[{"hash":"246998608663398917","title":"Developmental signaling and gene regulation","description":"The top GO terms point to signaling and kinase cascades (positive regulation of GTPase activity, TGF-beta stimulus response, positive regulation of serine/threonine kinase activity) alongside brain development, and also RNA processing elements (mRNA transport, RNA guanine-N7 methylation). This suggests a coherent theme of signaling during development that coordinately controls gene expression, though some terms reflect broad cellular processes like mitosis and protein quality control. ","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0071560","count":8},{"id":"GO:0050731","count":8},{"id":"GO:0007420","count":8},{"id":"GO:0071456","count":8}]},{"hash":"317990428218225415","title":"Innate immune cytoskeleton remodeling and endocytosis","description":"This cluster is dominated by actin-related processes (barbed-end actin filament capping, microspike assembly, podosome assembly) and membrane trafficking (caveolin-mediated endocytosis), alongside innate immune response and regulation of interferon signaling, suggesting a theme of cytoskeleton-driven immune cell remodeling and endocytosis. Some tissue-development GO terms appear ancillary rather than defining the cluster.","confidence":"High","size":29,"edges":37,"triangles":0,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":4},{"id":"GO:0060335","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0007507","count":3},{"id":"GO:0043552","count":3}]},{"hash":"880071298553779917","title":"Ion transport and innate immune signaling","description":"This cluster combines membrane-associated transport roles (sodium and potassium ion transmembrane transport, aromatic compound transport) with innate immune signaling pathways (TLR3/7/9 signaling, NF-kappaB regulation) and inflammatory response, suggesting proteins that link ion transport/vesicle dynamics to immune signaling at the membrane.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0035725","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0071260","count":3},{"id":"GO:0034154","count":3},{"id":"GO:0034138","count":3}]},{"hash":"705419719108446880","title":"Bacterial fatty acid biosynthesis and transport","description":"Most top GO terms point to fatty acid metabolism and lipid biosynthesis (fatty acid biosynthetic process; very long-chain and long-chain fatty acid metabolism; medium-chain fatty acid transport; long-chain fatty acid import). These suggest a cluster of enzymes and transporters involved in fatty acid production and uptake in bacteria. A few additional items (lipopolysaccharide biosynthesis; bioluminescence; obsolete terms) are related to broader lipid metabolism or artifacts, but do not override the central fatty acid theme.","confidence":"High","size":29,"edges":182,"triangles":490,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1902987","count":10},{"id":"GO:0009103","count":8},{"id":"GO:0019427","count":8},{"id":"GO:0043041","count":8},{"id":"GO:0000038","count":8}]},{"hash":"742359580598074889","title":"RNA splicing and translation initiation machinery","description":"The cluster is centered on mRNA processing and export (spliceosome-mediated splicing, mRNA export, stabilization) and on the assembly and regulation of translation initiation (preinitiation complex, eIF4F assembly, regulation of translational initiation, stress-related mRNA stability). This suggests a cohesive role connecting RNA processing to the initiation of translation, reflecting a shared function in gene expression control from splicing to translation.","confidence":"High","size":29,"edges":405,"triangles":3627,"max_degree":28,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0097010","count":3},{"id":"GO:1905663","count":3}]},{"hash":"1941980569368335453","title":"Nutrient-Responsive Transcription Regulation","description":"The cluster is dominated by GO terms about DNA-templated transcription and positive regulation of transcription from RNA polymerase II promoter, especially in response to nutrients (nonfermentable carbon sources and nitrogen catabolite activation). This suggests a module coordinating transcriptional activation in response to nutrient status, with links to nucleotide biosynthesis and calcium signaling as supporting regulatory layers.","confidence":"High","size":29,"edges":42,"triangles":0,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:2001158","count":4},{"id":"GO:0001080","count":4},{"id":"GO:1900399","count":4},{"id":"GO:0061414","count":4}]},{"hash":"1049945343990561009","title":"Nuclear DNA Replication, Repair, and Transcription","description":"The top GO terms are dominated by nuclear DNA processes: DNA replication, DNA repair, and DNA-templated transcription (each present twice). This indicates a cluster enriched for nuclear DNA metabolism and gene expression. Additional terms point to protein quality control and stress response pathways (ubiquitin-proteasome system, unfolded protein response), suggesting these proteins also participate in maintaining nuclear proteostasis during DNA-related processes. Overall, the theme is nuclear DNA maintenance with supporting quality-control mechanisms.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006895","count":1}]},{"hash":"1511552960535266337","title":"Diverse Membrane Transporters","description":"The proteins show a strong enrichment for transmembrane transport functions across a wide range of substrates (glucose, sialic acid, nitrite, sodium, vitamins, xenobiotics) and a specific role in neurotransmitter loading, indicating a shared theme of membrane transporter activity rather than a single substrate. The absence of edges suggests they are not tightly interconnected in this cluster, but the GO terms consistently point to membrane transport.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":3},{"id":"GO:1900754","count":2},{"id":"GO:0055085","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0015739","count":2}]},{"hash":"1729242094409249522","title":"Chloroplast and Mitochondrial Energy Production","description":"The top GO terms point to energy metabolism across organelles: photosynthesis (light reactions) and the TCA cycle, coupled with assembly of the ATP synthase complex and various transport processes. While some terms touch on peripheral biosynthetic tasks, the dominant signals are chloroplast- and mitochondria-centered energy production and material transport, justifying a label focused on organellar energy metabolism.","confidence":"High","size":28,"edges":359,"triangles":2821,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0019684","count":2},{"id":"GO:0006810","count":2},{"id":"GO:0033615","count":2},{"id":"GO:0046677","count":2}]},{"hash":"926364629492773257","title":"Glycerophospholipid biosynthesis and remodeling","description":"Most top GO terms cluster around lipid metabolism, especially biosynthesis and remodeling of glycerophospholipids such as phosphatidylcholine, cardiolipin, and ether lipids, plus CDP-diacylglycerol. This points to a coherent theme of membrane lipid production and acyl-chain remodeling, with supporting signals from platelet activating factor biosynthesis and triglyceride synthesis. A few terms (translation, T cell death regulation) are peripheral, likely reflecting multifunctional proteins in the cluster, but the lipid biosynthesis/remodeling theme dominates. ","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001246","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0002071","count":3},{"id":"GO:0019432","count":3},{"id":"GO:0006663","count":3}]},{"hash":"153526843456800669","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":12,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0019483","count":2}]},{"hash":"1599024401423180443","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":7},{"id":"GO:0000462","count":6},{"id":"GO:0042273","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0000472","count":5}]},{"hash":"1293081804882397494","title":"DNA Repair and Replication","description":"The top GO terms overwhelmingly point to DNA maintenance processes\u2014DNA recombination, DNA-templated replication, nucleotide-excision repair, and the SOS response\u2014indicating proteins in a DNA damage response and genome maintenance module. A few other terms (mRNA deadenylation, host gene expression suppression, glycolysis, cobalamin biosynthesis) appear, but they are sporadic and do not define the core function; the dominant signal is DNA repair/replication.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900153","count":2},{"id":"GO:0090305","count":1},{"id":"GO:0039657","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0006289","count":1}]},{"hash":"31245430433440973","title":"Nutrient-responsive liver and gut development","description":"The cluster combines GO terms for liver and midgut development with multiple nutrient- and hormone- response terms (response to amine, amino acid, food, glucagon stimulus, dexamethasone, starvation) and a related metabolic process (carbamoyl phosphate biosynthesis), suggesting a coordinated program linking digestive organ development to nutrient sensing and metabolic regulation.","confidence":"High","size":28,"edges":106,"triangles":103,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":6},{"id":"GO:0014075","count":6},{"id":"GO:0043200","count":6},{"id":"GO:0071377","count":6},{"id":"GO:0071548","count":5}]},{"hash":"1380879908363324849","title":"DNA replication and chromatin regulation","description":"The top terms cluster around DNA replication and repair, transcription, and especially chromatin organization and heterochromatin formation, including replication-dependent chromatin assembly. This points to a cohesive theme of DNA metabolism coupled with chromatin state maintenance, rather than a single isolated pathway, justifying a label focused on replication and chromatin regulation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":5},{"id":"GO:0006351","count":3},{"id":"GO:0006261","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1450155407938226798","title":"RNA