},{"id":"GO:0070086","count":2}]},{"hash":"602428536485492325","title":"Neuronal polarity and vesicle trafficking","description":"The cluster centers on processes related to establishing or maintaining cell polarity and adhesion, GPCR signaling, and especially regulation of synaptic vesicle exocytosis and endocytosis, all of which are key to neuronal communication. The inclusion of substantia nigra development reinforces a neural context, while mitotic spindle assembly is a looser link. Overall, the common theme is neuronal membrane signaling and vesicle trafficking tied to polarity and synaptic function.","confidence":"Medium","size":19,"edges":40,"triangles":9,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":3},{"id":"GO:0031532","count":3},{"id":"GO:0090136","count":3},{"id":"GO:0043547","count":3},{"id":"GO:2000300","count":3}]},{"hash":"1483490411920952093","title":"ERAD and Ubiquitin-Proteasome Quality Control","description":"The cluster is dominated by ubiquitin-related processes (deubiquitination, ubiquitin-dependent ERAD) and maintenance of unfolded proteins in the ER, pointing to protein quality control via the ubiquitin-proteasome system and ER-associated degradation. The presence of translation and cellular stress\u2013response terms supports a broader proteostasis role, with a few peripheral terms possibly reflecting connected regulatory pathways.","confidence":"High","size":18,"edges":152,"triangles":800,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":12},{"id":"GO:0030433","count":10},{"id":"GO:1904378","count":7},{"id":"GO:1900186","count":7},{"id":"GO:0010636","count":7}]},{"hash":"1949235535731509216","title":"Chromatin Silencing and Replication Licensing","description":"This cluster is dominated by terms for heterochromatin formation and transcriptional repression, alongside MCM complex assembly and DNA replication-related steps (including premeiotic replication). The presence of both silencing/heterochromatin terms and replication licensing suggests a cohesive theme around chromatin-based gene regulation coupled with replication initiation, consistent with meiosis and development contexts (e.g., female gamete generation, root meristem regulation). Confidence: Medium","confidence":"","size":18,"edges":34,"triangles":23,"max_degree":13,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030466","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0010082","count":5},{"id":"GO:0043966","count":5},{"id":"GO:0006348","count":4}]},{"hash":"503567097742447291","title":"Nuclear regulation and chromatin dynamics","description":"This cluster combines GO terms related to translation, protein deubiquitination, subtelomeric heterochromatin formation, meiotic chromosome movement, and cell polarity, pointing to intracellular regulation of gene expression and genome organization. The presence of sporulation and muscle development terms likely reflects broader annotation noise rather than a single functional pathway. Overall, the proteins seem linked to regulatory processes governing chromatin state and protein turnover, rather than a discrete, unified function.","confidence":"Medium","size":18,"edges":76,"triangles":138,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009258","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0016579","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0016344","count":3}]},{"hash":"928605751075897010","title":"Cell proliferation and nitric oxide biosynthesis","description":"Proteins in this cluster are enriched for cell division and DNA replication, pointing to a proliferation-related role, while also showing nitric oxide biosynthetic and S-nitrosylation activities, suggesting nitrosative signaling. The presence of xenobiotic catabolic processes further hints at detoxification links, aligning the name with both proliferative processes and nitric oxide\u2013related regulation.","confidence":"Medium","size":18,"edges":152,"triangles":800,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0014806","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0045429","count":1}]},{"hash":"1501681489417498803","title":"Oxidative Stress Response and Lipid Metabolism","description":"The top GO terms point to redox biology and detoxification (cellular oxidant detoxification, cellular response to hydrogen peroxide, cell redox homeostasis) combined with lipid metabolism (triglyceride metabolic process, prostaglandin biosynthetic process). There is also a translation component and a proliferation regulation term, suggesting some breadth beyond redox and lipids, but the core theme appears to be redox balance linked to lipid metabolism.","confidence":"Medium","size":18,"edges":68,"triangles":93,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006641","count":5},{"id":"GO:0070301","count":4},{"id":"GO:0046232","count":4}]},{"hash":"636899871151096318","title":"Somitogenesis and Notch Signaling Regulation","description":"The top terms center on somitogenesis and Notch signaling regulation, suggesting a cluster enriched for developmental signaling involved in somite formation. While there are a few metabolism-related terms, the dominant theme appears to be developmental regulation of signaling pathways rather than core metabolism.","confidence":"Medium","size":18,"edges":25,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001756","count":2},{"id":"GO:0043666","count":1},{"id":"GO:0005977","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0009966","count":1}]},{"hash":"1415163708754697070","title":"Mitochondrial energy metabolism and translation","description":"This cluster shows terms focused on mitochondrial functions: assembly of the ATP synthase complex, regulation of mitochondrial translation, fatty acid beta-oxidation, and iron homeostasis within mitochondria, along with protein stabilization/processing tied to mitochondria. A few terms are peripheral (e.g., cholesterol metabolism, plant root growth), but the core signal points to mitochondrial energy metabolism and protein handling. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033615","count":1},{"id":"GO:0008203","count":1},{"id":"GO:0006879","count":1},{"id":"GO:1902809","count":1},{"id":"GO:0006465","count":1}]},{"hash":"513439859580555480","title":"Amino acid biosynthesis and NADPH regeneration","description":"The Top Terms include multiple amino acid biosynthetic processes (valine, isoleucine, proline, tyrosine) and pantothenate biosynthesis, plus NADPH regeneration, suggesting a cohesive metabolic module centered on amino acid production and redox cofactors. The presence of a mitochondrial complex I assembly term adds an energy/metabolism context, but the core signal is biosynthesis of amino acids and NADPH-related metabolism.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0032981","count":2},{"id":"GO:0015940","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0009099","count":1}]},{"hash":"1563927544745876697","title":"Tight junction assembly and cell polarity regulation","description":"The top GO terms point to bicellular tight junction assembly, actin cytoskeleton organization, and basolateral membrane localization, indicating proteins involved in epithelial/neural cell polarity and junction maintenance. Receptor clustering and opioid signaling regulation suggest coordinated trafficking and signaling at polarized membranes. Ubiquitin-proteasome\u2013related processes imply regulated turnover of polarity/junction components. Together, these reflect a cluster focused on tight junction formation and polarity control.","confidence":"High","size":18,"edges":41,"triangles":39,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070830","count":6},{"id":"GO:0031146","count":5},{"id":"GO:0016579","count":5},{"id":"GO:0031145","count":5},{"id":"GO:0030036","count":5}]},{"hash":"1351341780134488695","title":"DNA Damage Response and Genome Integrity","description":"These proteins are linked to DNA replication, repair, damage response, telomere maintenance, and meiotic recombination resolution, implying a DNA damage response and genome integrity program. Some terms touch on immune system processes (somatic hypermutation, spleen development) that may share DNA modification machinery, but the dominant theme is genome maintenance.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990506","count":1},{"id":"GO:0000736","count":1},{"id":"GO:0008630","count":1},{"id":"GO:0048872","count":1},{"id":"GO:0009650","count":1}]},{"hash":"392225406897033433","title":"ER protein localization and processing","description":"This cluster is enriched for terms about protein localization to ER and endosomes, ER membrane localization, ER-associated degradation and retrograde ER-to-cytosol transport, as well as translation initiation, reflecting a broader theme of protein maturation, trafficking, and quality control within the secretory pathway. Some immune signaling and RNA processing 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:0001731","count":2},{"id":"GO:0033108","count":1},{"id":"GO:0010936","count":1},{"id":"GO:0036010","count":1},{"id":"GO:0030970","count":1}]},{"hash":"1156601702884011360","title":"Unknown","description":"The top GO terms are diverse (mRNA stability regulation, calcium release into cytosol, bile acid secretion, regulation of Rho signaling, pinocytosis, ubiquitination, cell growth, NOD2 signaling regulation, host-mediated viral genome activation, and plant hypersensitive response), with no single cohesive function tying the proteins together, suggesting heterogeneous roles or annotation noise; therefore no concise cluster label can be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":2},{"id":"GO:0051209","count":2},{"id":"GO:0032782","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0048549","count":2}]},{"hash":"467460392080800166","title":"Neural signaling regulators in brain development","description":"The top GO terms point to regulatory signaling activities (positive regulation of GTPase activity, serine/threonine kinase activity, and autophosphorylation) and processes linked to brain development and cell proliferation. Although many terms are broad, the cluster appears to group proteins that modulate signaling pathways and protein interactions during neural development, with potential roles in cell cycle control and assembly of protein complexes. The lack of detected edges suggests this is a loosely connected or multi-context set, but the neural development and signaling theme is coherent.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071456","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071902","count":3},{"id":"GO:0008284","count":3},{"id":"GO:0000278","count":3}]},{"hash":"2290968720207740865","title":"Genome maintenance and transcription regulation","description":"The cluster centers on DNA-templated transcription, Okazaki fragment processing, telomere maintenance, and regulation of apoptotic DNA fragmentation, pointing to genome stability and transcriptional control as the core theme; additional terms like mitochondria-nucleus signaling and ubiquitination can support regulatory networks around genome maintenance.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007018","count":4},{"id":"GO:0000209","count":4},{"id":"GO:0021510","count":4},{"id":"GO:0032212","count":3}]},{"hash":"889546759169620121","title":"Chromatin remodeling and histone modification","description":"This cluster is dominated by GO terms related to chromatin dynamics and histone modification (nucleosome mobilization, chromatin remodeling, histone H3 acetylation) and transcriptional regulation, indicating an epigenetic/Chromatin remodeling theme. A few terms about hormone processing and cholesterol transport appear, likely reflecting either multifunctional proteins or annotation noise, but do not override the central chromatin-focused signal.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":3},{"id":"GO:0010835","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0043044","count":2}]},{"hash":"2226715277212079258","title":"Carbohydrate Transmembrane Transporters","description":"The cluster\u2019s GO terms are dominated by transmembrane transport of sugars (galactose, arabinose, xylose, fructose) and other ions, with a tangential note on ER-to-Golgi vesicle transport, suggesting involvement in membrane transport and sugar uptake rather than a single specialized pathway. This supports a label centered on carbohydrate transport across membranes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060628","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0006817","count":1},{"id":"GO:1990539","count":1},{"id":"GO:0006004","count":1}]},{"hash":"426509304563169376","title":"Nuclear gene expression and genome maintenance","description":"Based on the Top Terms, the cluster is enriched for nuclear processes: regulation of transcription by RNA polymerase II, DNA replication and cell cycle regulation (including centrosome cycle), transcription-coupled DNA repair, RNA processing/maturation, and protein targeting. These collectively point to nuclear gene expression and genome maintenance functions. The presence of an embryonic morphogenesis term may reflect developmental regulation of transcription, but the dominant theme is nuclear/nucleic-acid\u2013related activities; the absence of edges suggests functional similarity without direct interactions in the network. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":6},{"id":"GO:0045944","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0010571","count":5},{"id":"GO:0007098","count":5}]},{"hash":"101982259052360232","title":"Steroid and sphingolipid metabolism","description":"This cluster is enriched for steroid-related and lipid metabolism GO terms, including C21-steroid hormone metabolic process and testosterone biosynthetic process, plus sphingolipid biosynthesis and 3-keto-sphinganine metabolic process. Additional lipid-associated terms (fatty acid elongation, retinal metabolic process, phylloquinone catabolic process) support a cohesive theme around lipid and steroid metabolism. Some antibiotic/drug-response terms appear, but the core signal points to lipid-based biosynthetic pathways and steroidogenesis.","confidence":"High","size":17,"edges":66,"triangles":106,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":13},{"id":"GO:0042376","count":12},{"id":"GO:0031427","count":12},{"id":"GO:0008207","count":12},{"id":"GO:0006666","count":12}]},{"hash":"446912810609770158","title":"Membrane Transporters for Ions and Small Molecules","description":"Top GO terms show transmembrane transport of ions (Na+, K+, phosphate), nutrients (fructose, fucose), vitamins, and xenobiotics, suggesting a group of membrane transporter proteins with broad substrate specificity. This pattern supports a cohesive transport-related function rather than a single pathway, hence the chosen label.","confidence":"High","size":17,"edges":53,"triangles":47,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":13},{"id":"GO:0006855","count":13},{"id":"GO:0071805","count":11},{"id":"GO:0042908","count":11},{"id":"GO:0042891","count":11}]},{"hash":"1855441289813816340","title":"Cell signaling and membrane trafficking","description":"This cluster combines terms tied to cellular signaling and membrane-associated processes: immune and stress signaling (dsRNA response, Fc receptor signaling, STAT phosphorylation), membrane trafficking (caveolin-mediated endocytosis), ion transport and homeostasis (potassium flux), and metabolic regulation (glucose response, glycogen catabolism). While diverse (including reproduction and mitotic attachment terms), the unifying theme is signaling and membrane/cargo handling in cells. ","confidence":"Medium","size":17,"edges":36,"triangles":17,"max_degree":8,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071333","count":5},{"id":"GO:0043330","count":5},{"id":"GO:0048240","count":5},{"id":"GO:0030007","count":5},{"id":"GO:0002774","count":4}]},{"hash":"1297894480121534301","title":"Bacterial energy metabolism: ETC, TCA, MK biosynthesis","description":"The dominant terms point to bacterial respiration and central carbon metabolism, including electron transport chain, tricarboxylic acid cycle, and menaquinone biosynthesis, plus pyruvate decarboxylation to acetyl-CoA. Other terms (DNA transcription/repair, tRNA queuosine biosynthesis, and various catabolic processes) are present but secondary to energy metabolism, suggesting the cluster mainly reflects energy-generating pathways in bacteria.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009234","count":2},{"id":"GO:0022900","count":2},{"id":"GO:0006086","count":2},{"id":"GO:0006099","count":2}]},{"hash":"578785544841939144","title":"Central carbon metabolism","description":"The cluster is dominated by terms for glycolysis, the TCA cycle, gluconeogenesis, and related central carbon metabolic pathways (plus 2-oxoglutarate metabolism and thiamine biosynthesis), pointing to core energy production and carbon flux. A few terms like liver development and starvation response are broader or stress-related annotations, but the overall signal is clear for central metabolism.","confidence":"High","size":17,"edges":66,"triangles":91,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0009098","count":3},{"id":"GO:0006096","count":3}]},{"hash":"1846291971904216377","title":"Bacterial cell envelope and cofactor biosynthesis","description":"The prominent GO terms are biosynthetic processes for lipopolysaccharide (LPS) and O antigen, plus cell wall organization, and biosynthesis of vitamins and cofactors (biotin, thiamine) and heme precursor (protoporphyrinogen IX). This points to a cluster of proteins involved in envelope component synthesis and essential cofactor production in bacteria. A minor term about DNA-templated transcription appears, but the shared theme remains biosynthesis in bacterial metabolism.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0006782","count":4},{"id":"GO:0046835","count":3},{"id":"GO:0009243","count":3}]},{"hash":"1141719046837692365","title":"Oxidative stress response and energy metabolism","description":"This cluster centers on GO terms related to responding to oxidative stress and regulating energy production (oxidative phosphorylation, aerobic respiration) with peroxisomal protein import, pointing to a shared theme of managing oxidative damage while coordinating metabolic activity. Some terms (transcription elongation, centriole elongation, blastocyst development) are broader or developmental, suggesting the proteins may have multiple roles, but the dominant signal is stress response coupled to metabolism.","confidence":"Medium","size":17,"edges":10,"triangles":1,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":7},{"id":"GO:0034599","count":7},{"id":"GO:0070987","count":7},{"id":"GO:1903862","count":7},{"id":"GO:0016562","count":7}]},{"hash":"817206315342368579","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0001193","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0006362","count":2},{"id":"GO:0032968","count":2}]},{"hash":"911151172318939432","title":"Plant photosynthesis and chlorophyll regulation","description":"This cluster is dominated by GO terms related to photosynthesis and chlorophyll biosynthesis regulation (e.g., photosynthesis, negative regulation of chlorophyll biosynthetic process), with additional annotations suggesting plant stress responses (cellular response to cadmium ion) and metabolic/regulatory processes (gluconeogenesis, protein modification). The terms point to a cohesive theme around chloroplast function and the control of photosynthetic and chlorophyll-related pathways, in a plant context. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1903646","count":4},{"id":"GO:0090526","count":4},{"id":"GO:0051291","count":3},{"id":"GO:1902325","count":3},{"id":"GO:0071276","count":3}]},{"hash":"1478437784007957692","title":"Carbohydrate metabolism and sugar biosynthesis","description":"The top GO terms cluster around trehalose biosynthesis, glycogen biosynthesis, and UDP-sugar metabolism (UDP-glucose and UDP-galactose), plus glucose-1-phosphate and related sugar pathways, pointing to a theme of carbohydrate metabolism and polysaccharide synthesis/energy storage. A few terms (somatic hypermutation in immunoglobulin genes and base-excision repair) appear unrelated and may reflect annotation noise, but the dominant pattern supports a carbohydrate metabolism cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005992","count":2},{"id":"GO:0052573","count":2},{"id":"GO:0006011","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0016446","count":2}]},{"hash":"1516779414336088606","title":"Ribosome biogenesis and RNA processing","description":"This cluster shows strong representation of ribosome-related processes: maturation of 5.8S rRNA and SSU rRNA, and ribosomal large subunit biogenesis, indicating a core function in ribosome assembly and RNA maturation. While there are additional signals like mRNA splicing and kinase regulation, they appear ancillary to the dominant ribosome biogenesis theme, justifying this label as representative.","confidence":"High","size":17,"edges":89,"triangles":206,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0051260","count":6},{"id":"GO:0000466","count":6},{"id":"GO:0000398","count":6},{"id":"GO:0043588","count":6}]},{"hash":"469752150401308700","title":"DNA-Templated Transcription Regulation","description":"The top terms are centered on DNA-templated transcription and its regulation, including regulatory ncRNA\u2013mediated silencing, indicating a cluster of transcriptional regulators. While there are auxiliary terms related to innate immune responses and other processes, the dominant signal points to transcriptional control as the shared function of these proteins.