[{"hash":"457012867813029837","title":"Mitochondrial energy metabolism and cofactor biosynthesis","description":"The top GO terms cluster around mitochondrial processes and essential cofactors: mitochondrial electron transport (GO:0006120), thiamine diphosphate biosynthesis (GO:0009229), and quinolinate biosynthetic process (GO:0019805) which ties to NAD biosynthesis, plus L-alanine catabolic process (GO:0042853) and tRNA methylation (GO:0030488). These point to energy metabolism in mitochondria and the production of key cofactors, with some additional stress-responsive terms (response to lipopolysaccharide/herbicide) likely reflecting broader cellular stress responses. Overall, the theme is mitochondrial metabolism and cofactor biosynthesis. ","confidence":"Medium","size":29,"edges":71,"triangles":80,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0043046","count":6},{"id":"GO:0032496","count":6},{"id":"GO:0006120","count":5},{"id":"GO:0042853","count":5}]},{"hash":"754701845887483427","title":"Neural development and innate immune signaling","description":"The cluster prominently features neural development terms like axonogenesis and corpus callosum development, along with dopamine response and broad transcriptional activity, while also showing innate immune signals (innate immune response, defense to Gram-positive bacterium, interferon-beta production). This suggests a thematic link between neural development processes and immune/signaling pathways, making the label representative though the terms span multiple functions. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":11},{"id":"GO:0071276","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0071260","count":7},{"id":"GO:0045359","count":7}]},{"hash":"1163453749105319525","title":"Unknown","description":"Top GO terms are scattered across development (dorsal/ventral axis specification, brain boundary development), adhesion (integrin activation, focal adhesion assembly), and other processes (cholesterol transport, autophagosome assembly, myelin assembly, immunoglobulin production). The lack of a unifying function and no reported interactions (Edges: 0) suggest these proteins do not form a coherent functional cluster. ","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007311","count":1},{"id":"GO:0009951","count":1},{"id":"GO:0033622","count":1},{"id":"GO:0030917","count":1},{"id":"GO:2001274","count":1}]},{"hash":"1188811446481734191","title":"Ubiquitination and Proteasomal Degradation","description":"The top GO terms cluster around ubiquitination processes (protein autoubiquitination, K48- and K6-linked ubiquitination), ubiquitin-dependent degradation pathways (SCF and ERAD), and related modification (neddylation). This points to a cohesive functional group of proteins involved in tagging substrates for proteasomal degradation and ubiquitin signaling, with additional associations to peroxisome import and DNA repair pathways that can interface with ubiquitination.","confidence":"High","size":28,"edges":104,"triangles":167,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0045116","count":7},{"id":"GO:0016032","count":7}]},{"hash":"680249191298655188","title":"RNA processing and translation control","description":"This cluster is enriched for post-transcriptional RNA regulation functions, including translation initiation (GO:0002188, GO:0097010; GO:0006446) and regulation of mRNA splicing via the spliceosome (GO:0000380, GO:0048025, GO:0000381), as well as mRNA export and stabilization (GO:0006406, GO:0048255). The combination of initiation factor assembly with spliceosome-mediated processing and mRNA handling indicates proteins coordinating RNA maturation and the control of translation, rather than a single, isolated pathway. ","confidence":"High","size":28,"edges":58,"triangles":4,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0097010","count":2},{"id":"GO:0000380","count":2},{"id":"GO:1903586","count":2},{"id":"GO:0006446","count":2}]},{"hash":"1909041724910890800","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0070059","count":5},{"id":"GO:0070317","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0000466","count":4}]},{"hash":"2043151799263154928","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms tied to protein synthesis and ribosome assembly\u2014translation, cytoplasmic translation, ribosome biogenesis (including small subunit biogenesis), and ribosomal subunit export\u2014along with tRNA modification. These consistently point to core ribosome/translation machinery, with a surrounding note of cell cycle coordination, but the central theme remains ribosome production and function.","confidence":"High","size":28,"edges":9,"triangles":0,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0007049","count":4},{"id":"GO:1901001","count":3},{"id":"GO:0006400","count":3}]},{"hash":"182486283261589012","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046638","count":2},{"id":"GO:0009636","count":2},{"id":"GO:2000114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1762719748292712891","title":"Angiogenesis and placental development","description":"The cluster is dominated by angiogenesis and placenta development terms, with supporting signals from focal adhesion assembly and mast cell differentiation, suggesting a vascular/placental development theme; a few terms (MHC I antigen presentation, meiotic spindle) may reflect broader or multifunctional annotations.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0014850","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0045766","count":3},{"id":"GO:0001525","count":3}]},{"hash":"366917256644579541","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (translation initiation, stress responses like cadmium and glucose limitation, various developmental pathways, transcription, cytoskeletal dynamics, and immune defense). There is no single coherent function tying these terms together, so a meaningful, specific label cannot be assigned beyond Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0001403","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0043547","count":3}]},{"hash":"2279169276878992659","title":"Innate immune cytokine signaling","description":"The terms point to innate immune functions: positive regulation of IL-8 production, regulation of cytokine production, and interferon production (including type II), plus inflammatory response and a MyD88-independent TLR signaling pathway, all indicating cytokine-driven innate immunity. There are a couple of plant-related GO terms present, but the dominant theme across the cluster is cytokine modulation and TLR-mediated innate immune signaling in response to pathogens such as fungi.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045416","count":1},{"id":"GO:0009729","count":1},{"id":"GO:0050707","count":1},{"id":"GO:0006963","count":1},{"id":"GO:0045359","count":1}]},{"hash":"1018104849814380872","title":"Mitotic Cell Cycle Regulation and Kinetochore Localization","description":"This cluster is dominated by mitosis-related GO terms: negative regulation of cyclin-dependent protein serine/threonine kinase activity points to cell cycle control; protein localization to kinetochore and chromosome passenger complex localization to spindle midzone implicate chromosome segregation machinery; mitotic cell cycle, mitotic cytokinesis checkpoint signaling, and positive regulation of mitotic sister chromatid biorientation all converge on mitosis and proper chromosome partitioning. The presence of transcription (DNA-templated transcription) and rhythm terms (circadian rhythm) likely reflect broader or pleiotropic annotations rather than a core theme, but do not override the clear mitotic signal. Therefore, the label 'Mitotic Cell Cycle Regulation and Kinetochore Localization' captures the cluster\u2019s main function with high confidence.","confidence":"High","size":27,"edges":45,"triangles":53,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045736","count":8},{"id":"GO:0034501","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0031647","count":5},{"id":"GO:0007601","count":5}]},{"hash":"463980889485123421","title":"Embryonic Development and Cell Division","description":"The cluster is dominated by terms for DNA replication, the mitotic cell cycle, and cell division, pointing to cellular proliferation. It also includes developmental processes such as nervous system development, mesoderm formation, and embryonic cranial skeleton morphogenesis, which together suggest roles in embryogenesis and tissue patterning. While there are immune signaling and RNA processing terms present, the prevailing pattern centers on growth and development, with proliferation linked to developmental processes. ","confidence":"Medium","size":27,"edges":41,"triangles":28,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0000278","count":8},{"id":"GO:0050852","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0048026","count":5}]},{"hash":"2028568113973007285","title":"Bacterial metabolism and biosynthesis","description":"This cluster is enriched for a variety of metabolic biosynthetic and catabolic processes, including antibiotic biosynthesis, glycolysis, fatty acid beta-oxidation, and biosynthesis of cofactors like menaquinone and phylloquinone, along with amino acid catabolism (valine, phenylacetate). This points to a broad metabolic module in bacteria. One outlier term (substantia nigra development) likely reflects misannotation, but does not disrupt the overall metabolic theme.","confidence":"Medium","size":27,"edges":153,"triangles":591,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0006574","count":7},{"id":"GO:0009245","count":7},{"id":"GO:0006096","count":6},{"id":"GO:0021762","count":6}]},{"hash":"985875035288249553","title":"Neurodevelopment and cellular stress responses","description":"The cluster is dominated by neural development terms (forebrain development, neural tube closure, multicellular organism development) suggesting a neurodevelopmental program, while other top terms point to transcription, cell cycle, and stress-related pathways (ER stress\u2013triggered apoptosis, cadmium response, immune defense). This pairing implies proteins involved in neurodevelopment that are modulated by cellular stress signals.","confidence":"Medium","size":27,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":16},{"id":"GO:0006351","count":14},{"id":"GO:0001403","count":14},{"id":"GO:0071276","count":14},{"id":"GO:0030900","count":14}]},{"hash":"1481314956064916878","title":"Cytosolic Translation and RNA Processing","description":"The cluster is strongly characterized by translation-related GO terms (translation; regulation of translation; cytosolic ribosome assembly) and RNA metabolism (negative regulation of mRNA splicing via spliceosome), pointing to a group of proteins involved in cytosolic protein synthesis and RNA processing/regulated splicing. While a few other terms appear, they are less central to the dominant theme, supporting a cohesive translation/RNA-processing cluster.","confidence":"High","size":27,"edges":314,"triangles":2156,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0009615","count":1},{"id":"GO:0045787","count":1},{"id":"GO:0006417","count":1}]},{"hash":"713285798312213448","title":"Amino acid biosynthesis and carbon metabolism","description":"This cluster is enriched for L-tyrosine and L-valine biosynthetic processes, plus several catabolic and glyoxylate-related metabolic terms, and NADPH regeneration. This combination points to a general metabolic module involved in amino acid production and broader carbon flux, rather than a single defined pathway. The sporulation term appears as an outlier; most terms cluster around biosynthesis and redox-balanced carbon metabolism, supporting a broad metabolic role.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006571","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042183","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0046487","count":2}]},{"hash":"579707735000282800","title":"Drosophila development and cell-cycle regulation","description":"This cluster features GO terms spanning developmental processes (fat cell differentiation, chitin-based larval cuticle pattern formation, oocyte localization) as well as core cell-cycle events (cell cycle, mitotic sister chromatid separation, cell migration). There are also regulatory processes such as positive regulation of kinase activity and mRNA decay/export, suggesting coordinated control of growth, differentiation, and division during development. The mix points to a theme of developmental growth regulation in Drosophila.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0033674","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0045444","count":2}]},{"hash":"645109522393056052","title":"TLR/NLRP3 Innate Immune Signaling","description":"The GO terms point to LPS detection, TLR signaling, NF-kB activation (I-kappaB phosphorylation), interferon-beta production, and NLRP3 inflammasome regulation, indicating a shared role in innate immune sensing and inflammatory signaling. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:1900227","count":1},{"id":"GO:0051901","count":1},{"id":"GO:0032497","count":1},{"id":"GO:0061364","count":1}]},{"hash":"1196509019936768195","title":"Autophagy-Linked Vesicle Trafficking","description":"The GO terms point to vesicle trafficking between the ER and Golgi and retrograde transport, along with autophagy-related processes (autophagosome maturation, Cvt pathway). This pattern suggests a functional cluster centered on vesicle trafficking that supports autophagy and vacuolar targeting, rather than chromatin or ribosomal modification functions. Some methylation-related terms are present but appear less representative of the main theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006890","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0097352","count":2},{"id":"GO:0050830","count":2}]},{"hash":"531135442542808864","title":"Energy metabolism and developmental processes","description":"The top GO terms point to metabolic regulation, including ketone body and short-chain fatty acid catabolism, response to starvation, and insulin secretion in response to glucose\u2014indicating energy metabolism and metabolic regulation. At the same time, there are developmental terms for heart, brain, and adipose tissue development, suggesting a link to developmental processes. Given this mix, the cluster seems to capture general metabolic energy handling with developmental associations rather than a single, tightly focused function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":1},{"id":"GO:0014823","count":1},{"id":"GO:0060612","count":1},{"id":"GO:0046952","count":1},{"id":"GO:0007420","count":1}]},{"hash":"1966206540314554184","title":"RNA Splicing and Surveillance Machinery","description":"The top GO terms cluster around spliceosome-mediated RNA processing (mRNA splicing, cis splicing, spliceosomal disassembly) and RNA quality control (nonsense-mediated decay, mRNA surveillance, post-transcriptional gene silencing), plus transcription termination, indicating a cohesive role in RNA processing and surveillance. Some terms relate to ribosomal biogenesis and DNA recombination but the dominant theme is splicing and RNA decay pathways.","confidence":"High","size":26,"edges":254,"triangles":1425,"max_degree":25,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":14},{"id":"GO:0031047","count":14},{"id":"GO:0006369","count":13},{"id":"GO:0045292","count":11},{"id":"GO:0042273","count":9}]},{"hash":"859997171344633881","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for rRNA maturation (LSU and 5.8S), ribosome biogenesis, and translation processes (preinitiation complex formation, initiation, and reinitiation), indicating a coherent role in ribosome assembly and protein synthesis. Some spliceosome-related and ncRNA silencing terms appear as ancillary processes, but the primary signal centers on ribosome formation and function.","confidence":"High","size":26,"edges":97,"triangles":190,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0000466","count":6},{"id":"GO:0000398","count":6},{"id":"GO:0042254","count":5}]},{"hash":"1548622456151028190","title":"Translation and Ribosome Biogenesis","description":"This cluster is dominated by GO terms for translation (including cytoplasmic translation and translational termination) and ribosome biogenesis, with supporting links to cell growth and division. A few terms such as response to antibiotic may reflect ribosome-targeted stress responses, but the core theme clearly centers on the protein synthesis machinery. ","confidence":"High","size":26,"edges":48,"triangles":123,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":3}]},{"hash":"2224260231146140163","title":"Mitotic spindle dynamics","description":"Top GO terms point to core mitotic machinery: plus-end microtubule depolymerization, spindle midzone assembly, mitotic centrosome separation, and metaphase chromosome recapture, indicating spindle assembly and chromosome segregation. Additional terms reference cytoskeletal organization, cell plate cytokinesis, and cell junction maintenance, suggesting broader cytoskeletal remodeling during cell division and development. Overall, the cluster appears to be enriched for proteins involved in mitotic spindle function and cytoskeletal dynamics.","confidence":"High","size":26,"edges":119,"triangles":254,"max_degree":25,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035617","count":12},{"id":"GO:0021685","count":11},{"id":"GO:0000911","count":11},{"id":"GO:0072092","count":11},{"id":"GO:0045218","count":11}]},{"hash":"2211433199758676146","title":"Nuclear RNA Processing and Ribosome Biogenesis","description":"This cluster is dominated by rRNA maturation (SSU/5.8S/LSU) and ribosomal large subunit biogenesis terms, plus spliceosome-mediated mRNA splicing, indicating a nucleolar/nuclear program of RNA processing and ribosome assembly. Additional terms point to protein quality control (ubiquitin-dependent ERAD) and regulation of protein kinases/GTPases, suggesting broader roles in cellular signaling and proteostasis, but the core signal remains RNA processing and ribosome biogenesis.","confidence":"Medium","size":26,"edges":16,"triangles":1,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":9},{"id":"GO:0000463","count":6},{"id":"GO:0042273","count":6},{"id":"GO:0000466","count":6},{"id":"GO:0000462","count":6}]},{"hash":"1170961551660865769","title":"Innate immunity and NLRP3 inflammasome regulation","description":"The cluster\u2019s top GO terms center on innate immune defense (defense response to virus, innate immune response, defense against Gram-positive bacteria) and specifically on regulation of the NLRP3 inflammasome, plus ubiquitination-related processes. While kidney development terms appear, the dominant signal ties to innate immunity and ubiquitin-mediated regulation of inflammasomes, suggesting a cohesive theme around immune defense and inflammasome control rather than kidney morphogenesis. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0072237","count":3},{"id":"GO:0036303","count":3},{"id":"GO:0050830","count":3}]},{"hash":"149719663804336172","title":"Lipid metabolism and vesicle trafficking regulation","description":"Most terms cluster around lipid metabolism (sphingolipid, phosphatidylcholine, phosphatidylinositol, fatty acid biosynthesis) and vesicle-related processes (IP3 signaling, vesicle fusion, insulin secretion), suggesting the proteins participate in membrane lipid biosynthesis and vesicle trafficking; a few terms like centriole elongation and ribosomal export are less central to this theme.","confidence":"Medium","size":26,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0061511","count":2},{"id":"GO:0090153","count":1},{"id":"GO:0032959","count":1},{"id":"GO:0046470","count":1},{"id":"GO:0032024","count":1}]},{"hash":"1207798708995485723","title":"Small-molecule and vitamin transmembrane transporters","description":"The top GO terms are dominated by transmembrane transport of diverse nutrients and compounds (amino acids, thiamine, vitamins, carbohydrates, glycerophosphodiesters) and even drug transport (daunorubicin), indicating a cluster enriched for membrane transporter proteins. A couple of terms about RNA processing/repair appear as outliers, but the core theme is membrane transport.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070651","count":2},{"id":"GO:0003333","count":2},{"id":"GO:0015888","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0043215","count":2}]},{"hash":"321344665322433195","title":"Transcription Regulation and Proteostasis","description":"The top GO terms cluster around two related axes: transcriptional regulation (positive regulation of DNA binding and transcription elongation by RNA Pol II) and protein quality control (protein unfolding, proteasome regulatory particle assembly, cellular response to misfolded protein), with supporting signals of stress response (corticosterone) and DNA repair (UV-damage excision repair). This suggests a cohesive theme of managing gene expression while maintaining proteome integrity under stress.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043388","count":2},{"id":"GO:0045654","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0051412","count":2}]},{"hash":"611911570714128186","title":"Mitochondrial redox metabolism","description":"The top GO terms are dominated by redox-related processes: cellular redox homeostasis, cellular oxidant detoxification, hydrogen peroxide biosynthetic process, and ubiquinone/quinolinate biosynthesis, plus sulfur oxidation, which all point to mitochondrial electron transport and oxidative stress management. There are a few brain-development terms (multicellular organism development, substantia nigra development, corticosterone response) that may reflect tissue-specific roles or secondary associations, but the strongest signal is mitochondrial redox metabolism. ","confidence":"High","size":25,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0051412","count":3}]},{"hash":"1754502998298486148","title":"Ribosome Biogenesis and Translation","description":"GO terms strongly indicate ribosome production and function: translation (GO:0006412), ribosome biogenesis (GO:0042254), large/ small subunit biogenesis (GO:0042273, GO:0000028) and rRNA maturation (GO:0000462). This pattern points to proteins involved in assembling ribosomes and supporting protein synthesis, with additional transcription-related terms likely reflecting shared RNA-processing steps rather than a different core function.","confidence":"High","size":25,"edges":146,"triangles":403,"max_degree":24,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:0042254","count":9},{"id":"GO:0042273","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0000028","count":3}]},{"hash":"1869365129475769815","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":3,"triangles":1,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000466","count":8},{"id":"GO:0000463","count":7},{"id":"GO:0000462","count":6},{"id":"GO:0042273","count":6},{"id":"GO:0000398","count":6}]},{"hash":"663376534709174616","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":10,"triangles":0,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0042273","count":4}]},{"hash":"1211593593289478368","title":"RNA processing and ribosome biogenesis","description":"Predominant terms point to RNA processing and ribosome biogenesis: transcription termination, splicing, tRNA processing, preribosome large subunit assembly, LSU/SSU rRNA maturation, and snRNP assembly. Together these indicate a nucleus-centric RNA maturation and ribosome assembly function; a few terms like ABA response and heterochromatin formation appear peripheral.","confidence":"High","size":25,"edges":26,"triangles":30,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0008033","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0000463","count":3}]},{"hash":"680964073464444377","title":"Lipid Biosynthesis and Membrane Trafficking Regulation","description":"Based on the top GO terms, the cluster centers on lipid metabolism (sphingolipid, phosphatidylcholine, phosphatidylinositol, fatty acid biosynthesis) and related signaling/membrane processes (regulation of synaptic vesicle exocytosis, IP3 biosynthesis). The presence of regulatory terms for vesicle exocytosis suggests a link to membrane trafficking, while lipid biosynthesis terms point to membrane dynamics. A few terms (mating projection growth, ribosomal export) are peripheral, but overall a coherent theme of lipid metabolism intertwined with vesicle regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010796","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0090153","count":2},{"id":"GO:0032959","count":2}]},{"hash":"373537420498897199","title":"Telomere maintenance and telomerase RNA localization to Cajal bodies","description":"The top GO terms cluster around telomerase activity and telomere maintenance via telomerase, including positive regulation of telomerase and RNA localization to Cajal bodies (and scaRNA localization). This suggests a shared function in telomere maintenance and RNA processing within Cajal bodies, with supporting signals from cell cycle-related terms; the cocaine/ischemia responses appear peripheral. ","confidence":"High","size":24,"edges":179,"triangles":713,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051973","count":8},{"id":"GO:0032212","count":8},{"id":"GO:1904874","count":7},{"id":"GO:0007049","count":7},{"id":"GO:0042220","count":7}]},{"hash":"40183399876801246","title":"ER-Golgi trafficking and reticulophagy","description":"The cluster is enriched for terms describing ER-to-Golgi transport, CVT pathway targeting, reticulophagy, and general protein translocation/localization, indicating a shared function in intracellular trafficking and ER-associated autophagy, with some peripheral stress-response terms.","confidence":"High","size":24,"edges":16,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0032258","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0071806","count":3}]},{"hash":"935258608821985893","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":46,"triangles":10,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032981","count":2},{"id":"GO:0009793","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0090617","count":2}]},{"hash":"897637442567985358","title":"Unknown","description":"The GO terms are highly heterogeneous, ranging from translation and elongation to various lipid, sterol, and nitrogen metabolism, plus tissue-specific processes like myelin maintenance and sebaceous gland differentiation. There is no single cohesive biological theme or shared pathway that ties these terms together, and the few metabolic terms span fungi and animals, making a precise, representative label inappropriate. Therefore, Unknown with None.","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0032286","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0001949","count":1},{"id":"GO:0006636","count":1}]},{"hash":"1598894872613336729","title":"Bacterial cell wall and LPS biosynthesis","description":"This cluster is dominated by GO terms for cell wall organization and biosynthesis of lipopolysaccharides, including O antigen and ether lipids, pointing to bacterial envelope assembly as the central theme. Additional terms like galactose catabolic process and DNA-templated transcription suggest broader metabolic and growth functions; however, the sparse connectivity (Edges: 1, Triangles: 0) means the envelope biosynthesis signal is plausible but not definitive.