processing and transcriptional regulation during cell cycle","description":"This cluster centers on mRNA processing (spliceosome-mediated splicing, polyadenylation) and transcriptional regulation, with links to cell cycle control and ubiquitin-mediated protein regulation, suggesting a coordinated program of RNA processing linked to cell-cycle progression and survival.","confidence":"High","size":28,"edges":16,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0043085","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1491070682878392892","title":"Neuronal RNA processing and vesicle trafficking","description":"The cluster is driven by RNA-centric processes (mRNA splicing via spliceosome, ribosome biogenesis, mRNA polyadenylation) and vesicle/trafficking activities (ER to Golgi transport, endocytosis). There are also neurally related terms (substantia nigra development, neuron apoptotic regulation) and metabolic/stress responses (response to glucose, xenobiotic stimulus), suggesting a neuron-focused theme around gene expression and protein handling. The presence of non-neuronal terms tempers the link, so the label reflects the strongest coherent pattern without overclaiming.","confidence":"Medium","size":28,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":3},{"id":"GO:0006897","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0009749","count":2}]},{"hash":"328993320590146130","title":"Cardiovascular and muscle development with angiogenesis","description":"The cluster is dominated by GO terms tied to developmental processes relevant to heart and muscle formation (heart development, myoblast fusion, multicellular organism development) and vascular formation (angiogenesis), plus supporting cell-cycle and localization signals common during differentiation (negative regulation of CDK activity, G2/M transition, kinetochore localization). This points to a coordinated program of cardiovascular and skeletal muscle development with associated angiogenesis. ","confidence":"High","size":28,"edges":17,"triangles":0,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":21},{"id":"GO:0034501","count":21},{"id":"GO:0007507","count":17},{"id":"GO:0007520","count":17},{"id":"GO:0007275","count":17}]},{"hash":"2216976452332889990","title":"RNA processing and ubiquitin-mediated turnover","description":"The top terms point to RNA processing (mRNA splicing via spliceosome and polyadenylation) alongside ubiquitin-related processes (protein ubiquitination and ubiquitin-dependent protein catabolic pathway, ERAD). This suggests a theme where RNA processing and protein quality control/degradation are coordinated, possibly in development contexts, despite a few outliers (e.g., SA node regulation, gluconate transport).","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0098907","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1441002581986404040","title":"Mitochondrial Energy Metabolism and Redox Regulation","description":"The top GO terms strongly point to mitochondrial energy production and redox balance, with keywords like mitochondrial electron transport, lipoate and dihydrolipoamide metabolic processes, beta-alanine biosynthesis, and regulation of membrane potential, plus cell redox homeostasis. A few developmental terms (in utero embryonic development, gastrulation, pituitary gland development) may reflect broad annotation or background noise rather than a unified developmental program in this cluster. Overall, the dominant theme is mitochondrial energy metabolism linked to redox control.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":6},{"id":"GO:0021983","count":4},{"id":"GO:0042135","count":4},{"id":"GO:0007369","count":4},{"id":"GO:0019483","count":4}]},{"hash":"1739335716506670150","title":"Developmental signaling and cell fate control","description":"This cluster centers on key signaling and transcriptional processes that govern cell fate, growth, and differentiation. The prominent GO terms include DNA-templated transcription, Wnt signaling, Hippo signaling, and keratinocyte differentiation, alongside apoptosis and telomere maintenance, all of which align with developmental regulation and tissue homeostasis. Although some terms like sperm capacitation and prostaglandin response are more context-specific, the shared theme is signaling networks that balance proliferation, differentiation, and survival.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006915","count":8},{"id":"GO:0030216","count":7},{"id":"GO:0090263","count":7},{"id":"GO:0035329","count":7}]},{"hash":"666692388297478106","title":"Ubiquitin-Proteasome Mediated NF-\u03baB Innate Immunity","description":"The cluster centers on ubiquitin-dependent protein degradation and NF-\u03baB pathway regulation, with several terms pointing to SCF and proteasomal ubiquitination, canonical and non-canonical NF-\u03baB signaling, TLR/NOD2 pathways, and inflammatory cytokine production. The overlap suggests proteins that modulate innate immune responses through controlled proteolysis of NF-\u03baB regulators, despite one odd term (defecation rhythm) likely being incidental. Overall, the set represents ubiquitin-proteasome control of NF-\u03baB\u2013driven inflammation.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":13},{"id":"GO:0042787","count":8},{"id":"GO:0070431","count":6},{"id":"GO:0032088","count":6},{"id":"GO:0043124","count":5}]},{"hash":"392246788217858823","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms revolve around translation and ribosome assembly (translation; cytoplasmic translation; ribosome biogenesis; ribosomal subunit assembly), indicating the cluster mainly represents the protein synthesis machinery. A couple of outliers exist (antibiotic response, cell fusion processes) but do not override the central ribosome/translation theme.","confidence":"High","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":21},{"id":"GO:0042254","count":8},{"id":"GO:0042274","count":6},{"id":"GO:0002181","count":5},{"id":"GO:0000027","count":4}]},{"hash":"1286723781423236169","title":"Meiosis/mitosis chromosome cohesion and spindle dynamics","description":"This cluster centers on processes governing chromosome behavior during cell division: meiotic and mitotic sister chromatid cohesion and separation, spindle elongation, and nuclear import, with additional signals related to kinase and GTPase regulation and post-translational modification like desumoylation. Despite some diverse terms, the dominant theme ties to coordinating chromosome segregation during meiosis and mitosis, suggesting a cohesive functional group of cell-cycle regulators rather than unrelated processes.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0006607","count":8},{"id":"GO:0051754","count":7},{"id":"GO:0033674","count":7},{"id":"GO:0051306","count":6}]},{"hash":"1331726417101427825","title":"Fatty acid oxidation and energy metabolism","description":"The cluster is dominated by energy-related metabolism terms, including fatty acid beta-oxidation (long-chain FA catabolic, acyl-CoA dehydrogenase/oxidase), carnitine biosynthesis, and glycogen biosynthesis, with additional involvement in leucine catabolism and thiamine biosynthesis. The presence of heart and liver development terms suggests tissue-specific energy metabolism roles, making a cohesive label around lipid oxidation and overall energy metabolism appropriate.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0006552","count":4},{"id":"GO:0042758","count":3},{"id":"GO:0033539","count":3}]},{"hash":"711202300561357469","title":"DNA replication and mitotic chromosome maintenance","description":"This cluster centers on nuclear processes: DNA replication, CENP-A chromatin assembly, and cell division, with microtubule dynamics supporting chromosome segregation. While there are peripheral hints of transcription regulation and protein quality control (proteasome/ubiquitin pathways) and some vesicle transport signals, the strongest shared theme is genome duplication and mitotic chromosome maintenance.","confidence":"High","size":27,"edges":158,"triangles":335,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0032968","count":5},{"id":"GO:0019079","count":5},{"id":"GO:0006888","count":5}]},{"hash":"357701786751900755","title":"Unknown","description":"The cluster shows a highly diverse set of GO terms\u2014from insulin signaling and phagocytosis to bone development, Hedgehog pathway regulation, metabolism, and stress responses\u2014without a clear, unifying function or pathway, and there are no edges linking the proteins to suggest a cohesive role. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0006909","count":2},{"id":"GO:0060348","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0006265","count":1}]},{"hash":"1241318133414469762","title":"DNA Repair and Genome Maintenance","description":"Based on the top GO terms, this cluster is enriched for base-excision repair, DNA recombination, and DNA catabolic processes, along with a cellular response to oxidative stress (hydrogen peroxide). These points collectively to genome maintenance and nucleic acid metabolism as the core theme. Some terms like corneocyte development and renal water transport appear unrelated and may reflect broader multifunctionality or noise, but the dominant signal supports a DNA repair/genome maintenance label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0046856","count":5},{"id":"GO:0006284","count":5},{"id":"GO:0006310","count":5},{"id":"GO:0090502","count":5},{"id":"GO:0070301","count":4}]},{"hash":"1925217011698836307","title":"Unknown","description":"The top GO terms cover a mix of embryonic development, multiple cell-type\u2013specific apoptotic processes (neuron, glial, nurse cell), heart and hemocyte development, wound healing, and scattered stress responses (antibiotic, cobalt ion) as well as sensory perception of sound, with no clear unifying pathway or context. The absence of edges and a cohesive functional theme makes it hard to assign a single representative label beyond Unknown.