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0030199","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1937505396530588531","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:0051301","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2}]},{"hash":"368673057759016714","title":"Ribosome Biogenesis and RNA Methylation","description":"The cluster's top terms are dominated by ribosome-related processes (ribosome biogenesis, cytosolic ribosome assembly) and RNA modification (rRNA base methylation, tRNA wobble base cytosine methylation), suggesting these proteins co-function in ribosome assembly and translation regulation. Other terms like heart development, fat cell differentiation, and stress responses occur at low counts and likely reflect annotation noise or pleiotropy rather than core cluster function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0045444","count":2}]},{"hash":"1592327776502468989","title":"Unknown","description":"The proteins show a highly diverse set of GO terms (mRNA processing, calcium signaling, various differentiation and stress responses, signaling pathways, ubiquitination) with no clear shared function or pathway, and there are no edges among them, making a cohesive cluster label unlikely.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0051209","count":3},{"id":"GO:0021707","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0035994","count":2}]},{"hash":"1959788267985718413","title":"RNA Processing and RNA Methylation","description":"The top GO terms cluster around RNA metabolism: mRNA splicing, translation initiation mechanisms on RNA, and RNA base methylation (rRNA), plus related methylation processes, suggesting a cohesive theme of RNA processing and modification. Some terms are peripheral or obsolete, but the dominant signal points to RNA-centric maturation and regulation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0070475","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1857740428195252754","title":"Placental Development with Immune and Metabolic Signaling","description":"The GO terms point to placental formation and development (maternal placenta development, labyrinthine layer blood vessel development, embryonic placenta\u2013related differentiation) while also highlighting metabolism and insulin signaling (insulin receptor signaling, response to insulin, hyaluronan metabolism) and immune differentiation (B cell affinity maturation, NK T cell differentiation, GM-CSF response, JNK cascade regulation). Together, these indicate a placenta-centric cluster with intertwined immune and metabolic pathways.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002344","count":2},{"id":"GO:0001893","count":2},{"id":"GO:0030212","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0060716","count":2}]},{"hash":"1664427766547714086","title":"Ubiquitin-Proteasome Regulation in Stress and Immunity","description":"This cluster centers on ubiquitin-mediated proteolysis, with deubiquitination and SCF-dependent proteasomal degradation, and it also shows links to stress and immune signaling (cadmium, salt, zinc, viral processes, and inflammatory regulation). Together, these terms imply proteins that coordinate protein turnover with defense and stress responses.","confidence":"High","size":16,"edges":46,"triangles":44,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":4},{"id":"GO:0010972","count":3},{"id":"GO:0010363","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0046686","count":3}]},{"hash":"668067399875163745","title":"Amino acid biosynthesis and nitrogen metabolism","description":"This cluster is dominated by GO terms for several amino acid biosynthesis pathways (tyrosine, phenylalanine, serine, homoserine) and a term related to nitrogen utilization, with additional related processes like serotonin biosynthesis and amino acid catabolism. The common thread appears to be amino acid production and nitrogen metabolism, with a few outliers (cell cycle, obsolete terms) likely noise. Confidence: Medium","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0019877","count":1},{"id":"GO:0006571","count":1}]},{"hash":"1978413938163031587","title":"Xenobiotic and oxidative stress response with DNA repair","description":"The cluster is enriched for GO terms related to responding to xenobiotic stimuli, oxidative stress (cell redox homeostasis and hydrogen peroxide response), and DNA repair (base-excision repair). This suggests a common functional theme around defense against toxic/oxidative damage and repairing DNA lesions, with additional signals of broader stress adaptation (mRNA stability regulation). ","confidence":"High","size":16,"edges":35,"triangles":12,"max_degree":7,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042493","count":6},{"id":"GO:0007568","count":6},{"id":"GO:0006284","count":6},{"id":"GO:0090502","count":5},{"id":"GO:2000327","count":5}]},{"hash":"1953394621902306165","title":"Mitochondrial Dynamics and Metabolism","description":"This cluster is dominated by GO terms tied to mitochondria\u2014membrane fission, membrane potential regulation, iron import, and genome maintenance\u2014indicating a cohesive theme around mitochondrial structure and energy metabolism; a few terms (e.g., liver regeneration, thiosulfate transport) may reflect ancillary metabolic or stress-related connections but do not negate the overall mitochondrial focus.","confidence":"High","size":16,"edges":15,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":9},{"id":"GO:0090149","count":9},{"id":"GO:0070542","count":8},{"id":"GO:0051881","count":7},{"id":"GO:0097421","count":7}]},{"hash":"971816664817700373","title":"RNA Processing and Translation Control","description":"This cluster centers on RNA processing and ribosome-related regulation, with terms for mRNA splicing, poly(A) tail regulation, processome assembly, and translation reinitiation, plus broader RNA-mediated gene silencing and regulatory processes. The combination suggests a cohesive theme of RNA metabolism and control of translation, rather than a single, narrow function.","confidence":"Medium","size":16,"edges":15,"triangles":2,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042981","count":1},{"id":"GO:0016579","count":1},{"id":"GO:0043392","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006376","count":1}]},{"hash":"1799137727702785806","title":"RNA processing and translation initiation control","description":"Top GO terms converge on translation initiation and reinitiation (preinitiation complex formation, translational initiation, IRES-dependent initiation, viral reinitiation) and on RNA processing via the spliceosome (mRNA splicing) plus ncRNA-mediated gene silencing and polyadenylation regulation. The shared theme is RNA metabolism with translational control, suggesting this cluster groups proteins involved in RNA processing and initiation regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0006446","count":4}]},{"hash":"2031584799988700170","title":"Meiosis-linked DNA repair and germ cell development","description":"The top terms cluster around double-strand break repair via homologous recombination, meiotic recombination, synaptonemal complex assembly, and germline development (spermatid development, oocyte fate). The gamma radiation response underscores a DNA damage response, consistent with meiotic DSB processing. Protein homooligomerization supports assembly of multi-subunit meiotic complexes, reinforcing a cohesive meiotic/germ-cell function.","confidence":"High","size":16,"edges":61,"triangles":83,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071480","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0010569","count":3},{"id":"GO:1990414","count":3},{"id":"GO:0007286","count":3}]},{"hash":"331153704862701187","title":"Small-molecule metabolism and detoxification","description":"The top GO terms cluster around catabolic processes for diverse small molecules (lipids, uracil, phenylpropanoids, alkaloids) and detoxification/response to toxins, with additional regulatory or biosynthetic roles in signaling lipids (strigolactone, endocannabinoid pathway). This indicates a cohesive theme of metabolite turnover and detoxification rather than a single narrow function.","confidence":"Medium","size":16,"edges":15,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":6},{"id":"GO:0055114","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0006212","count":4}]},{"hash":"1173486211098585586","title":"Developmental Transcription Regulation","description":"The top GO terms emphasize DNA-templated transcription and RNA polymerase II regulation, including preinitiation complex assembly, pointing to transcriptional control as a core function. The presence of diverse developmental terms (osteoblast development, neuroblast proliferation regulation, neuron migration, synapse assembly, seminiferous tubule development, surfactant homeostasis) suggests this cluster reflects transcriptional regulation across developmental contexts rather than a single pathway. The lack of edges supports a broad, common function rather than tight interaction, aligning with a developmental transcription theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006357","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0007406","count":1},{"id":"GO:0032147","count":1}]},{"hash":"1073626823284316365","title":"Lipid Metabolism and Transport","description":"GO terms show a strong emphasis on lipid processing and movement (phosphatidylcholine, ether lipids, N-acylphosphatidylethanolamine), vitamin A metabolism, and adipose tissue regulation, suggesting the proteins in this cluster function in lipid metabolism and lipid transport pathways. A few outlier terms (ascospore assembly, fibroblast migration, lead ion response) are present but do not dominate the theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031321","count":2},{"id":"GO:0006653","count":1},{"id":"GO:0042572","count":1},{"id":"GO:0070292","count":1},{"id":"GO:1904177","count":1}]},{"hash":"789827664572016247","title":"Ubiquitin-Dependent Proteostasis and Peroxisome Import","description":"The terms cluster around ubiquitin-mediated protein turnover and quality control (autoubiquitination, ubiquitin-dependent ERAD and proteasomal degradation, diverse ubiquitin linkages) with an additional peroxisomal import term tied to the PEX5 ubiquitination cycle. This points to a cohesive theme of ubiquitin-driven proteostasis, including peroxisomal protein handling, despite some less-specific or obsolete terms present. ","confidence":"High","size":16,"edges":7,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0085020","count":8},{"id":"GO:0070936","count":8}]},{"hash":"1813772928256708673","title":"Ubiquitin-Dependent Protein Degradation","description":"Most GO terms in this cluster point to ubiquitin-mediated turnover, including ubiquitin-dependent ERAD pathway, ubiquitin-dependent protein catabolic process, protein ubiquitination, and autoubiquitination. This indicates a core theme of tagging substrates with ubiquitin for degradation via ERAD and related proteasomal pathways. A few terms (Wnt receptor catabolic process, dosage compensation-related inactivation) are less directly tied but may reflect regulatory degradation roles; overall, the cluster centers on ubiquitin-driven protein turnover.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0038018","count":5},{"id":"GO:0060816","count":5},{"id":"GO:0070936","count":5},{"id":"GO:1900095","count":5}]},{"hash":"1840925769719038277","title":"Cell Wall Synthesis and Actin Organization","description":"This cluster centers on GO terms for peptidoglycan biosynthesis and cell wall organization, indicating roles in cell envelope construction and shape. Supporting terms about actin cortical patches and intracellular transport suggest cytoskeletal organization linked to maintaining cell morphology, with a secondary connection to trafficking. Some terms (e.g., neuron projection development) are less related, but the dominant themes point to cell wall biogenesis and cytoskeletal regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009252","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0070178","count":1},{"id":"GO:0030632","count":1}]},{"hash":"904952547562823441","title":"Ubiquitin-Dependent Autophagy and Endocytosis","description":"The most represented GO terms cluster around vesicle trafficking tied to autophagy and ubiquitin-dependent endocytosis, including substrate localization to autophagosomes and engulfment by autophagosomes. While there are other regulatory terms (nuclear export of ribosomal subunits and tRNA processing) in the mix, the autophagy/endocytosis-related processes appear to bind these proteins into a coherent functional theme\u2014vesicle turnover and protein degradation pathways. This suggests the cluster\u2019s function centers on autophagy-associated trafficking and ubiquitin-mediated turnover rather than a single metabolic pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070086","count":3},{"id":"GO:2000203","count":3},{"id":"GO:2000235","count":3},{"id":"GO:0061753","count":3},{"id":"GO:0061736","count":3}]},{"hash":"658064349560723975","title":"Unknown","description":"The terms cover multiple, unrelated processes (development, glycosylation, respiration, transport, signaling, and lipid metabolism) with no common function tying the proteins together, and there are no interactions or edges in this cluster. Therefore there isn't a coherent theme to label beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048366","count":1},{"id":"GO:0060117","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0009060","count":1}]},{"hash":"1411944817714159239","title":"Broad developmental regulation and differentiation","description":"Most terms point to development and tissue-specific differentiation (cerebellar granule cell, venous endothelial, epithelial prostate maturation) and related signaling and regulatory processes (vitamin D response, salicylic acid signaling, cell cycle, ubiquitination). The terms are from diverse tissues and do not converge on a single pathway, suggesting a broad, non-specific theme of developmental regulation rather than a defined function. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0021707","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0035994","count":3},{"id":"GO:2000031","count":3}]},{"hash":"997189819697187506","title":"Gene Regulation and DNA Metabolism","description":"The terms cluster around gene regulation and DNA metabolism: transcription initiation, DNA replication/Okazaki fragment processing, and chromatin modification, with signaling pathways (growth hormone, SREBP) and mitochondria-nucleus signaling that modulate gene expression. A vesicle trafficking term appears but seems peripheral.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":3},{"id":"GO:0060416","count":3},{"id":"GO:0031930","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0032933","count":2}]},{"hash":"1913357999342496925","title":"Neural and glial development with axonogenesis","description":"This cluster centers on neural and glial differentiation (Bergmann glial differentiation, Schwann cell development), plus axonogenesis and broader development signals (angiogenesis, insulin signaling), indicating a cohesive neural/glial developmental program.","confidence":"High","size":15,"edges":78,"triangles":200,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":14},{"id":"GO:0034501","count":14},{"id":"GO:0043065","count":12},{"id":"GO:0007275","count":12},{"id":"GO:0001525","count":12}]},{"hash":"1508935307845868080","title":"Unknown","description":"Top GO terms span diverse biosynthetic and transport processes (ubiquinone biosynthesis, tRNA wobble uridine modification, glycerol-3-phosphate metabolism, pantothenate biosynthesis, peptidoglycan and polysaccharide biosynthesis) plus xenobiotic transport and cytokinin catabolism; there is no single cohesive function linking the majority of terms, so a clear, representative label is not discernible.","confidence":"","size":15,"edges":30,"triangles":9,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0006855","count":1},{"id":"GO:0046167","count":1},{"id":"GO:0000271","count":1}]},{"hash":"275752732039708525","title":"Mitochondrial respiration and vacuolar transport","description":"The top GO terms point to mitochondrial electron transport and ATP synthesis (GO:0006120, GO:0034553, GO:0042777), indicating a respiration-related cluster. Additional signals for vacuolar processes (GO:0007033, GO:0006623, GO:0007035) and proton or ion transport (GO:0015991, GO:0006814, GO:0006878) suggest a link to vacuolar trafficking/maintenance and metal homeostasis. Together, this implies proteins involved in mitochondrial energy production with supporting roles in vacuolar function or targeting, a coherent yeast-like theme of organelle coordination.","confidence":"High","size":15,"edges":15,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":3},{"id":"GO:0034553","count":3},{"id":"GO:0042777","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0006623","count":1}]},{"hash":"602922164115730094","title":"Bone remodeling and ECM catabolism","description":"Based on enrichment for collagen catabolic process, bone resorption, intramembranous ossification, and broader proteolysis-associated terms (bradykinin/neuropeptide catabolic), this cluster appears centered on tissue remodeling via extracellular matrix degradation and bone development/remodeling. While some lung morphogenesis terms hint at remodeling in development, the dominant signal is bone/ECM remodeling. ","confidence":"High","size":15,"edges":59,"triangles":115,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":6},{"id":"GO:0060441","count":4},{"id":"GO:0001957","count":4},{"id":"GO:0050790","count":4},{"id":"GO:0060448","count":4}]},{"hash":"470364766550656916","title":"Ribosome biogenesis and translation","description":"The cluster is enriched for terms related to ribosomal assembly and protein synthesis: translation, cytoplasmic translation, ribosome biogenesis, and maturation of rRNA (both SSU and LSU). While a few outlier terms touch on RNA processing or other pathways, the strongest and most consistent signal ties to ribosome formation and the machinery of protein synthesis.","confidence":"High","size":15,"edges":63,"triangles":127,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0033119","count":2},{"id":"GO:0006378","count":2}]},{"hash":"666421598997381929","title":"Protein quality control and Golgi trafficking","description":"This cluster centers on protein folding and quality control (chaperone-dependent refolding, response to misfolded protein), proteasome assembly, and vesicle transport/retention in the Golgi, suggesting a cohesive role in maintaining protein homeostasis in the secretory pathway. Some terms like DNA replication or transformation competence appear less connected and may be noise. Medium","confidence":"","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0070682","count":4},{"id":"GO:0045053","count":4},{"id":"GO:0034214","count":3}]},{"hash":"563545120303408960","title":"Translation and mRNA quality control","description":"The set is dominated by translation-related processes (initiation, translation, termination) along with mRNA surveillance pathways (no-go decay, nonstop decay) and rRNA maturation, implying a module centered on protein synthesis with RNA quality control. Additional terms about cytoplasm-to-vacuole targeting and Golgi localization may reflect broader aspects of protein trafficking or turnover linked to these processes, but the core signal is translation machinery and RNA quality control.","confidence":"High","size":15,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0043547","count":2}]},{"hash":"985475748478521659","title":"RNA and protein methylation enzymes","description":"The top GO terms are dominated by methylation-related processes: N-terminal peptidyl-glycine methylation, peptidyl-lysine methylation (trimethylation and dimethylation), rRNA methylation, and tRNA wobble uridine modification. This points to a cluster enriched for methyltransferases that modify RNA and proteins, with a possible tie to chromatin regulation and cellular stress shown by the rDNA heterochromatin formation and apoptotic process terms. Overall, the core theme is RNA and protein methylation machinery. ","confidence":"Medium","size":15,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0009229","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0045454","count":2}]},{"hash":"999277645420840203","title":"Mitochondrial transport, energy metabolism, and apoptosis","description":"This cluster centers on mitochondrial function: apoptotic mitochondrial changes, regulation of membrane potential, mitochondrial iron import, thiosulfate and NAD transport, and the malate-aspartate shuttle, all pointing to mitochondrial metabolism and metabolite exchange. The presence of liver regeneration and necroptosis regulation terms suggests stress-response and cell-survival pathways linked to mitochondria. Overall, the proteins likely participate in mitochondrial energy metabolism and apoptosis regulation.","confidence":"High","size":15,"edges":19,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":7},{"id":"GO:0051881","count":6},{"id":"GO:0097421","count":6},{"id":"GO:0097274","count":6},{"id":"GO:0060546","count":6}]},{"hash":"882641765086015671","title":"Mitotic Chromatin Methylation","description":"The cluster\u2019s top terms center on mitosis (mitotic cell cycle, cell division, spindle checkpoint regulation) and histone methylation (H3-K4, K27, K79) with DNA-templated transcription, indicating proteins involved in coordinating chromatin state with cell division and transcription. Some older GO terms (e.g., ubiquitin-dependent ERAD, ER-Golgi transport) are less central and likely historical annotations, but the core theme is epigenetic regulation during mitosis. Overall, the proteins appear functionally cohesive around mitotic chromatin modification.