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:1902987","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0009103","count":3}]},{"hash":"1314840253059525150","title":"DNA replication and kinetochore cell cycle","description":"This cluster shows strong enrichment for nuclear processes tied to DNA replication (GO:0006260), kinetochore localization (GO:0034501), and meiotic cell cycle (GO:0051321), suggesting a module of chromosome duplication/segregation machinery. Additional terms hint at protein processing and stress responses (unfolded protein response, ER-to-Golgi transport) and peripheral signals (Schwann cell development, responses to morphine/cocaine/lead), indicating some functional breadth but a core cell-cycle signature.","confidence":"Medium","size":23,"edges":97,"triangles":252,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0014044","count":9},{"id":"GO:0043278","count":9},{"id":"GO:0010288","count":9}]},{"hash":"1631768500232831485","title":"Ribosome Biogenesis and rRNA Maturation","description":"The cluster is dominated by GO terms for ribosome biogenesis, ribosomal large subunit biogenesis, and maturation of both LSU- and SSU-rRNA, along with DNA-templated transcription, which together indicate proteins involved in ribosome assembly and rRNA processing. A separate defense response term appears less central to the core theme, likely an annotation artifact. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":4}]},{"hash":"701260665595848445","title":"Transmembrane Metabolite and Cofactor Transport","description":"The cluster is dominated by GO terms for transport of various metabolites and cofactors across membranes (deoxynucleotides, NAD, CoA, thiosulfate, mitochondrial ATP) and regulation of mitochondrial membrane potential, pointing to a cohesive role in transmembrane metabolite exchange and energy-related transport, with some growth/regeneration terms reflecting broader cellular contexts.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030302","count":6},{"id":"GO:0035352","count":6},{"id":"GO:0007565","count":6},{"id":"GO:1990544","count":6},{"id":"GO:0051881","count":6}]},{"hash":"579437302120846767","title":"Cilium Assembly and Motility","description":"The cluster is dominated by GO terms tied to cilia and flagella function: axoneme assembly, cilium movement, flagellated sperm motility, and left-right symmetry determination. While there are a few other terms, the recurrent theme is ciliogenesis and microtubule-based motility, indicating these proteins largely participate in ciliary structure and movement.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904526","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0060294","count":2},{"id":"GO:0003351","count":2},{"id":"GO:0007368","count":2}]},{"hash":"2177154819188332725","title":"Immune Receptor Signaling and Transcriptional Activity","description":"This cluster is dominated by GO terms for T cell and B cell receptor signaling, as well as VEGF receptor signaling and other serine/threonine kinase pathways, indicating a common theme of surface-receptor\u2013driven signaling leading to transcriptional responses. Additional terms about transcription (DNA-templated transcription, NF-kappaB activity) and protein turnover (proteasomal degradation) support a coherent signaling-to-transcription module in immune/vascular contexts, though a couple terms (corpus callosum development, pollen recognition) are less clearly connected and may reflect broader annotation. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033138","count":4},{"id":"GO:0032436","count":3},{"id":"GO:0022038","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0007178","count":3}]},{"hash":"401552388847686232","title":"Neural development and synaptic signaling","description":"The most represented GO terms center on neural development and function\u2014axonogenesis, Schwann cell development, visual perception, long-term potentiation, response to muscle activity, and multicellular organism development\u2014along with signaling-related terms like regulation of protein kinase activity and phosphorylation. While innate immune response and apoptosis regulation appear, the dominant theme ties to neural differentiation, development, and synaptic signaling. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007409","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0014044","count":3}]},{"hash":"1992460574840206704","title":"RNA processing and ribosome biogenesis","description":"Most top GO terms center on RNA maturation/processing (mRNA capping, m7 methylation) and rRNA maturation, plus ribosome biogenesis and translation-related activity. This pattern suggests a cluster tied to RNA metabolism and ribosome assembly, with a couple of outliers (DNA replication, sterol biosynthesis) that may reflect secondary associations rather than core function.","confidence":"High","size":22,"edges":37,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0006260","count":2}]},{"hash":"823822743327530843","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1990181","count":1},{"id":"GO:0015937","count":1},{"id":"GO:0015941","count":1},{"id":"GO:0006139","count":1}]},{"hash":"1597456563759815627","title":"Fatty acid metabolism and redox detoxification","description":"This cluster centers on lipid metabolism, with multiple terms for fatty acid biosynthesis, long-chain fatty acid metabolism, and long-chain fatty acid import, indicating active lipid processing. It is complemented by bile acid metabolism and cellular oxidant detoxification, suggesting a linked redox defense role in lipid pathways. The presence of some other catabolic terms does not outweigh the lipid-centric theme.","confidence":"High","size":22,"edges":56,"triangles":112,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0008206","count":4}]},{"hash":"1665688636154733390","title":"Innate Immune Signaling and Antiviral Defense","description":"Based on the enriched GO terms, the cluster centers on innate immunity and antiviral defense, including innate immune response, defense against virus, and NOD-like receptor signaling, with TNF signaling involvement. Other terms touch on immune regulation (T cell homeostasis, NF-kappaB activity) and unrelated processes (mRNA processing, vitamin D response, branching in blood vessels), but the dominant theme is innate immune signaling and antiviral defense.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0033280","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0051607","count":2}]},{"hash":"1677652147911842813","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":228,"triangles":1480,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0009793","count":1},{"id":"GO:0090617","count":1},{"id":"GO:1905639","count":1},{"id":"GO:0016554","count":1},{"id":"GO:0031425","count":1}]},{"hash":"2108200851716674245","title":"Fatty acid catabolism and endocannabinoid signaling","description":"This cluster is dominated by lipid-related catabolic and signaling processes: triglyceride and monoacylglycerol catabolism, phosphatidylserine catabolic process, prostaglandin catabolic process, epoxygenase P450 pathway, and regulation of endocannabinoid signaling. These terms collectively point to metabolism and signaling of fatty acids and lipid mediators. A few terms (e.g., secondary shoot formation, stilbene catabolic process) are less cohesive with the core theme and may reflect broader or off-target annotations, but the lipid metabolism signal is strong overall.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":5},{"id":"GO:0019433","count":5},{"id":"GO:0052651","count":5},{"id":"GO:0006660","count":5},{"id":"GO:2000124","count":5}]},{"hash":"827815484968747859","title":"Endomembrane vesicle trafficking","description":"The GO terms point mainly to intracellular transport within the endomembrane system, especially ER-Golgi and Golgi-ER trafficking as well as endosome-related transport. The presence of positive regulation of GTPase activity further supports a vesicle trafficking theme, making Endomembrane vesicle trafficking a concise, representative label, with a few peripheral terms that may reflect broader cellular roles or annotation noise.","confidence":"Medium","size":22,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0043007","count":2},{"id":"GO:0046959","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0007049","count":2}]},{"hash":"455921112389061322","title":"RNA Methylation Machinery","description":"The top GO terms are dominated by RNA methylation and processing functions, including RNA (guanine-N7)-methylation, rRNA and tRNA methylation, and 7-methylguanosine mRNA capping, which together point to a cohort of RNA-modifying enzymes involved in RNA maturation and ribosome biogenesis. While there are outliers related to biosynthetic processes (antibiotic/biotin biosynthesis) and other cellular responses, the repeated methyltransferase-associated terms strongly define a cohesive RNA modification theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0009102","count":7},{"id":"GO:0036265","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0000056","count":5}]},{"hash":"725967488370514879","title":"DNA Damage Repair and Recombination","description":"The GO terms are dominated by DNA repair and recombination processes (interstrand cross-link repair, meiotic mismatch repair, removal of nonhomologous ends, DNA recombination regulation, and DNA damage checkpoint signaling) with helicase activity modulation, indicating genome maintenance functions. Some terms like oxidative phosphorylation and lifespan are less central and likely incidental. Overall, the cluster aligns best with DNA damage response and recombination pathways.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0036297","count":1},{"id":"GO:0010777","count":1},{"id":"GO:0051096","count":1}]},{"hash":"1942172683647159616","title":"Proliferation and vascular development signaling","description":"The cluster centers on core growth and division processes (DNA replication, transcription, kinetochore localization) and a key growth pathway (PI3K/AKT signaling), with additional GO terms pointing to vascular development (angiogenesis and labyrinthine layer blood vessel development) and cellular stress responses (cadmium, glucose). Together, these terms suggest a theme of proliferative growth coupled with angiogenic signaling, rather than a single, narrow function.","confidence":"Medium","size":21,"edges":8,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006348","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0001525","count":4},{"id":"GO:0034501","count":3}]},{"hash":"364545903151776526","title":"RNA Splicing and Translational Regulation","description":"The top GO terms cluster around spliceosome-mediated mRNA processing (cis splicing, alternative splicing, and related regulatory processes) and control of translation (initiation, reinitiation, and initiation factor complex assembly). The presence of regulatory ncRNA-mediated gene silencing further supports a post-transcriptional regulatory theme. A few terms like regulation of Rho signaling appear, but the dominant signal is RNA processing and translation control, justifying a cohesive label focused on these processes.","confidence":"Medium","size":21,"edges":36,"triangles":1,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0097010","count":2}]},{"hash":"434617674819699419","title":"CNS neuron development and axonogenesis","description":"The cluster shows strong enrichment for neural development terms\u2014cerebral cortex development, optic nerve morphogenesis, CNS projection neuron axonogenesis, dendritic spine morphogenesis, and axon fasciculation\u2014indicating roles in neuronal differentiation and axon guidance/morphogenesis in the CNS. A few cell cycle\u2013related terms appear, but they are less central to the main neural theme, supporting a label focused on neural development rather than proliferation. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007095","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0006611","count":2}]},{"hash":"1307478687299474846","title":"Noncanonical NF-kappaB activation","description":"The top terms center on noncanonical NF-kappaB signaling, including positive regulation of non-canonical NF-kappaB transduction and activation of NF-kappaB-inducing kinase, pointing to initiation of the pathway. Additional terms tie to downstream immune responses, such as enhanced chemokine production, and ubiquitination-related regulation that commonly modulates NF-kappaB signaling. While some terms are obsolete or tangential, the core signal pertains to NF-kappaB pathway activation and immune regulation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090073","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0045623","count":1},{"id":"GO:0090309","count":1},{"id":"GO:1901224","count":1}]},{"hash":"2181258688467266588","title":"Ubiquitin-Dependent TNF/NF-\u03baB Signaling and Apoptosis","description":"These proteins show strong enrichment for ubiquitination-related processes (autoubiquitination and ubiquitin-dependent protein catabolic process) and are linked to key signaling pathways such as TNF-mediated signaling, NF-\u03baB activation, and JNK regulation, all associated with the control of apoptosis. The common thread is ubiquitin-mediated regulation of signaling and cell fate decisions, including inflammatory and stress responses. Therefore, the label reflects a ubiquitin-centric connection to TNF/NF-\u03baB signaling and apoptosis.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0036205","count":3},{"id":"GO:0042981","count":3},{"id":"GO:0090073","count":3}]},{"hash":"446607926272290010","title":"Translation Initiation and Spliceosome Regulation","description":"Top terms cluster around translation initiation (reinitiation, IRES-dependent initiation, preinitiation complex formation, mRNA capping) and spliceosome-mediated regulation of mRNA processing (alternative splicing, splicing regulation), suggesting a shared role in mRNA processing and translation control. A couple of germline stem cell terms seem incidental to the main theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1087729997626605782","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster is enriched for rRNA maturation and ribosome biogenesis, plus translation preinitiation complex formation, indicating a cohort of proteins involved in ribosome assembly and starting translation. Peripheral terms like angiogenesis and development may reflect broader functional annotation rather than a core shared activity.","confidence":"High","size":21,"edges":7,"triangles":0,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000462","count":4}]},{"hash":"1003802466865946020","title":"Developmental Gene Regulation and Neural Development","description":"This cluster is dominated by GO terms tied to broad developmental processes (multicellular organism development, forebrain development, skeletal system development, neural tube closure) and transcriptional regulation (DNA-templated transcription). While there are a few stress/immune-related terms present (cadmium response, defense to Gram-positive bacteria) that may reflect pleiotropic roles or annotation noise, the overall theme points to proteins involved in developmental regulation and neural formation.","confidence":"High","size":20,"edges":6,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0001403","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0030900","count":7}]},{"hash":"1415325134076396498","title":"Mitochondrial respiration and flavinylation","description":"The terms cluster around mitochondrial electron transport and assembly (Complex II/III), succinate metabolism, and flavin-dependent processes (protein-FAD linkage, flavinylation), plus magnesium/manganese ion homeostasis, which together point to mitochondrial oxidative phosphorylation and flavin-related functions. A single EMT-related term is likely incidental noise.","confidence":"High","size":20,"edges":21,"triangles":3,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010960","count":1},{"id":"GO:0030026","count":1},{"id":"GO:0006105","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0006121","count":1}]},{"hash":"726395419836826283","title":"RNA processing and translation machinery","description":"This cluster is dominated by GO terms for translation, mRNA splicing and export, ribosome biogenesis, and related RNA processing steps, pointing to a coherent RNA metabolism module that links transcription, RNA maturation, and protein synthesis. The presence of translation initiation regulation and ncRNA-mediated silencing supports a broader RNA-centric regulatory network, with a few peripheral terms (antibiotic response, telomerase assembly) not altering the core theme.","confidence":"High","size":20,"edges":57,"triangles":120,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0006406","count":2},{"id":"GO:1900363","count":2}]},{"hash":"1622301625406290286","title":"Nucleolar ribosome biogenesis and translation regulation","description":"This cluster centers on nucleolus organization, ribosomal subunit assembly, rRNA maturation, and translation, with related chromatin organization (nucleosome assembly). Together these terms point to a cohesive theme of ribosome biogenesis and protein synthesis. Additional terms such as actin filament severing and ER protein folding suggest broader cellular maintenance roles, but the dominant signal remains ribosome production and translation machinery; a few outliers reflect broader regulation rather than a separate function.","confidence":"Medium","size":20,"edges":18,"triangles":3,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0006334","count":2},{"id":"GO:0016239","count":2},{"id":"GO:0051014","count":2},{"id":"GO:0007000","count":1}]},{"hash":"2167077613989060836","title":"Developmental Regulation of Gene Expression","description":"This cluster includes proteins involved in development (brain and spermatid development, multicellular growth, cell division) and regulation of gene expression (translation initiation and reinitiation, alternative splicing), suggesting a coordinated role in developmental processes with post-transcriptional and chromatin-level regulation.","confidence":"Medium","size":20,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0030466","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0007420","count":2}]},{"hash":"335475397164696427","title":"Mitochondrial Translation and tRNA Methylation","description":"The cluster is strongly enriched for translation-related GO terms, including general translation, translational initiation/termination, and mitochondrial translation, with accompanying tRNA modification signals (tRNA methylation and RNA guanine-N7 methylation). A chlorophyll biosynthesis term appears but does not define the primary theme; overall, the proteins cluster around the translation machinery and RNA modification processes, especially mitochondrial translation. ","confidence":"High","size":20,"edges":10,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006413","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0036068","count":1}]},{"hash":"1879657271795350558","title":"DNA replication and cell cycle control","description":"The top GO terms are dominated by DNA replication, DNA repair, and mitotic cell cycle, with supporting terms on meiotic spindle organization and cyclin-dependent kinase activity regulation. While some terms hint at tissue-specific development, the strongest signal points to genome maintenance and progression through the cell cycle, justifying a label centered on replication/repair and cell cycle control.","confidence":"High","size":20,"edges":79,"triangles":158,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":17},{"id":"GO:0006281","count":16},{"id":"GO:0000278","count":16},{"id":"GO:0046827","count":16},{"id":"GO:0000212","count":15}]},{"hash":"1451831857361290437","title":"Nuclear RNA processing and ribosome biogenesis","description":"This cluster shows strong enrichment for splicing and spliceosome-related terms (mRNA splicing, spliceosomal complex disassembly, regulation of splicing) plus indications of transcription regulation and preribosome/rRNA maturation, suggesting a nuclear module centered on RNA processing and ribosome assembly.","confidence":"High","size":20,"edges":20,"triangles":7,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":8},{"id":"GO:0045944","count":7},{"id":"GO:1902626","count":7},{"id":"GO:0000463","count":7},{"id":"GO:0000398","count":7}]},{"hash":"240293156333332231","title":"Nuclear RNA processing and ribosome biogenesis","description":"This cluster centers on nucleolar processes: preribosome assembly for the large subunit and LSU rRNA maturation, complemented by broader RNA quality control and processing activities (nuclear mRNA surveillance, nonsense-mediated decay, spliceosomal disassembly, and related post-transcriptional regulation). Some DNA-related terms may be incidental context rather than core functions.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902626","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0006301","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000184","count":2}]},{"hash":"134740681040101671","title":"Proteostasis and organelle trafficking","description":"This cluster centers on protein quality control and handling across organelles: proteasome assembly, response to misfolded/unfolded proteins, protein unfolding, ER-to-Golgi transport, and mitochondrial intermembrane space import, along with linked energy-related processes (ATP biosynthesis and aerobic respiration) and stress responses (including UV damage repair). The recurring themes suggest a cohesive role in maintaining proteostasis and coordinating protein trafficking with cellular energy status.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":2},{"id":"GO:0071218","count":2},{"id":"GO:0070914","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0043335","count":2}]},{"hash":"315810640256761733","title":"Ubiquitin-mediated mitosis and antiviral defense","description":"This cluster shows strong signals for mitotic cell cycle and cell division, along with ubiquitin-dependent protein catabolic processes and K11-linked ubiquitination, indicating ubiquitin-mediated regulation of mitosis. It also includes innate immune/antiviral defense terms, suggesting a link between ubiquitin signaling and antiviral responses. The common thread is ubiquitin-dependent regulation influencing both cell division and antiviral defense, hence the label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0045842","count":3},{"id":"GO:0042787","count":3}]},{"hash":"450546885178575609","title":"Cell cycle control and proteolysis","description":"The cluster\u2019s GO terms mainly point to ubiquitin-proteasome\u2013mediated degradation, including SCF- and APC/C-dependent pathways, which are central to cell cycle regulation. Additional terms touch on DNA damage checkpoint signaling and mitotic control, supporting a unifying theme of coordinating division with proteostasis. Some terms (synaptic plasticity, invasive growth, histone acetylation) appear less connected and may reflect broader regulatory processes or noise. Overall, the set suggests a focus on cell cycle control through targeted protein degradation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031915","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0010659","count":1},{"id":"GO:0031930","count":1}]},{"hash":"279029635285389088","title":"ER-Golgi trafficking and reticulophagy","description":"The top GO terms point to ER-to-Golgi vesicle transport, COPII regulation, reticulophagy, and related endomembrane organization and vacuolar targeting, indicating a cluster of proteins involved in ER-Golgi trafficking and selective autophagy of the ER.","confidence":"High","size":19,"edges":22,"triangles":8,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0032258","count":6},{"id":"GO:0034629","count":5},{"id":"GO:0061709","count":5},{"id":"GO:0021766","count":5}]},{"hash":"644223544260514884","title":"Chromatin Remodeling and Cell Cycle","description":"GO terms center on chromatin dynamics (nucleosome mobilization, histone exchange, histone acetylation, heterochromatin formation) and DNA replication/cell cycle, with developmental terms like muscle and brain noted but less dominant. This suggests the cluster consists of chromatin modifiers and cell-cycle\u2013related proteins that coordinate chromatin state with replication and division.","confidence":"High","size":19,"edges":112,"triangles":378,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048741","count":7},{"id":"GO:0021762","count":7},{"id":"GO:0042220","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0042766","count":5}]},{"hash":"1621743520527421648","title":"Ubiquitin-Mediated Protein Degradation","description":"Dominant theme is ubiquitin-related protein regulation: protein autoubiquitination and K48-linked ubiquitination are present, along with a ubiquitin-dependent ERAD pathway term (noting it is listed as obsolete in the dataset). This points to a cluster centered on marking proteins for degradation. Some secondary terms (Wnt receptor catabolic process, negative regulation of organ growth, peroxisome matrix import) suggest broader links to protein turnover and cellular quality control, while transport terms for methotrexate/folate are less central. Overall, aligns with ubiquitin-mediated protein degradation.","confidence":"High","size":19,"edges":27,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0051958","count":3},{"id":"GO:0015885","count":3},{"id":"GO:1900095","count":2},{"id":"GO:0046621","count":2},{"id":"GO:0030433","count":2}]},{"hash":"295071712905920964","title":"Translation Initiation and Spliceosome Regulation","description":"These proteins show strong links to eukaryotic translation initiation (preinitiation complex formation, eIF4F assembly, translation reinitiation) and to spliceosome-mediated mRNA processing (alternative splicing regulation). The co-occurrence of initiation and splicing GO terms suggests a cohesive RNA-processing cluster where translation control is linked to splicing regulation.","confidence":"High","size":19,"edges":10,"triangles":1,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":10},{"id":"GO:0001731","count":10},{"id":"GO:1901407","count":9},{"id":"GO:0097010","count":8},{"id":"GO:0000380","count":8}]},{"hash":"193704937523912917","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":15,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1990569","count":1},{"id":"GO:0034221","count":1},{"id":"GO:0036085","count":1},{"id":"GO:0015786","count":1}]},{"hash":"2126369331783530538","title":"Amino acid catabolism and NAD biosynthesis","description":"The cluster\u2019s top GO terms center on amino acid metabolism (L-alanine, L-serine, and tryptophan pathways) and related NAD biosynthesis routes (kynurenine and quinolinate), along with pyruvate production. Notch signaling and cAMP response appear but are less central, making amino-acid catabolism and NAD precursor synthesis the most representative theme.","confidence":"Medium","size":19,"edges":34,"triangles":56,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0042853","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0007219","count":4},{"id":"GO:0006564","count":3},{"id":"GO:0019700","count":3}]},{"hash":"2054862666569213989","title":"Epidermal development and pigmentation","description":"Top GO terms center on skin development and pigmentation, with kinase signaling and GTPase regulation suggesting phosphorylation-driven signaling in epidermal differentiation. Although some terms like defense response and hypoxia are present, they appear peripheral to the core theme of epidermal development and pigment formation. This cluster likely represents proteins involved in skin-related development and pigment biosynthesis regulated by signaling pathways.