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0046677","count":7},{"id":"GO:0042060","count":3},{"id":"GO:0001700","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0043525","count":3}]},{"hash":"169464633033158326","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000390","count":2},{"id":"GO:0006378","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0016203","count":2}]},{"hash":"916043264093004802","title":"Bacterial quinone biosynthesis and lipid metabolism","description":"The top GO terms are dominated by quinone biosynthesis (phylloquinone, menaquinone) and fatty acid beta-oxidation, pointing to bacterial energy metabolism and cofactor production; other terms like Notch signaling are likely noise. Confidence: Medium","confidence":"","size":26,"edges":325,"triangles":2600,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0033512","count":7},{"id":"GO:0006635","count":6},{"id":"GO:0042372","count":6},{"id":"GO:0010124","count":6}]},{"hash":"1334455568894081174","title":"Diverse Membrane Transporters","description":"The top GO terms point to multiple transmembrane transport activities across a range of substrates (xenobiotics, vitamins, nitrite/nitrate, sodium, arabinose, fucose) and a related membrane-processing term (GPI anchor biosynthesis). This suggests a cluster of membrane transporter proteins with diverse substrate specificities, rather than a single-substrate transporter. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0006506","count":3},{"id":"GO:1900754","count":2},{"id":"GO:0098700","count":2}]},{"hash":"461630777631030615","title":"Unknown","description":"The top GO terms span development (heart development), apoptosis, growth control (hippo signaling), sensory perception, and various stress/immune responses ( xenobiotic and antibiotic responses, B cell homeostasis), plus general cellular processes like protein processing and cell cycle regulation. This broad, non-specific mix suggests there isn\u2019t a single coherent function tying the cluster together, so a precise, representative label isn\u2019t identifiable.","confidence":"","size":26,"edges":4,"triangles":0,"max_degree":2,"top_function":"wound healing","top_go_terms":[{"id":"GO:0007507","count":6},{"id":"GO:0097194","count":6},{"id":"GO:0035329","count":6},{"id":"GO:0007605","count":5},{"id":"GO:0051092","count":5}]},{"hash":"2167870867101300962","title":"Ion Transport and Membrane Potential Regulation","description":"Most terms describe transport of potassium across the plasma membrane (export/import), intracellular potassium homeostasis, and transmembrane transport of other ions (sodium, zinc, cadmium) that together stabilize membrane potential. A minority of terms point to transcriptional activity and pheromone-induced conjugation, but the dominant theme centers on ion transport and membrane potential maintenance.","confidence":"High","size":26,"edges":30,"triangles":11,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097623","count":8},{"id":"GO:0030007","count":8},{"id":"GO:0036376","count":7},{"id":"GO:0006351","count":7},{"id":"GO:1990573","count":6}]},{"hash":"1435114974066231802","title":"ER stress response and ribosome biogenesis","description":"The cluster\u2019s top GO terms cluster around endoplasmic reticulum quality control (ERAD), ER-stress\u2013triggered apoptosis, and key steps in initiating translation and ribosome maturation, pointing to a cohesive theme of how cells manage misfolded proteins and regulate protein synthesis under stress. While there are also notes on chromatin modification and a germ-cell development term (seminiferous tubule development), these appear less central to the core theme and may reflect contextual roles rather than a single unified function. Overall, the strongest signal is ER stress response coupled to translation/ribosome biogenesis.","confidence":"Medium","size":26,"edges":5,"triangles":0,"max_degree":5,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0030433","count":9},{"id":"GO:0050731","count":9},{"id":"GO:0070059","count":9},{"id":"GO:2000601","count":9},{"id":"GO:0001731","count":8}]},{"hash":"1038710882675426721","title":"Innate Immune Signaling and Inflammation","description":"This cluster is driven by GO terms tied to innate immune responses to pathogens (lipopolysaccharide response and signaling, dsRNA response, interferon-beta production) and the inflammatory response, with a few development-associated terms that may reflect broader tissue development roles. Overall, the core theme appears to be innate immune signaling and inflammation, with limited developmental context.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060427","count":2},{"id":"GO:0072224","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0043330","count":2},{"id":"GO:0045359","count":2}]},{"hash":"708904942146866597","title":"Stress-Responsive transcriptional repression and redox regulation","description":"The cluster\u2019s top GO terms converge on stress-responsive regulation of transcription (negative regulation of RNA Pol II transcription and DNA binding) combined with redox-related processes (protein deglutathionylation and cellular response to oxidative/ER stress). This suggests a cohesive theme where oxidative/ER stress triggers transcriptional repression and redox remodeling of proteins, even though the network shows no edges among members. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043392","count":2},{"id":"GO:0006662","count":1},{"id":"GO:0080058","count":1},{"id":"GO:1903206","count":1},{"id":"GO:1903026","count":1}]},{"hash":"22392263066827769","title":"TLR Signaling and Macrophage Activation","description":"This cluster is dominated by GO terms tied to Toll-like receptor signaling and innate immune responses, such as inflammatory response, MyD88-independent TLR signaling, Toll signaling pathway, macrophage activation, dendritic cell cytokine production regulation, and IFN production. These terms point to coordinated innate immune sensing and effector activation. A few outliers related to floral development appear in the list, likely annotation noise, but do not obscure the predominant immune-related theme.","confidence":"High","size":26,"edges":3,"triangles":1,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":4},{"id":"GO:0034158","count":4},{"id":"GO:0002730","count":4},{"id":"GO:0002756","count":4},{"id":"GO:0042116","count":4}]},{"hash":"1576067366583351458","title":"Translation initiation and mRNA processing","description":"The cluster is enriched for GO terms centered on translation initiation (formation of the translation preinitiation complex, regulation of translational initiation, eIF4F assembly, IRES-dependent initiation) and mRNA processing/export (mRNA splicing regulation, nuclear export, stress-related mRNA stability). This suggests a cohesive module of proteins involved in assembling and regulating translation initiation together with key mRNA maturation and export steps.","confidence":"High","size":26,"edges":267,"triangles":1590,"max_degree":25,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0075522","count":4},{"id":"GO:0048026","count":3}]},{"hash":"1766242241526970183","title":"DNA replication and repair with transcription regulation","description":"Top GO terms center on DNA replication and repair (leading strand elongation, replication, NER, translesion synthesis, checkpoint signaling). Transcription-related terms (RNA Pol II elongation, preinitiation complex assembly) hint at coordination with transcription during DNA metabolism. A few items (somatic hypermutation, viral genome replication) are context-specific but still related to DNA modification/replication processes. Overall, the cluster is best described as DNA replication and repair with transcription coordination.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070987","count":4},{"id":"GO:0006297","count":3},{"id":"GO:0033314","count":3},{"id":"GO:0016446","count":3}]},{"hash":"131282016207315968","title":"Lymphoid Homeostasis and Germinal Center Regulation","description":"The top GO terms cluster around T and B cell homeostasis, T follicular helper differentiation, and regulation of IL-2 and germinal center formation, indicating a theme of adaptive immune regulation and germinal center biology. Lymph node development also appears, supporting a lymphoid-focused function, while a few developmental terms are present but less central.","confidence":"Medium","size":26,"edges":9,"triangles":0,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0043029","count":5},{"id":"GO:0001782","count":5},{"id":"GO:0061470","count":4},{"id":"GO:0045085","count":4},{"id":"GO:0002635","count":4}]},{"hash":"709154949774865389","title":"Unknown","description":"The top GO terms span very diverse areas (bacterial SOS response; box H/ACA snoRNP assembly; RNA processing and telomere biology; neuronal axon fasciculation and synaptic signaling; various signaling pathways; bronchus morphogenesis), with no clear, shared biological function linking the proteins. This lack of a cohesive theme across most terms suggests no single representative function for the cluster.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0000493","count":1},{"id":"GO:2000233","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0097155","count":1}]},{"hash":"827135679446345056","title":"Unknown","description":"The top terms show a mix of epithelial adhesion/cytoskeleton-related terms (zonula adherens maintenance, epithelial cell\u2013cell adhesion, microtubule anchoring) and distinct lipid metabolism processes (triglyceride and phosphatidylcholine catabolism, acyl-chain remodeling), plus neuronal development and cell budding. This heterogeneity makes it difficult to assign a single coherent function to the cluster.