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0090231","count":2},{"id":"GO:0051568","count":2}]},{"hash":"651236214080277082","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0071805","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0006189","count":3},{"id":"GO:0009089","count":2}]},{"hash":"729117283053133296","title":"Diverse membrane substrate transporters","description":"The top GO terms show transmembrane transport for a wide variety of substrates (arabinose, nitrite, nitrate, potassium, sialic acid, phosphate, vitamins, xenobiotics, etc.), indicating a cluster of membrane transporter proteins with broad substrate specificity. While there is a metabolism term (fucose), the prevalence of multiple transport-related terms supports a transporter-focused theme.","confidence":"Medium","size":15,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0006855","count":2}]},{"hash":"961000838504873878","title":"Membrane signaling and endocytosis","description":"The top GO terms cluster around membrane-associated signaling and trafficking: Fc receptor inhibitory signaling, caveolin-mediated endocytosis, response to epidermal growth factor, and regulation of integrin-mediated adhesion, complemented by tyrosine phosphorylation of STAT. These collectively point to receptor-driven signaling at the cell surface and associated endocytic processes, with other terms (metabolic regulation, apoptosis, ovulation) likely reflecting broader pathway cross-talk. Overall, the cluster seems best described by membrane signaling and endocytosis, with some peripheral processes included.","confidence":"Medium","size":14,"edges":42,"triangles":17,"max_degree":8,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0002774","count":6},{"id":"GO:0006813","count":6},{"id":"GO:0072584","count":6},{"id":"GO:0051316","count":6},{"id":"GO:0042517","count":6}]},{"hash":"2124114078823036372","title":"Fungal ER stress response and cell wall biosynthesis","description":"This cluster shows strong signals for SRP-dependent cotranslational targeting to membranes (secretory pathway), ER stress\u2013related apoptotic regulation, and fungal-type beta-glucan biosynthesis, pointing to a fungal growth program centered on the secretory pathway and cell wall biogenesis. DNA replication and morphogenesis are present but less defining for the cluster\u2019s core function. ","confidence":"Medium","size":14,"edges":83,"triangles":281,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0090084","count":7},{"id":"GO:1903382","count":7},{"id":"GO:0016226","count":7}]},{"hash":"2095094643261674124","title":"Unknown","description":"The GO terms span disparate areas (photoreceptor localization, cell cycle regulation, protein heterooligomerization, chlorophyll biosynthesis, dsRNA response, chaperone folding, cadmium response, protein modification regulation, innate immunity, histone methylation) with no single cohesive biological theme. This suggests the cluster is functionally heterogeneous or an artifact of the network data, rather than representing a specific, unified biological module.","confidence":"","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:1903546","count":2},{"id":"GO:0045842","count":2},{"id":"GO:0051291","count":2},{"id":"GO:1902325","count":2},{"id":"GO:0071360","count":2}]},{"hash":"1214644926409740047","title":"Embryonic Development and Neural Patterning","description":"Top terms cluster around embryonic development and tissue patterning: glial cell fate determination, hair placode formation, cranial skeletal system development, and zona limitans intrathalamica formation point to neural and craniofacial lineage specification. Lung induction further supports an overall developmental theme. The presence of intermediate filament bundle assembly and regulation of cell cycle/apoptotic processes suggests coordinated growth and differentiation rather than a single signaling pathway, while a proton transmembrane transport term appears ancillary. Overall, the cluster seems to reflect developmental patterning and lineage specification.","confidence":"Medium","size":14,"edges":87,"triangles":320,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0007050","count":8},{"id":"GO:0015991","count":7},{"id":"GO:0060492","count":6},{"id":"GO:0043065","count":6},{"id":"GO:0060789","count":6}]},{"hash":"1843838393487563709","title":"Translation Initiation and RNA Processing","description":"The top GO terms are dominated by translation initiation, including viral IRES-dependent and reinitiation, plus formation of the preinitiation complex and regulation of initiation. Additional terms point to RNA processing tasks such as splicing and polyadenylation, along with mRNA surveillance and cellular signaling (EGF response) that can influence translation. Taken together, these proteins likely function around initiating translation and related RNA metabolism activities, with both viral and cellular relevance.","confidence":"Medium","size":14,"edges":20,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2}]},{"hash":"1059750725675564416","title":"RNA Processing and Translation Regulation","description":"This cluster centers on RNA metabolism and translation control: it includes mRNA splicing (splice site recognition), assembly of small-subunit processomes, mRNA modification and poly(A) tail regulation, mRNA stability under stress, and translation initiation/reinitiation (preinitiation complex formation and reinitiation), plus regulatory ncRNA\u2013mediated gene silencing. This cohesion suggests functional grouping around post-transcriptional gene regulation at both RNA processing and translation levels.","confidence":"High","size":14,"edges":20,"triangles":9,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0075525","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0060211","count":2},{"id":"GO:1900363","count":2}]},{"hash":"506642262583085418","title":"Fatty acid oxidation and carnitine biosynthesis","description":"This cluster is enriched for lipid metabolism and energy pathways, highlighted by fatty acid beta-oxidation (GO:0033539) and carnitine biosynthetic process (GO:0045329), pointing to mitochondrial fatty acid catabolism. Related terms such as regulation of gluconeogenesis and response to starvation support a broader energy-homeostasis theme. Some terms are obsolete, introducing noise, but the core signal remains metabolic energy production.","confidence":"Medium","size":14,"edges":16,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042594","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045730","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0009791","count":1}]},{"hash":"629134610154305358","title":"Translation and Splicing Machinery","description":"This cluster is dominated by translation-related GO terms (translation, translational initiation, maintenance of translational fidelity, ribosome disassembly), suggesting a core theme of protein synthesis. A spliceosome-related term also appears, indicating RNA processing involvement alongside translation. The presence of some cell-cycle terms likely reflects broader cellular context, but the main signal points to components of translation and RNA splicing. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2}]},{"hash":"2076960495409761213","title":"Vesicle trafficking and organelle homeostasis","description":"The dominant signals are SNARE complex assembly, endosome-to-lysosome transport, and Golgi maintenance, indicating vesicle trafficking and organelle homeostasis as the cluster's theme; other terms are peripheral stress or developmental processes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090207","count":1},{"id":"GO:0098779","count":1},{"id":"GO:0043552","count":1},{"id":"GO:0097680","count":1},{"id":"GO:0051684","count":1}]},{"hash":"1421828043849403886","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0034414","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0030420","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1833137465481297025","title":"Peroxisome Biogenesis and Fission","description":"Most of the top GO terms center on peroxisomes: inheritance, ER-dependent organization, membrane biogenesis, and fission, suggesting the proteins cluster around peroxisome assembly and division. Additional terms like protein exit from ER and protein stabilization relate to broader protein handling but can accompany peroxisome-related processes. A few terms (viral process, nucleotide-excision repair, obsolete urea homeostasis) appear less connected and may reflect annotation noise or multifunctionality.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0070911","count":2},{"id":"GO:0032527","count":1},{"id":"GO:0045033","count":1}]},{"hash":"199225340169927721","title":"Mitochondrial protein import and respiration","description":"The top GO terms point to mitochondrial-specific processes: import into the mitochondrial matrix and inner membrane, insertion into the inner membrane, and electron transport/respiration including complex III assembly. While a chloroplast import term appears, the strongest signal is mitochondrial targeting and respiratory chain-related activities, suggesting this cluster centers on mitochondrial protein import and respiration/assembly machinery.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":4},{"id":"GO:0030150","count":3},{"id":"GO:0000002","count":3},{"id":"GO:0032094","count":3},{"id":"GO:0045037","count":3}]},{"hash":"1438132393365600066","title":"Redox homeostasis and mitochondrial metabolism","description":"The top GO terms cluster around redox control and mitochondrial function (cellular oxidant detoxification, redox homeostasis, regulation of mitochondrial membrane potential), suggesting a shared role in maintaining cellular redox balance and mitochondrial energy status. Additional terms point to aromatic amino acid metabolism and starvation response, reinforcing a broader metabolic-regulatory theme; a few outliers (platelet aggregation, germ cell proliferation) may reflect broader regulatory networks but do not override the core redox/metabolic signal.","confidence":"Medium","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":10},{"id":"GO:0045454","count":8},{"id":"GO:0051881","count":5},{"id":"GO:0060316","count":5},{"id":"GO:0009072","count":5}]},{"hash":"406178845508890149","title":"ER proteostasis and redox homeostasis","description":"This cluster centers on protein folding in the endoplasmic reticulum and responses to oxidative stress, including ER stress, unfolded protein response, and detoxification of reactive oxygen species. The dominant GO terms point to maintaining ER proteostasis under redox challenges, with several terms explicitly noting redox homeostasis and hydrogen peroxide response. Although a few terms are listed as obsolete, the core theme remains consistent. ","confidence":"High","size":13,"edges":33,"triangles":34,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0098869","count":6},{"id":"GO:0034975","count":6},{"id":"GO:0019430","count":5}]},{"hash":"1097793884650646702","title":"Mitochondrial Energy Metabolism and Transport","description":"The cluster centers on mitochondrial processes: regulation of membrane potential, NAD and malate-aspartate shuttles, iron import into mitochondria, and ATP transport, indicating a cohesive theme of mitochondrial energy production and metabolite trafficking. Peripheral terms like liver regeneration and thiosulfate transport may reflect broader metabolic roles but do not override the mitochondrial focus.","confidence":"High","size":13,"edges":33,"triangles":20,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":9},{"id":"GO:0097421","count":9},{"id":"GO:0097274","count":9},{"id":"GO:0060546","count":9},{"id":"GO:0015709","count":9}]},{"hash":"842429158077836672","title":"Neuronal development and ER-Golgi vesicle trafficking","description":"The top terms emphasize brain development and growth together with ER-Golgi trafficking processes (COPII budding and retrograde Golgi-ER transport) and regulation of synaptic vesicle exocytosis, suggesting a cohesive theme of neuronal development guided by secretory vesicle trafficking; the mitotic terms may reflect proliferating neural progenitors rather than mature neurons.","confidence":"High","size":13,"edges":35,"triangles":28,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0006888","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0008283","count":3},{"id":"GO:2000300","count":3}]},{"hash":"316665628675815644","title":"Unknown","description":"The GO terms span diverse biological themes (DNA-templated transcription, multiple developmental processes across tissues, lactation, liver regeneration, meiosis, chromatin modification, and immune-related viral suppression) with no single unifying function linking the cluster. Therefore a coherent, specific label cannot be assigned.","confidence":"","size":13,"edges":17,"triangles":5,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0060749","count":7},{"id":"GO:0033327","count":7},{"id":"GO:0097421","count":7},{"id":"GO:0044828","count":7}]},{"hash":"1311858770155410943","title":"RNA and protein methylation","description":"This cluster is dominated by methylation-related GO terms: RNA guanine-N7 methylation, mRNA capping, rRNA and tRNA methylation, and protein arginine/histone methylation, suggesting a common theme of methylation-modification activities. A few unrelated terms (cobalamin and vitamin E biosynthesis, nodulation) are likely noise, but the overarching pattern supports a methylation-centric interpretation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0030488","count":2}]},{"hash":"211400985421628296","title":"Lysosome-targeting and TORC1 signaling proteins","description":"The top GO terms cluster around lysosome-related trafficking and signaling: protein targeting to lysosome, Golgi to lysosome transport, intracellular protein transport, and TORC1 signaling. These terms imply a shared involvement in lysosome biology and nutrient-sensing pathways. Other terms (Pol III transcription regulation, lamellipodium assembly, synaptonemal complex assembly, antigen processing via MHC Ib) are more disparate and may reflect annotation noise or multifunctionality. Overall, the strongest signal points to lysosome-directed protein trafficking and TORC1 pathway interactions, suggesting a cohesive functional group centered on lysosomal targeting and related signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045945","count":2},{"id":"GO:0006622","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0090160","count":2},{"id":"GO:0010592","count":2}]},{"hash":"569342923956039998","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018023","count":1},{"id":"GO:0046944","count":1},{"id":"GO:0045454","count":1},{"id":"GO:1902376","count":1},{"id":"GO:0036129","count":1}]},{"hash":"187815332895495106","title":"Membrane signaling and endocytic trafficking","description":"Based on the top GO terms, most proteins appear involved in signaling at the plasma membrane and in endocytic/adhesive processes (Fc receptor inhibitory signaling, caveolin-mediated endocytosis, EGF response, regulation of integrin-mediated adhesion, and tyrosine phosphorylation of STAT). Potassium ion transport and reproduction-related terms suggest additional membrane or cytoskeletal roles, but the strongest common thread is membrane-associated signaling and trafficking.","confidence":"Medium","size":12,"edges":46,"triangles":71,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0002774","count":11},{"id":"GO:0006813","count":11},{"id":"GO:0072584","count":11},{"id":"GO:0051316","count":11},{"id":"GO:0042517","count":11}]},{"hash":"932405593891911854","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":17,"triangles":6,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0009408","count":4},{"id":"GO:0006458","count":4},{"id":"GO:0006452","count":4},{"id":"GO:0070843","count":4}]},{"hash":"387714848716119227","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000494","count":1},{"id":"GO:1990258","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0008033","count":1}]},{"hash":"2196714322032026003","title":"Cell cycle progression and kinetochore localization","description":"Based on the Top Terms, the cluster is dominated by cell cycle and chromosome segregation processes (DNA replication, G1/S transition, meiotic cell cycle, kinetochore localization). Some terms point to neural, hormonal, or microbial pathways that may reflect annotation noise or multifunctional proteins, but the strongest shared theme is cell cycle progression and kinetochore-related localization.