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031954","count":5},{"id":"GO:0043588","count":5},{"id":"GO:0071902","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0032516","count":4}]},{"hash":"756594337365652354","title":"Nuclear gene expression and proteostasis","description":"The terms cluster around transcription (DNA-templated), ribosome biogenesis, chromatin-related processes (histone H3 acetylation), and proteostasis (SCF-ubiquitin-proteasome\u2013dependent degradation, protein kinase signaling). The presence of cell-cycle and DNA damage response terms (anaphase-promoting complex\u2013dependent catabolic process, G1 checkpoint signaling) suggests a coordinated regulation of gene expression, chromatin state, and protein turnover that links transcription with growth control and stress responses. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0071902","count":5},{"id":"GO:0010659","count":5},{"id":"GO:0031930","count":5}]},{"hash":"14010132083520541","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms are dominated by ribosome biogenesis and rRNA processing, including large-subunit biogenesis and nuclear export, plus rRNA processing steps. While a few terms touch other processes, the predominant signal points to ribosome assembly and maturation as the cluster\u2019s core function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035522","count":2},{"id":"GO:0034599","count":1},{"id":"GO:0035335","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0042254","count":1}]},{"hash":"935030646170146938","title":"Carbohydrate catabolism and chemical stress responses","description":"The top GO terms point to sugar metabolism, including D-sorbitol and D-xylulose-5-phosphate pathways and pyruvate fermentation to ethanol, suggesting a core in carbohydrate processing. The presence of terms related to copper ion and antineoplastic agent responses, along with nitrosylation, indicates broader chemical stress handling. Taken together, the cluster seems to combine carbohydrate catabolism with general chemical/stress response capabilities rather than a single, tightly focused pathway.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0019518","count":5},{"id":"GO:0006062","count":4},{"id":"GO:0043458","count":4},{"id":"GO:0018119","count":4},{"id":"GO:0045777","count":4}]},{"hash":"1451667731446612659","title":"Ubiquitin-Dependent ERAD and Proteolysis","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes, the ER-associated degradation (ERAD) pathway, and various ubiquitination activities, including K11-linked ubiquitination and autoubiquitination. Unfolded protein response and innate immune/defense signaling also appear, suggesting a core role in ubiquitin-mediated protein quality control that intersects with cell cycle processes. Overall, the common theme is ubiquitin-driven proteolysis related to ER stress and quality control, with secondary ties to immune response and division.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0051865","count":3}]},{"hash":"253640514716679835","title":"Inhibition of angiogenesis","description":"This cluster includes GO terms that point to negative regulation of vascular development, such as endothelial differentiation, VEGF signaling, and vasculogenesis. Other terms relate to metabolism and transport (e.g., ferredoxin/xanthine catabolic processes, ATP-linked electron transport, sodium transport). The vascular development terms provide the core theme, suggesting modulation of angiogenesis alongside broader metabolic roles.","confidence":"Medium","size":18,"edges":25,"triangles":14,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":4},{"id":"GO:0045602","count":3},{"id":"GO:1900747","count":3},{"id":"GO:0006124","count":3},{"id":"GO:2001213","count":3}]},{"hash":"729761553798076857","title":"Intracellular protein transport and Rab signaling","description":"The cluster's top GO terms point to intracellular trafficking and signaling roles, notably protein transport and Rab protein signal transduction, as well as protein heterooligomerization. Although some terms relate to development or metabolism in specific tissues, the prominent transport and signaling terms suggest the proteins function together primarily in trafficking and communication rather than a single tissue-specific process.","confidence":"Medium","size":18,"edges":14,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0015031","count":2},{"id":"GO:0050771","count":2},{"id":"GO:0032482","count":2}]},{"hash":"1422909053407731231","title":"DNA replication and mitotic cell cycle","description":"The cluster\u2019s top GO terms are dominated by DNA replication, mitotic processes, and transcription (DNA replication, mitotic G2 checkpoint signaling, DNA-templated transcription, mitotic cell cycle, meiotic spindle organization). This points to a core function in nuclear DNA metabolism and cell division, even though a few terms (mast cell differentiation, placenta development, visual perception, interferon-beta production) suggest additional, broader roles or tissue-specific contexts. Overall, the prevailing theme is DNA replication and mitosis.","confidence":"Medium","size":18,"edges":13,"triangles":3,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0007095","count":10},{"id":"GO:0006351","count":10},{"id":"GO:0018108","count":10},{"id":"GO:0000278","count":10}]},{"hash":"1066896937393459954","title":"Regulation of Cell Signaling and Apoptosis","description":"The top GO terms repeatedly emphasize regulatory roles across processes like cell cycle control, transcriptional repression, protein ubiquitination, apoptosis/necroptosis, and signaling pathways (including TLR and cell surface receptor signaling). This suggests a cluster of proteins that primarily function as regulators of signaling and cell fate decisions, rather than as components of a single pathway, making the label appropriate though broad. Edge topology is minimal, which fits a set of diverse regulators rather than a tightly connected complex.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0060544","count":3}]},{"hash":"1317228399692732950","title":"Vacuolar transport and proton/ion homeostasis","description":"The cluster centers on vacuolar processes\u2014vacuole organization and protein targeting to the vacuole\u2014along with proton transmembrane transport and proton motive force\u2013driven activities, plus ion homeostasis (copper and sodium). This points to a cohesive function in vacuolar trafficking, acidification, and maintenance of ionic and energy balance.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0007033","count":2}]},{"hash":"1702545458385524866","title":"ER Stress and Protein Quality Control","description":"This cluster is dominated by GO terms tied to the endoplasmic reticulum (ER) folding world: protein folding in the ER, response to unfolded protein, ER stress\u2013related regulation of translation initiation, and ubiquitin-proteasome\u2013mediated quality control including ERAD and nuclear quality control. Together, these terms point to ER-associated protein quality control and the unfolded protein response as a unifying theme, with a few unrelated terms (e.g., mesoderm formation) likely representing pleiotropic proteins or annotation noise.","confidence":"High","size":18,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0006986","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0032781","count":1}]},{"hash":"2124862008452879565","title":"TOR signaling and translation regulation","description":"The top GO terms cluster around nutrient sensing and protein synthesis: positive regulation of TOR signaling, cellular response to amino acid stimulus, translation initiation and reinitiation, and eIF4F complex assembly, suggesting a growth-control module linking nutrient status to translation; some terms related to folate transport and intraflagellar transport appear as outliers, but the core theme remains growth signaling and translation control.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051958","count":2},{"id":"GO:0015885","count":2},{"id":"GO:0032008","count":1},{"id":"GO:0071230","count":1},{"id":"GO:0035735","count":1}]},{"hash":"2274340067218624043","title":"Spindle assembly and microtubule organization","description":"The top GO terms cluster around microtubule dynamics and spindle machinery, including mitotic spindle assembly, astral microtubule anchoring, cortical microtubule organization, meiotic cell cycle, and spindle-related processes in meiosis and mitosis, suggesting the proteins function in spindle assembly and microtubule organization. A few outliers (metabolic salvage and antibiotic response) exist, but the dominant theme is clear and coherent.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019284","count":2},{"id":"GO:0019509","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0098863","count":1},{"id":"GO:0007058","count":1}]},{"hash":"290728387180617611","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001824","count":2},{"id":"GO:0000389","count":1},{"id":"GO:0000350","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000387","count":1}]},{"hash":"899160191539071380","title":"Unknown","description":"The cluster contains a varied set of GO terms spanning DNA replication, transcription elongation, ribosome assembly, cilium movement, vesicle and gas vesicle organization, chaperone/cofactor-dependent protein refolding, proteasome assembly, misfolded protein response, and UV-damage repair. This broad mix lacks a single cohesive functional theme, so a specific label cannot be confidently assigned.","confidence":"","size":17,"edges":5,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:1990048","count":5},{"id":"GO:0000027","count":5},{"id":"GO:0003341","count":5},{"id":"GO:0031412","count":5}]},{"hash":"2276635854061876507","title":"Membrane lipid metabolism and ER-Golgi trafficking","description":"This cluster is dominated by GO terms related to lipid biosynthesis and membrane processes (unsaturated fatty acid biosynthesis, sphingolipid metabolism, ergosterol regulation) and vesicle transport from ER to the Golgi, pointing to membrane biogenesis and lipid handling. Some terms are general metabolism or other processes, but the lipid/trafficking theme is strongest.","confidence":"Medium","size":17,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0006809","count":2}]},{"hash":"644435549126714662","title":"Calcium signaling in neural development","description":"The cluster features several calcium-related GO terms (calcium detection, postsynaptic calcium regulation, calcium-release channel activity, and calcineurin-NFAT signaling) and a clear neural/glial development angle (Schwann cell development), plus associated secretory pathway activity (ER-to-Golgi transport). While other terms (DNA replication, tissue remodeling) are present, the dominant, cohesive signal is calcium-dependent signaling in neural development, particularly Schwann cells. Confidence: Medium","confidence":"","size":17,"edges":23,"triangles":0,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006888","count":4},{"id":"GO:0001569","count":3},{"id":"GO:0033173","count":3},{"id":"GO:0099566","count":3}]},{"hash":"1712310154950613582","title":"Neural Development and Synaptic Plasticity","description":"This cluster is dominated by GO terms related to neural development and synaptic function, including visual perception, Schwann cell development, axonogenesis, and long-term synaptic potentiation, suggesting a role in neural differentiation and synaptic signaling. Some terms (e.g., kinase regulation and kinetochore localization) are more general or cell-cycle related, but the prominent neural-focused terms support the chosen theme.","confidence":"Medium","size":17,"edges":133,"triangles":636,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":11},{"id":"GO:0045736","count":11},{"id":"GO:0014044","count":11},{"id":"GO:0043065","count":11},{"id":"GO:0034501","count":11}]},{"hash":"1229289870590154235","title":"Unknown","description":"The enriched GO terms span plant defense (salicylic acid biosynthesis, response to microbial phytotoxin, hydrogen peroxide regulation) and animal/developmental processes (MHC biosynthesis regulation, meiotic spindle elongation, cerebellar granular layer organization, ureteric bud invasion) with no single shared function or pathway, and the network has no edges, so no coherent label can be assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010310","count":2},{"id":"GO:0010188","count":2},{"id":"GO:0009697","count":2},{"id":"GO:0045347","count":2},{"id":"GO:0051232","count":2}]},{"hash":"63774184893354019","title":"Developmental differentiation and translation initiation","description":"The top GO terms point to developmental processes (brain and lung development) and cell differentiation steps (G1 to G0 transition, negative regulation of epithelial proliferation), which suggest a developmental theme. The presence of translation-related terms (translational initiation and formation of the cytoplasmic translation initiation complex) indicates regulation of protein synthesis accompanying differentiation. Some metabolic terms and the absence of interaction edges hint at heterogeneity, but the consistent thread is development intertwined with translation initiation control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0006413","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0001732","count":1},{"id":"GO:0046360","count":1}]},{"hash":"395423798022642225","title":"Neural Development and Organogenesis","description":"This cluster includes multiple development-related GO terms, notably neural development: midbrain dopaminergic neuron differentiation, superior colliculus development, and medulla oblongata development, plus oviduct and root development, suggesting a shared role in developmental programs across tissues. Some terms refer to general cellular processes (DNA replication, ERAD, stress granule disassembly), but the dominant signal is developmental/neural in nature.","confidence":"Medium","size":17,"edges":101,"triangles":308,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015991","count":6},{"id":"GO:0048364","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0035617","count":6}]},{"hash":"1188883477567484565","title":"Vacuolar amino acid transport","description":"The top GO terms center on transmembrane transport of amino acids into and out of the vacuole (arginine, lysine, serine, histidine, proline), plus a general amino acid transport term. While a couple of unrelated terms appear, the dominant theme is vacuolar amino acid transporters.","confidence":"High","size":17,"edges":19,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0090518","count":2},{"id":"GO:0003333","count":2},{"id":"GO:0089707","count":2},{"id":"GO:0090516","count":2},{"id":"GO:0090517","count":2}]},{"hash":"551400511100617175","title":"Oxidative Stress Response and Aging","description":"This cluster centers on ROS detoxification and redox processes (removal of superoxide radicals, oxidation-reduction, response to ROS) with links to aging and DNA repair, suggesting a module dedicated to stress defense and genome maintenance. Some outlier terms (e.g., pigment differentiation, vascular signaling) may reflect organism-specific or broader stress-related roles rather than core themes.","confidence":"Medium","size":17,"edges":15,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048773","count":2},{"id":"GO:0001320","count":2},{"id":"GO:0010447","count":2},{"id":"GO:0001302","count":2},{"id":"GO:0071291","count":2}]},{"hash":"1962365428090021078","title":"Chloroplast RNA processing and ribosome biogenesis","description":"The terms point to RNA maturation and ribosome assembly in chloroplasts, with chloroplast mRNA processing, rRNA acetylation for SSU maturation, ribosomal SSU biogenesis, and tRNA acetylation forming a cohesive theme. A few terms relate to broader plant processes (meristem development, telomere maintenance) or general regulation, which are likely annotations not specific to the cluster\u2019s core function. Overall, the dominant signal is chloroplast RNA processing and ribosome biogenesis.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048507","count":1},{"id":"GO:0031426","count":1},{"id":"GO:0006744","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0010239","count":1}]},{"hash":"2025863518194931095","title":"Vacuolar amino acid transport","description":"The top GO terms point to transmembrane transport of various amino acids into and out of the vacuole (arginine, lysine, serine, histidine, proline, etc.), indicating a cluster of proteins functioning as vacuolar amino acid transporters. A few non-specific terms are present, but the dominant pattern is amino acid movement across the vacuolar membrane, supporting a cohesive transporter-related theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090518","count":2},{"id":"GO:0089707","count":2},{"id":"GO:0090516","count":2},{"id":"GO:0090517","count":2},{"id":"GO:0048829","count":2}]},{"hash":"964376459433184029","title":"Neuronal development and dendrite morphogenesis","description":"This cluster shows several neural development and morphogenesis terms (hippocampus development, CNS projection neuron axonogenesis, layer formation in cerebral cortex, dendrite morphogenesis, visual perception, and axon-related processes), suggesting a neuronal development theme. A few terms (pseudohyphal growth, glycerol catabolic process) appear unrelated and may be noise, but they do not dominate the overall pattern.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0007124","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0021766","count":2}]},{"hash":"2298320235039283646","title":"Unknown","description":"The top GO terms span metabolism (thiamine biosynthesis, thiamine diphosphate biosynthesis, TCA cycle, amino acid catabolism) and distinct processes such as tRNA modification and various protein modifications (lipidation, urmylation, sumoylation) along with a signaling pathway (Notch). This mix does not reveal a single cohesive function or pathway tying the cluster together, so a specific functional label is not identifiable. ","confidence":"","size":16,"edges":42,"triangles":63,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":4},{"id":"GO:0009229","count":3},{"id":"GO:0002143","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0097053","count":3}]},{"hash":"2275647696675206758","title":"Bacterial metal transport and polymer degradation","description":"The cluster includes GO terms for metal ion transport (copper, iron, arsenate), iron assimilation, nitrate assimilation, and redox-related processes, plus catabolic processes for cellulose and lignin. The presence of FtsZ-dependent cytokinesis also points to bacterial cell division. Together these suggest a bacterial toolkit for nutrient uptake and processing of plant-derived substrates, rather than a single narrow function. ","confidence":"Medium","size":16,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042128","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006825","count":1},{"id":"GO:0043093","count":1}]},{"hash":"1726906886750770745","title":"SRP-Dependent Membrane Targeting & ER Stress Regulation","description":"The top GO terms point to SRP-dependent cotranslational protein targeting to the membrane and SRP-dependent/ post-translational targeting to membranes, indicating a strong theme of guiding proteins to membranes (especially the ER). There are also terms about regulation of ER stress\u2013induced apoptotic signaling and inclusion body assembly, suggesting links to ER quality control and stress responses, with some additional but looser signals related to nucleic/cell morphogenesis pathways. Overall, the cluster seems centered on membrane targeting of proteins and ER stress regulation.","confidence":"Medium","size":16,"edges":45,"triangles":48,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0070389","count":3},{"id":"GO:1903382","count":3},{"id":"GO:1900035","count":3},{"id":"GO:1902037","count":3}]},{"hash":"1748283690990716936","title":"Ubiquitin-Dependent Proteostasis and Aggresome Assembly","description":"The cluster shows strong enrichment for ubiquitin-mediated protein catabolic processes (ERAD pathway, general ubiquitin-dependent degradation, autoubiquitination) and K63-linked ubiquitination, plus aggresome assembly. This points to a cohesive theme of ubiquitin-dependent protein quality control and turnover, with proteostasis being the dominant function among the terms. A transcription-related term is present but secondary to the ubiquitin/polyubiquitination signals.","confidence":"High","size":16,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0051865","count":2}]},{"hash":"194833628434139876","title":"Chromosome maintenance and mitosis","description":"This cluster\u2019s dominant signals are chromosome maintenance and cell division, including DNA replication, DNA recombination, CENP-A\u2013containing chromatin assembly, mitotic cell cycle, cell division, and microtubule severing, suggesting a focus on chromosome segregation machinery. Some terms relate to vesicle trafficking and protein quality control, but they appear as less central context compared to the mitosis/DNA practices.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0006888","count":4},{"id":"GO:0006310","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0019079","count":3}]},{"hash":"1007331290011056590","title":"Translation and Ribosome Biogenesis","description":"The dominant GO terms center on translation, its regulation, ribosome biogenesis, and translational initiation, with additional signals for SRP-dependent cotranslational targeting to membranes. This points to a cohesive module of protein synthesis machinery and associated membrane targeting, with a few secondary signals (cell division, signaling) that are less central. Confidence in this label is High.