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010923","count":1},{"id":"GO:0031175","count":1},{"id":"GO:0045218","count":1},{"id":"GO:0090136","count":1},{"id":"GO:0034453","count":1}]},{"hash":"890813959465839618","title":"Neural development gene regulation","description":"This cluster centers on DNA-templated transcription and chromatin regulation (histone H3-K4 methylation) and is enriched for developmental processes such as multicellular organism development, forebrain development, and neural tube closure. The convergence on transcriptional regulation and neural/developmental milestones suggests these proteins act as regulators of developmental gene expression, especially in neural tissues, rather than core metabolic functions. Some terms are marked obsolete, but the core theme remains neural development and gene regulation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0030433","count":5},{"id":"GO:0051568","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0030900","count":4}]},{"hash":"1335989855162178234","title":"Mitochondrial energy metabolism and insulin signaling","description":"The cluster centers on mitochondrial functions (membrane potential regulation, alpha-ketoglutarate and ornithine transport) and nutrient-growth signaling (insulin/IGF responses, amino acid starvation, liver regeneration), suggesting proteins involved in mitochondrial energy homeostasis linked to metabolic and growth signaling. Confidence is Medium.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":8},{"id":"GO:0060546","count":8},{"id":"GO:0097421","count":8},{"id":"GO:0051881","count":8},{"id":"GO:0034198","count":8}]},{"hash":"1947670209993851220","title":"ER-Golgi vesicle trafficking","description":"The top GO terms cluster around vesicle transport between the endoplasmic reticulum and Golgi (anterograde and retrograde), plus related pathways like Golgi-to-lysosome transport and protein sorting, indicating a primary theme of intracellular trafficking within the endomembrane system. Other terms (cell division, rRNA processing) are less central to this theme, so the label focuses on the dominant function.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0006890","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0070262","count":4},{"id":"GO:0000447","count":4}]},{"hash":"1281400271487548314","title":"Unknown","description":"The Top Terms span vesicle transport between the ER and Golgi, brain and seminiferous tubule development, mitotic spindle assembly and chromosome segregation, Rac signaling, proteolysis, ribosome biogenesis/translation initiation, translational frameshifting regulation, and rRNA maturation. This broad mix covers several distinct cellular processes with no single cohesive function, so there isn\u2019t a clear, representative theme to label the cluster beyond Unknown.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0016601","count":2},{"id":"GO:0006508","count":2}]},{"hash":"908526231381591483","title":"Unknown","description":"The top terms cover diverse processes: heart and posterior midgut development, intestinal smooth muscle contraction, innate immune response, dopamine signaling, IP3 biosynthesis, and mitochondrial electron transport. This broad spread suggests there is no single unifying function tying these proteins together, so the cluster appears functionally heterogeneous.","confidence":"","size":25,"edges":16,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0022900","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0060160","count":1}]},{"hash":"1254681459834557176","title":"RNA processing and translation initiation control","description":"This cluster is dominated by GO terms related to mRNA processing and splicing regulation (positive and negative regulation via spliceosome), mRNA export, and translation initiation steps (formation of the preinitiation complex, eIF4F complex assembly, translation reinitiation). The co-occurrence of splicing, mRNA maturation, and translation initiation suggests a coordinated RNA metabolism module linking processing with translation control.","confidence":"High","size":25,"edges":81,"triangles":82,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":13},{"id":"GO:0048026","count":11},{"id":"GO:0031047","count":11},{"id":"GO:0048025","count":9},{"id":"GO:0001731","count":9}]},{"hash":"123173990801746329","title":"Unknown","description":"The top terms are a scattered mix covering lipid metabolism (triglyceride catabolic process, lipid droplet organization, phosphatidylinositol dephosphorylation), nucleotide metabolism (uracil catabolic process), protein modification (diphthamide formation), transcription regulation (negative regulation of RNA polymerase II), and immune signaling (T cell differentiation in thymus). This lack of a unifying function or pathway makes it unclear what common role ties these proteins together.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":2},{"id":"GO:0019740","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0017183","count":2},{"id":"GO:0033089","count":2}]},{"hash":"116463079738632965","title":"Ribosome Biogenesis and Translation","description":"The proteins cluster around ribosome-related processes: translation (GO:0006412), ribosome biogenesis (GO:0042254), maturation of LSU-rRNA, and export of the large subunit from the nucleus, with additional translation regulation and cell cycle associations. This combination points to a coordinated role in ribosome assembly and protein synthesis control, with minor hints of other processes like transposition, but not altering the core theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000470","count":2}]},{"hash":"951740086477784283","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0052704","count":1},{"id":"GO:0009116","count":1},{"id":"GO:0006541","count":1}]},{"hash":"442195346691655200","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for ribosome biogenesis and translation (cytoplasmic translation, ribosomal subunit biogenesis, and export), indicating a cohesive set of proteins involved in ribosome assembly and protein synthesis; a few cell-cycle and stress-response terms appear but are likely ancillary.","confidence":"High","size":25,"edges":113,"triangles":186,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":7},{"id":"GO:0007049","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0042273","count":3}]},{"hash":"1307964044436196492","title":"Ribosome Biogenesis and RNA Processing","description":"The set is dominated by terms for rRNA maturation (5.8S, SSU/LSU) and ribosome biogenesis, with several spliceosome- and ncRNA-mediated RNA processing terms, indicating a primary function in RNA maturation and ribosome assembly; auxiliary terms like SOS response and cobalt transport seem ancillary.","confidence":"Medium","size":25,"edges":13,"triangles":1,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0009432","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0031047","count":3}]},{"hash":"1068820850499208807","title":"DNA Replication and Repair Core","description":"The cluster is dominated by GO terms for DNA replication (GO:0006260) and DNA repair (GO:0006281) with high counts (21 and 20), indicating proteins primarily involved in genome maintenance. Other terms include developmental and adhesion-related processes and differentiation/migration terms, which are less central and may reflect multifunctional proteins or annotation spillover. Overall, the strongest shared function across the proteins is DNA replication and repair, supporting the chosen label.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":21},{"id":"GO:0006281","count":20},{"id":"GO:0051893","count":19},{"id":"GO:0043552","count":18},{"id":"GO:0060434","count":18}]},{"hash":"2102496116157122206","title":"Ubiquitin-Dependent Proteostasis and RNA Processing","description":"The cluster heavily features ubiquitin-dependent protein degradation via SCF-proteasome and ERAD, plus stress-induced apoptotic signaling, indicating proteostasis under ER stress. It also contains RNA-processing and translation-related terms (spliceosome splicing, translation preinitiation, frameshifting regulation, rRNA maturation), suggesting a link between protein turnover and RNA maturation/translation. Together, these terms describe a module combining proteostasis with RNA processing/translation control.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0070059","count":2}]},{"hash":"1755039032283259836","title":"RNA processing and translation initiation","description":"This cluster is dominated by terms related to RNA metabolism and translation control, including miRNA-mediated silencing, mRNA export, splicing regulation, rRNA maturation, and assembly of translation initiation complexes. Together with components involved in preinitiation complex formation and eIF4F assembly, the proteins appear to coordinate RNA processing, export, and the initiation steps of protein synthesis, suggesting a cohesive RNA metabolism/translation machinery module.","confidence":"High","size":25,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":3},{"id":"GO:0032781","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0000466","count":2}]},{"hash":"2026358869350178638","title":"Unknown","description":"The top GO terms include immune and antibiotic responses, hormone response, development (embryo and heart), Hippo signaling, oxidative stress, wound healing, sensory perception, and neuronal apoptosis. This spread indicates no single cohesive function or pathway unites the 25 proteins, so a confident, specific label cannot be assigned. ","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0046677","count":10},{"id":"GO:0043029","count":9},{"id":"GO:0032355","count":9},{"id":"GO:0035329","count":9},{"id":"GO:0042542","count":9}]},{"hash":"1383878428014244922","title":"Neural signaling and intracellular transport","description":"The top GO terms point to diverse signaling pathways (GTPase regulation, Wnt, IGF receptor signaling), broad intracellular signaling, and vesicle trafficking (Golgi\u2013ER transport, microtubule movement), with spinal cord development suggesting a neural context. This suggests a cluster of proteins coordinating signaling