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0014044","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0051321","count":5},{"id":"GO:0034501","count":5},{"id":"GO:0060079","count":5}]},{"hash":"391795983060309409","title":"Xenobiotic Detoxification","description":"This cluster is enriched for GO terms tied to processing and breaking down xenobiotics and environmental chemicals (insecticides, alkaloids, ozone). The presence of xenobiotic catabolic process, insecticide metabolic process, alkaloid catabolic process, and related response terms supports a detox/metabolic function. A few terms (retinoic acid biosynthesis, methylation) reflect broader metabolism but do not negate the detox theme. Therefore, a succinct label \"Xenobiotic Detoxification\" captures the main function of this cluster.","confidence":"Medium","size":12,"edges":14,"triangles":4,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":5},{"id":"GO:0042904","count":5},{"id":"GO:0042738","count":5},{"id":"GO:0010193","count":5},{"id":"GO:0032259","count":5}]},{"hash":"1819143865669176107","title":"Unknown","description":"The top GO terms cover a broad mix of DNA replication/recombination, various signaling pathways (endocannabinoid, cAMP, calcineurin-NFAT), development (Schwann cell and skeletal muscle), and metabolism (lipid and lipid A biosynthesis). There is no single cohesive function or pathway that ties these terms together, and the lack of edges suggests little direct functional coupling among the proteins. Therefore, no specific cohesive label can be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:2000124","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0071320","count":3}]},{"hash":"1725467006796967776","title":"Golgi-ER vesicle trafficking and protein transport","description":"The cluster is dominated by GO terms related to vesicle fusion and transport between the Golgi and the ER/ERGIC, Golgi ribbon formation, and general protein transport, indicating a cohesive theme of Golgi- and ER-associated trafficking; other terms like TNF signaling and oxidative detoxification appear less central to the core function of this cluster.","confidence":"High","size":12,"edges":18,"triangles":7,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0090161","count":1},{"id":"GO:1990668","count":1},{"id":"GO:0034197","count":1}]},{"hash":"419498330768741255","title":"Unknown","description":"The top GO terms cover diverse, largely unrelated processes (cell division components like spindle assembly and centrosome cycle; chromatin modification; autophagy regulation; signaling; and various developmental morphogenesis terms), and there are no edges connecting the proteins. This heterogeneity makes it impossible to assign a single coherent function label to the cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0045869","count":2},{"id":"GO:0043972","count":2},{"id":"GO:2000864","count":2}]},{"hash":"1386980522978286036","title":"Unknown","description":"There is no clear functional theme across the top GO terms; the terms span diverse processes such as drug and osmolyte transport, lipid movement, secretion, ribosome biogenesis, morphogenesis, and pheromone export, suggesting multiple unrelated functions rather than a single cohesive cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900753","count":1},{"id":"GO:0031460","count":1},{"id":"GO:0045332","count":1},{"id":"GO:0030253","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1466389307860088022","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0035308","count":1},{"id":"GO:1903361","count":1},{"id":"GO:0045943","count":1},{"id":"GO:0007472","count":1},{"id":"GO:0031929","count":1}]},{"hash":"549886545198246540","title":"Protein assembly and secretory trafficking","description":"The proteins cluster around oligomerization (hexamerization, homooligomerization), and trafficking processes in the secretory pathway (ER-to-Golgi transport, dense core vesicle transport), plus a cellular response to misfolded proteins, all pointing to protein assembly and quality control in the secretory system. Some transcription- and DNA-related terms may reflect moonlighting roles or annotation noise, but the dominant theme is protein assembly/trafficking and folding quality control.","confidence":"Medium","size":11,"edges":22,"triangles":25,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0034214","count":2}]},{"hash":"699574462906331438","title":"Nucleolar ribosome biogenesis and transcription","description":"The cluster is dominated by nucleolar and ribosome-related functions (rRNA transcription by RNA Pol I, tRNA transcription by RNA Pol III, and ribosome biogenesis), with indications of broader transcriptional activity (RNA Pol II) and nucleologenesis, linking ribosome assembly to nuclear transcription processes.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0001172","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1078474454179519319","title":"Translation Machinery and Regulation","description":"The cluster is dominated by GO terms tied to protein synthesis and its control: translation, initiation, termination, and elongation, including cytoplasmic translation and selenocysteine incorporation. The presence of deadenylation-dependent mRNA decay suggests linked post-transcriptional regulation. A couple of terms (glial cell proliferation, response to antibiotic) are less central but may reflect context-specific roles. Overall, this cluster appears to group proteins involved in the translation apparatus and its regulation.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0046677","count":4},{"id":"GO:0006415","count":3},{"id":"GO:0014009","count":2},{"id":"GO:0006413","count":2}]},{"hash":"867629359792822021","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0008153","count":3},{"id":"GO:0006526","count":3},{"id":"GO:0032094","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0006508","count":3}]},{"hash":"501862469327132643","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1903358","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0051083","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0051260","count":1}]},{"hash":"291243428000127883","title":"Acetylation-linked metabolism and chromatin processes","description":"The top GO terms cluster around acetylation-related events (N-terminal acetylation, putrescine acetylation, N-acetylglucosamine metabolism) and multiple biosynthetic pathways (melatonin, putrescine, ectoine, arginine). There are also chromatin-related terms (subtelomeric heterochromatin formation, centromeric cohesion), suggesting a tie between acetylation-regulated metabolism and chromatin maintenance. However, the mix of diverse metabolic processes implies only a broad association rather than a single coherent pathway, so the label captures a plausible theme without overcommitting.","confidence":"Medium","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":8},{"id":"GO:0046208","count":7},{"id":"GO:0009447","count":7},{"id":"GO:0030187","count":7},{"id":"GO:0006526","count":7}]},{"hash":"1371484754744604898","title":"SCF-Mediated Ubiquitination and Mitotic Progression","description":"The cluster is dominated by SCF-dependent ubiquitination, various ubiquitin linkages (K11, K48, K6), protein neddylation, and mitotic cell cycle terms (G2/M transition, cell division), indicating a coherent role in ubiquitin-proteasome\u2013driven regulation of mitosis. While embryonic development and viral processes appear among the terms, the strongest signal is proteasomal degradation linked to cell-cycle control via SCF/neddylation pathways.","confidence":"High","size":11,"edges":50,"triangles":127,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":8},{"id":"GO:0031146","count":7},{"id":"GO:0000278","count":6},{"id":"GO:0000086","count":6},{"id":"GO:0001701","count":6}]},{"hash":"1345974988329890954","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010950","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0006458","count":2},{"id":"GO:0006452","count":2},{"id":"GO:0070843","count":2}]},{"hash":"1168870338950075419","title":"Detoxification and Aromatic Compound Metabolism","description":"These proteins show enrichment for detox-related and aromatic/secondary metabolite pathways (response to toxic substances, cellular oxidant detoxification, beta-ketoadipate/aromatic compound catabolism, alkaloid metabolism). The presence of strigolactone biosynthesis points to plant-specific secondary metabolism, while prostaglandin catabolic and endocannabinoid signaling terms indicate broader lipid-related regulation. Overall, the cluster centers on detoxification and metabolism of aromatic/secondary metabolites and related lipid signaling processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0009820","count":3},{"id":"GO:0019380","count":3},{"id":"GO:1901601","count":3},{"id":"GO:2000124","count":3}]},{"hash":"417496005310932591","title":"Golgi- and synaptic vesicle trafficking","description":"This cluster's GO terms center on vesicle trafficking and exocytosis involving the Golgi apparatus and synaptic-like processes. Terms include Golgi ribbon formation, Golgi-to-vacuole transport, synaptic vesicle docking, vesicle fusion with Golgi and endosome-to-Golgi transport, plus neurotransmitter secretion and acrosome reaction. The common theme is vesicle trafficking and regulated secretion across Golgi- and synapse-related pathways.","confidence":"High","size":11,"edges":23,"triangles":18,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":2},{"id":"GO:1904050","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0016081","count":2},{"id":"GO:0007340","count":2}]},{"hash":"2144144432681569761","title":"Neuronal differentiation and microtubule dynamics","description":"The prominent GO terms center on neuron differentiation and cytoskeletal microtubule processes (microtubule nucleation, cytoplasmic microtubule organization, spindle-related duplication), with additional signaling responses (epinephrine, insulin, cAMP, nutrients, hypoxia) that together point to a program coordinating neuronal development with microtubule remodeling and cell signaling.","confidence":"Medium","size":10,"edges":38,"triangles":76,"max_degree":9,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0030182","count":6},{"id":"GO:0071872","count":5},{"id":"GO:0051591","count":5},{"id":"GO:0051301","count":4},{"id":"GO:1903087","count":4}]},{"hash":"1132271660195644189","title":"Transcription, Chromatin Assembly, and Cell Cycle Machinery","description":"Based on the top GO terms, the proteins cluster around DNA-templated transcription, CENP-A\u2013containing chromatin assembly, and cell division-related processes (e.g., microtubule severing, translation initiation/preinitiation complexes). Although there are hints of ER-Golgi transport and oligomerization, the prevailing theme is gene expression regulation and mitotic/chromosomal machinery, supporting a cohesive cell cycle\u2013related module.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0061641","count":4}]},{"hash":"1036259289627037447","title":"Glycolysis, TCA, and NADH Electron Transport","description":"This cluster is dominated by GO terms for core energy metabolism: glycolytic process, tricarboxylic acid cycle, and mitochondrial NADH to ubiquinone electron transport, along with redox homeostasis and thiamine biosynthesis, all pointing to central carbon metabolism and energy production. A couple of terms related to development appear, likely annotation noise or cross-species artifacts, but the overall theme clearly centers on carbohydrate metabolism and NADH-driven energy generation.","confidence":"High","size":10,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0006096","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0045454","count":3}]},{"hash":"630932511692711024","title":"Phospholipid biosynthesis and remodeling","description":"The cluster centers on lipid metabolism, with strong representation of phospholipid-related biosynthesis and remodeling (phosphatidylcholine, cardiolipin, ether lipids), triglyceride synthesis, and CDP-diacylglycerol pathways. Mitochondrial lipid remodeling and energy-related terms (cardiolipin remodeling and ATP synthesis coupling) reinforce a membrane/lipid-assembly theme. Some developmental terms may reflect tissue contexts, but the dominant signal is lipid biosynthesis and remodeling. ","confidence":"High","size":10,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":5},{"id":"GO:0036151","count":4},{"id":"GO:0010143","count":4},{"id":"GO:0002071","count":4},{"id":"GO:0016024","count":4}]},{"hash":"1811758500069316793","title":"Ribosome biogenesis and translation","description":"The dominating GO terms are centered on translation (cytoplasmic and mitochondrial) and ribosome biogenesis/assembly, plus rRNA processing steps, pointing to a cluster of ribosome-related proteins and factors involved in assembling and translating ribosomes. Some peripheral terms exist, but the core signal clearly indicates ribosome function.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0070126","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0042254","count":2}]},{"hash":"755356685880404220","title":"Transmembrane Transport of Sugars and Ions","description":"Top GO terms show multiple transmembrane transport activities: fructose, galactose, arabinose, and D-xylose transport across the plasma membrane, plus phosphate ion and sodium ion transport and selenite transport. Some terms touch on fucose metabolic process, but the unifying signal is membrane transport of diverse solutes, especially sugars and ions. Therefore the label Transmembrane Transport of Sugars and Ions captures the cluster's likely function.","confidence":"Medium","size":10,"edges":17,"triangles":14,"max_degree":7,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006817","count":4},{"id":"GO:1990539","count":4},{"id":"GO:0006004","count":4},{"id":"GO:0035725","count":4},{"id":"GO:0052106","count":4}]},{"hash":"917006869763210356","title":"Multitissue Development and Protein Processing","description":"This cluster combines GO terms tied to development across multiple tissues (brain regions like substantia nigra and hippocampus; skin/keratinocytes) with protein processing-related terms (ubiquitination, Golgi localization) and general cellular responses, implying roles in broad differentiation and protein handling rather than a single pathway.","confidence":"Medium","size":10,"edges":24,"triangles":18,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0003334","count":3},{"id":"GO:0051683","count":3}]},{"hash":"1340015217584397513","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms linking ribosome assembly and translation initiation: formation of the translation preinitiation complex, ribosome biogenesis, translation reinitiation, and maturation of SSU-rRNA. These consistently point to proteins involved in making and initiating translation. A few terms (chromatin organization, collagen catabolic, transcription-related) are likely less central or incidental noise within the set.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0034724","count":2}]},{"hash":"1457632210328208755","title":"Nuclear RNA processing and splicing regulation","description":"These proteins cluster around nuclear RNA metabolism: multiple GO terms point to splicing (mRNA splicing via spliceosome, cis splicing of mRNA), mRNA export from the nucleus, transcription termination, and ncRNA-mediated gene silencing. Additional terms cover nuclear rRNA maturation, polyadenylation-dependent mRNA decay, and transcription-coupled DNA repair, all consistent with a module focused on RNA processing, surveillance, and transcription-linked regulation in the nucleus.","confidence":"High","size":10,"edges":39,"triangles":81,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0016973","count":5},{"id":"GO:0006369","count":5},{"id":"GO:0045292","count":4}]},{"hash":"341693482100527612","title":"RNA processing and transcription regulation","description":"This cluster is enriched for mRNA splicing, various DNA-templated transcription processes, and regulatory effects on transcription, indicating a core focus on RNA processing and transcription control. Dendrite morphogenesis and growth terms appear less central, possibly reflecting developmental contexts of some proteins.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048813","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0006353","count":1},{"id":"GO:0052704","count":1}]},{"hash":"591626924976349140","title":"Retroviral replication and integration","description":"Top GO terms cluster around steps of the viral life cycle, especially retroviral processes: virion assembly, fusion and release from host cells, RNA-templated DNA biosynthesis (reverse transcription), viral life cycle, and establishment of integrated proviral latency, which collectively indicate retroviral replication and genome integration. A couple of terms (like sepal formation and leukocyte migration) appear as noise or host-response context, but do not override the core viral theme. ","confidence":"High","size":10,"edges":17,"triangles":9,"max_degree":9,"top_function":"protein folding","top_go_terms":[{"id":"GO:0019076","count":6},{"id":"GO:0048453","count":6},{"id":"GO:0050900","count":6},{"id":"GO:0019064","count":6},{"id":"GO:0006278","count":6}]},{"hash":"1773461846117654310","title":"DNA Repair and Genome Maintenance","description":"The cluster is enriched for DNA repair processes (base-excision repair, DNA recombination, alkylation repair, depurination) and includes a negative regulation of apoptosis, consistent with a core role in maintaining genome stability. Additional terms related to responses to xenobiotics, estradiol, and folic acid suggest broader stress and signaling contexts that connect to DNA damage response pathways. Overall, this set appears to group proteins involved in sensing and repairing DNA damage and promoting cell survival.","confidence":"High","size":10,"edges":37,"triangles":68,"max_degree":9,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0033158","count":2}]},{"hash":"1944748492625774729","title":"Lipid Metabolism and Membrane Trafficking","description":"The cluster is enriched for lipid-related processes (ergosterol biosynthesis, unsaturated fatty acid biosynthesis, MIPC sphingolipid metabolism) and vesicle trafficking between ER, Golgi, and vacuole, suggesting a cohesive role in lipid production and membrane transport; a few terms may reflect broader metabolism or tissue-specific contexts, rather than a distinct new function.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0006636","count":3}]},{"hash":"1745501242413809252","title":"Polyamine metabolism and related biosynthesis","description":"This cluster centers on polyamine catabolism (spermine, putrescine), acetylation of putrescine, and arginine biosynthesis, suggesting a shared theme of small-molecule biosynthesis and turnover with related post-translational modifications. Some other GO terms in the set (angiogenesis, melatonin biosynthesis, ectoine biosynthesis, sporulation) are more divergent, but the core pattern points to metabolism and modification of amine-containing compounds.","confidence":"Low","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":5},{"id":"GO:0018003","count":5},{"id":"GO:0046208","count":4},{"id":"GO:0006348","count":4},{"id":"GO:0009447","count":4}]},{"hash":"219855139551628799","title":"Dendritic spine morphogenesis and vesicle exocytosis regulation","description":"This cluster is strongly enriched for neuronal development and synaptic function terms, including positive regulation of dendritic spine development and morphogenesis, regulation of synaptic vesicle exocytosis, and hippocampus development, all pointing to coordinated spine formation and presynaptic vesicle regulation. The presence of Rac signaling and lamellipodium/ruffle assembly terms supports actin cytoskeleton remodeling common to neuron structure and synapse formation, with a broader touch of cytoskeletal dynamics seen in mating projection growth. Overall, the data suggest a coherent theme of synapse formation and cytoskeletal regulation.","confidence":"High","size":10,"edges":33,"triangles":44,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":4},{"id":"GO:2000300","count":4},{"id":"GO:0010592","count":4},{"id":"GO:0021766","count":4},{"id":"GO:0010796","count":4}]},{"hash":"1230287806026624408","title":"Transcription Regulation in Embryonic Development","description":"The cluster centers on transcriptional control, with GO terms for regulation of DNA-templated transcription and RNA polymerase II\u2013mediated transcription, complemented by several embryonic development processes across organs (pituitary gland and endocrine pancreas development, ureteric bud branching morphogenesis, neural crest migration, digestive tract morphogenesis, megakaryocyte differentiation). This suggests a unifying theme of transcriptional regulation guiding organogenesis, though a metabolic term (L-alanine catabolic process) appears less connected. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042853","count":2},{"id":"GO:0021983","count":2},{"id":"GO:0031018","count":2}]},{"hash":"2007799024548320395","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090201","count":2},{"id":"GO:0030330","count":2},{"id":"GO:2001140","count":2},{"id":"GO:0045332","count":2},{"id":"GO:1902166","count":2}]},{"hash":"128712110914670944","title":"Acetyl-CoA-driven central carbon metabolism","description":"This cluster is dominated by GO terms tied to acetyl-CoA production and core energy pathways: malonyl-CoA biosynthesis, pyruvate-to-acetyl-CoA formation, the TCA cycle, glycolysis, gluconeogenesis, and fatty acid biosynthesis, with several amino-acid catabolism routes funneling into acetyl-CoA. While a few terms touch on nucleotide metabolism or ion transport, the main signal is central carbon metabolism centered on acetyl-CoA flux.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:2001295","count":5},{"id":"GO:0006086","count":5},{"id":"GO:0006099","count":5},{"id":"GO:0006213","count":5},{"id":"GO:0006814","count":5}]},{"hash":"280676561228385630","title":"Unknown","description":"The GO terms span chromatin regulation, cytoskeletal/axoneme assembly, immune signaling, fungal cell wall organization, neuronal development, DNA damage tolerance, ubiquitination, and peroxisomal protein import. This mix shows no single cohesive function or pathway tying the proteins together, so a concise, specific label cannot be assigned beyond Unknown.","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0061186","count":9},{"id":"GO:0007288","count":9},{"id":"GO:0033128","count":9},{"id":"GO:0071347","count":9},{"id":"GO:0031505","count":9}]},{"hash":"1513320262737667898","title":"Mitochondrial translation and tRNA aminoacylation","description":"The dominant GO term is translation, with 7 proteins, and there are several mitochondrial tRNA aminoacylation activities (threonyl-, alanyl-, prolyl-), indicating a focus on mitochondrial protein synthesis and tRNA charging; other terms like ribosome biogenesis and mitochondrial DNA processes appear but are less represented, supporting a cohesive mitochondrial gene-expression theme.","confidence":"High","size":9,"edges":21,"triangles":18,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":3},{"id":"GO:0006407","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0070159","count":2}]},{"hash":"509184258814002676","title":"Ribosome Biogenesis and Translation","description":"The GO terms strongly point to the protein synthesis machinery: translation, cytoplasmic translation, translation initiation, and maturation/assembly of ribosomal subunits (SSU/LSU). This suggests the cluster comprises factors involved in ribosome biogenesis and protein translation. A few single annotations (DNA metabolic process, osteoblast differentiation, IL-4 response) appear incidental and do not define the core function.