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006417","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006616","count":2}]},{"hash":"796962199184921470","title":"Transcription and DNA replication with proteostasis","description":"The top GO terms cluster around RNA polymerase II transcription regulation (elongation and preinitiation complex assembly), DNA replication, and cell division, with accompanying proteostasis processes (aggresome formation, proteasome assembly, misfolded-protein response) and Golgi/vesicle handling. This suggests a unit linking nuclear gene expression and genome maintenance with protein quality control, justifying the label Transcription and DNA replication with proteostasis.","confidence":"Medium","size":16,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032968","count":3},{"id":"GO:0070842","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0045053","count":3},{"id":"GO:0070676","count":3}]},{"hash":"1858042970864311998","title":"GPCR Signaling and Calcium Transport","description":"The listed GO terms largely point to cellular signaling, especially GPCR-mediated pathways (acetylcholine receptor signaling; bitter taste) and calcium signaling (calcium ion transport; IP3 biosynthesis). Additional terms touch on growth factor signaling, immune signaling, and developmental processes, suggesting a broad signaling-connected cluster rather than a single, narrow function. Overall, calcium dynamics and GPCR signaling appear to be the core motif tying these terms together, with other terms representing downstream or parallel pathways.","confidence":"Low","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032959","count":1},{"id":"GO:0003073","count":1},{"id":"GO:0007343","count":1},{"id":"GO:0035722","count":1},{"id":"GO:0032835","count":1}]},{"hash":"1452170200593499734","title":"RNA Polymerase Assembly and Transcription Machinery","description":"The cluster centers on core transcription-related processes: assembly of RNA polymerase I, II, and III complexes, DNA-templated transcription, and transcription elongation, suggesting a coherent theme of nuclear gene expression and transcription machinery. Some terms also touch on cell division and protein folding, but the dominant signal is transcription apparatus and regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033601","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1990114","count":1}]},{"hash":"1187574119436655212","title":"Ciliogenesis and Flagellar Motility","description":"The terms cluster around exocytosis and exocyst-mediated trafficking to the plasma membrane, Golgi-to-PM transport, and axoneme/flagellum processes (sperm axoneme assembly, flagellated sperm motility) with tubulin polyglycylation. Together they point to proteins involved in building and operating cilia/flagella and their secretory support, especially in sperm cells. Therefore this label captures the shared function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006887","count":1},{"id":"GO:0051601","count":1},{"id":"GO:0048309","count":1},{"id":"GO:0001927","count":1},{"id":"GO:0006893","count":1}]},{"hash":"34543265675557487","title":"Chromatin organization and heterochromatin formation","description":"This cluster centers on chromatin-level processes, with items like CENP-A\u2013containing chromatin assembly, pericentric heterochromatin formation, and histone methylation regulation, suggesting a core function in chromatin organization and heterochromatin maintenance. A few terms reference spermatogenesis and morphogenesis, which may reflect developmental contexts rather than core chromatin activity, but the dominant signal is chromatin-related. ","confidence":"Medium","size":15,"edges":15,"triangles":1,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":2},{"id":"GO:1904693","count":1},{"id":"GO:0031508","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1914675742983872835","title":"Ribosome Biogenesis and Translation","description":"This cluster shows strong representation of ribosome-related processes: ribosome biogenesis, small subunit (SSU) assembly, and translation, indicating a core involvement in ribosome production and protein synthesis. Additional terms point to regulatory roles in signaling and cytoskeletal dynamics and transcription regulation, suggesting broader coordination, but the dominant theme remains ribosomal function.","confidence":"High","size":15,"edges":14,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0035024","count":2},{"id":"GO:0043149","count":2}]},{"hash":"13898188016806327","title":"Proteostasis and ER-to-Golgi trafficking","description":"Dominant terms cluster around protein quality control and trafficking: misfolded protein response, ER-associated degradation, proteasome assembly, and ER-to-Golgi transport, with protein import into mitochondria and protein unfolding supporting overall proteostasis across organelles. The presence of UV-damage repair and transcription elongation terms hints at broader stress response connections. Overall, the theme best captures the core set of functions linking folding, degradation, and trafficking under stress.","confidence":"Medium","size":15,"edges":13,"triangles":2,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0070682","count":4},{"id":"GO:0071218","count":4}]},{"hash":"1725155014019988619","title":"ER Stress and Protein Folding","description":"The top GO terms point to endoplasmic reticulum\u2013associated proteostasis: response to unfolded protein, ER protein folding, ERAD, and translation initiation in response to ER stress, suggesting a cohesive ER stress response and quality-control network. A few terms related to development or mitochondrion targeting appear unrelated and may be background noise.","confidence":"High","size":15,"edges":24,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0036494","count":3},{"id":"GO:0070389","count":3},{"id":"GO:1901621","count":2}]},{"hash":"370957020620899803","title":"Ribosome Biogenesis and Translation","description":"The proteins in this cluster center on ribosome assembly and the translation machinery, including maturation of rRNA, formation of translation preinitiation complexes, and initiation (including IRES-dependent routes). The GO terms indicate coordinated roles in ribosomal subunit biogenesis, rRNA maturation, and general translation processes.","confidence":"High","size":15,"edges":29,"triangles":42,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0042273","count":3}]},{"hash":"1776439546893736058","title":"ER Stress Response and Protein Quality Control","description":"The cluster is dominated by GO terms tied to endoplasmic reticulum proteostasis: protein folding in the ER, response to unfolded protein, ERAD-related ubiquitin pathways, and translation initiation regulation during ER stress, plus nuclear protein quality control by the ubiquitin-proteasome system. These collectively point to an ER stress response/UPR and associated quality-control mechanisms. A few development-related terms (mesoderm formation, neural tube patterning) may be incidental and not central to the main theme.","confidence":"High","size":15,"edges":20,"triangles":2,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0032781","count":2}]},{"hash":"137960725165532917","title":"Vacuolar amino acid transport","description":"The terms point to transport of amino acids into and out of the vacuole (arginine, lysine, serine) and general amino acid transmembrane transport, suggesting a cohesive cluster of vacuolar transporter proteins targeting amino acid movement. Peripheral terms like palmitoylation and development appear less central but may relate to membrane association and broader biology.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0018230","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0090518","count":1},{"id":"GO:0003333","count":1}]},{"hash":"977345999788232008","title":"Calcineurin-NFAT calcium signaling","description":"The cluster is dominated by GO terms related to calcium signaling and dephosphorylation, especially regulation and activity of the calcineurin-NFAT pathway, along with postsynaptic calcium regulation and peptidyl-serine dephosphorylation, pointing to calcium-dependent phosphatase signaling. Some developmental terms (Schwann cell development, vascular branching) may reflect broader calcium-mediated developmental roles, but the core theme is calcium-dependent NFAT signaling and phosphatase activity.","confidence":"Medium","size":15,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":3},{"id":"GO:0051531","count":3},{"id":"GO:0001569","count":2},{"id":"GO:0006685","count":2},{"id":"GO:0033173","count":2}]},{"hash":"237793859865016096","title":"Dopamine Regulation and Serotonin Secretion","description":"The cluster shows a clear tilt toward monoamine neurotransmitter regulation, with dopamine catabolic process and positive regulation of dopamine metabolism, along with negative regulation of serotonin secretion. This suggests a core theme around dopaminergic/serotonergic signaling. The presence of other terms (alternative splicing, xenobiotic response, metal ion responses, and thiamine biosynthesis) indicates additional, more general roles or multi-function proteins, but they do not outweigh the dominant neurotransmitter-related terms. Overall, the label captures the main functional thread with moderate confidence due to some heterogeneity. ","confidence":"Medium","size":14,"edges":21,"triangles":9,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":5},{"id":"GO:0000380","count":4},{"id":"GO:0010044","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0042420","count":4}]},{"hash":"1058514889034168657","title":"Unknown","description":"The GO terms in this cluster cover a wide and unrelated range of functions\u2014from metabolism and RNA localization to neuronal structure, immune isotype switching, vesicle transport, integrin regulation, chromatin modification, ion channel regulation, and DNA replication initiation. With only a single edge and no clear shared function, there isn\u2019t a single coherent theme to name the cluster beyond Unknown.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":2},{"id":"GO:0019509","count":2},{"id":"GO:0051237","count":2},{"id":"GO:0021693","count":2},{"id":"GO:0045190","count":2}]},{"hash":"2128701158245172354","title":"Central Metabolism and Redox Homeostasis","description":"This cluster shows strong signals for core energy metabolism: glycolysis, the TCA cycle, 2-oxoglutarate metabolism, and mitochondrial electron transport, plus redox homeostasis. The presence of related biosynthetic processes (folate metabolism and capsule polysaccharide biosynthesis) suggests a linked metabolic flux supporting energy and precursor synthesis; some terms are historical annotations but do not change the overall theme.","confidence":"High","size":14,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0045227","count":3},{"id":"GO:0046653","count":3},{"id":"GO:0042135","count":3}]},{"hash":"1542029179844271522","title":"Membrane trafficking and immune signaling","description":"The cluster is dominated by vesicle transport and membrane organization terms (ER-to-Golgi transport, COPII coat regulation, CVT pathway, lysosomal membrane organization), indicating a core role in membrane trafficking. Immune-related terms (T cell receptor signaling, Th1 response) and small GTPase\u2013mediated signaling align with trafficking regulation and immune cell signaling, suggesting a broader theme of vesicle-mediated transport coupled with signaling processes.","confidence":"Medium","size":14,"edges":13,"triangles":2,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":10},{"id":"GO:0032258","count":8},{"id":"GO:0045453","count":8},{"id":"GO:0050852","count":8},{"id":"GO:0006888","count":8}]},{"hash":"968689217439237648","title":"Regulated Stress Signaling","description":"The top terms show involvement in detoxification, starvation response, ubiquitin-mediated proteolysis, and multiple signaling pathways (TNF, TLR, dopamine signaling), plus roles in endosome-Golgi transport, neural morphogenesis, and epithelial polarity. This suggests the proteins collectively modulate diverse stress responses and signaling rather than a single pathway, so a label emphasizing regulated signaling under stress fits best.","confidence":"Medium","size":14,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0010804","count":2},{"id":"GO:0042594","count":2},{"id":"GO:0042787","count":2},{"id":"GO:1903125","count":2}]},{"hash":"2273390151762153402","title":"Fungal Lipid Biosynthesis and Vesicle Trafficking","description":"The top GO terms cluster around fungal membrane lipid pathways: MIPC metabolism, unsaturated fatty acid biosynthesis, and ergosterol biosynthesis regulation, paired with Golgi to vacuole transport, pointing to lipid production and intracellular trafficking in fungi. Some terms (nitrate assimilation, nitric oxide) are more general, but they don\u2019t override the dominant lipid/trafficking theme. Confidence: Medium","confidence":"","size":14,"edges":12,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":4},{"id":"GO:0032286","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006636","count":2}]},{"hash":"1805266486884487284","title":"CNS Neuron Development and Transcription Regulation","description":"The top terms cluster around nervous system development, especially CNS neuron development and dendrite morphogenesis, indicating a role in neural differentiation and maturation. Complementary transcription-related terms (DNA-templated transcription, termination of RNA Pol II transcription) and signaling/regulatory processes (positive regulation of JNK cascade, proteasomal ubiquitin-dependent protein catabolic process) suggest coordinated control of gene expression during neural development. Confidence: High","confidence":"","size":14,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046330","count":2},{"id":"GO:0032435","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0048813","count":2}]},{"hash":"2131799349648439688","title":"TORC1 Growth Signaling and Trafficking","description":"This cluster shows enrichment for TORC1 signaling, amino-acid\u2013stimulated cellular responses, and growth-related processes (cell division, proliferation) along with vesicle transport between Golgi and ER and GTPase regulation, all suggesting a unit coordinating nutrient sensing with protein trafficking and growth.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006890","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0038202","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1298865500506662253","title":"Bacterial sugar metabolism and phosphorylation","description":"This cluster's GO terms are dominated by carbohydrate metabolism and phosphorylation, with multiple entries for glucose, xylose, arabinose, rhamnose catabolic processes, and general phosphorylation/dephosphorylation, plus a sugar-related lipopolysaccharide biosynthesis note. A few terms like response to cocaine appear as minor outliers, but the prevailing theme centers on sugar metabolism.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":4},{"id":"GO:0006006","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0009103","count":2}]},{"hash":"2170392703151823613","title":"ER Stress and Protein Folding Quality Control","description":"The cluster is enriched for endoplasmic reticulum\u2013related processes such as protein folding in the ER, response to unfolded protein, and ER-associated degradation, with additional terms on ER stress\u2013driven translation and nuclear quality control; together these define a proteostasis/ER stress signature, though a few development terms may reflect broader roles or annotation noise.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032781","count":4},{"id":"GO:1901621","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0001707","count":3}]},{"hash":"2213135601417211436","title":"Spliceosome-Mediated mRNA Processing","description":"GO terms are centered on mRNA cis splicing via spliceosome and related RNA processing (including mRNA decay). This strongly indicates a cluster of spliceosome components and post-transcriptional regulators. Some development-related terms may reflect contextual roles, but the core function ties to RNA splicing.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0010555","count":1},{"id":"GO:0070564","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0035214","count":1}]},{"hash":"707206549011282140","title":"Sulfur metabolism and H2S signaling","description":"The cluster is enriched for sulfur-containing amino acid metabolism: transsulfuration, cysteine biosynthesis via cystathionine, and hydrogen sulfide biosynthesis. These terms cluster with redox-related modifications (peptidyl-cysteine S-nitrosylation) and H2S's role as a gasotransmitter linked to blood pressure regulation, suggesting a core theme of sulfur metabolism and redox signaling. While there are other metabolic terms present (fatty acid biosynthesis, PPP), they appear secondary to the sulfur/H2S-focused processes.","confidence":"High","size":13,"edges":74,"triangles":246,"max_degree":12,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0006633","count":5},{"id":"GO:0019343","count":5},{"id":"GO:0019346","count":5},{"id":"GO:0070814","count":5},{"id":"GO:0009097","count":4}]},{"hash":"695935962361954482","title":"Core cellular process regulators","description":"This set is enriched for broad regulators of fundamental cellular activities, including translation (protein synthesis) and cell cycle/division, as well as multiple negative regulatory processes (neuron apoptosis, RNA splicing, cell motility) and ubiquitin-protein transferase activity. The presence of an interleukin-1 response term suggests some signaling context, but the dominant pattern points to proteins that modulate core cellular processes rather than a single, cohesive pathway. Name reflects this general regulatory role across essential functions.","confidence":"Medium","size":13,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071347","count":2},{"id":"GO:0051443","count":2}]},{"hash":"845543804987393267","title":"Neuronal development and synaptic signaling","description":"The GO terms point to neural development and function: tangential migration to the olfactory bulb, regulation of neuron maturation and nerve branching, GABAergic synaptic transmission, dopamine response, and GPCR signaling. Mitochondrial fission aligns with energy needs during neuronal formation, and cell cycle fits proliferating neural progenitors. The kidney size term is an outlier, but the dominant theme is neural development and synaptic activity, supporting this label.","confidence":"High","size":13,"edges":12,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1902499","count":3},{"id":"GO:0051932","count":3},{"id":"GO:0000266","count":3},{"id":"GO:0022028","count":3},{"id":"GO:2000172","count":3}]},{"hash":"1014794078491432641","title":"Nucleolar ribosome biogenesis and rRNA processing","description":"The cluster is dominated by rRNA maturation (SSU/LSU, 5.8S) and ribosomal large subunit biogenesis, plus related rRNA processing steps, consistent with nucleolar ribosome assembly; splicing signals and other nucleus-associated terms appear but are secondary.","confidence":"High","size":13,"edges":32,"triangles":34,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0016441","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0016584","count":5},{"id":"GO:0042766","count":5}]},{"hash":"709221777403122537","title":"TGF-\u03b2/BMP Signaling Regulation","description":"The cluster is enriched for GO terms tied to TGF-\u03b2 and BMP signaling, including cellular response to TGF-\u03b2 stimulus, negative regulation of TGF-\u03b2 receptor signaling, BMP signaling, and SMAD complex regulation, indicating regulators of this pathway. The presence of peptidyl-threonine dephosphorylation suggests phosphatases modulating TGF-\u03b2/BMP signaling. Some terms appear less related (e.g., vacuole fusion, photosystem stoichiometry), but the core theme centers on TGF-\u03b2/BMP pathway control and SMAD activity.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":4},{"id":"GO:0035970","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0080005","count":3},{"id":"GO:0030512","count":3}]},{"hash":"446096902343138060","title":"DNA Replication and Cell Cycle Regulation","description":"The cluster\u2019s top GO terms are centered on DNA replication, the centrosome cycle, and transcription related to DNA-templated processes, including positive regulation of nuclear DNA replication, which together point to cell cycle control and DNA replication. While there are developmental terms (forebrain, cranial skeleton morphogenesis, multicellular development) that reflect roles in embryogenesis, the dominant signal is cell cycle/DNA replication regulation; a few stress-response terms (cadmium response, invasive growth under glucose limitation) may reflect broader regulatory contexts but do not override the core theme.","confidence":"Medium","size":13,"edges":13,"triangles":3,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0048701","count":6},{"id":"GO:0007098","count":5},{"id":"GO:0010571","count":5},{"id":"GO:0006351","count":5}]},{"hash":"2133385984169769672","title":"RNA processing and translation initiation regulation","description":"This cluster shows strong representation of mRNA splicing (spliceosome activity), mRNA export, stabilization, and regulation of translational initiation, including eIF4F complex assembly, indicating a group involved in RNA maturation/processing and control of translation.","confidence":"High","size":13,"edges":29,"triangles":8,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":1},{"id":"GO:0097010","count":1},{"id":"GO:0000380","count":1},{"id":"GO:1903586","count":1},{"id":"GO:0006446","count":1}]},{"hash":"372441741750154816","title":"Mitotic Chromosome Segregation and Chromatin Assembly","description":"The cluster centers on mitosis and chromosome maintenance, with GO terms for cell division, mitotic sister chromatid segregation, CENP-A\u2013containing chromatin assembly, microtubule severing, and ubiquitin-related regulation, suggesting a core function in chromosome segregation and spindle dynamics; some annotations (cadmium response, ER\u2013Golgi transport, gonad development) are more peripheral or broader functional terms.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0071276","count":2}]},{"hash":"702072046835876552","title":"Proteostasis and post-translational modification","description":"The terms point to protein quality control and turnover (misfolded-protein response, mitophagy, ubiquitination) and to post-translational modifications affecting protein function (diphthamide formation, tRNA wobble modification). While some entries relate to growth and neural remodeling, the dominant theme is maintaining protein homeostasis through degradation, autoubiquitination, and translation-modifying modifications. Overall, a cohesive but not perfect connection, hence Medium confidence.","confidence":"Medium","size":13,"edges":13,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007117","count":1},{"id":"GO:0017183","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0060997","count":1},{"id":"GO:0071218","count":1}]},{"hash":"1012726436980300713","title":"Neuron maturation linked to ubiquitin-proteasome and mitochondria","description":"The top GO terms cluster around ubiquitin-related proteostasis (monoubiquitination, autoubiquitination, proteasomal degradation) and mitochondrial regulation (membrane potential, ATP synthesis, cytochrome c release), alongside neuron maturation. This suggests a coordinated program in developing neurons that ties protein turnover to mitochondrial health to support maturation and anti-apoptotic stability. ","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0006513","count":1},{"id":"GO:0090201","count":1},{"id":"GO:0032436","count":1},{"id":"GO:0051865","count":1}]},{"hash":"1944030722197931369","title":"ER-Golgi Vesicle Transport","description":"Dominant GO terms point to ER\u2013Golgi vesicle transport, COPII vesicle coating regulation, and Golgi localization, suggesting a cohesive function in vesicle trafficking and Golgi organization. Small GTPase\u2013mediated signaling supports trafficking control, while other terms hint at broader roles in endothelial signaling and development, but the vesicle trafficking theme is strongest.","confidence":"High","size":13,"edges":10,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0097212","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0003400","count":2},{"id":"GO:0097498","count":2}]},{"hash":"432619326646740352","title":"Translation Machinery and Membrane Targeting","description":"GO terms cluster around translation (initiation, elongation, termination, frameshifting) and membrane insertion/targeting, indicating a ribosome-associated translation module linked to membrane trafficking; antibiotic responses likely reflect translation stress rather than separate processes. The dense network (78 edges, 286 triangles) supports a cohesive functional group.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0006452","count":1},{"id":"GO:0006413","count":1}]},{"hash":"648293137402893640","title":"Steroid and Retinoid Metabolism in Lung Development","description":"The cluster is dominated by hormone-related and retinoid metabolism terms: androgen and estrogen biosynthesis/metabolic processes, plus retinoic acid, retinal, and retinol metabolic processes, all of which align with steroid and vitamin A (retinoid) pathways. The presence of lung development reinforces a developmental context where retinoid signaling and steroid metabolism influence tissue maturation. Some terms like melanin biosynthesis and response to antibiotic appear ancillary, and one obsolete oxidation-reduction term is likely noise. Overall, the core theme ties steroid and retinoid metabolism to development.","confidence":"High","size":13,"edges":12,"triangles":4,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0046677","count":9},{"id":"GO:0008209","count":8},{"id":"GO:0030324","count":8},{"id":"GO:0042438","count":8}]},{"hash":"362271427889133795","title":"ER Stress Response and Protein Quality Control","description":"This cluster is dominated by GO terms for protein folding in the endoplasmic reticulum, response to unfolded proteins, ERAD/ubiquitin-proteasome\u2013mediated quality control, and ER-stress\u2013related translation regulation, which together point to ER homeostasis and protein quality control as the shared function. A developmental term appears less central and may be incidental to a subset of proteins.","confidence":"High","size":13,"edges":18,"triangles":10,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":5},{"id":"GO:0034975","count":5},{"id":"GO:0006986","count":5},{"id":"GO:0001707","count":5},{"id":"GO:0032781","count":5}]},{"hash":"1062773195434949679","title":"RNA Processing and mRNA Export","description":"Based on GO terms like primary miRNA processing, siRNA processing, regulation of translational initiation, nonsense-mediated decay, and mRNA export from nucleus, the proteins in this cluster appear to be involved in post-transcriptional RNA metabolism, including processing and surveillance of RNA species, as well as regulation of translation. The presence of unrelated terms (hair follicle maturation, male germ-line cyst formation, meiotic cell cycle transition) might reflect pleiotropy or annotation noise, but the dominant signal is RNA processing.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031053","count":1},{"id":"GO:0000184","count":1},{"id":"GO:0030307","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0030422","count":1}]},{"hash":"965815402602625025","title":"Translation initiation & ribosome biogenesis","description":"This cluster is dominated by GO terms related to translation initiation and ribosome assembly, including translation reinitiation, formation of the translation preinitiation complex, ribosome biogenesis, and eIF4F complex assembly. While there are a few terms touching on splicing regulation, the strongest and most frequent signals point to initiation of translation and ribosome biogenesis as the core function of these proteins.","confidence":"High","size":13,"edges":16,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0097010","count":1},{"id":"GO:0000380","count":1}]},{"hash":"1577384327052329362","title":"Ribosome Biogenesis and Protein Synthesis","description":"The top GO terms cluster around ribosome assembly and function\u2014maturation of LSU rRNA, ribosome biogenesis, cytoplasmic translation, and mRNA capping/methylation\u2014pointing to production and use of ribosomes for protein synthesis. Some terms (chromatin organization, collagen catabolic process) appear less related and may reflect background annotations, but the core signal supports this theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0034724","count":2},{"id":"GO:0034396","count":2},{"id":"GO:0035551","count":2},{"id":"GO:0030574","count":2}]},{"hash":"1155662747543297838","title":"Neural and organismal development","description":"This cluster centers on developmental processes across an organism, including forebrain development, neural tube closure, skeletal system development, and multicellular organism development, indicating a neural/organismal development theme. While ion transport and stress-response terms appear, they do not override the dominant developmental signal, so the label reflects the core function with moderate confidence.