with intracellular transport in neural development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007584","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0097011","count":2}]},{"hash":"290687601470914078","title":"Mitochondrial Protein Import and Translation","description":"This cluster is dominated by GO terms for protein import into the mitochondrial intermembrane space and mitochondrial matrix, alongside translation, and general housekeeping processes like cell division and various biosynthetic pathways. The presence of chaperone-related refolding and ERAD-related terms (even if labelled obsolete) supports a theme of protein quality control in mitochondria, tying the assembly together as a mitochondrial protein handling and basic metabolism cluster.","confidence":"Medium","size":24,"edges":81,"triangles":79,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0045041","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0070389","count":2}]},{"hash":"1901635592527500719","title":"Cellular metabolism and redox homeostasis","description":"The top GO terms point to a broad mix of metabolic activities (glycolysis, L-alanine and organic phosphonate catabolism, proteolysis, transsulfuration) alongside redox-related processes (oxidation-reduction, redox homeostasis) and stress/ detox responses, with mitochondrial translation/tRNA biosynthesis suggesting a mitochondrial angle. This pattern indicates a cluster centered on general metabolism with a strong emphasis on maintaining redox balance, rather than a single tight pathway.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0006508","count":3}]},{"hash":"1087453525553956255","title":"Small-molecule metabolism and detoxification","description":"This cluster centers on diverse small-molecule metabolic processes, including biosynthesis of vitamins and secondary metabolites (biotin, antibiotics, alkaloids), various catabolic pathways (uracil, 3-phenylpropionate, triglycerides), redox processes, and response to toxic substances, suggesting a general theme of metabolism and detoxification rather than a single, cohesive pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":6},{"id":"GO:2000124","count":5},{"id":"GO:0019433","count":5},{"id":"GO:0055114","count":5}]},{"hash":"925339813360859947","title":"Rho/Rac Signaling and Phagocytosis","description":"These proteins cluster around cytoskeletal signaling through Rho and Rac GTPases and the phagocytic process, suggesting a module focused on immune cell\u2013mediated uptake and cell movement. The presence of EGFR signaling and adaptive immune response terms indicates broader signaling roles that can influence migration and activation, but the core theme appears to be Rho/Rac-driven cytoskeletal dynamics linked to phagocytosis. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035176","count":3},{"id":"GO:0006909","count":3},{"id":"GO:0007173","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0002250","count":3}]},{"hash":"1447628903246398478","title":"RNA processing and translational control","description":"The cluster shows strong representation of RNA processing and mRNA export (splicing, export from nucleus, stress-related mRNA stability) alongside translation initiation and reinitiation (formation of preinitiation complex, translation reinitiation, regulation of translational initiation). Viral translation initiation terms further support a focus on translational control. Some vesicle transport and ERAD terms appear peripheral and do not redefine the main theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":8},{"id":"GO:0002188","count":8},{"id":"GO:0000398","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0006406","count":5}]},{"hash":"1533582070844040287","title":"Chromatin regulation and transcription","description":"The proteins are enriched for chromatin-related processes (heterochromatin formation, DNA methylation\u2013dependent chromatin states) and RNAP II\u2013driven transcription/elongation, with supporting links to DNA replication and repair, suggesting a coherent module coordinating chromatin state with transcription and genome maintenance.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0070869","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0006351","count":2}]},{"hash":"48240121773215037","title":"Developmental transcriptional signaling regulators","description":"The terms point to transcriptional regulation (DNA-templated transcription) and developmental processes (hippocampus development, embryonic digit morphogenesis, sensory perception of sound), with several entries on signaling pathways and cell-cycle regulation (insulin signaling, PI3K/AKT, G1/S). The cluster seems to mix developmental gene regulation with modulated signaling rather than a single clean function, making this a plausible but not definitive theme. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032196","count":2},{"id":"GO:0021766","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046627","count":1}]},{"hash":"2289972958423606418","title":"Developmental Morphogenesis Signaling","description":"Top GO terms cluster around angiogenesis, multicellular organism development, cell morphogenesis, and Rho-mediated signal transduction, suggesting a developmental signaling program focused on tissue morphogenesis and cytoskeletal remodeling. Some terms (DNA repair, sperm capacitation, obsolete entries) are peripheral, indicating partial noise but not negating the core theme. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":2},{"id":"GO:0045766","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0001525","count":2}]},{"hash":"30194166358423914","title":"NER DNA Repair Proteins","description":"The top GO terms point to nucleotide-excision repair, including global genome NER and NER itself, indicating a cluster enriched for DNA damage repair functions. Other terms (developmental or signaling-related) appear less central, so the main theme is DNA repair via NER rather than a single cohesive developmental or signaling pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0048820","count":2},{"id":"GO:0016525","count":2}]},{"hash":"1154412768112315428","title":"Hematopoiesis and Immune Signaling","description":"The top GO terms cluster around hematopoietic and immune biology (hemopoiesis, NK T cell differentiation, cellular response to GM-CSF) and associated signaling pathways (PI3K/Akt, JNK regulation) plus cell migration. Additional terms involving hyaluronan metabolism and prostaglandin response suggest extracellular remodeling and inflammatory signaling linked to immune development. Although the network has no edges here, the converging themes point to proteins involved in immune cell formation, movement, and signaling rather than a single, cohesive pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0097011","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0071380","count":3},{"id":"GO:0007507","count":3}]},{"hash":"1326218822879658309","title":"Unknown","description":"The top GO terms span a broad and incoherent mix of functions\u2014from ascospore formation and regulation of cell shape to visual perception, transcriptional initiation, and glycan processing\u2014without a unifying biological theme. The cluster also appears edge-less, suggesting no cohesive functional module. Therefore no specific label beyond Unknown is appropriate.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0072205","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0006491","count":2}]},{"hash":"1855048884408706785","title":"Meiosis and Mitosis with Apoptotic Regulation","description":"The cluster centers on cell division (mitosis and meiosis) with terms for sister chromatid separation and chromatid cohesion, plus apoptotic signaling and morphogenesis, and includes nuclear pore assembly and desumoylation regulation that connect nuclear transport and protein modification to division and cell fate. ","confidence":"High","size":23,"edges":183,"triangles":767,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015991","count":10},{"id":"GO:0051301","count":9},{"id":"GO:0051306","count":7},{"id":"GO:2001241","count":7},{"id":"GO:0042518","count":7}]},{"hash":"428649936311753849","title":"Cell Cycle and Proliferation Signals","description":"This cluster is driven by core cell cycle terms such as DNA replication and cell division, suggesting a shared function in promoting cell proliferation. The presence of related signaling terms (adenosine receptor signaling, cAMP biosynthesis, and forskolin response) indicates integrated pathways that regulate this proliferation, which can also be linked to early development (blastocyst development). Overall, the dominant theme is coordination of DNA synthesis and division with signaling cues that modulate growth.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0098779","count":2},{"id":"GO:0061635","count":2}]},{"hash":"1120623262720897974","title":"GTPase/Rac signaling regulators","description":"The cluster is dominated by GO terms tied to regulation of GTPase activity, especially Rac signaling, and related downstream processes like threonine phosphorylation and cytoskeletal dynamics, which points to a cohesive role in modulating small GTPase pathways. While a few terms touch on broader developmental or neural contexts (e.g., myelination, synaptic potentiation), these likely reflect the diverse roles of GTPase signaling in different cell types. Overall, the unifying theme appears to be regulation of GTPase/Rac signaling and its downstream effects.