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000027","count":3},{"id":"GO:0000462","count":2},{"id":"GO:1901194","count":1},{"id":"GO:0001649","count":1}]},{"hash":"1269884642099345968","title":"Unknown","description":"The GO terms span metabolism, signaling, and development across diverse organisms with no clear common function linking the proteins. Because there is no cohesive theme, the cluster cannot be given a specific functional name.","confidence":"","size":9,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006784","count":1},{"id":"GO:0033173","count":1},{"id":"GO:0014044","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0009742","count":1}]},{"hash":"400266063341231146","title":"Mitochondrial fatty acid oxidation and acetyl-CoA metabolism","description":"The GO terms cluster around fatty acid beta-oxidation, acetyl-CoA catabolic processes, and ketone body biosynthesis, all pointing to mitochondrial energy metabolism. The linked apoptotic regulation term also ties to mitochondrial function, reinforcing a mitochondria-centered metabolic theme. A few terms like brain development or sporulation are broader contexts and not dominant, but do not override the core metabolic signal.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1901029","count":4},{"id":"GO:0014070","count":4},{"id":"GO:0046951","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0006635","count":4}]},{"hash":"1977093027152829470","title":"Synaptic vesicle trafficking and brain development","description":"The GO terms cluster around regulation of synaptic vesicle exocytosis, brain development, multivesicular body sorting, filopodium assembly, and neuronal differentiation, indicating a coherent theme of neuronal vesicle trafficking and brain morphogenesis.","confidence":"High","size":9,"edges":30,"triangles":51,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0010796","count":6},{"id":"GO:0031384","count":6},{"id":"GO:1903434","count":5}]},{"hash":"1063707663217745341","title":"Unknown","description":"The GO terms are highly diverse, spanning transcription, development, metabolism, immune signaling, transport, endocytosis, and spindle attachment, with no single shared mechanism tying the proteins together. This suggests no coherent cluster function can be assigned.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060716","count":3},{"id":"GO:0016126","count":2},{"id":"GO:0035754","count":2},{"id":"GO:0002774","count":2}]},{"hash":"1590321472274153610","title":"Light-regulated transcription and circadian control in plants","description":"The cluster centers on transcriptional regulation (nucleosome assembly and RNA Pol II regulation) and plant-specific light signaling (far-red phototransduction and far-red signaling) with circadian rhythm control and hormone responses (jasmonic acid, gibberellin), suggesting a module coordinating light perception with transcriptional timing in plants.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0045944","count":2},{"id":"GO:0006355","count":1},{"id":"GO:0009585","count":1}]},{"hash":"682205328186771171","title":"Unknown","description":"The top GO terms span diverse processes across species (animal signaling pathways like TGF\u03b2/BMP and NF-\u03baB, plant development and photosystem adjustments, and general processes like dephosphorylation and nuclear export), with no single dominant function tying the cluster together. The heterogeneity and low connectivity suggest the proteins do not form a coherent functional module.","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042347","count":6},{"id":"GO:0030514","count":6},{"id":"GO:0030512","count":6},{"id":"GO:0071560","count":6},{"id":"GO:0010074","count":6}]},{"hash":"2277401920725170839","title":"Cell Cycle and Morphogenesis","description":"The top terms cluster around cell division and DNA replication (mitotic/meiotic cell cycle, G1/S transition, DNA replication) and developmental processes (cell morphogenesis, budding, Schwann cell development). Some terms like innate immune response and neural signaling appear but do not override the core themes of proliferation and development, making a label that captures both appropriate and representative.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000902","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0007118","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0014044","count":4}]},{"hash":"825133925018212762","title":"Metabolic Biosynthesis and Response Pathways","description":"This cluster centers on metabolic biosynthetic processes (fatty acid, pyruvate, D-xylulose-5-phosphate, retinoic acid metabolism) and includes components related to signaling regulation and responses to drugs and metal stress. The combination of core metabolic terms with signaling and response terms suggests a theme of metabolism connected to cellular signaling and stress responses, rather than a single isolated pathway.","confidence":"Medium","size":8,"edges":23,"triangles":32,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0006633","count":6},{"id":"GO:0019518","count":4},{"id":"GO:0042866","count":3},{"id":"GO:0018119","count":3},{"id":"GO:1900116","count":3}]},{"hash":"1917284576235267044","title":"Ribosome biogenesis and translation","description":"Enriched for translation and ribosome assembly, plus ITS2 rRNA processing, indicating involvement in ribosome biogenesis and protein synthesis; a minor antibiotic response term likely reflects translation-targeting stress rather than a core function.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":1},{"id":"GO:0000448","count":1},{"id":"GO:0042255","count":1},{"id":"GO:0017148","count":1}]},{"hash":"860710472113393263","title":"Plant RNA processing and chromatin dynamics under stress","description":"The cluster centers on nuclear RNA processing and RNA biogenesis activities, including transcription termination, mRNA splicing and snRNP assembly, P-body involvement, and maturation of rRNA, along with nuclear import and chromatin-related processes like heterochromatin formation. Plant stress signals (ABA response and water deprivation) are also represented, suggesting the proteins function in RNA processing and chromatin regulation within stressed plant cells. Thus the shared theme is RNA processing and chromatin dynamics in plant stress contexts.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":7},{"id":"GO:0042633","count":5},{"id":"GO:0009737","count":5},{"id":"GO:0045292","count":5},{"id":"GO:0033962","count":5}]},{"hash":"1363495788987815257","title":"Nuclear RNA export and cell cycle regulation","description":"The top GO terms point to nuclear export/import of RNA and ribosomal subunits, transcriptional regulation in the nucleus, and localization to centrosomes/kinetochores, indicating a theme of nuclear transport linked to cell cycle control.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":5},{"id":"GO:0006609","count":5},{"id":"GO:0046825","count":5},{"id":"GO:0010824","count":5},{"id":"GO:0042176","count":5}]},{"hash":"1359991172961201187","title":"GlcNAc Metabolism and UDP-GlcNAc Biosynthesis","description":"The top GO terms cluster around carbohydrate metabolism, including N-acetylglucosamine catabolic processes, UDP-N-acetylglucosamine biosynthesis, glucosamine catabolism, and the pentose-phosphate shunt. This points to a shared function in GlcNAc metabolism and UDP-GlcNAc production, which is central for protein glycosylation and related pathways. A couple of terms (translation, heat response) are broader and less specific to this cluster, but the dominant signal supports the GlcNAc/UDP-GlcNAc theme.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0009051","count":1},{"id":"GO:0006046","count":1},{"id":"GO:0005975","count":1}]},{"hash":"2207418607713450852","title":"Isoprenoid Biosynthesis","description":"The TOP terms include farnesyl diphosphate, geranyl and geranylgeranyl diphosphate biosynthesis, monoterpene biosynthesis, and cholesterol/quinone biosynthesis, all central to isoprenoid/terpenoid production. While a couple of terms (like protein folding or autophagosome assembly) appear unrelated, the dominant pattern points to terpenoid/isoprenoid biosynthetic activity as the cluster\u2019s core function.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045337","count":1},{"id":"GO:0043693","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0033386","count":1},{"id":"GO:0051290","count":1}]},{"hash":"276903744285996461","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070842","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000162","count":2},{"id":"GO:0006189","count":1},{"id":"GO:0009231","count":1}]},{"hash":"1690300343945217642","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":8,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0006949","count":2},{"id":"GO:0009828","count":2},{"id":"GO:0019953","count":2},{"id":"GO:0006458","count":1}]},{"hash":"377397990030032440","title":"Filopodium Dynamics and GTPase Signaling","description":"This cluster's strongest signals are filopodium assembly and its regulation, plus small GTPase-mediated signaling and related actin/cytoskeletal remodeling processes linked to cell spreading. While there are a few outliers (e.g., macrophage differentiation, chromatin-related terms), the dominant theme ties to actin-driven protrusions and adhesion dynamics governed by GTPase pathways.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046847","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0051489","count":2}]},{"hash":"1723984142269352709","title":"MVB/Exosome trafficking and mitotic processes","description":"The listed GO terms cluster around vesicle trafficking via multivesicular bodies (exosome regulation, sorting, and MVB-lysosome fusion) and core mitotic events (exit from mitosis, mitotic chromosome condensation) along with related processes like abscission and nucleus organization. This suggests a functional theme where vesicle trafficking interfaces with cell division and nuclear dynamics. Some terms (e.g., suppression of viral release, response to anoxia) may reflect broader stress or host-defense contexts but still align with vesicle trafficking-linked cellular states.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903541","count":1},{"id":"GO:0006997","count":1},{"id":"GO:0010458","count":1},{"id":"GO:0061763","count":1},{"id":"GO:0071985","count":1}]},{"hash":"1540906499924335350","title":"Retinoid metabolism and sensory organ development","description":"The cluster is dominated by retinoid-related terms (retinal and retinol metabolic processes) and several developmental terms linked to eye/ear and brain formation (embryonic camera-type eye development, inner ear morphogenesis, hindbrain development), plus associated neural metabolism (GABA shunt). This points to a coherent theme of retinoid signaling influencing sensory organ and neural development, justifying a label that highlights both retinoid metabolism and sensory organ development.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":7},{"id":"GO:0042572","count":7},{"id":"GO:0021983","count":4},{"id":"GO:0031076","count":4},{"id":"GO:0042904","count":4}]},{"hash":"1114970304496427399","title":"Mitotic Spindle Assembly and Cytokinesis","description":"The cluster is enriched for cell division, mitosis, and microtubule organization terms (mitotic cytokinesis, cell cycle, microtubule nucleation, cytoplasmic microtubule organization, spindle pole body duplication, cell division), indicating a cohesive role in spindle assembly and cytokinesis. A couple of metabolic terms (TCA cycle and oxidation-reduction) are present but do not dominate the signal, so the primary theme is mitosis and cytoskeletal dynamics.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0043093","count":2},{"id":"GO:1902408","count":2},{"id":"GO:0071353","count":2}]},{"hash":"50899935966464599","title":"Unknown","description":"The GO terms are highly diverse, spanning mitochondrial assembly, lipid biosynthesis, neural/fibroblast development, meiotic processes, transcription, limb development, and iron homeostasis, with no clear single shared function tying the cluster together.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0033108","count":1},{"id":"GO:0006655","count":1},{"id":"GO:0007406","count":1},{"id":"GO:0006311","count":1},{"id":"GO:0048147","count":1}]},{"hash":"143226347888138099","title":"SRP-Dependent Membrane Targeting","description":"The top GO terms include explicit references to SRP-dependent cotranslational targeting to membranes and translocation, indicating these proteins cluster around membrane targeting and the secretory pathway; other terms (UPR, metabolism, development) appear ancillary rather than defining the cluster\u2019s core function.","confidence":"Medium","size":7,"edges":18,"triangles":20,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0007165","count":1},{"id":"GO:0044781","count":1}]},{"hash":"1834428426240817113","title":"Broad Metabolic Catabolism","description":"The top GO terms point to a mix of catabolic and central metabolic processes (glycolysis, amino acid and carbohydrate catabolism, mandelate and galactonate pathways, and even menaquinone biosynthesis), suggesting the cluster is enriched for general metabolism and energy-yielding breakdown rather than a single specific pathway. Some terms (tRNA processing, vacuole regulation, tissue regeneration) are more peripheral but likely reflect broader cellular context or annotation noise. Overall, a broad label capturing diverse catabolic metabolism fits best.","confidence":"Medium","size":7,"edges":9,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0009234","count":1},{"id":"GO:0019596","count":1},{"id":"GO:0016998","count":1}]},{"hash":"513689555685152967","title":"Nuclear RNA Splicing & Processing","description":"The cluster is dominated by GO terms for splicing and RNA processing (mRNA cis splicing via spliceosome, spliceosomal snRNP assembly, termination of RNA polymerase II transcription, maturation of SSU-rRNA, P-body assembly, and import into nucleus). These indicate a shared role in RNA maturation and nuclear RNA metabolism, with additional terms reflecting broader stress responses and chromatin-related processes that may be context-specific. Overall, the core theme is RNA processing in the nucleus and related RNA metabolism pathways.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042633","count":4},{"id":"GO:0009737","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0033962","count":4},{"id":"GO:0000387","count":4}]},{"hash":"2139938917297936203","title":"Sugar and ion membrane transporters","description":"The top GO terms show transmembrane transport of phosphate and sodium ions and import of several sugars (fructose, galactose, arabinose, D-xylose) across the plasma membrane, plus related metabolism. This pattern strongly supports a cluster of membrane transporter proteins with broad substrate specificity for monosaccharides and ions, rather than enzymes. Therefore, \"Sugar and ion membrane transporters\" is a concise, representative label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":1},{"id":"GO:1990539","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0052106","count":1}]},{"hash":"2136277593341475727","title":"Plasma Membrane Sugar and Ion Transport","description":"This cluster centers on proteins involved in transport across the plasma membrane, with several GO terms for sugar import (fructose, galactose, arabinose, xylose) and various ion/transmembrane transports (sodium, phosphate, selenite). The common theme is membrane-mediated uptake of sugars and ions, indicating a transporter program at the cell surface rather than a single substrate or signaling role.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":1},{"id":"GO:1990539","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0052106","count":1}]},{"hash":"1820224873583434945","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":9,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006098","count":2},{"id":"GO:0042538","count":1},{"id":"GO:0010224","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0008615","count":1}]},{"hash":"1298699020345824339","title":"TORC1 signaling and mitotic transcription","description":"The top GO terms point to TORC1 signaling and DNA-templated transcription, with supporting notions of mitotic cell cycle, GTPase regulation, and mRNA transport. Although the cluster has no edges, these terms together suggest a growth-and-division regulatory module in which TORC1 coordinates transcription and cell-cycle progression, potentially via small GTPases and RNA trafficking mechanisms.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0038202","count":3},{"id":"GO:0000278","count":3}]},{"hash":"112700039010473257","title":"Protein complex assembly and vesicle trafficking","description":"Top terms indicate a focus on protein oligomerization/assembly (homooligomerization, hexamerization, chaperone-mediated assembly) and intracellular trafficking (Golgi retention, intralumenal vesicle formation, anterograde vesicle transport), with additional signals of cytoskeletal involvement (cell division, microtubule depolymerization). Taken together, the cluster seems best described as proteins involved in assembling complexes and routing them within the secretory pathway or cytoskeleton, rather than a single specific function.","confidence":"Medium","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0051131","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045053","count":2}]},{"hash":"911181385644282573","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA metabolism: spliceosome complex and snRNP assembly, rRNA processing, and ribosomal large subunit biogenesis, suggesting a core theme of RNA processing and ribosome assembly. A few outlier terms (nitrile biosynthesis, CD40 signaling, glycoprotein catabolic process, necroptosis regulation, nuclear division) are present but do not dominate the cluster\u2019s functional theme. Overall, the label captures the strongest shared function among the terms.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080028","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0023035","count":1},{"id":"GO:0060546","count":1}]},{"hash":"441212565760890282","title":"Osmotic Stress and Cell Wall Remodeling","description":"The shared GO terms point to osmotic stress response and cell wall-related processes (water homeostasis, cellular response to osmotic stress, cell wall biosynthesis/organization, and mannoprotein biosynthesis), suggesting the cluster functions in adapting the cell wall under osmotic challenge. Some terms about translation initiation and GTPase activity may reflect broader stress-regulation, but the core theme is osmotic response with cell wall remodeling.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0034220","count":2},{"id":"GO:0009992","count":2},{"id":"GO:0071470","count":2}]},{"hash":"1349355105597386860","title":"Xenobiotic and oxidative stress response with DNA repair","description":"The cluster shows GO terms tied to xenobiotic stimulus response, oxidative stress (hydrogen peroxide and redox homeostasis), and DNA repair (base-excision repair), suggesting a set of proteins involved in stress response and genome maintenance. Some terms are obsolete, but the common theme appears to be cellular defense against xenobiotics and oxidative damage with DNA repair processes.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0090502","count":2},{"id":"GO:2000327","count":2},{"id":"GO:0045454","count":2}]},{"hash":"1815356567772469160","title":"Neuronal Synaptic Signaling and Autophagy","description":"The GO terms lean toward neuronal communication (GABAergic synaptic transmission; retrograde signaling by neuropeptides) and intracellular trafficking/quality control (ubiquitin-dependent endocytosis; autophagosome substrate localization), with some broader cell-maintenance processes (apoptosis, centriole elongation) also noted. Together they suggest a cluster centered on neuronal synaptic signaling coupled with autophagy/vesicle trafficking.