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006813","count":9},{"id":"GO:0001403","count":8},{"id":"GO:0071276","count":8},{"id":"GO:0030900","count":8},{"id":"GO:0006349","count":8}]},{"hash":"968244665253736427","title":"Keratinocyte Differentiation and MAPK Signaling","description":"The terms show a clear focus on keratinocyte differentiation (GO:0030216) and multiple signaling pathways (ERK1/ERK2 cascade, p38 MAPK cascade) with connections to Wnt and Hippo signaling, as well as apoptosis and stimulus responses (PMA, GM-CSF). This suggests a cluster of proteins coordinating epithelial differentiation through MAPK- and growth-signaling networks. ","confidence":"High","size":12,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0060044","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0035329","count":3}]},{"hash":"1661084367891165440","title":"Chromatin Organization and Transcription Regulation","description":"This cluster centers on chromatin dynamics: CENP-A\u2013containing chromatin assembly and pericentric heterochromatin formation, plus negative regulation of transcription by RNA polymerase II and RNA polymerase I\u2013driven rRNA transcription. The GO terms point to chromatin structure maintenance and transcription control, with a few development-related terms that likely reflect broader roles of chromatin regulators in development. Overall, it seems to group proteins involved in chromatin organization and transcription regulation during development.","confidence":"Medium","size":12,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904693","count":1},{"id":"GO:0031508","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0030466","count":1}]},{"hash":"1312818502870678600","title":"Chemical Response and Metabolism","description":"The top GO terms point to responses to various chemical stimuli (herbicide, fungicide, ethanol) and signaling (cellular response to cAMP), as well as core metabolic processes (thiamine diphosphate and tetrahydrofolate metabolism, guanine metabolism). This suggests a cluster of proteins involved in broad chemical response together with fundamental metabolic pathways, rather than a single, cohesive biological process. Confidence: Medium","confidence":"","size":12,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009635","count":4},{"id":"GO:0009229","count":4},{"id":"GO:0071320","count":4},{"id":"GO:0045648","count":4},{"id":"GO:0045654","count":4}]},{"hash":"1898080563627458132","title":"Ubiquitin-Proteasome System and ERAD","description":"This cluster is dominated by ubiquitination-related processes (autoubiquitination, ubiquitin chain polymerization, SCF- and APC/C-dependent proteasomal degradation) and ERAD, indicating a core theme of protein quality control and degradation. Additional terms on interferon signaling, ER stress\u2013induced apoptosis, and DNA repair reflect ubiquitin's broader regulatory roles. Together, these terms point to a cohesive UPS/ERAD-centered cluster.","confidence":"High","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0030433","count":12},{"id":"GO:0070911","count":12},{"id":"GO:0060340","count":11},{"id":"GO:0010994","count":11}]},{"hash":"2159838797898371871","title":"DNA Repair and Calcium Signaling","description":"This cluster shows strong representation of DNA repair processes (base-excision and nucleotide-excision repair), indicating a DNA damage response core. It also features calcium signaling components (calcineurin-NFAT, postsynaptic calcium regulation, and ryanodine receptor activity) and xenobiotic/cadmium stress responses, suggesting cross-talk between DNA repair and calcium-dependent signaling under stress. A few terms like blood vessel branching and obsolete aging appear as less relevant noise but do not override the main theme.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0006289","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1825999970390159630","title":"Small GTPase signaling and endocytosis","description":"This label reflects the prominence of GO terms for small GTPase-mediated signal transduction and regulation of GTPase activity, along with multiple endocytosis-related terms such as endocytosis, regulation of synaptic vesicle endocytosis, and engulfment of apoptotic cells. The cluster likely groups proteins involved in GTPase-driven signaling and trafficking/endocytic processes, with additional hints of broader signaling (Wnt) and ER stress responses that indicate auxiliary regulatory roles.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903206","count":5},{"id":"GO:0007264","count":5},{"id":"GO:0034260","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0034976","count":4}]},{"hash":"519621026692403083","title":"Nuclear signaling and RNA processing regulators","description":"This cluster centers on nuclear regulatory processes: RNA splicing via the spliceosome and assembly of transcription-related protein complexes (SMAD and steroid hormone receptor), with modulation by activin signaling, sumoylation, and protein quality control through refolding. The heart development term hints at developmental signaling roles, tying these regulatory and stress-response functions to tissue morphogenesis. ","confidence":"Medium","size":12,"edges":13,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0007183","count":1},{"id":"GO:0006463","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0061077","count":1}]},{"hash":"414964535338181879","title":"Translation Initiation and mRNA Surveillance","description":"Most of the prominent GO terms are about translation initiation (initiation, regulation, IRES-dependent initiation, preinitiation complex formation), which points to a cluster of proteins involved in the translation machinery. The presence of an mRNA surveillance term (nonsense-mediated decay) and a proteasomal degradation term suggests coupling to mRNA/protein quality control, while stem cell terms appear infrequently and are not central. Thus, the core theme is translation initiation with related RNA quality-control processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1987144673043185210","title":"Calcium-Dependent Signaling in Cell Cycle and Development","description":"The cluster centers on calcium-dependent signaling (calcineurin-NFAT cascade, postsynaptic calcium regulation, and dephosphorylation) intertwined with cell cycle and DNA damage control (G1/S transition, DNA damage checkpoint signaling and its regulation). This suggests a common theme where calcium-mediated transcriptional programs influence proliferation and developmental processes, including lung and vascular morphogenesis; some terms reflect broader stress responses and membrane lipid metabolism that can intersect with calcium signaling.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0031573","count":3},{"id":"GO:0001569","count":2}]},{"hash":"2274236663647895761","title":"ER Stress and Cell Cycle Control","description":"The strongest signals are the endoplasmic reticulum unfolded protein response and several cell cycle\u2013related terms (cell division, G2/M transition, regulation of cyclin-dependent kinase activity, and transcription by RNA Pol II). This suggests a functional cluster where ER stress signaling interfaces with transcriptional and cell-cycle regulation, despite some peripheral terms that reflect broader transcriptional control or tissue-specific roles. ","confidence":"High","size":12,"edges":9,"triangles":3,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030968","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0001302","count":2},{"id":"GO:0071157","count":2}]},{"hash":"598709060027628040","title":"RNA methylation and oxidative stress response","description":"This cluster shows notable enrichment for RNA modification activities (guanine-N7 methylation in RNA, rRNA, and tRNA methylation) alongside oxidative stress-related responses (response to hydrogen peroxide, xenobiotic stimulus) and PPP-related metabolism, pointing to a group of proteins that couple RNA modification with redox defense and related biosynthetic capacity. The presence of cobalamin, ubiquinone, and vitamin E biosynthesis hints at redox-associated metabolism.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0006098","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0070476","count":2},{"id":"GO:0036265","count":2}]},{"hash":"1375272789129565467","title":"Maternal-Effect Development and Axis Specification","description":"This cluster\u2019s terms cluster around maternal control of embryogenesis and axis formation (maternal specification of dorsal/ventral axis; Wnt secretion; placental development; egg-laying regulation). Other terms touch general cellular processes (ER protein handling, mitochondrial autophagy, respiration) that are active during development but don\u2019t define a single molecular function, supporting a thematic link to maternal influence on development rather than a precise shared pathway. Confidence: Medium","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010259","count":1},{"id":"GO:0000422","count":1},{"id":"GO:0043457","count":1},{"id":"GO:0007311","count":1},{"id":"GO:0070863","count":1}]},{"hash":"209704217760023474","title":"Unknown","description":"The GO terms span immune signaling (interferon-\u03b2 production, IL-1 signaling, IL-3 production, MAPK cascade) and diverse developmental/sensory processes (mast cell differentiation, placenta and hippocampus development, visual perception) with no single cohesive biological theme linking all terms. Therefore a specific, representative label cannot be assigned beyond Unknown.","confidence":"","size":12,"edges":35,"triangles":45,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0060374","count":11},{"id":"GO:0000212","count":11},{"id":"GO:0001893","count":11},{"id":"GO:0007601","count":11},{"id":"GO:0045359","count":11}]},{"hash":"2222092662919904597","title":"Neural development and cytoskeletal dynamics","description":"The top GO terms show a mix of neural development (nervous system development, neurogenesis) and cytoskeletal organization/remodeling (nuclear migration along microtubules, microtubule anchoring at centrosome, actin filament bundle assembly), with supportive themes of vesicle transport (ER to Golgi) and developmental morphogenesis. Together, these points suggest a cluster of proteins coordinating neural development and cytoskeletal-directed processes essential for cell movement and morphogenesis, rather than a single isolated function.","confidence":"Medium","size":12,"edges":12,"triangles":2,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0030473","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0007283","count":1},{"id":"GO:0007476","count":1}]},{"hash":"1746947209379549383","title":"Growth and secretory pathway proteins","description":"The cluster centers on ribosome biogenesis and ER-Golgi trafficking via COPII, plus cell-proliferation and development terms, indicating a growth-related program that links protein synthesis with secretory transport.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0008283","count":2}]},{"hash":"533964136431761406","title":"DNA Replication & Cell Cycle","description":"The dominant GO terms are DNA replication, DNA strand elongation, mitotic DNA replication initiation, and cell cycle, which together point to a replication/cell-cycle function. A few terms related to photosynthesis and heterochromatin formation are present but appear secondary or incidental to the core replication theme.","confidence":"High","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006271","count":4},{"id":"GO:0042140","count":3},{"id":"GO:1902450","count":3}]},{"hash":"1347410736574691174","title":"Developmental transcription and chromatin regulation","description":"The top GO terms cluster around transcription (DNA-templated transcription), protein regulation (regulation of protein stability, phosphorylation) and chromatin-associated processes (nucleosome density/positioning), with developmental signals such as embryonic cranial skeleton morphogenesis and synapse localization, suggesting a theme of gene expression control during development and chromatin dynamics.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031647","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035418","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0006260","count":3}]},{"hash":"2186081833615310076","title":"Transmembrane nutrient and ion transport","description":"This cluster centers on multiple transmembrane transport GO terms for diverse substrates (nitrate, galactose, phosphate, sialic acid, vitamins, potassium ions), suggesting a group of membrane transporters handling uptake and efflux of nutrients and ions. While there are also metabolic terms like nitrate assimilation, the preponderance of transport terms supports a transporter-focused theme.","confidence":"High","size":11,"edges":17,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015757","count":2}]},{"hash":"599340439166428811","title":"Xenobiotic Response and Nucleotide Metabolism","description":"The terms show a clear thread of responding to xenobiotic stimuli and antibiotics, combined with strong signals for nucleotide-related metabolism (folate interconversion, dUMP/dihydrofolate, uracil) and glycolysis, with some bone/cartilage development terms likely reflecting broader growth signals. This suggests a cluster focused on stress response to xenobiotics plus core metabolic and nucleotide turnover processes.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0051216","count":1}]},{"hash":"1555396064564128019","title":"Telomere maintenance and Cajal body RNA localization","description":"The strongest signals are telomerase-related terms and RNA localization to Cajal bodies, pointing to a role in telomere maintenance and nuclear RNA processing. Additional terms about nuclear pore assembly and cell cycle fit with nuclear organization and division, supporting a coherent nuclear regulatory cluster.","confidence":"High","size":11,"edges":25,"triangles":31,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051973","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0007100","count":4},{"id":"GO:0002931","count":3}]},{"hash":"792349289734921833","title":"Immune and growth signaling pathways","description":"Most of the top GO terms point to signaling and immune-related processes (defense response to Gram-positive bacteria, LPS signaling, interferon-beta production) as well as growth-factor-related signaling (ERBB pathway, tyrosine kinase activity regulation, PI3K signaling). A few terms touch on cell division and brain development, but the dominant theme across the cluster is signaling in immune and growth contexts, justifying a label centered on immune and growth signaling. ","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":3},{"id":"GO:0007100","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0038127","count":2},{"id":"GO:0061099","count":2}]},{"hash":"335391225118112786","title":"Ribosome biogenesis and translation initiation","description":"The cluster is enriched for ribosome-related processes (ribosome biogenesis, cytosolic ribosome assembly, translation reinitiation, and eIF4F complex assembly) and translation initiation, indicating a core theme of ribosome production and initiation of protein synthesis; a spliceosome assembly term appears but is much less represented, while several terms refer to unrelated cellular processes, suggesting a mostly ribosome/translation-focused cluster with some noise.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0030595","count":1},{"id":"GO:0048539","count":1},{"id":"GO:0030282","count":1}]},{"hash":"2204201132976276460","title":"Wnt and Hippo growth signaling with differentiation","description":"The terms cluster around growth-control signaling pathways (Wnt, Hippo, TGF-\u03b2 receptor signaling) and their regulation of cell proliferation, fate decisions, and differentiation (e.g., keratinocyte differentiation), with supporting roles from GTPase activity and apoptosis. Although a term like visual perception is present, the dominant theme is growth signaling and differentiation control.","confidence":"High","size":11,"edges":44,"triangles":112,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":5},{"id":"GO:0030512","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0030216","count":3}]},{"hash":"464398272191686335","title":"Cardiac calcium signaling and conduction regulation","description":"The top GO terms converge on calcium signaling and cardiac electrical conduction: regulation of ryanodine receptor\u2013mediated calcium release, store-operated calcium channels, calcineurin-NFAT signaling, and regulation of electrical coupling in cardiac conduction, with supporting hints from kinase activity and cell shape. These collectively suggest a function focused on calcium-dependent control of cardiac conduction and related vascular processes.","confidence":"High","size":11,"edges":13,"triangles":6,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060316","count":4},{"id":"GO:0001569","count":3},{"id":"GO:1901339","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0071902","count":3}]},{"hash":"269511320391070570","title":"Cell Division and Protein Synthesis Machinery","description":"This cluster centers on mitotic processes (sister chromatid cohesion, microtubule severing), DNA repair, transcription, ribosome biogenesis, translation initiation, and ER-Golgi transport, pointing to a cohesive module that supports cell proliferation, gene expression, and genome maintenance.","confidence":"High","size":11,"edges":12,"triangles":2,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000724","count":4},{"id":"GO:0007064","count":4},{"id":"GO:0002188","count":3}]},{"hash":"170203471218119506","title":"ER\u2013Golgi vesicle trafficking and lysosome targeting","description":"This cluster is dominated by GO terms tied to ER-to-Golgi and Golgi-to-ER transport, COPII vesicle coating, intracellular protein transport, Golgi-to-lysosome transport, protein targeting to lysosome, and macroautophagy, pointing to a cohesive role in vesicle trafficking and lysosomal degradation pathways. Ubiquitin-dependent MVB sorting further supports a degradation/quality-control theme. The translation preinitiation complex term appears incidental to this shared trafficking/degradation function.","confidence":"High","size":11,"edges":15,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0043162","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1134923121650525173","title":"ER Stress and Protein Quality Control","description":"The cluster is dominated by GO terms on endoplasmic reticulum proteostasis (protein folding in the ER, response to unfolded protein, ERAD, ER stress\u2013related translation regulation, and ubiquitin-proteasome\u2013mediated quality control), indicating a cohesive ER stress and protein quality control theme; a couple of developmental terms may reflect broader roles or pleiotropy.","confidence":"High","size":11,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0032781","count":2}]},{"hash":"1451243081440983797","title":"DNA replication and repair machinery","description":"The cluster is enriched for core genome maintenance terms: DNA replication, nucleotide-excision repair, and double-strand break repair in meiotic recombination, plus translesion synthesis, indicating a shared role in DNA replication/repair processes. Additional terms for proteasome assembly and ER-Golgi transport may reflect supporting proteostasis and trafficking needed for genome maintenance, but the dominant theme is DNA replication and repair.","confidence":"Medium","size":11,"edges":30,"triangles":41,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0070682","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0070987","count":2}]},{"hash":"1334056747465706373","title":"Vacuole function and ion transport","description":"The cluster is dominated by vacuolar-related terms (vacuolar acidification, vacuole organization, protein targeting to vacuole) and proton transport processes (proton transmembrane transport, proton motive force-driven ATP synthesis), suggesting a core role in vacuole biology and ion homeostasis. Copper and sodium ion transport terms further support a theme of ion balance linked to vacuolar/vesicular function. Some annotations for transcription or multicellular growth appear incidental to this core function. ","confidence":"High","size":11,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006626","count":1},{"id":"GO:0015991","count":1}]},{"hash":"1859202683151230793","title":"ER Stress and Protein Folding","description":"Based on enrichment for GO terms related to protein folding in the endoplasmic reticulum, response to unfolded protein, ERAD, and translation initiation regulation in response to ER stress, the cluster centers on ER proteostasis and the unfolded protein response; a few developmental terms are present but appear incidental to the dominant ER-related functions.","confidence":"Medium","size":11,"edges":12,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006337","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0001707","count":2}]},{"hash":"404690112214083302","title":"Neural development and synaptic plasticity","description":"The GO terms cluster around nervous system development and function: visual perception (retina), forebrain and multicellular organism development, Schwann cell development, and long-term synaptic potentiation, plus transcriptional regulation, all pointing to neuronal/glial differentiation and synaptic activity. Some terms reflect stress responses (cadmium) or metabolic signals, but the dominant theme is neural development and synaptic plasticity.","confidence":"High","size":11,"edges":8,"triangles":0,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0014044","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0010800","count":4},{"id":"GO:0001403","count":4}]},{"hash":"594997247342505897","title":"Unknown","description":"The top GO terms span toxic response, placenta development, cell polarity and division, visual perception, and immune cytokine production, with no clear single theme tying them together. The network is sparsely connected (one edge, no triangles), suggesting the proteins do not form a coherent functional module in this dataset. Therefore, no intuitive, concise label can capture a common function.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009636","count":4},{"id":"GO:2000114","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0060374","count":2}]},{"hash":"2202054749512164309","title":"Unknown","description":"The GO terms are diverse (proteolysis, hypoxia response, glycolysis, angiogenesis regulation, differentiation, and even plant cytokinin biosynthesis), with no single clear function tying the cluster together. While some themes hint at stress/metabolic responses, the mixture prevents a specific, cohesive label. ","confidence":"","size":11,"edges":38,"triangles":59,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0009691","count":2},{"id":"GO:0031639","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0030855","count":2}]},{"hash":"746354999718699386","title":"DNA Replication and Cell Cycle","description":"The top GO terms are dominated by nuclear DNA processes (replication, repair, DNA-templated transcription) and mitotic/cell-cycle activities (mitotic cell cycle, meiotic spindle organization), suggesting a core theme of DNA metabolism and cell division. Other terms (wounding response, mast cell differentiation, placenta development, visual perception, interferon-beta production) are more peripheral and don't define a single cohesive function for the cluster, so the label reflects the primary signal with caveats.","confidence":"Medium","size":11,"edges":14,"triangles":6,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0006281","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0009611","count":7}]},{"hash":"664207010767957174","title":"Potassium Ion Transport and Membrane Excitability","description":"The top GO terms are dominated by potassium ion transport, intracellular potassium homeostasis, and regulation/stabilization of membrane potential, which together point to a shared role in ion balance and cellular excitability. A few terms (hematopoietic differentiation, saliva secretion, mechanosensation) seem less central and may reflect annotation noise or multifunctional proteins, but they do not override the dominant potassium/membrane themes.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901532","count":2},{"id":"GO:1902035","count":2},{"id":"GO:0006919","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0046541","count":1}]},{"hash":"2246059557043219937","title":"Unknown","description":"The cluster\u2019s GO terms span several unrelated areas (cell growth and spindle assembly, telomere maintenance, immune signaling, vascular development, sensory perception, and signaling regulation). There is no single cohesive biological process uniting these terms, and the absence of network edges further suggests a lack of a common function. Therefore, a concise, representative label cannot be assigned with confidence.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0051225","count":1},{"id":"GO:0097497","count":1},{"id":"GO:0045083","count":1},{"id":"GO:2000031","count":1}]},{"hash":"1427278418346647228","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by ribosome-related terms (ribosome biogenesis, ribosomal subunit biogenesis/export, cytoplasmic translation) and tRNA modification, pointing to a module of ribosome assembly and protein synthesis; a few cell division-related terms appear but are secondary to the ribosome-centered processes.","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903833","count":3},{"id":"GO:1901001","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0002181","count":2}]},{"hash":"293553239009358837","title":"Purine Nucleotide Metabolism","description":"This cluster is dominated by GO terms for purine nucleotide synthesis and processing (ADP biosynthesis, GTP metabolism, AMP salvage, nucleoside monophosphate phosphorylation, purine ribonucleotide interconversion, ITP metabolism). The presence of DNA replication initiation suggests a link to nucleotide supply for synthesis. Brain and liver development terms appear incidental to the core nucleotide-focused theme. Overall, the core function is purine nucleotide metabolism.","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006172","count":2},{"id":"GO:0006270","count":2},{"id":"GO:0046939","count":2},{"id":"GO:0046940","count":2},{"id":"GO:0007420","count":2}]},{"hash":"1500511404190883677","title":"Central carbon metabolism and signaling","description":"The proteins cluster around core metabolic pathways (glycolysis, glyoxylate cycle, malate/oxaloacetate metabolism) and energy-related NADH processes, while also showing multiple signaling/response connections (glucose, estrogen, hydrogen peroxide, cAMP) and apoptotic regulation. This points to a group involved in central carbon metabolism coupled with cellular stress and hormonal signaling, rather than a single specialized function.