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0022011","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0010800","count":2},{"id":"GO:0071574","count":2}]},{"hash":"920521469913585630","title":"Amino acid catabolism and central carbon metabolism","description":"The top GO terms cluster around amino acid degradation (L-alanine, L-kynurenine) and central carbon metabolism (pyruvate biosynthesis, TCA cycle, oxaloacetate and 2-oxoglutarate metabolism), with a secondary tie to porphyrin biosynthesis. The Notch signaling term appears as an outlier, not tying into the metabolic theme. Overall, the cluster seems to represent metabolic pathways rather than a single signaling or regulatory function.","confidence":"Medium","size":23,"edges":237,"triangles":1468,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":10},{"id":"GO:0007219","count":9},{"id":"GO:0097053","count":9},{"id":"GO:0042866","count":8},{"id":"GO:0006099","count":7}]},{"hash":"1635591512274742577","title":"Chaperone-assisted folding and ER targeting","description":"This cluster is dominated by GO terms related to protein folding quality control and targeting to membranes via the secretory pathway (SRP-dependent cotranslational targeting, post-translational targeting, and cellular response to unfolded protein), plus chaperone/cofactor-dependent refolding and ER stress\u2013related signaling. While a few terms touch on other processes like DNA replication or cell wall biosynthesis, the strongest and most cohesive theme is chaperone-mediated folding and delivery of proteins to membranes/secretory routes.","confidence":"High","size":23,"edges":103,"triangles":166,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0070389","count":6},{"id":"GO:0006880","count":6},{"id":"GO:0070880","count":6},{"id":"GO:1902037","count":6}]},{"hash":"1047596353566815887","title":"Unknown","description":"The top terms cover a wide, unrelated mix of ribosome assembly, plant shoot development, amino acid starvation response, rRNA export, hemidesmosome assembly, meristem initiation, chromatin remodeling, transcription elongation, pH response, and viral genome activation. There is no clear shared function or pathway among these terms, and the cluster has no edges or connectivity, suggesting it is not a coherent functional group. ","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000028","count":1},{"id":"GO:2000032","count":1},{"id":"GO:0034198","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0031581","count":1}]},{"hash":"1712810548375982461","title":"Ribosome Biogenesis and Translation Initiation","description":"This cluster is dominated by terms on ribosome maturation (LSU and 5.8S rRNA) and translation initiation/controls, with GO terms for preinitiation complex formation and regulation of translational frameshifting, suggesting a coherent ribosome- and translation-focused group, while a few terms like brain development or cellular fusion appear as noise.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0000747","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0071560","count":5}]},{"hash":"350350269075575113","title":"RNA Polymerase III Transcription Machinery","description":"The cluster shows multiple terms tied to transcription by RNA polymerase III and its preinitiation complex assembly (e.g., 5S rRNA transcription by Pol III, Pol III preinitiation complex assembly), suggesting a core theme around Pol III transcription machinery. Other terms like ER unfolded protein response and host\u2013virus interaction may reflect broader cellular stress contexts but do not override the stronger Pol III transcription signal. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044791","count":2},{"id":"GO:0044828","count":2},{"id":"GO:0030968","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0033197","count":2}]},{"hash":"856391112175927678","title":"Substrate-Specific Membrane Transporters","description":"This cluster is enriched for GO terms describing transport of various substrates across membranes (sialic acid, carbohydrates, vitamins, sodium ions, xenobiotics, etc.) and a general transmembrane transport term, with an additional note on neurotransmitter loading into synaptic vesicles. The common thread is proteins involved in moving diverse substrates across membranes, rather than a single cohesive pathway, so a transporter-focused label is appropriate.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":2},{"id":"GO:0006412","count":2},{"id":"GO:1900754","count":1},{"id":"GO:0055085","count":1},{"id":"GO:0035461","count":1}]},{"hash":"2054189255009133567","title":"Motile cilium assembly and left-right symmetry","description":"The strongest signals are cilia-related: axonemal dynein complex assembly and motile cilium assembly, plus determination of left/right symmetry, pointing to ciliogenesis and ciliary motility as the core cluster function. Supporting terms like intracellular signal transduction and secretory granule localization fit with ciliary signaling and transport roles; other terms reflect general cellular responses but do not override the ciliopathy-related theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042149","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0044458","count":2},{"id":"GO:0070286","count":2}]},{"hash":"2100075179071528157","title":"RNA processing and translation machinery","description":"The cluster centers on translation-related processes (cytoplasmic and mitochondrial translation, ribosome dynamics, and selenocysteine incorporation) and RNA processing (spliceosome changes), suggesting a cohesive theme of protein synthesis and RNA maturation.","confidence":"High","size":22,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0014009","count":3},{"id":"GO:1990145","count":3},{"id":"GO:2000767","count":3},{"id":"GO:1990416","count":3}]},{"hash":"759285686570537740","title":"Developmental endocytosis and cytoskeleton dynamics","description":"The top GO terms cluster around endocytosis, neuronal projection development, and barbed-end actin filament capping, with additional developmental terms like heart development and cell fate specification. This suggests a theme where endocytic trafficking and cytoskeleton remodeling support developmental processes, particularly in neural and cardiac contexts.","confidence":"Medium","size":22,"edges":23,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:0010976","count":2},{"id":"GO:0033132","count":1},{"id":"GO:1904960","count":1},{"id":"GO:0008535","count":1}]},{"hash":"1665178276283120994","title":"Unknown","description":"The top GO terms span plant lignin biosynthesis, various metabolic biosynthetic processes, immune signaling, and physiological regulation, with no clear single function tying all proteins together. This makes a precise, representative label unreliable.","confidence":"","size":22,"edges":168,"triangles":620,"max_degree":21,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0009809","count":8},{"id":"GO:0032496","count":8},{"id":"GO:1901159","count":7},{"id":"GO:0006633","count":7},{"id":"GO:0045777","count":7}]},{"hash":"2108684654195978954","title":"Unknown","description":"The top GO terms span stress and environmental responses, hormonal/metabolic processes, eye development, and xenobiotic metabolism, with no single cohesive function linking all proteins. Given the diversity, a specific, representative label isn\u2019t supported.","confidence":"","size":22,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":9},{"id":"GO:0032342","count":9},{"id":"GO:0090350","count":9},{"id":"GO:0033072","count":9},{"id":"GO:0033280","count":9}]},{"hash":"1959837991331915080","title":"Mitochondrial Energy Metabolism under Starvation","description":"These terms cluster around mitochondrial energy production and nutrient stress responses: fatty acid oxidation, carnitine metabolism, and electron transport/complex II assembly, plus a starvation response and energy storage (glycogen biosynthesis). The presence of oxidative stress and transcription regulation terms may reflect broader mitochondrial regulation. Overall, the group represents mitochondrial energy metabolism under nutrient limitation.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019254","count":3},{"id":"GO:0033540","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0001890","count":2}]},{"hash":"375216716276103128","title":"Bacterial transcription regulation and LPS biosynthesis","description":"The most frequent GO terms are centered on DNA-templated transcription and its regulation, alongside lipopolysaccharide biosynthetic processes, which together point to bacterial transcriptional control and outer-membrane polysaccharide production. Some terms appear noisy (mesodermal differentiation, testosterone response), but the core signal supports a bacterial transcription-regulation with LPS biosynthesis theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0009103","count":3},{"id":"GO:0042619","count":3}]},{"hash":"324010192282512741","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0010951","count":1},{"id":"GO:0097309","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000494","count":1}]},{"hash":"1648752404475328797","title":"Ribosome Biogenesis and rRNA Maturation","description":"The top GO terms are dominated by maturation of LSU-rRNA, maturation of 5.8S rRNA, and maturation of SSU-rRNA, plus ribosome biogenesis and large subunit biogenesis, indicating a shared role in ribosome assembly and rRNA processing. Protein homooligomerization may reflect ribosomal protein interactions, while DNA-templated transcription is a less central signal for this cluster. Overall, these terms point to a ribosome-focused biogenesis function.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0051260","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000462","count":3}]},{"hash":"220327375579090267","title":"Cardiac GPCR Signaling and Heart Contraction","description":"The top GO terms cluster around GPCR-mediated signaling in cardiac contexts (tachykinin and acetylcholine receptor pathways), desensitization/internalization of GPCR signaling, and regulation of heart contraction, indicating a cohesive theme of signaling control of cardiac function; a couple more general terms (sterol biosynthesis, mRNA capping) are less specific but do not negate the cardiac signaling pattern.