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":2},{"id":"GO:0038028","count":1},{"id":"GO:0070086","count":1},{"id":"GO:0061753","count":1},{"id":"GO:1905433","count":1}]},{"hash":"1978358360093668203","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":6},{"id":"GO:0006452","count":6},{"id":"GO:0006458","count":6},{"id":"GO:0070843","count":6},{"id":"GO:0046825","count":6}]},{"hash":"1976922704497301939","title":"Meiotic Chromosome Condensation and Genome Organization","description":"This cluster is dominated by terms related to chromosome condensation during cell division (mitosis and meiosis), synaptonemal complex assembly, and meiotic chromosome dynamics, including microsporogenesis and regulation of meiotic DSB formation. It also features genome organization processes like tRNA gene clustering and heterochromatin formation in mating-type regions. A couple of terms refer to plant organelle positioning (amyloplasts) and gravitropism, which may reflect broader cellular architecture in the dataset. Overall, the connected theme is chromosome structure and genome organization during division and meiosis.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007076","count":3},{"id":"GO:0070058","count":3},{"id":"GO:1903342","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0010032","count":3}]},{"hash":"1702778159583251837","title":"Mitochondrial Electron Transport and Protein Assembly","description":"Dominant signal is mitochondrial electron transport (ubiquinol to cytochrome c) and protein complex assembly (heterooligomerization/homotetramerization). Some unrelated/obsolete terms (viral process, PQQ biosynthesis) add noise, but the core theme points to mitochondrial respiration and assembly of protein complexes.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":3},{"id":"GO:0008340","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0071432","count":2},{"id":"GO:0006627","count":2}]},{"hash":"1812013246905749617","title":"Oxidative Stress Response and MAPK Signaling","description":"Reasoning: Top GO terms are dominated by cellular response to hydrogen peroxide and regulation of stress-activated MAPK cascades, with I-kappaB phosphorylation suggesting involvement in inflammatory/signal transduction pathways. A few other terms (DNA-templated transcription, magnesium transport) are peripheral or obsolete, so the core theme is oxidative stress response and associated signaling.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0006308","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0007252","count":1},{"id":"GO:0019471","count":1}]},{"hash":"1362806433728273041","title":"Nuclear transcription and DNA replication","description":"Most represented terms point to nuclear processes: DNA-templated transcription, Okazaki fragment processing in mitotic DNA replication, mRNA branch site recognition, and rRNA maturation. These collectively indicate involvement in gene expression and DNA replication/RNA processing within the nucleus. Supportive terms on chromatin modification and signaling hint at broader regulatory context, but the core theme is nuclear gene expression and DNA replication.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007584","count":4},{"id":"GO:0031930","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0032933","count":3},{"id":"GO:0006351","count":3}]},{"hash":"236662655449679255","title":"Microtubule-driven mitosis and spindle dynamics","description":"This cluster\u2019s top GO terms center on microtubule-based processes: nuclear migration along microtubules, plus-end directed microtubule sliding, spindle-kinetochore attachments, and centrosome separation, all key aspects of mitosis and spindle function. The presence of cytokinesis-related terms supports a broader theme of microtubule dynamics coordinating cell division. A few terms touch on stress granule disassembly or chloroplast movement, which can involve microtubules as well, but they do not override the dominant mitotic/spindle signal.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030473","count":6},{"id":"GO:0031535","count":6},{"id":"GO:0000911","count":6},{"id":"GO:0099607","count":6},{"id":"GO:0007100","count":6}]},{"hash":"354750235834302002","title":"Ubiquitin-dependent protein turnover and vesicle trafficking","description":"This cluster is enriched for ubiquitin-mediated degradation and trafficking processes (ubiquitin-dependent catabolic process, endocytosis, ER-Golgi transport, intracellular transport), plus related quality-control and turnover roles (autophagosome localization, protein isomerization). The common theme ties protein quality control to vesicle trafficking and turnover.","confidence":"High","size":6,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0048260","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006886","count":2}]},{"hash":"2154056634959638210","title":"Developmental Transcription and Stress Response","description":"The cluster\u2019s top GO terms cluster around developmental processes (multicellular organism development, forebrain and neural tube development, skeletal system development) and DNA-templated transcription along with cell cycle processes, suggesting proteins involved in developmental regulation and proliferation. Additional terms for ER-stress\u2013triggered apoptotic signaling and defense response imply these proteins also participate in cellular stress responses, potentially linking development with adaptive signaling. Overall, this points to a group of transcription regulators involved in development with stress-responsive roles.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0006351","count":4}]},{"hash":"1944503914579239671","title":"DNA Replication Machinery and Protein Oligomerization","description":"The top GO terms indicate a core of DNA-related processes (DNA biosynthetic process, DNA replication, DNA replication initiation) and substantial protein oligomerization (homooligomerization and hexamerization), suggesting a cluster of replication-associated proteins that assemble into oligomeric complexes. While other terms point to stress responses or miscellaneous functions, the dominant signal centers on replication machinery and protein complex formation.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0071897","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006270","count":3},{"id":"GO:0034214","count":3}]},{"hash":"634852038549144304","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0071042","count":2},{"id":"GO:0006605","count":2},{"id":"GO:0034476","count":2},{"id":"GO:0034475","count":2}]},{"hash":"1531992238906522508","title":"Unknown","description":"The top terms span RNA modification, fatty acid oxidation, heme biosynthesis, and responses to several metal ions and hypoxia, with an immune signal (IL-4) included. There is no clear, single function tying these proteins together, so a unified label cannot be confidently assigned.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":1},{"id":"GO:0033539","count":1},{"id":"GO:0009437","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0010039","count":1}]},{"hash":"626147918462818742","title":"Unknown","description":"The six proteins show GO terms across diverse processes (toxic substance response, liver regeneration, cytokine response, intestinal maturation, methylation, hormone and nutrient responses, nucleotide metabolism, and antibiotic response). There is no single dominant function or shared pathway evident among them, so a cohesive, specific label isn\u2019t justifiable.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0034097","count":1},{"id":"GO:0060574","count":1},{"id":"GO:0032259","count":1}]},{"hash":"2018994754764854314","title":"Unknown","description":"The GO terms are highly heterogeneous, including vasodilation, oxidative stress responses, metal ion response, pH response, differentiation, and apoptosis, with several obsolete terms. There is no clear single function or pathway linking these proteins, so a specific, representative label cannot be assigned.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0003069","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0019430","count":1},{"id":"GO:0071291","count":1},{"id":"GO:0001302","count":1}]},{"hash":"811096475907693822","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by translation and ribosome-related processes (translation, maturation of LSU-rRNA, ribosomal large subunit biogenesis, regulation of translation), pointing to a cluster centered on protein synthesis machinery. The retina development terms and cell-cycle terms appear incidental, possibly due to shared domains or annotation noise. Overall, the functional theme is the protein synthesis apparatus.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000470","count":2},{"id":"GO:0006417","count":1},{"id":"GO:0031290","count":1},{"id":"GO:0021554","count":1}]},{"hash":"485204678470835809","title":"Ribosome biogenesis and transcription regulation","description":"Cluster centers on RNA metabolism and gene expression: translation and ribosome biogenesis are prominent (translation, ribosome biogenesis, rRNA methylation), with supporting signals for transcription regulation and chromatin-related processes (RNA Pol II regulation, transcription elongation fidelity). A few terms appear noisy or obsolete (neural tube closure, nucleosome density), but overall the proteins seem linked to ribosome-associated functions and transcription control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0001843","count":1},{"id":"GO:0031167","count":1},{"id":"GO:1903758","count":1}]},{"hash":"1823954534668894645","title":"RNA and Protein Methylation","description":"Most GO terms cluster around methylation processes: tRNA methylation, rRNA modification, RNA cap methylation, RNA guanine-N7 methylation, and peptidyl-arginine/histone methylation. This points to a group of methyltransferases acting on RNA and proteins, with some involvement in methylation-related biosynthetic steps (cobalamin and vitamin E) and related bacterial processes like nodulation. Confidence in this as the representative theme is High.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":5},{"id":"GO:0009236","count":5},{"id":"GO:0006370","count":4},{"id":"GO:0000154","count":4},{"id":"GO:0010189","count":4}]},{"hash":"1490055289633673603","title":"Vacuolar trafficking and ion homeostasis","description":"The GO terms cluster around vacuole-related processes (vacuole organization, protein targeting to vacuole, vacuolar acidification) and ion/homeostasis (sodium and copper transport, proton transmembrane transport, polyphosphate metabolism). Together these suggest a functional grouping focused on vacuolar trafficking and ion storage/homeostasis, with some related energy/transport processes. Confidence: Medium.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042777","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0006878","count":1}]},{"hash":"509164821677601216","title":"Chromatin regulation and cell polarity dynamics","description":"This cluster is enriched for chromatin-related terms (subtelomeric heterochromatin formation; histone H4-K12 acetylation) and for processes governing cell shape/polarity (establishment/maintenance of cell polarity regulating cell shape), with additional diverse terms pointing to endocytosis regulation, sporulation, and muscle development. The common thread appears to be regulation of genome organization and cellular architecture rather than a single cohesive pathway, so the label emphasizes chromatin regulation together with polarity dynamics.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":6},{"id":"GO:0016344","count":6},{"id":"GO:0002121","count":6},{"id":"GO:0048741","count":6},{"id":"GO:0043503","count":6}]},{"hash":"1143737565167978755","title":"DNA-Templated Transcription Initiation and Regulation","description":"The cluster is dominated by GO terms related to transcription initiation by RNA polymerase II and III, including preinitiation complex assembly, promoter opening, and start-site selection, with additional terms for transcriptional regulation. These together suggest a cohesive function in initiating and regulating transcription rather than other processes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0002574","count":1},{"id":"GO:0070898","count":1},{"id":"GO:0051123","count":1}]},{"hash":"1005337744834936500","title":"RNA processing and translation regulation","description":"The top GO terms cluster around mRNA processing (spliceosome-mediated splicing, cis splicing, polyadenylation, mRNA stabilization) and translational control (translation reinitiation, IRES-dependent initiation, formation of the preinitiation complex, and regulation of translational initiation). This suggests the proteins participate in RNA maturation and in regulating how transcripts are translated, including contexts involving viral translation. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075522","count":2}]},{"hash":"2272226367905094119","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006796","count":1},{"id":"GO:0009970","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0050428","count":1}]},{"hash":"2051762301823128771","title":"RNA processing and gene silencing","description":"The top GO terms cluster around RNA metabolism\u2014ncRNA-mediated and post-transcriptional gene silencing, splicing regulation, rRNA maturation, and mRNA turnover\u2014suggesting a core function in RNA processing and gene expression control. Outliers related to DNA repair and cold response are present but less representative.","confidence":"Medium","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0000716","count":3},{"id":"GO:0071042","count":3},{"id":"GO:0070417","count":3}]},{"hash":"1816953668733166661","title":"Sphingolipid and Phospholipid Metabolism","description":"The terms converge on lipid metabolism: sphingosine and sphinganine-1-phosphate metabolic processes, along with phospholipid biosynthesis, catabolism, and dephosphorylation, point to sphingolipid and glycerophospholipid metabolism. While there are a couple of oxidation-detoxification terms and some obsolete Wnt entries, the dominant signal is lipid-related metabolism and signaling.","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0044330","count":1},{"id":"GO:0015760","count":1},{"id":"GO:0006670","count":1},{"id":"GO:0006655","count":1}]},{"hash":"2035679559735865503","title":"DNA Replication and Repair","description":"This cluster is dominated by GO terms for DNA replication, recombination, SOS response, and translesion synthesis, pointing to genome maintenance and DNA damage response as the core theme; additional terms related to transcription and oxidative stress support a broader stress signaling context, but the primary signal is replication- and repair-focused.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0051260","count":2}]},{"hash":"1214773328255860914","title":"Unknown","description":"The top GO terms cover a wide and unrelated mix of processes (neural and muscle development, lymphangiogenesis, plant hormone signaling, lipid A biosynthesis, cell budding, translation regulation, glycogen metabolism, DNA repeat maintenance). There is no clear, single biological function or pathway tying these proteins together, suggesting no coherent cluster label beyond Unknown.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0033173","count":5},{"id":"GO:0014044","count":5},{"id":"GO:0009245","count":5},{"id":"GO:0009742","count":5},{"id":"GO:0048741","count":5}]},{"hash":"1306429054444813211","title":"Unknown","description":"The top GO terms span a wide range of distinct processes (DNA replication, endocytosis, ion transport, signaling, cell cycle, metabolism, apoptosis, ovulation) with no clear shared function or pathway across the five proteins, and there are no observed interactions. Because there isn\u2019t a unifying theme tying these proteins together, a specific, representative label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0002774","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0072584","count":2},{"id":"GO:0051316","count":2}]},{"hash":"1126056164574964422","title":"DNA replication and cell cycle factors","description":"Based on the strongest, recurring GO terms in the cluster, the proteins are predominantly linked to DNA replication, DNA replication initiation, and cell cycle processes, suggesting a functional grouping around replication machinery and cell cycle regulation. While there are a few outlier terms (e.g., cilium movement, gas vesicle organization) that are less clearly connected, the core signal centers on DNA synthesis and cell cycle activities, justifying a label focused on replication/cell cycle functions. The lack of observed edges does not contradict this, as annotation-based clustering can occur without direct interactions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006270","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0003341","count":2},{"id":"GO:0031412","count":2}]},{"hash":"270802931398062295","title":"Apoptosis and cell cycle regulation","description":"Dominant terms center on apoptotic processes and cell division components (apoptosis, centrosome cycle, attachment of meiotic spindle microtubules to kinetochore), suggesting a cluster of proteins involved in cell fate decisions during division. Some other terms (endocytosis, glycogen metabolism, amino acid starvation response) appear less connected and do not override the main theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0002774","count":1},{"id":"GO:0006813","count":1}]},{"hash":"493513250466792984","title":"Heat-shock and immune response proteins","description":"The top GO terms cluster around heat response and protein refolding (classic heat-shock/chaperone activity) while also including immune signaling terms (B cell cytokine production, T cell\u2013mediated tumor cell response), suggesting proteins involved in stress responses that modulate immune pathways; a few terms are tangential (cadmium response, protein translocation into host cytoplasm), but the dominant theme is heat-shock/immune function.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":5},{"id":"GO:0002368","count":5},{"id":"GO:0002842","count":5},{"id":"GO:0042026","count":5},{"id":"GO:0044053","count":5}]},{"hash":"52313463450229666","title":"Ribosome Biogenesis and RNA Pseudouridylation","description":"The strongest signals are in translation and ribosome biogenesis, plus specific RNA modification activities (rRNA and tRNA pseudouridine synthesis) that underpin translational fidelity. While a few transcription-related terms appear, the core theme centers on the ribosome assembly/function and RNA modification essential for translation. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006353","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0031119","count":1}]},{"hash":"1849645683798052933","title":"Fatty acid metabolism and energy balance","description":"Top GO terms mostly indicate lipid metabolism and energy regulation (fatty acid beta-oxidation, acyl-CoA and carnitine biosynthesis) and starvation response, with some developmental terms as context. The common thread is fatty acid metabolism and energy balance.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009791","count":2},{"id":"GO:0019439","count":2},{"id":"GO:1904070","count":2},{"id":"GO:0042594","count":2}]},{"hash":"729480123904773116","title":"DNA Damage Repair and Stress Response","description":"The top GO terms point to DNA repair processes (nucleotide-excision repair, DNA alkylation repair, depurination, depyrimidination) and related damage-response signaling, with additional references to apoptosis regulation and stress responses (cadmium exposure, estradiol, folic acid) and inflammation. This combination suggests proteins in this cluster primarily engage in DNA damage repair and cellular stress responses rather than a single pathway, warranting a DNA damage repair and stress response label.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033158","count":1},{"id":"GO:0006307","count":1},{"id":"GO:0032355","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0045007","count":1}]},{"hash":"1185227387835185492","title":"Ubiquitin-mediated protein regulation","description":"The top terms are dominated by various forms of protein ubiquitination (K6-, K48-, and linear polyubiquitination) plus the general GO term protein ubiquitination, suggesting the proteins in this cluster participate in ubiquitin-dependent regulation of substrates. Some related regulatory themes (TORC1 signaling, necroptosis) appear as secondary hints, and a couple terms touch on mitotic chromatid cohesion, but the strongest signal is ubiquitin signaling.