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006097","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0006108","count":3},{"id":"GO:0009749","count":3},{"id":"GO:0006107","count":3}]},{"hash":"2229140364323763073","title":"Developmental Growth and Cell Cycle Control","description":"The cluster centers on embryonic development (cranial skeleton morphogenesis, placenta development) and proliferative processes (DNA replication, cell cycle regulation), with regulatory layers including transcriptional control, ubiquitination, apoptosis avoidance, and TLR signaling, suggesting a coordinated development\u2013proliferation program.","confidence":"Medium","size":10,"edges":14,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0009636","count":2},{"id":"GO:2000114","count":2},{"id":"GO:0001890","count":2}]},{"hash":"1384750603230224357","title":"Mitochondrial respiration, Complex II assembly","description":"The top GO terms point to mitochondrial electron transport from NADH to ubiquinone and to the assembly of respiratory chain complex II, indicating the proteins are tied to oxidative phosphorylation and Complex II biogenesis.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1}]},{"hash":"135187405944141665","title":"ER stress and protein folding quality control","description":"This cluster centers on ER-associated proteostasis: translation, protein folding in the ER, unfolded protein response, and ERAD, indicating a cohesive group involved in managing protein synthesis and folding under ER stress. A few non-core terms (e.g., mesoderm formation, obscure ER targeting) appear but do not define the main function.","confidence":"High","size":10,"edges":22,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0032781","count":3},{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006986","count":2}]},{"hash":"832401992005861787","title":"RNA processing and ribosome maturation","description":"This cluster centers on RNA metabolism, with GO terms for transcription, RNA folding, splicing (including Group I intron splicing), SSU-rRNA maturation, and translation/fidelity, pointing to ribosome biogenesis and RNA processing as the shared function.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0034337","count":1}]},{"hash":"1220275576310785427","title":"Developmental and Cell-Cycle Regulation","description":"The terms point to broad regulatory roles in growth and development, including cell division (centrosome/pericentriolar material localization), root meristem growth, and plant hormone signaling (auxin polar transport, cytokinin signaling). The mix of plant- and animal-related developmental terms and lack of a single cohesive pathway suggest a general regulatory cluster rather than a specific pathway. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0060430","count":2},{"id":"GO:2000299","count":2},{"id":"GO:2000012","count":2},{"id":"GO:1905793","count":2}]},{"hash":"1846809322221110560","title":"Transmembrane transport of ions and nutrients","description":"The GO terms show diverse plasma membrane transport for ions and small solutes (K+, nitrate, nitrite, vitamins, dehydroascorbic acid, D-xylose, selenite, etc.), with a couple items related to epithelial maintenance and glucose starvation response, supporting a transporter-centric cluster.","confidence":"High","size":10,"edges":11,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043252","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0070837","count":1},{"id":"GO:0015707","count":1}]},{"hash":"241639095212003032","title":"Post-transcriptional RNA processing and translation control","description":"The GO terms converge on RNA-level regulation, with several terms tied to translation initiation and reinitiation (EIF4F complex assembly, regulation of translational initiation, translation reinitiation) as well as spliceosome-mediated mRNA splicing and its regulation. Additional terms about differentiation may be broad associations, but the core signal is RNA processing and translational control.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":2},{"id":"GO:0048235","count":2},{"id":"GO:0040015","count":2},{"id":"GO:0002188","count":1},{"id":"GO:0097010","count":1}]},{"hash":"2107112619761362282","title":"Splicing and Translation Initiation Regulation","description":"This cluster is enriched for spliceosome-mediated mRNA splicing (cis and alternative) and components involved in translation initiation (preinitiation complex formation, eIF4F assembly) as well as regulation of translational initiation, indicating a cohesive group of proteins that connect RNA processing with control of translation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0097010","count":3}]},{"hash":"997124263749776744","title":"Mixed Developmental Signaling and Cellular Stress","description":"The top terms span developmental signaling (negative regulation of a neural patterning pathway, mesoderm formation) and core cellular processes (DNA replication, ER protein folding/unfolded protein response), plus a few miscellaneous terms. This suggests a cluster with no single cohesive function, but rather a mix of developmental signaling and general cellular maintenance with some noise from obsolete terms.","confidence":"Low","size":10,"edges":11,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0034975","count":1}]},{"hash":"1354041082357824145","title":"Mitochondrial Transporters and Membrane Potential","description":"The cluster shows a pattern of transmembrane transport activities, including deoxynucleotide, NAD, coenzyme A, thiosulfate, and specifically mitochondrial ATP transport, along with regulation of the mitochondrial membrane potential. This combination suggests a theme of mitochondrial metabolite transport and energy regulation. A few terms (pregnancy, IGF stimulus, superoxide response) are less directly tied to transport and may reflect broader cellular signaling in the dataset.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":3},{"id":"GO:0030302","count":3},{"id":"GO:0035352","count":3},{"id":"GO:0007565","count":3},{"id":"GO:1990544","count":3}]},{"hash":"1229943527950493508","title":"Unknown","description":"The GO terms are highly diverse, ranging from peptidoglycan biosynthesis to cerebellar cortex development and tarsal gland development, with no clear shared function. The cluster has only a single edge and no triangles, indicating very weak connectivity and no cohesive biological theme. Therefore there is no reliable, representative label beyond Unknown.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009252","count":2},{"id":"GO:1903699","count":2},{"id":"GO:0071168","count":2},{"id":"GO:0045128","count":2},{"id":"GO:0008360","count":2}]},{"hash":"98246344653011285","title":"Ribophagy and Autophagy-Related Trafficking","description":"The cluster\u2019s top GO terms point to autophagy- and ribophagy-related processes (engulfment by autophagosome, substrate localization to autophagosome, ribophagy) and linked vesicle trafficking, with additional hints of ribosome/nuclear export regulation and endocytosis. This suggests the proteins collectively participate in autophagic cargo processing and ribosome turnover, with membrane trafficking involvement.","confidence":"High","size":10,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000203","count":2},{"id":"GO:0045723","count":2},{"id":"GO:0010794","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0061736","count":2}]},{"hash":"170294960789185431","title":"Ubiquitination and Protein Quality Control","description":"This cluster shows strong enrichment for ubiquitin- and SUMO-related processes (proteasomal ubiquitin-dependent protein catabolic process, protein autoubiquitination, protein sumoylation) and related protein quality-control functions (deglycosylation, ER stress/apoptotic regulation, PML body organization). The mixture of these PTM pathways with regulators of vesicle formation and innate immune signaling (MyD88-dependent TLR pathway) suggests a collective role in maintaining protein homeostasis and regulated signaling, rather than a single, narrow function.","confidence":"High","size":9,"edges":16,"triangles":13,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0002109","count":3},{"id":"GO:0006517","count":3},{"id":"GO:0032436","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0034126","count":3}]},{"hash":"1693804314307114465","title":"Mitochondrial membrane regulation and lipid biosynthesis","description":"The strongest signals are mitochondrial in nature: regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, with concurrent enrichment for triglyceride biosynthesis, pointing to a mitochondria-centric role in membrane dynamics and lipid metabolism. Some terms touch on cell cycle regulation and proteasome assembly, which can relate to mitochondrial quality control, while a couple of terms reference broader signaling (Wnt) that may be secondary. Overall, the cluster appears to represent mitochondria-focused regulation of membrane properties and lipid metabolism.","confidence":"High","size":9,"edges":13,"triangles":5,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:0010867","count":4},{"id":"GO:2000134","count":4},{"id":"GO:1903740","count":4},{"id":"GO:0030150","count":4}]},{"hash":"394237370464300729","title":"Mitotic spindle dynamics and ciliogenesis","description":"GO terms point to microtubule-based movement, spindle orientation, and mitotic cycle, plus intraflagellar transport for cilium assembly, with related vesicle trafficking and GTPase regulation; developmental terms suggest broader growth roles.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0035735","count":2}]},{"hash":"1587906179642793946","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":7,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2}]},{"hash":"787918785852552158","title":"Oxidative Stress Response and Redox Homeostasis","description":"The top GO terms cluster around cellular oxidant detoxification, redox homeostasis, and responses to reactive oxygen species (hydrogen peroxide and superoxide). This points to a coherent redox/antioxidant module among the proteins, with deglutathionylation aligning with redox regulation; a few transcription-related terms appear but do not define the main function of the cluster.","confidence":"High","size":9,"edges":8,"triangles":2,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0042267","count":3},{"id":"GO:0019430","count":3}]},{"hash":"1208309841679586402","title":"Mitochondrial tRNA modification and redox metabolism","description":"The cluster shows enrichment for tRNA modification terms (methylation and wobble uridine modification) together with redox-related processes (redox homeostasis, NAD+ biosynthesis, mitochondrial electron transport). This suggests a coherent module combining mitochondrial tRNA processing/modification with energy production and redox balance, rather than a single isolated function. Some amino acid catabolism terms appear less central to the core theme but may reflect ancillary metabolic links.","confidence":"Medium","size":9,"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:0045454","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0009435","count":2}]},{"hash":"1444480912279605163","title":"ER-Golgi Trafficking and Autophagy","description":"The cluster\u2019s top GO terms cluster around intracellular vesicle transport (ER\u2192Golgi, Golgi\u2192vacuole, intra-Golgi, CvT pathway), Golgi to vacuole transport, and autophagosome maturation, indicating a cohesive role in ER-Golgi trafficking and autophagy. A few terms (cornified envelope assembly, neurotransmitter secretion, T cell cytotoxicity) are more distant but may reflect broader annotation contexts rather than core function.","confidence":"High","size":9,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061669","count":2},{"id":"GO:0006896","count":2},{"id":"GO:1903575","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0032258","count":2}]},{"hash":"1766987650476446283","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to ribosome production and function (ribosome biogenesis, ribosomal subunit export from the nucleus, and cytoplasmic translation) as well as tRNA modification, which together indicate a core theme of assembling and using ribosomes for protein synthesis. Additional cell cycle terms appear as general growth-associated processes but the ribosome-related terms are most frequent, supporting a label focused on ribosome biology.","confidence":"High","size":9,"edges":9,"triangles":1,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000055","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0007049","count":5},{"id":"GO:1901001","count":4},{"id":"GO:0042254","count":4}]},{"hash":"53808732281844866","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for cytoplasmic translation, ribosome biogenesis, large subunit maturation/export, and rRNA/tRNA processing, indicating a shared role in ribosome assembly and protein synthesis. A minority of terms reference conjugation with cellular fusion and cell division, which may reflect broader cellular coordination rather than a primary function of this cluster, and a couple relate to stress response. High","confidence":"High","size":9,"edges":9,"triangles":1,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000747","count":3}]},{"hash":"2121926966200785428","title":"Hormone and carbohydrate metabolism","description":"These proteins appear enriched for hormone-related metabolism (androgen, progesterone, prostaglandin response) and diverse carbohydrate pathways (xylose, arabinose, sorbitol) along with pyridoxal (vitamin B6) biosynthesis. Ancillary terms include daunorubicin metabolism, oxidative stress response, and potassium transport, but the core signal centers on hormone and carbohydrate metabolic processes. Confidence: Medium","confidence":"","size":9,"edges":11,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071799","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0042821","count":2},{"id":"GO:0044597","count":2},{"id":"GO:0008209","count":2}]},{"hash":"1545552766935905417","title":"Metal ion transport and ion homeostasis","description":"The top GO terms cluster around transport and regulation of metal ions (cadmium, zinc, copper) and overall ion balance, including potassium homeostasis and membrane potential stabilization, suggesting a functional group of ion transporters and homeostatic regulators. Some signaling/modulatory terms (dephosphorylation, calcineurin-NFAT signaling, PKA activity) hint at regulatory connections to ion flux, while a couple of metabolic terms (L-serine biosynthesis) may be ancillary. Overall, the dominant theme is ion transport and maintenance of cellular ion balance.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030322","count":3},{"id":"GO:0070574","count":3},{"id":"GO:0071577","count":3},{"id":"GO:0030007","count":3},{"id":"GO:2000481","count":2}]},{"hash":"584814427915893155","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0006398","count":1},{"id":"GO:0010197","count":1},{"id":"GO:0031126","count":1}]},{"hash":"974269471078731258","title":"Broad-spectrum membrane transporters","description":"GO terms cluster around transmembrane transport of diverse substrates (amino acids, thiamine, vitamins, carbohydrates, phytosterols) and xenobiotics, suggesting a group of solute transport proteins. An outlier nucleotide-excision repair term is present, but the dominant theme is membrane transport function.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055099","count":1},{"id":"GO:0099133","count":1},{"id":"GO:0003333","count":1},{"id":"GO:0015888","count":1},{"id":"GO:0043215","count":1}]},{"hash":"2273115699541095406","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0000480","count":1},{"id":"GO:0000472","count":1},{"id":"GO:1901917","count":1},{"id":"GO:0000973","count":1}]},{"hash":"702609605672161012","title":"Oxidative Stress and DNA Metabolism","description":"The top GO terms center on responses to oxidative and chemical stress (hydrogen peroxide, xenobiotic stimuli) and DNA-related processes (recombination, DNA catabolic processes), suggesting a cluster focused on stress-induced DNA handling. A corneocyte development term is present but appears less representative than the oxidative/DNA-related terms; some obsolescent terms are present, which may reflect annotation noise rather than core biology. Overall, the cluster seems to group proteins involved in stress responses that link to DNA metabolism.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0070301","count":2},{"id":"GO:0003335","count":2},{"id":"GO:0006310","count":2},{"id":"GO:2000327","count":2}]},{"hash":"1804935815027618910","title":"Mitochondrial Translation and Electron Transport","description":"The top GO terms point to mitochondrial processes: assembly of respiratory chain complex II and NADH-to-ubiquinone electron transport, plus maturation of LSU rRNA and translation, which collectively map to mitochondrial ribosome assembly and mitochondrial protein synthesis involved in oxidative phosphorylation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0006412","count":1}]},{"hash":"769846333487127913","title":"Membrane targeting and vesicle trafficking","description":"This cluster is dominated by GO terms for SRP-dependent cotranslational targeting to membrane and Golgi-to-plasma membrane transport, plus small GTPase\u2013mediated signaling, which together point to membrane-associated protein targeting and vesicle trafficking. Additional terms such as iron ion import and osmotic response involve membranes but are peripheral to the central trafficking theme; a few entries (chitin-based cuticle formation, chlorophyll biosynthesis) may reflect species-specific or annotation noise rather than a cohesive core function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":3},{"id":"GO:0006972","count":2},{"id":"GO:0098707","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0035293","count":2}]},{"hash":"5164459452338522","title":"Genome Maintenance and Protein Quality Control","description":"These proteins cluster around genome maintenance functions (DNA repair, UV-damage excision repair, DNA recombination, replication initiation) together with protein quality control processes (response to misfolded proteins, protein processing, mitochondrial protein import), plus links to mRNA export and ER organization. Overall, the theme is maintaining genome integrity and proteostasis under stress, making this label appropriate and representative.","confidence":"Medium","size":8,"edges":11,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0071218","count":2},{"id":"GO:0070914","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0045041","count":2}]},{"hash":"1856735003518120991","title":"DNA Repair and Translesion Synthesis","description":"GO terms cluster around DNA repair, translesion synthesis (both error-free and error-prone), nucleotide-excision repair, UV-C response, and DNA-templated replication, pointing to DNA damage tolerance and repair pathways. A couple of terms for peptidoglycan biosynthesis and cell shape regulation appear as outliers, but the core signal is DNA damage response and TLS.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":2},{"id":"GO:0006281","count":1},{"id":"GO:0071897","count":1},{"id":"GO:0071494","count":1},{"id":"GO:0006297","count":1}]},{"hash":"670445249768873918","title":"Bone Remodeling and Matrix Degradation","description":"The top GO terms cluster around bone and extracellular matrix turnover: collagen catabolic process, bone resorption, and intramembranous ossification point to matrix remodeling and bone turnover. Additional terms related to proteolysis, proteasome storage granule assembly, and autophagy regulation suggest cellular protein turnover accompanying remodeling. Some terms like decidualization and xenobiotic response are less directly related but may reflect broader proteolytic and stress-response activities that accompany matrix remodeling. Overall, the cluster appears to group proteins involved in bone remodeling and extracellular matrix degradation.","confidence":"Medium","size":8,"edges":22,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":5},{"id":"GO:0046697","count":3},{"id":"GO:0001957","count":3},{"id":"GO:1990237","count":3},{"id":"GO:0042493","count":3}]},{"hash":"1112992887026356137","title":"Selective autophagy in yeast","description":"The proteins in this cluster are enriched for autophagy-related processes, including autophagy of mitochondrion, the cytoplasm-to-vacuole targeting (Cvt) pathway, and piecemeal microautophagy of the nucleus, indicating a core theme of selective autophagic turnover in yeast. Additional terms like sumoylation and deglycosylation point to regulation of protein turnover, supporting a cohesive autophagy/quality-control theme, even though a few unrelated terms may appear due to annotation noise. ","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0044805","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0034727","count":2}]},{"hash":"94349109424925226","title":"Spliceosome and mRNA decay cluster","description":"This cluster's top GO terms center on RNA metabolism, including transcription termination by RNA Pol II, mRNA decapping, spliceosome-mediated splicing and snRNP assembly, and P-body formation. Together these indicate proteins involved in RNA processing and post-transcriptional regulation, including mRNA decay and splicing. Some ABA/water-stress terms may reflect broader transcriptional regulation under stress but do not override the core RNA-related signals.","confidence":"High","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":3},{"id":"GO:0000290","count":2},{"id":"GO:1990141","count":2},{"id":"GO:0030490","count":2},{"id":"GO:0000387","count":2}]},{"hash":"925131837205062767","title":"Mitochondrial quality control and autophagy","description":"The cluster shows enrichment for mitochondrial inheritance, apoptosis, and macroautophagy, along with redox/ROS detox and hydrogen peroxide response, suggesting a coordinated mitochondrial maintenance and stress-response program. Ribosome biogenesis appears as a minor association, not central to the main theme.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0016236","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1656448774571829597","title":"Proteostasis and protein quality control","description":"Top GO terms emphasize degradation and handling of misfolded proteins (ubiquitin-dependent ERAD, misfolded protein response, proteasome assembly, protein unfolding), pointing to a proteostasis-focused cluster involved in protein quality control and degradation. Some terms related to DNA repair, transcription elongation, and energy production may reflect broader stress responses, but the central theme remains proteostasis.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0070682","count":2},{"id":"GO:0071218","count":2},{"id":"GO:0070914","count":2}]},{"hash":"1371134124014876311","title":"Neuronal vesicle trafficking and SNARE assembly","description":"This cluster centers on vesicular transport in the neuronal secretory pathway, including ER\u2013Golgi trafficking, intra-Golgi transport, SNARE complex assembly, and vesicle fusion, with links to postsynaptic receptor insertion and long-term potentiation, indicating a cohesive synaptic vesicle trafficking/function theme.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006891","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0090161","count":2}]},{"hash":"1764143871901908435","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":11,"triangles":5,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000462","count":3}]},{"hash":"1413535076538557101","title":"mRNA processing and translation regulation","description":"Based on the top GO terms, this cluster centers on post-transcriptional control: regulation of translation initiation and reinitiation, assembly of the eIF4F complex, and regulation of mRNA splicing and spliceosome activity, with accompanying stress-related mRNA stability regulation. These collectively indicate a coherent theme of mRNA processing and translation control.","confidence":"High","size":8,"edges":11,"triangles":4,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0002188","count":3},{"id":"GO:0097010","count":3},{"id":"GO:0000380","count":3}]},{"hash":"493623768259906558","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900264","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0007064","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0035753","count":1}]},{"hash":"1160597986265519833","title":"Membrane lipid metabolism and repair","description":"This cluster centers on lipid biosynthesis and phospholipid metabolism (sphingolipid, phosphatidylcholine, phosphatidylinositol; inositol trisphosphate and fatty acid biosynthesis) and includes plasma membrane repair, indicating a theme of membrane lipid homeostasis and remodeling. A few other terms (GTPase regulation, insulin secretion, angiogenesis) may reflect broader regulatory connections to signaling and metabolism but are less central to the core theme.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0016525","count":2},{"id":"GO:0001778","count":2},{"id":"GO:0090153","count":1},{"id":"GO:0032959","count":1}]},{"hash":"849569754842168293","title":"Cell cycle regulation and development","description":"The prominent terms revolve around DNA replication, mitotic cell cycle, spindle organization, and regulation of cyclin-dependent kinases, pointing to a core cell cycle control theme. The remaining terms cover developmental processes (placenta/hippocampus/mast cell differentiation) and immune signaling, suggesting the cluster includes proteins with cell-cycle roles plus broader developmental regulation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0060374","count":6},{"id":"GO:0000212","count":6},{"id":"GO:0001893","count":6}]},{"hash":"1181324813468417036","title":"Unknown","description":"The GO terms include plant carbohydrate catabolic processes (raffinose, inulin, sucrose) and storage, but also immune and neural/developmental terms, offering no single cohesive function for the eight proteins.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034484","count":1},{"id":"GO:0080167","count":1},{"id":"GO:1902927","count":1},{"id":"GO:0005987","count":1},{"id":"GO:0071370","count":1}]},{"hash":"2111403419087251839","title":"Lipid Biosynthesis and Remodeling","description":"This cluster shows several GO terms tied to lipid metabolism, including CDP-diacylglycerol biosynthetic process, phosphatidylcholine acyl-chain remodeling, ether lipid biosynthetic process, and triglyceride biosynthetic process. While there are additional terms related to RNA modification and energy production, the lipid biosynthesis/remodeling terms provide the clearest shared theme among the proteins. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0016024","count":1},{"id":"GO:0036151","count":1}]},{"hash":"676058770335631153","title":"Muscle and neural tissue development and homeostasis","description":"The top GO terms point to development and maintenance across muscle, brain, and eye (skeletal muscle fiber adaptation, substantia nigra development, retina homeostasis), suggesting a theme of tissue-specific development and homeostasis. Additional terms like potassium ion transport and hypoxia response reflect shared physiology of excitable tissues, while positive regulation of gene expression indicates control of these programs. Together, these indicate a cross-tissue development/adaptation and homeostasis signature rather than a single narrow function.","confidence":"Medium","size":7,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006813","count":3},{"id":"GO:0001666","count":3},{"id":"GO:0043981","count":3},{"id":"GO:0043982","count":3}]},{"hash":"697943132244805071","title":"Proteasome-Ubiquitin Proteolysis and Wnt Signaling","description":"The top GO terms point to the core proteasome assembly and ubiquitin-dependent protein degradation pathways (SCF and APC-related catabolic processes), indicating a proteostasis-centered cluster. Additionally, several terms involve Wnt signaling and planar cell polarity, suggesting these degradation components may interface with Wnt pathway regulation. The presence of related immune antigen processing and stress-response terms can reflect broader cellular roles of the ubiquitin\u2013proteasome system. Overall, the cluster seems best characterized by proteasome- and ubiquitin-mediated regulation with connections to Wnt signaling.","confidence":"Medium","size":7,"edges":9,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0080129","count":4},{"id":"GO:0060071","count":4},{"id":"GO:0061418","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0006521","count":4}]},{"hash":"1475571076954874692","title":"Proteasome-ubiquitin-mediated degradation in cell cycle","description":"This cluster centers on ubiquitin-proteasome\u2013driven protein turnover, including SCF- and APC/c-mediated pathways and proteasome assembly, which regulate cell-cycle progression and signaling. While a viral process term appears, the core pattern reflects degradation machinery governing mitosis and pathway regulation (e.g., Wnt signaling). ","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0080129","count":1},{"id":"GO:0060071","count":1},{"id":"GO:0061418","count":1},{"id":"GO:0090090","count":1}]},{"hash":"1533387946795722634","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006369","count":6},{"id":"GO:0006605","count":6},{"id":"GO:0008306","count":5},{"id":"GO:0000184","count":5},{"id":"GO:0006310","count":5}]},{"hash":"562513163854418323","title":"Proteostasis and Unfolded Protein Response","description":"This cluster centers on translation, protein folding in the endoplasmic reticulum, response to unfolded protein, and ubiquitin-dependent protein catabolic processes, indicating a proteostasis/quality-control network. The presence of ER folding and UPR-related terms strongly supports this theme, with translation and refolding as core aspects. A couple of developmental terms (mesoderm formation, neural tube patterning) may reflect multifunctional roles or annotation noise, but they do not outweigh the dominant proteostasis signal.","confidence":"Medium","size":7,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:1904158","count":2},{"id":"GO:0010198","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0042026","count":2}]},{"hash":"740574684828700002","title":"DNA replication and chromosome maintenance","description":"The cluster is dominated by GO terms related to DNA replication, chromosome segregation/separation, recombination, and fork progression, suggesting proteins involved in DNA replication and chromosome maintenance. A few items (like carbohydrate metabolism and an unusual viral RNA replication term) seem weakly related or are likely annotation noise. Overall, the core theme is DNA replication and chromosome dynamics.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0035552","count":1},{"id":"GO:0000819","count":1},{"id":"GO:0045870","count":1}]},{"hash":"1546772613265822322","title":"Unknown","description":"The terms cover a broad, incongruent mix of signaling and development processes (immune cytokine production, cellular responses to GM-CSF, serotonin metabolism, retinal and oocyte development, cardiac hypertrophy), with no clear, unifying function tying all proteins together.","confidence":"","size":7,"edges":10,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043949","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0046549","count":2},{"id":"GO:0042428","count":2},{"id":"GO:0032754","count":2}]},{"hash":"1380788847677471852","title":"DNA replication and cell cycle","description":"The most represented processes are DNA replication (5) and mitotic cell cycle (4), with additional support from DNA-templated transcription (3), indicating a core set of nuclear activities tied to genome duplication and cell division. While signaling pathways (Wnt, ephrin, T cell receptor) and development terms appear, they are secondary and do not outweigh the central cell-cycle\u2013related functions. Thus the cluster is best described as DNA replication and cell cycle control.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0021766","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0000186","count":3}]},{"hash":"1231365194143209981","title":"TNF/NF-\u03baB inflammatory signaling and apoptosis regulation","description":"The GO terms cluster around TNF-mediated signaling, NF-kappaB activation, regulation of the JNK cascade, and control of apoptotic processes, pointing to a module of inflammatory stress signaling linked to cell survival decisions. A few terms (response to cold, histone catabolic process, X-chromosome dosage compensation) are less directly connected but may reflect broader stress response or epigenetic regulation contexts.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0036205","count":1},{"id":"GO:0042981","count":1},{"id":"GO:0046328","count":1}]},{"hash":"1069041237667699707","title":"Meiosis, Chromosome Pairing, and DNA Repair","description":"The cluster is enriched for meiotic processes (homologous chromosome pairing, chiasma assembly, meiosis I), along with cell cycle regulation and a DNA repair function (base-excision repair). Together, these terms point to proteins coordinating chromosome behavior during meiosis while maintaining genome integrity, with some broader cell-cycle associations. A single term on histoblast morphogenesis appears incidental.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0007129","count":1},{"id":"GO:0051026","count":1},{"id":"GO:0007488","count":1}]},{"hash":"583509188076261798","title":"Ribosome biogenesis and translation","description":"The top GO terms cluster around ribosome biogenesis (including small subunit biogenesis), translation, and SSU-rRNA maturation/rRNA processing, with related rRNA methylation and TOR signaling, indicating a focus on ribosome assembly and protein synthesis. A few immune-related terms are likely incidental noise.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0043065","count":1},{"id":"GO:0048821","count":1}]},{"hash":"307553431273414812","title":"Mitochondrial Transporters and Energy Regulation","description":"The cluster is characterized by multiple transmembrane transport GO terms for mitochondrial cofactors and metabolites (NAD, CoA, ATP, deoxynucleotides, thiosulfate) and by regulation of mitochondrial membrane potential, pointing to a mitochondrial transport/energy metabolism theme; oxidative stress response and IGF/pregnancy signaling terms appear as related, secondary facets of mitochondrial function.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0030302","count":2},{"id":"GO:0035352","count":2},{"id":"GO:0007565","count":2}]},{"hash":"2240531494422085069","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042594","count":2},{"id":"GO:0006564","count":1}]},{"hash":"317563543844947870","title":"Acetylation-Linked Chromatin Regulation","description":"Several top GO terms center on acetylation events (histone H4 acetylation, N-terminal acetylations, spermine acetylation, etc.) and a term for subtelomeric heterochromatin formation, which together point to regulation of chromatin structure via protein acetylation. Although there are some metabolic and sporulation terms in the list, the acetylation and chromatin-related terms are the most recurrent clues, suggesting the proteins as a cluster involved in acetylation-modulated chromatin dynamics.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006041","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0043967","count":2},{"id":"GO:0017198","count":2},{"id":"GO:0032919","count":2}]},{"hash":"579300271363346803","title":"Lipid metabolism and sphingolipid biosynthesis","description":"Top GO terms are centered on lipid metabolism, including unsaturated fatty acid biosynthesis, sphingoid catabolic processes, and sphingolipid-related metabolism (MIPC) as well as sterol regulation (ergosterol). The inclusion of myelin maintenance and brown fat/ sebaceous gland differentiation supports a theme of lipid-rich tissues and lipid-derived signaling, despite a few outliers (nitrate assimilation, NO biosynthesis, mitochondrial inheritance). Overall, the cluster appears to group lipid metabolism and sphingolipid-related processes across diverse contexts.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0006809","count":2}]},{"hash":"1232359616529044426","title":"Mitotic spindle and microtubule dynamics","description":"Most top terms point to mitosis and microtubule machinery (centrosome separation, spindle midzone, plus-end depolymerization, metaphase chromosome recapture). This suggests the cluster primarily participates in spindle assembly and microtubule dynamics. A few terms reference development and cell junctions, but they don\u2019t override the core mitotic signature.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0021685","count":7},{"id":"GO:0000911","count":7},{"id":"GO:0072092","count":7},{"id":"GO:0045218","count":7},{"id":"GO:1990942","count":7}]},{"hash":"768721724408354671","title":"ER Stress and Protein Quality Control","description":"The terms cluster around endoplasmic reticulum functions: protein folding in the ER, response to unfolded proteins/ER stress, ER-associated degradation, and ubiquitin-proteasome\u2013mediated quality control, indicating a coherent ER stress/quality control module.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0001707","count":2}]},{"hash":"34747036386870264","title":"GTPase and vesicle trafficking signaling cluster","description":"The top GO terms point to various signaling pathways (small GTPase signaling, GPCR signaling, TORC2) and vesicle dynamics (synaptic vesicle budding and recycling), suggesting a coherent theme around intracellular signaling linked to vesicle trafficking. Some terms (placenta development, apoptosis, fatty acid oxidation, antigen receptor signaling) are broader or context-specific but do not negate the central vesicle/signaling focus. Confidence: Medium","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010572","count":1},{"id":"GO:0007264","count":1},{"id":"GO:0016185","count":1},{"id":"GO:0038203","count":1},{"id":"GO:0001893","count":1}]},{"hash":"2067564345895277557","title":"Proteostasis and Stress Response","description":"The cluster centers on protein quality control and cellular stress management, with proteins involved in folding/unfolding, handling misfolded proteins, proteasome assembly, and oxidative stress response. The presence of UV-damage repair suggests genome maintenance under stress as well, complemented by peroxisomal import and metabolic regulation that can tie into stress adaptation. Overall, these terms point to a cohesive theme of maintaining proteome integrity and genome stability under stressful conditions.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0070682","count":1},{"id":"GO:0071218","count":1}]},{"hash":"1525037686682854443","title":"Mitochondrial Transport and Energy Metabolism","description":"This cluster is dominated by GO terms for transport of various metabolites across membranes, especially into/out of mitochondria (deoxynucleotides, NAD, CoA, thiosulfate, ATP), as well as regulation of mitochondrial membrane potential and oxidative stress response. While a few terms touch broader contexts (IGF signaling, liver regeneration, pregnancy), the strongest recurring theme is mitochondrial transport and energy metabolism, suggesting proteins involved in mitochondrial metabolite exchange and energetic regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030302","count":7},{"id":"GO:0035352","count":7},{"id":"GO:0007565","count":7},{"id":"GO:1990544","count":7},{"id":"GO:0051881","count":7}]},{"hash":"769859670015753477","title":"Unknown","description":"The GO terms are spread across transcriptional regulation, nuclear transport control, diverse development (brain, placenta, mast cells), and immune signaling, with no single cohesive function linking all terms. This makes a specific, representative label unclear.","confidence":"","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0060374","count":1},{"id":"GO:0000212","count":1},{"id":"GO:0001893","count":1}]},{"hash":"1590051979915488641","title":"Chromatin assembly and transcription regulation in development","description":"This cluster centers on chromatin-related processes: CENP-A\u2013containing chromatin assembly, pericentric heterochromatin formation, and regulation of histone methylation, along with negative transcription regulation. The presence of developmental terms like midbrain morphogenesis and spermatogenesis suggests chromatin-based control of gene expression across development, including germline silencing, despite some diverse GO terms. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904693","count":3},{"id":"GO:0031508","count":3},{"id":"GO:0007283","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0030466","count":3}]},{"hash":"655258775610191169","title":"Calcium signaling in neural and cardiac systems","description":"The cluster centers on calcium dynamics, including calcium ion transport and regulation of ryanodine receptor\u2013mediated calcium release, plus GO terms tied to neural activity (long-term synaptic potentiation) and cardiac conduction (electrical coupling). While a kidney development term appears, the dominant theme is calcium-dependent signaling affecting neural and heart function, with some cytoskeletal/transcriptional context.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0072205","count":1},{"id":"GO:0006816","count":1},{"id":"GO:1901844","count":1},{"id":"GO:1900271","count":1},{"id":"GO:0042554","count":1}]},{"hash":"812915818947916823","title":"Unknown","description":"The GO terms are highly diverse and do not point to a single coherent function or pathway. They include cellular responses to nitric oxide and ethylene, amino acid starvation regulation, translational initiation regulation (cytoplasmic and general), positive regulation of GTPase activity, oligodendrocyte development, and even decidualization, with some terms being obsolete. This mix suggests no clear, unified theme for a concise, representative label, so the cluster is best described as Unknown.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071732","count":1},{"id":"GO:1903833","count":1},{"id":"GO:0019284","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0006446","count":1}]},{"hash":"1233895132963034757","title":"Lipidation and ubiquitin-like modifications","description":"The top GO terms cluster around post-translational modifications of proteins, especially lipidation at the C-terminus and ubiquitin-like pathways (urmylation, sumoylation, ufmylation) along with related cysteine modifications. While a few terms related to vitamin cofactor biosynthesis appear, the dominant pattern is protein modification, justifying a label focused on lipidation and ubiquitin-like modifications.","confidence":"Medium","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006501","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0061504","count":1},{"id":"GO:0016925","count":1},{"id":"GO:1990592","count":1}]},{"hash":"1777021938898053173","title":"Protein post-translational modifications (lipidation and ubiquitin-like)","description":"The top GO terms cluster around various protein modification processes\u2014C-terminal lipidation, urmylation, sumoylation, ufmylation, and a cysteine-based modification\u2014pointing to a shared function in modifying proteins after synthesis. Some other terms (cofactor biosynthesis and the CVT pathway) are less directly related and may reflect broader cellular roles or annotation noise. Overall, the strongest signal is a set of PTMs, hence this label.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006501","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0061504","count":1},{"id":"GO:0016925","count":1},{"id":"GO:1990592","count":1}]},{"hash":"2249139965286848343","title":"Redox Homeostasis and Mitochondrial Electron Transport","description":"The cluster is defined by GO terms focused on cellular oxidant detoxification, redox homeostasis, and energy production via electron transport, pointing to a cohesive role in managing oxidative stress and mitochondrial respiration. A few terms about endothelial regulation and lactation are present but appear incidental to the main redox/energy theme.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0045602","count":1},{"id":"GO:1900747","count":1}]},{"hash":"667645859485785079","title":"Developmental Tissue Formation and ECM Biosynthesis","description":"These proteins cluster around developmental processes (lung and liver development, pregnancy) and collagen biosynthesis, suggesting a shared role in tissue formation and extracellular matrix construction. Additional terms for cytokine signaling (IL-4, TGF-beta) and stress/xenobiotic responses support a broader developmental signaling environment that accompanies ECM remodeling. Overall, the most coherent theme is developmental tissue formation tied to ECM biosynthesis, hence this label. ","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048678","count":1},{"id":"GO:0070301","count":1},{"id":"GO:0007565","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0009635","count":1}]},{"hash":"1714829024623924267","title":"Ribosome biogenesis and rRNA maturation","description":"The top GO terms center on maturation of LSU and 5.8S rRNA from tricistronic transcripts and RNA guanine-N7 methylation, plus ribosome biogenesis, which together point to roles in rRNA processing and ribosome assembly. Some other terms relate to protein turnover and cell-cycle signaling, but the dominant theme is ribosome biogenesis and rRNA maturation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0071902","count":1}]},{"hash":"82862958297815372","title":"Unknown","description":"The GO terms are highly diverse, including kinase activity regulation, neural development, lipid and sterol metabolism, nitrogen metabolism, and mitochondrial inheritance, with no single shared process tying all six proteins together. There isn\u2019t a cohesive theme or common pathway to label this cluster, so it is best described as Unknown with no confidence.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0032286","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0001949","count":1},{"id":"GO:0006636","count":1}]},{"hash":"98792546133779019","title":"Ribosome Biogenesis and Translation","description":"Dominant translation and ribosome-associated terms (GO:0006412; GO:0015968) point to a core function in ribosome assembly and protein synthesis; supporting terms like translational termination reinforce this, while a few regulatory and stress-response terms likely reflect broader cellular context rather than changing the primary function.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":1},{"id":"GO:0015968","count":1},{"id":"GO:0006415","count":1},{"id":"GO:0050821","count":1}]},{"hash":"455938704961504326","title":"Unknown","description":"The top GO terms are highly diverse and do not point to a single cohesive function for the cluster. Terms range from CNS myelin maintenance and sebaceous gland differentiation to nitrate assimilation, unsaturated fatty acid and ergosterol-related lipid metabolism, nitric oxide biosynthesis, sphingolipid metabolism, mitochondrial inheritance, and even obsolete RNA processing. This lack of a consistent shared pathway or molecular function makes it impossible to assign a specific, representative label; thus Unknown with None confidence.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0001949","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0006809","count":1}]},{"hash":"619582641517816421","title":"Oxidative stress response and metabolism","description":"The cluster\u2019s GO terms cluster around oxidative processes and detoxification (oxidation-reduction, cellular oxidant detoxification), along with various metabolic activities (aromatic amino acid and methylamine metabolism, toxin catabolic processes) and transport. An outlier term for photosynthesis likely reflects annotation noise rather than a common function. Taken together, the proteins seem tied to oxidative stress response plus general metabolism rather than a single precise function, justifying the label \u201cOxidative stress response and metabolism.\u201d","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019684","count":1},{"id":"GO:0006810","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0030416","count":1}]},{"hash":"991409625335786707","title":"Ribosome Biogenesis and Translation","description":"These proteins show strong enrichment for GO terms tied to ribosome biology and protein synthesis (tRNA modification, translation, cytoplasmic translation, ribosome biogenesis, and ribosomal subunit export), suggesting they function together in ribosome assembly and the translation process. The other terms (cell cycle, septum assembly) appear secondary and do not override the core ribosomal theme.","confidence":"High","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":3},{"id":"GO:0006412","count":3},{"id":"GO:1901001","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2}]},{"hash":"832012756462813773","title":"Virus-host Interaction and Transcription Regulation","description":"Top terms point to viral life cycle steps (virion assembly, viral release) alongside host transcription and RNA processing regulation (miRNA catabolic process, transcription regulation by RNA polymerase II and related processes), suggesting the cluster centers on virus-host interaction and modulation of host gene expression.","confidence":"Low","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":1},{"id":"GO:0010767","count":1},{"id":"GO:0010587","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0019068","count":1}]},{"hash":"2112167986772618906","title":"ER Protein Folding & Unfolded Protein Response","description":"These proteins cluster around endoplasmic reticulum quality control, with GO terms emphasizing ER protein folding, unfolded protein response, and ER-stress\u2013driven translation regulation. A few unrelated terms (molybdopterin biosynthesis, mesoderm formation) appear but do not override the dominant ER stress/theme.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0006986","count":1},{"id":"GO:0001707","count":1}]},{"hash":"2121507808329388432","title":"RNA Metabolism and Transcription Regulation","description":"This cluster centers on gene expression control, with GO terms for mRNA decapping and deadenylation-dependent decay, as well as transcription elongation and its regulation by RNA polymerase II. These together point to a cohesive theme of RNA processing and transcription regulation, even though a few terms touch on other processes. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006919","count":1},{"id":"GO:1901532","count":1},{"id":"GO:1902035","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0000288","count":1}]},{"hash":"796876914192070096","title":"Spliceosome-driven RNA processing and silencing","description":"This cluster is dominated by GO terms for mRNA splicing and spliceosome activity (e.g., mRNA splicing via spliceosome, spliceosomal complex disassembly) along with post-transcriptional gene silencing and nuclear mRNA surveillance (nonsense-mediated decay). While a few terms touch on DNA recombination, the overall signal centers on RNA maturation, splicing, and quality control through RNA silencing pathways, justifying this label.","confidence":"High","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0000184","count":2},{"id":"GO:0006310","count":2}]},{"hash":"937603580228060227","title":"Plant nutrient and ion transport","description":"The cluster's GO terms are dominated by membrane transport of diverse substrates (amino acids, potassium, thiamine, vitamins, carbohydrates, daunorubicin) and ABA-related stomatal signaling, pointing to a core function in plant transporter activity. Peripheral terms like cadmium detox, uracil salvage, and transcription termination are less central but do not override the transport theme.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0098849","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0006223","count":2},{"id":"GO:1901527","count":1},{"id":"GO:0003333","count":1}]},{"hash":"1027434236437221299","title":"ER Protein Folding and Quality Control","description":"This cluster centers on ER-based proteostasis: protein folding in the ER, unfolded protein response, ER stress signaling, and related quality-control processes (proteasome/nuclear quality control), with a few developmental terms likely due to pleiotropy or annotation noise.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0032781","count":2}]},{"hash":"806129880210132659","title":"NK cell signaling and IFN pathway regulation","description":"The top GO terms cluster around natural killer cell cytotoxicity and regulation of interferon signaling, including IFN-\u03b2 production and negative regulation of IFN and IL-6 pathways, along with control of STAT phosphorylation. This points to a cohesive set of proteins involved in innate immune signaling and NK-related regulation, with ancillary redox-related terms likely reflecting broader cellular context in immune cells.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042267","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0042524","count":1},{"id":"GO:0060336","count":1}]},{"hash":"2116275989963404670","title":"Neuronal development and growth-factor response","description":"The strongest signals are neuron projection morphogenesis and cellular response to nerve growth factor, pointing to neural development and growth-factor\u2013driven signaling. Supporting terms like cranial skeletal development and nitric oxide response further fit a developmental/neural context, while transcription, endocytosis, and immune synapse terms suggest broader cellular roles but are less central. Overall, the cluster seems best described by neural development and growth factor\u2013mediated signaling.