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990758","count":2},{"id":"GO:0060546","count":2},{"id":"GO:1904262","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0016567","count":2}]},{"hash":"1631410714450350202","title":"Cell Division and Protein Oligomerization","description":"The cluster centers on cell division and chromatin organization, with several terms describing protein self-assembly (homooligomerization, hexamerization). This points to a theme of coordinating cell-cycle processes with the formation of protein complexes essential for division and genome organization, possibly including mitotic machinery. Some unrelated or obsolete terms appear, but the core signal remains cell-cycle and protein assembly.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0030574","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0035551","count":1}]},{"hash":"1952213591952495492","title":"GTPase-regulated vesicle trafficking and cytoskeletal remodeling","description":"Based on GO terms centered on regulation of GTPase activity, vesicle transport (ER-Golgi and endosome-to-plasma membrane), podosome assembly, and mitotic cleavage furrow ingression, the cluster points to membrane trafficking and cytoskeletal dynamics governed by small GTPases. Some terms about apoptosis and floral organ abscission are less central but may reflect broader cell remodeling processes tied to trafficking and adhesion.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0097284","count":4},{"id":"GO:0010227","count":4},{"id":"GO:1905751","count":4},{"id":"GO:0033028","count":4}]},{"hash":"906827474355529577","title":"Unknown","description":"The GO terms span protein sumoylation, protein neddylation, negative regulation of DNA-templated transcription, amygdala development, thiamine diphosphate biosynthesis, and autophagy/vacuolar targeting, among others. This diversity suggests no single cohesive function ties all proteins together, so a concise label cannot be confidently assigned.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0045892","count":3},{"id":"GO:0021764","count":3},{"id":"GO:0061504","count":3},{"id":"GO:0051726","count":3}]},{"hash":"2239006830792955188","title":"Telomere maintenance and recombination repair","description":"This cluster is dominated by GO terms related to telomere protection, subtelomeric heterochromatin, telomeric D-loop disassembly, and replication-born double-strand break repair via sister chromatid exchange, with additional references to meiotic recombination regulation. These together point to a module focused on genome stability at chromosome ends and during recombination, rather than broad metabolic processes, despite some noisy terms. ","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031848","count":3},{"id":"GO:0035390","count":3},{"id":"GO:0072362","count":3},{"id":"GO:0010520","count":3},{"id":"GO:1903770","count":3}]},{"hash":"1038584467740216666","title":"Bacterial sugar catabolism","description":"This cluster centers on degradation and processing of various sugars (xylose, fucose, gluconate, glucuronate) and glycerol, plus glycerol-3-phosphate biosynthesis, indicating bacterial carbohydrate metabolism. The presence of antibiotic biosynthetic process and quorum sensing hints at regulatory/metabolic connections, but the primary theme remains sugar catabolism.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0046835","count":1},{"id":"GO:0046167","count":1},{"id":"GO:0019521","count":1}]},{"hash":"842026912182942199","title":"Synaptic Transmission and Endocytic Trafficking","description":"This cluster is dominated by GO terms for neurotransmitter secretion, regulation of synaptic transmission (GABAergic), and ubiquitin-dependent endocytosis, indicating a core theme of synaptic vesicle cycling and receptor trafficking at the neuronal synapse. Additional terms about autophagosome localization and trans-synaptic signaling modulation fit within the broader trafficking and signaling context, while some terms (like centriole elongation and RNA Pol III transcription) are less tied to the main theme. Overall, the label captures the principal function of the cluster.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007269","count":3},{"id":"GO:0038028","count":2},{"id":"GO:0070086","count":2},{"id":"GO:0061753","count":2},{"id":"GO:1905433","count":2}]},{"hash":"1677658669632440950","title":"Nuclear gene expression and DNA processing","description":"Based on the top GO terms, the cluster centers on nuclear functions related to gene expression and genome maintenance, including DNA-templated transcription, Okazaki fragment processing during replication, maturation of rRNA, and RNA processing (branch site recognition). Additional terms point to chromatin modification (histone acetylation) and protein complex formation, with a few outliers like mitochondria-nucleus signaling and SREBP signaling that may reflect broader regulatory connections. Overall, the set suggests a core, nucleus-focused housekeeping module rather than a single cohesive pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051441","count":1},{"id":"GO:0031930","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1722295248088691904","title":"ECM Remodeling in Bone and Lung Morphogenesis","description":"This cluster pulls together GO terms related to extracellular matrix turnover and skeletal development (bone resorption, intramembranous ossification, collagen catabolic process, proteolysis) and lung morphogenesis (epithelial tube branching, terminal unit subdivision). While there are some broader catabolic terms, the predominant pattern is matrix remodeling driving tissue morphogenesis in bone and lung, supporting a cohesive theme of ECM remodeling during development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":4},{"id":"GO:0060441","count":3},{"id":"GO:0001957","count":3},{"id":"GO:0050790","count":3},{"id":"GO:0060448","count":3}]},{"hash":"1027166955633868033","title":"ER-Golgi vesicle trafficking and oxidative stress response","description":"The top GO terms cluster around ER-to-Golgi vesicle transport, cellular responses to hydrogen peroxide, and redox homeostasis, with auxiliary signals in RNA stability regulation and xenobiotic response. This suggests a cohesive group involved in secretory pathway trafficking plus oxidative stress signaling. Some terms are obsolete, but the core theme remains vesicle transport coupled with stress response.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0042493","count":1},{"id":"GO:0090502","count":1},{"id":"GO:2000327","count":1},{"id":"GO:0045454","count":1}]},{"hash":"2215790913530349963","title":"Unknown","description":"There are no GO terms or functional connections among these proteins (no edges, no triangles, and the top terms list is empty), so there is no clear common function to name the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1513390381426822427","title":"Cell polarity and membrane trafficking regulation","description":"This cluster centers on terms about regulation of cell fusion/conjugation, Rho signaling, and establishing or maintaining cell polarity and cell shape, complemented by trafficking-related processes like protein transport into membrane rafts and organelle organization (ER and nuclear pore). Together these suggest a cohesive module that coordinates cytoskeletal dynamics, polarity, and membrane trafficking rather than a single isolated pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031139","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0032005","count":2},{"id":"GO:2000769","count":2},{"id":"GO:0032596","count":1}]},{"hash":"2251716364460825874","title":"Plant secondary metabolism: alkaloids and strigolactones","description":"The GO terms point to plant-specific secondary metabolism, with alkaloid metabolic process, strigolactone biosynthesis, and phenylpropanoid-related catabolic processes as prominent themes. Some terms are broader or less plant-specific (lipid catabolism, nitrogen utilization, menaquinone/prostaglandin-related processes, endocannabinoid signaling regulation, and an obsolete redox term), suggesting annotation noise. Nonetheless, the core signal is biosynthesis and degradation of plant secondary metabolites, supporting a label centered on plant secondary metabolism.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":1},{"id":"GO:0009820","count":1},{"id":"GO:0019380","count":1},{"id":"GO:0006660","count":1}]},{"hash":"629004126064375694","title":"Unknown","description":"The top terms span glycosylation (O-linked, via serine/threonine, N-acetyl-galactosamine) and a mix of plant polysaccharide metabolism (xylan, arabinan, L-arabinose) plus unrelated processes (extracellular matrix secretion, immunoglobulin production, and negative regulation of translation). There is no single coherent function uniting these terms, so there isn\u2019t a clear label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018243","count":1},{"id":"GO:0017148","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0018242","count":1},{"id":"GO:0070278","count":1}]},{"hash":"2303610086658410369","title":"Unknown","description":"The GO terms span unrelated processes\u2014from chromatin regulation and histone modification to sperm axoneme assembly, immune signaling, fungal cell wall organization, neuron development, DNA damage tolerance, and various ubiquitination and protein trafficking events\u2014indicating no coherent, single functional theme for the cluster. Therefore, the cluster is labeled Unknown with no confident representative function.","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0061186","count":3},{"id":"GO:0007288","count":3},{"id":"GO:0033128","count":3},{"id":"GO:0071347","count":3},{"id":"GO:0031505","count":3}]},{"hash":"2177297899317877591","title":"Neural development and cell-cycle proteins","description":"The top GO terms cluster around developmental processes (multicellular organism development, forebrain development, neural tube closure, skeletal system development) and fundamental cellular activities (DNA-templated transcription, DNA replication, mitotic cell cycle). This indicates a cohesive theme of developmental regulation paired with cell proliferation, with an outlier immune-related term contributing less to the overall signal.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0006351","count":2}]},{"hash":"201255950710738645","title":"Chloroplast division machinery","description":"This cluster is characterized by GO terms tied to chloroplast/plastid division and cytokinesis, including chloroplast fission, division septum assembly, FtsZ-dependent cytokinesis, division site positioning, and microtubule nucleation, which together point to plastid division machinery. Other terms such as DNA-templated transcription and cell cycle are broader or incidental and do not define the core function as strongly. ","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006012","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000917","count":1},{"id":"GO:0043093","count":1}]},{"hash":"459708980882840335","title":"Germline RNA processing and ncRNA silencing","description":"Top GO terms cluster around RNA processing and regulatory ncRNA pathways (pre-miRNA and snoRNA processing, miRNA metabolic process, regulatory ncRNA-mediated gene silencing, and rRNA catabolic process), suggesting a core function in RNA maturation and turnover. The presence of germline development terms (germarium-derived oocyte fate determination, germarium-derived female germ-line cyst formation, and polarity specification) implies these RNA processes are linked to germline development in this group.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0010586","count":1},{"id":"GO:0007294","count":1},{"id":"GO:0009944","count":1}]},{"hash":"966119495262199691","title":"Diverse Metabolic Pathways","description":"This cluster shows a mix of biosynthetic processes (menaquinone, phylloquinone, terpenoid, and antibiotic biosynthesis) and catabolic/central metabolism (valine catabolic process, phenylacetate catabolic process, TCA cycle), plus a tRNA modification term. The broad spread of metabolism-related GO terms suggests no single dominant function, so a broad label for diverse metabolic pathways is most representative.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002949","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006635","count":1},{"id":"GO:0006574","count":1}]},{"hash":"1402092180827501833","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006458","count":1},{"id":"GO:1903779","count":1},{"id":"GO:0055010","count":1},{"id":"GO:0042026","count":1}]},{"hash":"351489982308090139","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000716","count":2},{"id":"GO:0071042","count":2},{"id":"GO:0070417","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006605","count":2}]},{"hash":"647115033637230016","title":"Ribosome Biogenesis and Translation","description":"The GO terms are dominated by ribosome-related processes: cytoplasmic translation, ribosome biogenesis (including small and large subunit biogenesis and export), and tRNA modification, suggesting a cluster centered on protein synthesis machinery. Additional terms related to cell division align with growth connected to ribosome activity. This combination points to ribosome assembly and function as the core theme.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":1},{"id":"GO:0002181","count":1},{"id":"GO:1903833","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006400","count":1}]},{"hash":"1411541581769107109","title":"LPS and outer membrane biosynthesis","description":"Most terms point to biosynthesis of components of the bacterial outer membrane and cell envelope (lipid A, lipopolysaccharide core, and O antigen), with a broader note on cell wall organization. While one term mentions cell wall mannoprotein biosynthesis (more typical for fungi) and another starch biosynthesis, the dominant signal is LPS-related pathways, suggesting a cluster tied to envelope component production rather than general metabolism or signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0009243","count":1},{"id":"GO:0071555","count":1}]},{"hash":"2162424333701073687","title":"Unknown","description":"There are no top GO terms provided to guide a functional label, so no clear shared function can be inferred for these four proteins.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"979770295988126800","title":"Stress-Responsive Metabolism and Detoxification","description":"The set includes trehalose biosynthesis and heat response terms, pointing to stress protection, along with multiple catabolic processes (tyrosine/phenylalanine, methylglyoxal, xenobiotic) and antibiotic response, suggesting a cluster of proteins involved in metabolic adjustment and detoxification during stress. The RNA polymerase II transcription regulation term is less directly connected but may reflect broader regulatory ties under stress.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0005992","count":1},{"id":"GO:0070413","count":1},{"id":"GO:0034605","count":1},{"id":"GO:0006357","count":1},{"id":"GO:0006572","count":1}]},{"hash":"2097921348213747793","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0061470","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0070371","count":1},{"id":"GO:0043029","count":1}]},{"hash":"922275837839679067","title":"Golgi vesicle trafficking","description":"These proteins show strong enrichment for GO terms related to Golgi function and vesicle transport, including ER\u2194Golgi traffic (retrograde and ER\u2192Golgi), Golgi localization/inheritance, and Golgi-to-vacuole transport\u2014consistent with components of the Golgi trafficking machinery. A few terms appear to be noise (pigmentation, obsolete toxin transport), but the dominant pattern supports Golgi vesicle trafficking as the cluster theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0048313","count":1},{"id":"GO:0051645","count":1},{"id":"GO:0006896","count":1}]},{"hash":"1682541877649134876","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0006452","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0046825","count":1}]},{"hash":"1784496115068653612","title":"RNA Processing and Translation Regulation","description":"This cluster shows a set of GO terms centered on mRNA processing (splicing, polyadenylation, mRNA modification), mRNA stability, and translation initiation/reinitiation, including spliceosome-related processes and the small-subunit processome. The recurring theme is post-transcriptional RNA processing coupled with translation control, suggesting these proteins collectively govern mRNA maturation and translation reinitiation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0060211","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0034462","count":2}]},{"hash":"1147660184772384855","title":"Synaptic vesicle exocytosis and calcium signaling","description":"The top GO terms point strongly to neuronal communication, with emphasis on regulation of synaptic vesicle exocytosis, neurotransmitter secretion, calcium ion response, and long-term potentiation. While additional terms span broader signaling and non-neuronal processes (e.g., plant ABA signaling, VEGF pathway, apoptosis), the most representative cluster theme is calcium-driven synaptic transmission and vesicle release. This supports labeling the cluster as focused on synaptic vesicle exocytosis and calcium signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0007269","count":2}]},{"hash":"1322723461134432127","title":"Unknown","description":"The GO terms are extremely diverse, covering signaling cascades (calcineurin-NFAT, brassinosteroid), development (Schwann cells, skeletal muscle, lymphangiogenesis), translational control, metabolism, and even a bacterial lipid A biosynthesis term. With only four proteins and a single edge, there is no clear, cohesive functional theme tying these terms together, so this cluster appears heterogeneous and unlabeled. ","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033173","count":1},{"id":"GO:0014044","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0009742","count":1},{"id":"GO:0048741","count":1}]},{"hash":"2074287165283008704","title":"Deoxyribonucleotide Biosynthesis","description":"The cluster centers on thymidine and other deoxyribonucleotide biosynthesis processes (dTMP, dTDP, dTTP, dUDP) and nucleoside monophosphate phosphorylation, indicating a shared role in generating DNA precursors. A few unrelated terms (estrogen response, growth factor signaling, cadmium response) appear sparsely but do not outweigh the nucleotide biosynthesis theme.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046044","count":1},{"id":"GO:0046940","count":1},{"id":"GO:0043627","count":1},{"id":"GO:0006233","count":1},{"id":"GO:0046939","count":1}]},{"hash":"2010654246100924643","title":"Ion Transport and Hormone Signaling","description":"Top GO terms emphasize potassium and magnesium ion transport across the plasma membrane and regulation of cation channel activity, pointing to ion homeostasis and channel modulation. The presence of hormone- and ligand-response terms (nicotine, estradiol, testosterone) suggests hormone-responsive signaling that can interface with ion transport. Together, these indicate a cluster centered on ion transport with hormone-associated regulation rather than a single distinct function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051877","count":1},{"id":"GO:0050877","count":1},{"id":"GO:0010107","count":1},{"id":"GO:0071316","count":1},{"id":"GO:0033574","count":1}]},{"hash":"637930898697272377","title":"Osmoprotectant sugar biosynthesis and autophagy","description":"This cluster centers on biosynthesis of osmoprotectant sugars (trehalose, glucosylglycerol) and autophagy-related processes (glycophagy, macroautophagy), with associated cellular responses to heat and desiccation. The co-occurrence of trehalose/glucosylglycerol biosynthetic processes and autophagy terms suggests a stress-adaptation module targeting osmoprotection via sugar production and autophagic turnover.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005992","count":1},{"id":"GO:0046959","count":1},{"id":"GO:0090441","count":1},{"id":"GO:0061723","count":1},{"id":"GO:0016239","count":1}]},{"hash":"998736115130723558","title":"Zinc and Cadmium Ion Homeostasis and Detoxification","description":"GO terms point to zinc and cadmium detoxification, zinc transport, and intracellular homeostasis, including regulation of zinc import. This suggests the cluster groups proteins that coordinate metal ion detoxification and balance across cellular compartments.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010312","count":1},{"id":"GO:0098849","count":1},{"id":"GO:0071577","count":1},{"id":"GO:0071584","count":1},{"id":"GO:0070574","count":1}]},{"hash":"434284192449718616","title":"Mitochondrial respiration and complex II assembly","description":"This cluster is best labeled by mitochondrial energy metabolism, highlighted by GO terms for mitochondrial electron transport (NADH to ubiquinone) and mitochondrial respiratory chain complex II assembly, which point to core mitochondrial function. The other terms (translation, differentiation, histone demethylation) are more general or less mitochondria-specific and may reflect broader cellular contexts or annotation noise in a small cluster. Overall, the mitochondrial terms provide the strongest and most coherent theme for this group.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030154","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0048477","count":1},{"id":"GO:0030961","count":1}]},{"hash":"1928495703428525659","title":"Unknown","description":"The GO terms are highly diverse, spanning development, DNA replication, signaling, endocytosis, spindle attachment, transport, metabolism, and apoptosis. There isn\u2019t a single coherent function that clearly links all three proteins, so a precise label cannot be confidently assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0002774","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0072584","count":2}]},{"hash":"2179661991521495337","title":"Protein quality control and trafficking","description":"This cluster centers on proteostasis and protein handling: terms for protein catabolic processes and misfolded-protein response, alongside vesicle- and Golgi-related transport and oligomerization processes, suggesting a cohesive theme of maintaining protein integrity and intracellular trafficking, with some links to stress responses and cytoskeletal dynamics.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030163","count":2},{"id":"GO:0034214","count":2},{"id":"GO:1990048","count":2},{"id":"GO:0030420","count":2},{"id":"GO:0051260","count":2}]},{"hash":"149408254013748753","title":"EGF Signaling and Caveolin-mediated Endocytosis","description":"This cluster is best described by membrane receptor signaling and endocytic trafficking, highlighted by terms for response to epidermal growth factor and caveolin-mediated endocytosis. The other terms (translation, potassium transport, spindle attachment, etc.) may reflect incidental associations in a small cluster, so the functional connection is moderate.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0002774","count":1},{"id":"GO:0006813","count":1},{"id":"GO:0072584","count":1},{"id":"GO:0051316","count":1}]},{"hash":"2045876789251149399","title":"Unknown","description":"The top GO terms span diverse processes including immune signaling, endocytosis, cytoskeletal attachments, metabolism, cell adhesion, and development, with no single unifying function across the cluster. The scattered terms and lack of edges suggest the proteins do not share a coherent biological role detectable from these annotations.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002774","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0072584","count":2},{"id":"GO:0051316","count":2},{"id":"GO:0042517","count":2}]},{"hash":"761591845951524056","title":"Unknown","description":"The Top Terms span diverse processes from development (placenta, thymus) and cell migration to immune signaling, endocytosis, ion transport, and meiosis-related spindle attachment, with no single unifying function. This makes it unclear how these proteins function as a coherent cluster, so I assign Unknown with no confidence.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0000187","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1008537050073267968","title":"Microbial vitamin biosynthesis and metabolism","description":"The GO terms point to a metabolism-centric cluster with several biosynthetic processes (menaquinone/phylloquinone, antibiotic biosynthesis) and catabolic pathways (fatty acid beta-oxidation, valine/phenylacetate catabolism), suggesting a group of microbial enzymes involved in vitamin production and broader metabolism rather than a single coherent pathway. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006635","count":1},{"id":"GO:0006574","count":1},{"id":"GO:0042372","count":1}]},{"hash":"248171718899748265","title":"Central carbon metabolism and energy production","description":"This cluster is dominated by core energy pathways\u2014glycolytic process and TCA cycle\u2014with related redox homeostasis and broad catabolic processes (amino acids, fatty acids) that feed into energy generation. The mix of metabolic activities suggests a cohesive group focused on central carbon metabolism and energy production, with some auxiliary biosynthetic terms reflecting broader metabolic versatility in microbes.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0045454","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0019521","count":1}]},{"hash":"443557750836519922","title":"Mitochondrial respiration and redox regulation","description":"This cluster's GO terms are dominated by mitochondrial energy production and redox processes (electron transport, membrane potential, superoxide detoxification, cellular oxidant detoxification). While a few terms touch on growth or differentiation, the central theme is mitochondrial function and oxidative stress management.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":3},{"id":"GO:0006120","count":2},{"id":"GO:0042391","count":2},{"id":"GO:0019430","count":2},{"id":"GO:0010976","count":2}]},{"hash":"535649876629385601","title":"Ribosome Biogenesis Factors","description":"The strongest signals are GO terms for ribosomal small and large subunit biogenesis, suggesting these proteins are involved in ribosome assembly. The other GO terms (propionate and propanediol catabolism, acetyl-CoA biosynthesis, phosphorylation) are more diffuse and could reflect multifunctionality or annotation noise, making the ribosome-biogenesis signal the most representative here. Given the small cluster size and lack of interactions, the label is plausible but with limited confidence.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0019543","count":1},{"id":"GO:0070689","count":1}]},{"hash":"1976696870543058122","title":"Development and Lipid Metabolism","description":"This cluster centers on lipid- and energy-related GO terms (fatty acid beta-oxidation, fatty-acyl-CoA biosynthesis, carnitine biosynthesis, and regulation of gluconeogenesis), with additional development-related terms (post-embryonic development, heart and liver development). The combination suggests a coupling between metabolic state and developmental processes, potentially including nematode-specific ascaroside biosynthesis and starvation response. Therefore, \u201cDevelopment and Lipid Metabolism\u201d best captures the shared theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009791","count":1},{"id":"GO:0019439","count":1},{"id":"GO:1904070","count":1},{"id":"GO:0042594","count":1},{"id":"GO:0006111","count":1}]},{"hash":"327863857618384178","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031581","count":1},{"id":"GO:0006407","count":1},{"id":"GO:2000032","count":1},{"id":"GO:0090506","count":1},{"id":"GO:0000028","count":1}]},{"hash":"2249279932253808280","title":"Ribosome biogenesis and translation","description":"Most terms point to ribosome biogenesis and translation (SSU rRNA maturation, small-subunit assembly, ribosome biogenesis, translation, and translation reinitiation), supported by small-subunit processome assembly and related processes, with a few ancillary RNA-processing terms that may reflect broader nuclear RNA handling.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0075525","count":1}]},{"hash":"2227044940990601715","title":"Pantothenate-CoA biosynthesis and mitochondrial respiration","description":"This cluster centers on pantothenate (vitamin B5) biosynthesis and beta-alanine metabolism, which feed into CoA production, along with mitochondrial respiration terms (NADH to ubiquinone, complex II assembly). The combination suggests a theme tying CoA biosynthesis to mitochondrial energy metabolism. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019482","count":1},{"id":"GO:0033317","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0034553","count":1}]},{"hash":"181648533706077975","title":"Mitotic cytokinesis and microtubule organization","description":"This cluster is dominated by GO terms related to mitosis, cytokinesis, cell division, and microtubule organization/nucleation (e.g., FtsZ-dependent cytokinesis; mitotic cytokinesis; cell cycle; cell division; microtubule nucleation; cytoplasmic microtubule organization; mitotic spindle pole body duplication). These collectively point to a shared role in mitotic progression and spindle/microtubule dynamics, making the label representative. Some unrelated terms appear but are likely non-revalued annotations rather than core functions of the cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043093","count":1},{"id":"GO:1902408","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0007049","count":1},{"id":"GO:1905792","count":1}]},{"hash":"2267638306907013065","title":"SSU ribosome biogenesis","description":"Top GO terms cluster around ribosome biogenesis, maturation of SSU-rRNA, and small subunit assembly, plus related transcription and translation terms; together they indicate involvement in producing the small ribosomal subunit and initiating translation, supporting the label.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0030490","count":2},{"id":"GO:0006407","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0006412","count":1}]},{"hash":"819451560300468354","title":"Nuclear transcription and RNA processing components","description":"The top GO terms center on DNA-templated transcription (GO:0006351), mRNA branch site recognition (GO:0000348), maturation of 5.8S rRNA (GO:0000466), and Okazaki fragment processing in mitotic DNA replication (GO:1903461), which together point to nuclear gene expression and RNA processing. Several other terms (mitochondria-nucleus signaling, SREBP signaling, ubiquitin ligase activity in meiosis) are less directly connected, suggesting peripheral or broader roles. Overall, the core theme is nuclear transcription and RNA maturation, justifying this label with moderate confidence.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051441","count":2},{"id":"GO:0031930","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2055268746935051275","title":"Actin-driven cell migration and endosomal trafficking","description":"The top GO terms cluster around actin cytoskeleton remodeling (filopodium assembly, microspike assembly, actin cortical patch assembly) and cell migration/shape/polarity regulation, indicating actin-driven protrusive motility. Several terms also point to vesicular trafficking and phagosome/endosome dynamics (endosomal vesicle fusion, phagosome reneutralization, post-lysosomal vacuole size), suggesting a coordination between cytoskeletal remodeling and membrane trafficking. A development term appears incidental. Overall, the cluster likely represents proteins involved in actin-driven motility linked to vesicle trafficking.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044655","count":1},{"id":"GO:0044656","count":1},{"id":"GO:0030049","count":1},{"id":"GO:0021592","count":1},{"id":"GO:0071963","count":1}]},{"hash":"400142437086553694","title":"Oxidative stress response and DNA repair","description":"The proteins appear linked to managing oxidative damage and genome maintenance: terms include cell redox homeostasis, cellular response to hydrogen peroxide, and base-excision repair, alongside xenobiotic response. The presence of these stress-response and repair processes suggests a cluster focused on protecting cells from oxidative damage and maintaining DNA integrity, with a few broader regulatory terms that may reflect auxiliary roles.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":1},{"id":"GO:0090502","count":1},{"id":"GO:2000327","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0046856","count":1}]},{"hash":"1284628216995961486","title":"Chromatin silencing and transcription regulation","description":"These proteins cluster around chromatin-related processes: heterochromatin formation, regulation of transcription, and nucleosome density. The recurrent GO terms indicate roles in chromatin silencing and DNA-templated transcription, suggesting a core function in regulating chromatin state and gene expression, despite a few obsolete terms that may reflect outdated annotations. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061186","count":3},{"id":"GO:0045668","count":3},{"id":"GO:0000117","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0061587","count":3}]},{"hash":"2143441415693318881","title":"Mitochondrial Bioenergetics and Transport","description":"The Top Terms are dominated by mitochondrial functions: regulation of membrane potential, various mitochondrial transport processes (NAD, thiosulfate, iron, ATP), and metabolic shuttles like malate-aspartate. This suggests the cluster groups proteins involved in mitochondrial energy production and metabolite movement rather than other cellular processes. A liver regeneration term appears less central and likely incidental. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0097274","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0015709","count":1}]},{"hash":"728545165289546298","title":"Unknown","description":"The top terms span transcription regulation, neural development, metabolism, cell cycle, protein modification, and autophagy with no clear unifying function across the three proteins. The diversity and small cluster size suggest no coherent biological theme, so a generic Unknown label is appropriate. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045892","count":2},{"id":"GO:0021764","count":2},{"id":"GO:0061504","count":2},{"id":"GO:0051726","count":2},{"id":"GO:0009229","count":2}]},{"hash":"362931018006393347","title":"ER Membrane Targeting and Insertion","description":"The prominent GO terms point to ER-associated protein handling, including post-translational targeting to the ER membrane and tail-anchored membrane protein insertion into the ER membrane, with vesicle-mediated transport also relevant. Although several terms are obsolete, the remaining terms consistently reflect ER localization and membrane insertion/trafficking, suggesting a small cluster focused on ER membrane targeting/insertion processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046855","count":2},{"id":"GO:0016192","count":1},{"id":"GO:1904378","count":1},{"id":"GO:0071816","count":1},{"id":"GO:0048767","count":1}]},{"hash":"1007311403713489407","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms related to ubiquitination and proteasomal degradation (protein ubiquitination, autoubiquitination, and SCF-dependent ubiquitin-mediated protein catabolic processes), indicating a shared role in tagging proteins for degradation. A few other terms about meiotic chromosome movement and DNA repair appear but are less central to the main theme. Overall, the proteins seem to function within the ubiquitin-proteasome system.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051759","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0000717","count":1}]},{"hash":"2025944226455497247","title":"Glycolysis and glycogenolysis","description":"The top GO terms are strongly glycolysis- and carbohydrate metabolism-centered, including canonical glycolysis, glycolysis from storage polysaccharide, fructose-6-phosphate metabolism, and glycogen catabolic process, pointing to enzymes involved in glucose generation and utilization. A few RNA-processing and transcription-related terms appear but do not define the main function, suggesting possible multifunctional annotations or incidental associations. Thus, the cluster is best characterized as glycolysis/glycogenolysis with high confidence.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":1},{"id":"GO:0006002","count":1},{"id":"GO:0005980","count":1},{"id":"GO:0093001","count":1},{"id":"GO:0061621","count":1}]},{"hash":"498712736708519404","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071035","count":1},{"id":"GO:0071033","count":1},{"id":"GO:0000973","count":1},{"id":"GO:1901917","count":1},{"id":"GO:0034476","count":1}]},{"hash":"1512902258738465283","title":"Nuclear transcription and DNA replication","description":"The most represented GO terms center on nuclear genome information processing, including DNA-templated transcription and Okazaki fragment processing during mitotic DNA replication, with supporting signals from rRNA maturation. While a few terms (e.g., mitochondria-nucleus signaling, SREBP pathway) are less cohesive with this core theme, the evident pattern suggests involvement in nuclear transcription and DNA replication processes, hence the label. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051441","count":3},{"id":"GO:0031930","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0032933","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1707661488817891756","title":"Golgi- and vacuole-targeted vesicle trafficking","description":"The GO terms indicate a core role in Golgi-related vesicle transport (ER-to-Golgi, intra-Golgi, Golgi to vacuole, retrograde endosome-to-Golgi, and vesicle fusion with Golgi) and protein localization to vacuoles and membranes, with an overarching theme of Golgi-mediated trafficking and organelle-targeting. The outlier term for muscle movement appears unrelated to the main trend, which does not undermine the predominant Golgi trafficking pattern.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006891","count":1},{"id":"GO:0048280","count":1},{"id":"GO:0006896","count":1}]},{"hash":"339445346237597912","title":"Nuclear RNA Processing and Translation Control","description":"This cluster centers on RNA processing and gene expression regulation in the nucleus and during translation. Top GO terms touch on splicing site recognition, regulation of mRNA poly(A) tail shortening/polyadenylation, small-subunit processome assembly, and mRNA stability under stress, plus translation reinitiation and ncRNA-mediated gene silencing. The combination of nuclear RNA processing steps with translation initiation/reinitiation and regulatory ncRNA activity suggests a coherent theme of preparing and regulating mRNA transcripts for translation, possibly under stress or viral contexts. Thus a label like Nuclear RNA Processing and Translation Control captures the shared functional themes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051457","count":1},{"id":"GO:0042517","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006376","count":1},{"id":"GO:0060211","count":1}]},{"hash":"712144726359471146","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0006452","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0046825","count":1}]},{"hash":"1086989018124559121","title":"Metal Ion Transport and Homeostasis","description":"The terms show strong signals for zinc, copper, and cadmium ion transport and calcium ion homeostasis, pointing to a shared role in cellular metal balance. Less consistent terms (carbohydrate metabolism, testosterone response) are present but appear secondary to metal ion transport.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006045","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0033574","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0005975","count":2}]},{"hash":"187579357297552696","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"These proteins are collectively annotated with mitochondrial transport and energy metabolism processes: regulation of mitochondrial membrane potential, transmembrane transport of NAD, iron, ATP, and malate-aspartate shuttle activity. The presence of thiosulfate transport and a negative regulation of necroptotic process fits with mitochondrial roles in metabolism and cell death control, with a potential link to tissue regeneration contexts. Thus the label Mitochondrial Transport and Membrane Potential Regulation captures the main theme.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0097274","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0015709","count":1}]},{"hash":"329617805823913178","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0006452","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0046825","count":1}]},{"hash":"1788368713629091111","title":"Multi-substrate catabolic metabolism","description":"This cluster centers on various catabolic processes across multiple substrates (carbohydrates, monosaccharides, glycerol, alanine, ketones, 6-sulfoquinovose) and related oxidative metabolism, suggesting a broad role in energy-yielding breakdown rather than a single substrate pathway. A few tokens (immune signaling regulation, potassium transport) may be incidental annotations, but the dominant theme is diverse catabolic metabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":1},{"id":"GO:0019588","count":1},{"id":"GO:0046365","count":1},{"id":"GO:0039534","count":1},{"id":"GO:0042182","count":1}]}]