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":1},{"id":"GO:0048096","count":1},{"id":"GO:0007264","count":1},{"id":"GO:0001771","count":1},{"id":"GO:0045953","count":1}]},{"hash":"1024222797554495696","title":"Unknown","description":"The top GO terms span many unrelated processes (transcription by RNA Pol III, interferon production, gland/uterus development, metabolic and chromatin regulation, and tubulin modification) with no cohesive function across the cluster, so a single representative label cannot be assigned.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":1},{"id":"GO:0032728","count":1},{"id":"GO:1903699","count":1},{"id":"GO:0010835","count":1},{"id":"GO:0010742","count":1}]},{"hash":"1272578404596600458","title":"Membrane lipid metabolism and vesicle transport","description":"The top GO terms cluster around lipid biosynthesis and membrane composition (unsaturated fatty acid biosynthesis, ergosterol metabolism, sphingolipid-related processes) and membrane trafficking/organization (vacuolar transport, cell polarity and shape regulation, organelle inheritance). While a couple of terms (nitrate assimilation, nitric oxide biosynthesis) are more metabolic signaling related, the overall theme points to coordinated lipid synthesis with membrane trafficking and organelle dynamics. Confidence: Medium","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0001949","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0006809","count":1}]},{"hash":"1501120987561321213","title":"ER protein folding and stress response","description":"The dominant terms describe endoplasmic reticulum\u2013associated protein folding, the unfolded protein response, ER-associated degradation, and stress-regulated translation, collectively indicating an ER quality-control module; a couple of developmental terms may reflect pleiotropy but do not override this core theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0006986","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0032781","count":1}]},{"hash":"1099625111548418087","title":"Unknown","description":"The top GO terms are highly diverse, covering redox metabolism, CoA biosynthesis, phosphorylation, antioxidant detoxification, transcription regulation, ER protein folding, nuclear transport regulation, DNA binding regulation, and even viral processes. There is no single unifying function tying these proteins together, so a concise, meaningful label cannot be assigned beyond Unknown.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0015937","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0098869","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1198368407212747783","title":"Chromatin Regulation and Transcription Control","description":"Proteins in this cluster are linked to chromatin organization and transcriptional control, including CENP-A chromatin assembly, heterochromatin formation, and regulation of histone methylation and RNA polymerase\u2013mediated transcription. While there are a few development-related terms (midbrain and pericardium morphogenesis, spermatogenesis), the dominant signals point to chromatin state management and gene expression regulation. This suggests a cohesive function in chromatin remodeling and transcriptional control.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1904693","count":1},{"id":"GO:0031508","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0030466","count":1}]},{"hash":"1518132676626826091","title":"Glucocorticoid receptor signaling and ER stress","description":"The dominant GO terms point to glucocorticoid/nuclear receptor signaling and steroid receptor complex assembly, complemented by indicators of ER stress and unfolded protein response, with additional metabolic regulation signals (gluconeogenesis, fatty acid biosynthesis). This suggests a cluster centered on steroid receptor\u2013mediated signaling intertwined with cellular stress responses and metabolic control. The presence of hydrogen peroxide response also supports a general stress context. ","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000324","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0090526","count":2}]},{"hash":"1638931176699486196","title":"Ribosome Biogenesis and rRNA Processing","description":"The terms cluster around ribosome biogenesis, cytosolic ribosome assembly, and maturation of LSU rRNA, with several rRNA/tRNA methylation processes pointing to RNA modification during ribosome production; a chlorophyll biosynthesis term may reflect plastid context but does not overshadow the ribosome-focused signal.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0042256","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0070476","count":1}]},{"hash":"431275115016463089","title":"Central metabolism and quinone biosynthesis","description":"The cluster\u2019s GO terms converge on core metabolic pathways (glycolysis, TCA cycle, beta-oxidation, amino acid catabolism to acetyl-CoA) and quinone biosynthesis (menaquinone and phylloquinone), with additional malonyl-CoA production. This suggests proteins involved in energy generation and essential cofactors, rather than a single specialized pathway. Confidence: High","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0009234","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0006635","count":2}]},{"hash":"1991853218873237344","title":"Unknown","description":"The GO terms in this cluster cover immune signaling (IFN-\u03b2 and IL-1 pathways, IL-3 production, MAPK cascades) as well as developmental and sensory processes (mast cell differentiation, placenta and hippocampus development, visual perception) and cell-cycle related terms (meiotic spindle organization, CDK activity). This broad mix suggests there is no single cohesive function tying all members together, so an Unknown label with no confidence is appropriate.","confidence":"","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0060374","count":4},{"id":"GO:0000212","count":4},{"id":"GO:0001893","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0045359","count":4}]},{"hash":"1009862643671747837","title":"Golgi-vacuolar vesicle trafficking","description":"This cluster's top GO terms center on vesicle transport linked to the Golgi and vacuole, including ER-to-Golgi transport, intra-Golgi transport, endosome-to-Golgi retrograde transport, vacuole fusion, Golgi ribbon formation, and vacuolar acidification, indicating a cohesive function in Golgi/vacuolar vesicle trafficking.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0042144","count":2}]},{"hash":"308722110805909895","title":"Mitochondrial Translation and Complex IV Assembly","description":"The top GO terms cluster around mitochondrial protein synthesis (mitochondrial translation and termination) and the assembly/regulation of the mitochondrial respiratory chain, especially complex IV (cytochrome-c oxidase) activity. This suggests a core function in mitochondrial protein production and electron transport complex assembly; a few peripheral terms (DNA repair, dexamethasone response, heart/brain development) are likely secondary annotations. ","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0071549","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0070126","count":1},{"id":"GO:0007507","count":1}]},{"hash":"725290968616255485","title":"Mitochondrial Transport and Energetics","description":"The cluster repeatedly features transmembrane transport terms, especially involving mitochondria\u2014deoxynucleotide, NAD, CoA, and thiosulfate transport, plus mitochondrial ATP transport and regulation of membrane potential\u2014indicating a group of proteins linked to mitochondrial transport and energy metabolism. Some terms map to broader physiology (pregnancy, liver regeneration, IGF signaling) but the core pattern centers on membrane transport and mitochondrial energetics, justifying this label.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030302","count":2},{"id":"GO:0035352","count":2},{"id":"GO:0007565","count":2},{"id":"GO:1990544","count":2},{"id":"GO:0051881","count":2}]},{"hash":"671784102892265877","title":"Motile cilium assembly and movement","description":"Based on the top GO terms, the strongest signal in this cluster is ciliary: axoneme assembly, motile cilium assembly, and cilium movement, pointing to ciliogenesis and motility of motile cilia/flagella. While other terms (protein transport, endocytosis regulation, translation-related processes) appear, they do not cohere as a dominant functional theme. Therefore, the cluster most likely reflects motile cilium assembly and movement.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0050715","count":1},{"id":"GO:0045806","count":1},{"id":"GO:0045956","count":1},{"id":"GO:0060294","count":1}]},{"hash":"1134726394601174302","title":"Mitochondrial transport and membrane potential regulation","description":"The Top Terms point to transport across mitochondrial membranes for various metabolites (deoxynucleotides, NAD, CoA, thiosulfate, ATP) and regulation of mitochondrial membrane potential, indicating a cohesive mitochondrial transport/energy metabolism theme. A few terms like liver regeneration or pregnancy appear peripheral, but do not detract from the core mitochondrial transport signal.","confidence":"Medium","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030302","count":2},{"id":"GO:0035352","count":2},{"id":"GO:0007565","count":2},{"id":"GO:1990544","count":2},{"id":"GO:0051881","count":2}]},{"hash":"1131453562822798096","title":"Golgi-ER Vesicle Trafficking and Lysosome Organization","description":"This cluster is dominated by GO terms related to intracellular transport and membrane dynamics\u2014lysosomal membrane organization, COPII vesicle coating regulation, Golgi localization, and small GTPase-mediated signaling\u2014pointing to a shared role in vesicle trafficking between the ER, Golgi, and lysosomes. While some terms relate to development or physiology, the strongest link among the proteins is the vesicle trafficking machinery and organelle membrane organization.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097212","count":1},{"id":"GO:0007264","count":1},{"id":"GO:0003400","count":1},{"id":"GO:0097498","count":1},{"id":"GO:0000042","count":1}]},{"hash":"1108085834427155606","title":"Mitochondrial Transport and Energy Regulation","description":"This cluster is characterized by multiple GO terms describing transport across membranes (deoxynucleotides, NAD, thiosulfate, CoA, and mitochondrial ATP transport) and regulation of mitochondrial membrane potential, pointing to a cohesive theme of mitochondrial transport and energy homeostasis. While a few terms touch on broader processes like IGF signaling, pregnancy, or liver regeneration, the dominant signal relates to mitochondrial transport and energy metabolism.","confidence":"High","size":5,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030302","count":2},{"id":"GO:0035352","count":2},{"id":"GO:0007565","count":2},{"id":"GO:1990544","count":2},{"id":"GO:0051881","count":2}]},{"hash":"1105505874887756665","title":"Meiosis-Linked DNA Repair and Recombination","description":"The top terms cluster around DNA repair and recombination, including interstrand cross-link repair, double-strand break repair via homologous recombination, meiotic joint molecule formation, and meiosis-specific processes, indicating a coherent role in DNA damage response with meiosis. ","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":1},{"id":"GO:0036297","count":1},{"id":"GO:0051106","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0009951","count":1}]},{"hash":"1717166450842073765","title":"COPII-mediated ER-to-Golgi vesicle trafficking","description":"The top GO terms emphasize transport from the ER to the Golgi via COPII vesicles, COPII coat regulation, and Golgi localization, pointing to a secretory pathway\u2013focused cluster. Additional terms on lysosomal membrane organization and small GTPase signaling support a vesicle-trafficking/regulatory network, with some vascular-associated terms reflecting contexts where trafficking is important. Overall, the core theme is COPII-dependent ER-to-Golgi transport and Golgi localization.","confidence":"Medium","size":5,"edges":6,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0097212","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0003400","count":3},{"id":"GO:0097498","count":3}]},{"hash":"1291425796770818162","title":"DNA replication, repair, and telomere maintenance","description":"The top GO terms center on DNA metabolism\u2014DNA repair, replication, recombination, and mitotic checkpoint signaling\u2014with a clear link to telomere localization, indicating chromosome maintenance and genome integrity. Translation-related terms and tRNA aminoacylation appear, but the dominant theme is genome maintenance rather than protein synthesis. ","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006281","count":4},{"id":"GO:0071915","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0072581","count":4},{"id":"GO:0006422","count":4}]},{"hash":"1619432121486960470","title":"Endocytic recycling and Golgi-lysosome transport","description":"The GO terms cluster mainly around endocytic recycling, endosome-to-Golgi retrograde transport, Golgi-to-vacuole/lysosomal transport, and sphingolipid homeostasis, all indicating a coherent theme of intracellular membrane trafficking and lipid regulation within the secretory/endomembrane system. A few terms related to development or locomotion may be incidental annotations, but the primary signal is trafficking.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0090156","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0010668","count":2}]},{"hash":"967247168086641955","title":"Detoxification and lipid metabolism","description":"The cluster\u2019s GO terms cluster around detoxification and oxidation-reduction balance (response to toxic substance, cellular oxidant detoxification) and multiple lipid catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine catabolism, stilbene and prostaglandin catabolic processes). This suggests a common theme of clearing toxins and metabolizing lipid-derived molecules, despite some plant- or signaling-related terms that appear less central. Overall, a concise label focusing on detox and lipid breakdown captures the main functional signal.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0046272","count":2}]},{"hash":"1971160609041870249","title":"Redox-Regulated Transcription and ER Stress","description":"This cluster shows a common theme of transcriptional regulation (DNA-templated transcription, RNA Pol II regulation and DNA binding) intertwined with redox biology (deglyutathionylation, cellular oxidant detoxification, and redox homeostasis) and an ER stress response. Together these terms suggest proteins that modulate gene expression in response to oxidative and ER stress, rather than a single metabolic pathway. The presence of both positive/negative transcription regulation terms further supports a regulatory rather than purely catalytic role under stress conditions.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0080058","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0043388","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0045454","count":1}]},{"hash":"197086245908937157","title":"Neural development and axonogenesis","description":"The top GO terms cluster around neural development and neuronal differentiation (multicellular organism development, Schwann cell development), axonogenesis, and synaptic plasticity (long-term potentiation, visual perception). There are also signaling-related terms (positive regulation of protein serine/threonine kinase activity, TORC1 regulation) that fit growth and plasticity in neural contexts. A couple of broad cell-cycle terms may reflect developmental precursors, but the dominant signal points to neural development and axon growth/plasticity.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0051304","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0007601","count":2}]},{"hash":"1268135182449476423","title":"Protein quality control and modification","description":"This cluster centers on proteostasis-related processes: unfolded protein response, ER-associated ubiquitin-dependent proteolysis, and APC-dependent catabolic processes, plus post-translational modifications like tyrosine sulfation. The presence of protein localization to photoreceptor outer segments and interferon response hints at broader stress signaling, but the core theme is protein quality control and turnover through PPtM/ubiquitin pathways.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090526","count":3},{"id":"GO:0006478","count":3},{"id":"GO:1902391","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0035457","count":3}]},{"hash":"215972966308275427","title":"Unknown","description":"The GO terms are highly diverse, ranging from translation and rRNA maturation to ion transport, osmotic stress, development, vision, and immune signaling, with no clear shared function tying all proteins together. This makes it impossible to assign a coherent, specific label to the cluster.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0034220","count":1},{"id":"GO:0009992","count":1},{"id":"GO:0071470","count":1}]},{"hash":"620059092313571592","title":"Folate and methotrexate transporters","description":"The cluster\u2019s top GO terms are methotrexate transport and 5-formyltetrahydrofolate transport, indicating a shared role in transporting folate-related substrates and antifolate drugs. With four proteins showing these transport-related functions, the label captures the core theme without overgeneralizing to other activities.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051958","count":1},{"id":"GO:0015885","count":1}]},{"hash":"535773079913584901","title":"Multisubstrate membrane transporters (nutrients and xenobiotics)","description":"Most GO terms emphasize transmembrane transport of diverse substrates: vitamins, xenobiotics, carbohydrates, and specific compounds like daunorubicin and thiamine. An outlier repair term likely reflects annotation noise, but the dominant signal is membrane transporter activity for nutrients and xenobiotics. Confidence in this functional grouping is high.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0042891","count":2},{"id":"GO:0003333","count":2},{"id":"GO:0015888","count":2}]},{"hash":"583793744925988618","title":"Regulators of signaling and stress responses","description":"The GO terms cluster around positive regulation of signaling and related processes (nitric oxide biosynthesis, kinase activity, protein binding), as well as regulation of the cell cycle and cell size, plus immune signaling and stress responses (interleukin-4, interferon signaling, salt stress). This suggests a group of proteins that modulate signaling networks and cellular stress pathways. One term about virion attachment to host cell is an outlier, possibly reflecting host factors co-opted in viral infection rather than a core function of the cluster.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045429","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0019062","count":1},{"id":"GO:0032092","count":1}]},{"hash":"1365165267815772162","title":"Metabolic Regulation of Glycolysis and Biosynthesis","description":"The terms center on regulation of metabolic pathways, including glycolysis (negative regulation of glycolytic process; fructose 2,6-bisphosphate metabolism), PPP shunt regulation, and biosynthesis (L-serine and cobalamin). While some terms reflect broader stress or tissue-specific responses (xenobiotic response; cardiac muscle apoptotic regulation), the dominant theme is coordinated metabolic pathway regulation rather than a single pathway.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":1},{"id":"GO:0016311","count":1},{"id":"GO:1904024","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0033133","count":1}]},{"hash":"1739351343351928807","title":"Neuronal development and Golgi dynamics","description":"This cluster includes GO terms pointing to neuronal development and synaptic plasticity (substantia nigra development; regulation of synaptic plasticity), suggesting a neuronal function theme. It also contains Golgi-related terms (Golgi localization and Golgi reassembly), indicating concurrent Golgi apparatus remodeling. While other terms hint at broader cellular processes, the strongest coherent signal is neuronal development with Golgi-facing dynamics.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006713","count":1},{"id":"GO:0048167","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0000079","count":1},{"id":"GO:0008630","count":1}]},{"hash":"47546914377153548","title":"Mitotic Regulation and Spindle Checkpoint","description":"The top GO terms are dominated by mitosis-related processes: negative regulation of cyclin-dependent protein kinases, spindle midzone localization, mitotic cytokinesis checkpoint signaling, and positive regulation of sister chromatid biorientation. These strongly point to control of cell cycle progression and chromosome segregation during mitosis, with translation and immune-signaling terms appearing as ancillary associations. Overall, the cluster appears to capture proteins involved in mitotic regulation and spindle checkpoint functions.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0042524","count":1},{"id":"GO:0060336","count":1},{"id":"GO:0035853","count":1},{"id":"GO:0044878","count":1}]},{"hash":"583552943388078718","title":"Ribosome Biogenesis and Protein Kinase Activation","description":"The cluster is enriched for GO:0042254 (ribosome biogenesis) and GO:0032147 (activation of protein kinase activity), suggesting a link between ribosome assembly and kinase signaling that could coordinate growth-related protein production. The small size and modest connectivity imply a cohesive but not tightly defined functional module.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0032147","count":3}]},{"hash":"362037076574303479","title":"Unknown","description":"Top Terms are empty, giving no shared functional signal among the three proteins; without GO term enrichment, I cannot identify a coherent theme for this cluster.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"793874021919903307","title":"Mitochondrial energy metabolism","description":"The top GO terms cluster around mitochondrial energy production, including the respiratory electron transport chain, TCA cycle, and ATP synthesis linked to oxidative phosphorylation, indicating proteins associated with mitochondrial respiration. A few terms (e.g., flagellum assembly, actin depolymerization, DNA repair, polysaccharide transport) may be less related or annotation noise, but the core theme is energy metabolism in mitochondria.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0022904","count":1},{"id":"GO:0044780","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0006281","count":1}]},{"hash":"485103729419287837","title":"Unknown","description":"The GO terms are highly diverse, covering proton transport, multiple xenobiotic/catabolic pathways (carbazole and toluene), sialic acid metabolism, photosynthesis and nonphotochemical quenching, and heme A biosynthesis. There is no single, coherent function linking these three proteins, so a specific label isn\u2019t warranted. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":1},{"id":"GO:0046381","count":1},{"id":"GO:0046232","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0015979","count":1}]},{"hash":"1328775935061387118","title":"ER Proteostasis and Unfolded Protein Response","description":"These proteins cluster around endoplasmic reticulum\u2013associated proteostasis: protein folding in the ER, response to unfolded proteins, ERAD/ubiquitin-proteasome quality control, and ER stress\u2013driven regulation of translation. A few developmental terms are present but do not define the main theme, which is ER protein folding and degradation pathways.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0032781","count":2}]},{"hash":"1878489708339670522","title":"Iron-Sulfur Cluster Biogenesis and Iron Homeostasis","description":"The top GO terms point mainly to iron-sulfur (Fe-S) cluster assembly and intracellular iron ion homeostasis, suggesting the proteins are involved in Fe-S biogenesis and iron management. While some terms like nitrogen fixation, phosphate transport, and nucleotide metabolism appear, they are ancillary to the Fe-S focus. This makes the Fe-S cluster biogenesis theme the most representative for the cluster.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0006879","count":1},{"id":"GO:0006817","count":1}]},{"hash":"1226187553187519675","title":"Nucleotide metabolism and cofactor biosynthesis","description":"The cluster\u2019s top GO terms cluster around nucleotide and cofactor biosynthesis and interconversion (ADP biosynthesis, nucleotide phosphorylation, AMP salvage, purine ribonucleotide interconversion, NAD+ and coenzyme A biosynthesis, ITP metabolism). The brain and liver development terms appear as secondary annotations, but the dominant theme is nucleotide/cofactor metabolism, suggesting these proteins function in nucleotide metabolism pathways. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006172","count":1},{"id":"GO:0046939","count":1},{"id":"GO:0046940","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0009435","count":1}]},{"hash":"2058104513629211424","title":"RNA processing and translation regulation","description":"The top GO terms cluster around mRNA maturation steps (splicing via spliceosome, polyadenylation, export, and stabilization) and also include regulation of translation initiation. Together they indicate a functional group involved in mRNA processing and the control of protein synthesis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0002188","count":1},{"id":"GO:0097010","count":1},{"id":"GO:0000380","count":1},{"id":"GO:1903586","count":1}]},{"hash":"1670379192987683286","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051084","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0022417","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0032543","count":1}]},{"hash":"1027166979612485787","title":"Calcium signaling and cardiac conduction","description":"The GO terms show a coherent emphasis on calcium regulation (store-operated calcium channels, postsynaptic calcium, calcineurin-NFAT signaling) and processes tied to cardiac electrical activity (electrical coupling in cardiac conduction). Other terms are ancillary or context-specific, but the dominant theme is calcium signaling linked to cardiac conduction, justifying this label. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":2},{"id":"GO:1901339","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0033173","count":2}]}]