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0002031","count":2},{"id":"GO:0060048","count":2}]},{"hash":"1489810818245880434","title":"Developmental Transcriptional Regulation and Chromatin Remodeling","description":"This cluster is dominated by GO terms related to transcriptional control and chromatin remodeling, with additional links to differentiation of skeletal muscle and glial cells, indicating a developmental program where transcription regulation and chromatin dynamics coordinate lineage differentiation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0000973","count":2}]},{"hash":"1494230187890656925","title":"Embryonic eye development","description":"The top GO terms are strongly skewed toward eye-related development and morphogenesis (neural crest cell migration, embryonic eye morphogenesis, camera-type eye development, and related branching). While there are some general cellular processes in the list (tRNA processing, transcription, mitotic events), the dominant signal points to ocular development as the shared theme of this cluster. This justifies naming it Embryonic eye development.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001755","count":2},{"id":"GO:0048048","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0043010","count":2},{"id":"GO:0060441","count":2}]},{"hash":"1822016940109228578","title":"Innate Immunity and RNA Regulation","description":"This cluster centers on innate immune signaling and inflammatory response terms (innate immune response, inflammatory response, type II interferon signaling) alongside strong signals for post-transcriptional RNA regulation (deadenylation-dependent decapping, poly(A) tail shortening, and miRNA-mediated silencing). Together they suggest a theme of immune modulation through RNA turnover and silencing mechanisms. Some tissue-development terms appear but are less characteristic of the core function. Given the lack of interaction data (Edges 0) the label is plausible but not definitive.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006954","count":2},{"id":"GO:0000289","count":2},{"id":"GO:0000290","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0035195","count":2}]},{"hash":"2097888796172018388","title":"Mitosis-Chromatin Regulation via Ubiquitin-Proteasome","description":"Key terms point to mitosis (spindle assembly, cohesion) and chromatin regulation (localization to chromatin, histone-related modifications), with several ubiquitin-proteasome\u2013mediated degradation processes (SCF-dependent ubiquitination and polyubiquitination). This suggests a cohesive theme of chromosome segregation control through chromatin state and regulated proteolysis, though a few terms (like mRNA processing) may be less central.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0071169","count":3},{"id":"GO:0007064","count":2},{"id":"GO:0007275","count":2}]},{"hash":"509634124149128514","title":"Actin Cytoskeleton Remodeling in Migration and Organelle Inheritance","description":"This cluster is dominated by GO terms for actin nucleation and polymerization (Arp2/3, actin filament assembly/bundling), lamellipodium formation, and cell migration, indicating a central theme of actin-driven cytoskeletal remodeling related to movement. The presence of organelle inheritance terms (mitochondrion and vacuole inheritance) suggests actin\u2019s role in positioning and inheritance of organelles as well. Overall, the terms point to cohesive actin-mediated dynamics guiding migration and organelle inheritance.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0000147","count":3},{"id":"GO:0034314","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0030032","count":2}]},{"hash":"1871891971213238858","title":"ER Proteostasis and Ubiquitin-Proteasome Degradation","description":"This cluster is enriched for protein quality-control processes: ubiquitin-dependent degradation, ER-assisted protein folding, and responses to unfolded proteins, along with redox homeostasis. Together these point to a cohesive theme of maintaining proteome integrity via the ubiquitin-proteasome system and ER stress pathways, with a few outlying terms likely represent noise or context-specific annotations.","confidence":"Medium","size":21,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006986","count":2}]},{"hash":"230492812451707298","title":"Insect follicle epithelium development and ion transport","description":"The GO terms cluster around insect ovarian follicle epithelium processes (polarity maintenance, cell adhesion) and chitin biosynthesis, with several ion/transmembrane transport terms (potassium, sodium, arsenite, phosphate). This suggests a cohesive module linking follicular epithelial development with membrane transport and chitin-related components in insect oogenesis.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":2},{"id":"GO:0006031","count":2},{"id":"GO:0001744","count":2},{"id":"GO:0042248","count":2},{"id":"GO:0007299","count":2}]},{"hash":"1791124060923784627","title":"DNA replication and damage repair response","description":"This cluster is dominated by DNA replication terms (DNA replication, primer synthesis, DNA unwinding, topological changes) and DNA damage response processes (SOS response, nucleotide-excision repair). Nonsense-mediated decay and hypoxia response add broader stress-context signals, but the strongest common thread is replication-associated maintenance and repair. Hair cell differentiation stands out as less connected but may reflect secondary roles or annotation noise. Overall, the proteins likely participate in DNA replication and DNA damage response pathways.","confidence":"High","size":21,"edges":18,"triangles":12,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0006269","count":9},{"id":"GO:0009432","count":9},{"id":"GO:0000184","count":9},{"id":"GO:0006268","count":9}]},{"hash":"703001681445453914","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009561","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000480","count":1}]},{"hash":"1296606664748167191","title":"RNA processing and translation initiation","description":"The cluster shows strong representation of mRNA splicing, transcription, formation of the translation preinitiation complex, and ribosomal RNA maturation, indicating involvement in gene expression from transcription through translation. Some terms are older annotations or unrelated, but the core theme centers on RNA processing and initiation of protein synthesis.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0001731","count":3}]},{"hash":"1459292997250414422","title":"Heart morphogenesis and Ca2+ signaling","description":"The top GO terms are dominated by heart development and calcium signaling, including left ventricular cardiac muscle morphogenesis, Purkinje myocyte signaling to ventricular cells, outflow tract morphogenesis, and calcium release from the sarcoplasmic reticulum, plus cGMP-related signaling. Some outliers (immune response, meiosis, bone development) exist but are fewer, so the core theme centers on cardiac development and calcium-mediated signaling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0009395","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0043060","count":2}]},{"hash":"1117900596667784504","title":"Epigenetic Regulation and Transcription","description":"The top GO terms emphasize arginine methylation (PRMT activity), histone methylation, and DNA-templated transcription, pointing to chromatin-level control of gene expression. While other terms touch on signaling, growth, and metabolism, the core theme is epigenetic regulation of transcription.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0043985","count":2}]},{"hash":"440799415107281765","title":"Cell Cycle and Proliferation Core","description":"The cluster shows strong enrichment for mitotic cell cycle, cell division, and proliferation-related GO terms, suggesting a shared role in cell cycle progression and growth regulation. While translation-related terms appear, the dominant theme is cell cycle control and proliferation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0008284","count":4},{"id":"GO:0001731","count":3}]},{"hash":"675703313887557456","title":"Signaling and membrane trafficking","description":"The cluster centers on GO terms tied to signaling regulation (ERK1/ERK2 cascade, peptidyl-serine phosphorylation, protein binding) and membrane trafficking (ubiquitin-dependent endocytosis), complemented by various transport functions (branched-chain amino acids, cobalt ions, doxorubicin) and stress-related responses. Although there are outliers (visual perception, mercury ion response), the strongest cohesive theme is signaling coupled with membrane trafficking and transport. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032092","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0070086","count":2}]},{"hash":"1634123852286358943","title":"Embryonic Organ Morphogenesis","description":"The proteins are associated with diverse embryonic development and organ morphogenesis across several tissues (pituitary, uterus, pharyngeal system, inner ear, cranial skeleton), plus the broad multicellular organism development term. This cross-tissue developmental theme best explains the cluster, so the label emphasizes embryonic organ formation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":5},{"id":"GO:0021902","count":4},{"id":"GO:0003309","count":4},{"id":"GO:0060065","count":4},{"id":"GO:0060037","count":4}]},{"hash":"616446904253032322","title":"tRNA Modification and Processing","description":"The strongest coherent signal in the terms is tRNA processing and wobble-base modification (lysidine biosynthesis and uridine thiolation), indicating a set of enzymes dedicated to RNA maturation and modification. Other terms (stress response, cell growth, CoA biosynthesis) are more general or incidental, so the dominant theme appears to be RNA modification machinery. ","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0085014","count":3},{"id":"GO:0006950","count":3},{"id":"GO:0015937","count":3},{"id":"GO:0048549","count":2},{"id":"GO:0016049","count":2}]},{"hash":"1005322677439042674","title":"Methyltransferase-Rich Biosynthesis and RNA Modification","description":"The top GO terms include several biosynthetic processes (antibiotic, cobalamin, polyamine) together with RNA and protein modification steps (tRNA wobble uridine modification, 7-methylguanosine capping, N-terminal peptidyl-alanine trimethylation, historical histone methylation). This pattern suggests a shared role for methyltransferase activities linking biosynthesis pathways and RNA/protein modification. Some xenobiotic and stress-related responses appear as ancillary features, but the core signal centers on methylation-related functions across different substrates. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009236","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0018012","count":4},{"id":"GO:0090398","count":4}]},{"hash":"25945947091725727","title":"Innate Immunity and K63-Linked Ubiquitination","description":"The cluster is strongly enriched for innate immune response and defense against virus, along with K63-linked ubiquitination, which together point to antiviral signaling regulated by ubiquitination. While other terms (developmental and lipid transport) appear, the most representative shared theme among the top terms is immune signaling modulated by ubiquitination. This justifies a label focused on innate immunity and ubiquitination rather than broader or unrelated processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007368","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2}]},{"hash":"2292647790746155872","title":"Ubiquitin-Mediated Innate Immune Response","description":"This cluster centers on innate immune activity linked with ubiquitination processes (ubiquitin-dependent proteolysis, protein ubiquitination, autoubiquitination, and K63-linked ubiquitination) and antiviral defense, suggesting a cohesive theme of ubiquitin-regulated innate immune signaling and cell fate decisions during viral defense, despite some peripheral terms like vitamin D response.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0070534","count":5}]},{"hash":"1475257892548860801","title":"Melanin biosynthesis and pigmentation","description":"Most top GO terms point to pigment production and melanin biology (melanin biosynthetic process, melanosome organization, pigmentation, and positive regulation of melanin biosynthesis), suggesting this cluster mainly encompasses pigment cell function. A few neural development terms may reflect the neural crest origin of melanocytes but do not outweigh the pigmentation theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002052","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0032438","count":4},{"id":"GO:0006583","count":4},{"id":"GO:0021847","count":4}]},{"hash":"536535688127476584","title":"Unknown","description":"The top terms span many unrelated processes (insulin signaling, chromatin organization, collagen catabolism, RNA splicing, DNA damage checkpoints, gastrulation, fungal spindle remodeling) and include obsolete entries, indicating no single cohesive function for the cluster. Therefore, the appropriate label is Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":2},{"id":"GO:0035551","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0030574","count":1}]},{"hash":"1341425323195189076","title":"Mitotic division and DNA replication regulation","description":"The top GO terms cluster around mitosis (cell division, mitotic cell cycle, G2/M transition) and regulation/ initiation of DNA replication, with spindle microtubule attachment and related cell-shape changes; together these indicate proteins coordinating mitotic progression and replication control in multicellular organisms.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0008360","count":2}]},{"hash":"998227574709818001","title":"Mitochondrial Metabolism and Amino Acid Biosynthesis","description":"The terms converge on mitochondria-centered biology, with mitochondrial translation and multiple metabolic/biosynthetic pathways (thiamine, leucine, lysine, acetyl-CoA, TCA cycle, fatty acid metabolism) suggesting a cluster of proteins involved in mitochondrial energy production and amino acid biosynthesis. Some terms are flagged as obsolete, but they point to related metabolic activities within the same mitochondrial context.","confidence":"High","size":20,"edges":14,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0009098","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0006099","count":2}]},{"hash":"119584686150737833","title":"ER proteostasis and unfolded protein response","description":"The top GO terms converge on protein folding homeostasis and stress responses: unfolded protein response, positive regulation of translation initiation in ER stress, and nuclear/ubiquitin-proteasome\u2013mediated protein quality control, plus post-translational targeting to membranes. While a few terms (DNA replication, tRNA import) are less directly related, the dominant signal is proteostasis and ER-associated stress response, suggesting a cluster centered on managing protein folding and degradation under stress.","confidence":"Medium","size":20,"edges":21,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":2},{"id":"GO:0030447","count":1},{"id":"GO:0051259","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0071374","count":1}]},{"hash":"323892093157412399","title":"Ribosome biogenesis and rRNA maturation","description":"The top GO terms cluster around ribosome biogenesis, rRNA maturation/processing, and translation, with multiple entries for maturation of SSU/LSU rRNA from tricistronic transcripts, plus related transcription and DNA processes. The dominant signal points to ribosome assembly and RNA maturation as the core function of this cluster.","confidence":"High","size":20,"edges":19,"triangles":10,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0008033","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1792111936795738233","title":"Unknown","description":"The listed top GO terms are highly diverse (nitrate assimilation, antibiotic response, redox homeostasis, spliceosome-mediated splicing, propylene catabolism, development, lipid metabolism, fatty acid response, photoinhibition, and water loss regulation) and include obsolete terms, suggesting no single coherent function or pathway ties these proteins together. Therefore there isn\u2019t a recoverable, representative theme for this cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0042208","count":2}]},{"hash":"877172052892279729","title":"Unknown","description":"The top GO terms span nitrogen metabolism, lipid/sterol biosynthesis, membrane-related processes, and metal homeostasis across diverse organisms, with no single cohesive function tying the proteins together. Therefore, no clear, representative label can be assigned.","confidence":"","size":20,"edges":41,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0006809","count":4},{"id":"GO:0001949","count":4},{"id":"GO:0006675","count":4},{"id":"GO:0000001","count":4}]},{"hash":"795927284340906919","title":"Ribosome biogenesis and RNA processing","description":"The proteins are linked to ribosome biogenesis (including large subunit assembly) and RNA processing/splicing, with involvement across RNA polymerases I\u2013III and spliceosome-related activities, indicating a cohesive nuclear module coordinating transcription, RNA processing, and ribosome production.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":8},{"id":"GO:0042273","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0006385","count":3},{"id":"GO:0001172","count":3}]},{"hash":"1113536274530390199","title":"DNA Transcription Regulation Cluster","description":"The top terms are dominated by DNA-templated transcription and regulation of DNA-templated transcription, pointing to a core role in transcriptional control. The other GO terms (immune signaling, cell migration, detoxification, metabolism, proteolysis) imply additional, diverse roles or multifunctionality, but the transcription regulation theme is the strongest signal. ","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001662","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0060244","count":1}]},{"hash":"426553051752725170","title":"Nuclear DNA Maintenance and Viral Integration","description":"The dominant GO terms point to nuclear DNA metabolism (DNA replication/removal of RNA primer, DNA integration, recombination, RNA-templated DNA biosynthesis) and virus-host interactions (viral entry into the host nucleus, proviral latency). A couple of terms related to neurogenesis and pain appear incidental. Overall, the cluster seems to reflect nuclear DNA processing with viral integration features rather than a single, cohesive neural function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006409","count":2},{"id":"GO:0019233","count":1},{"id":"GO:0022008","count":1},{"id":"GO:0075732","count":1},{"id":"GO:0075713","count":1}]},{"hash":"621845769337960297","title":"Cell cycle and genome maintenance","description":"The cluster is dominated by GO terms related to cell cycle, cell division, and genome integrity (protein phosphorylation, DNA repair, DNA recombination, cell cycle). These point to a cohesive theme of cell proliferation control and genome maintenance, with a few neural-related terms appearing but likely secondary. Confidence in this label is High.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006468","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006281","count":2}]},{"hash":"569878605353354195","title":"Unknown","description":"The GO terms span mechanosensory response, glycogen metabolism, cyclin-dependent kinase regulation, calcium signaling, autophagy, vacuole fusion, polyprenol/wax metabolism, and circadian rhythm, with no single pathway uniting all 20 proteins. Therefore a specific, representative label is not supported.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0005979","count":1},{"id":"GO:0000079","count":1},{"id":"GO:0050849","count":1},{"id":"GO:0016242","count":1}]},{"hash":"1153066542606597940","title":"Retina Development and Opsin Signaling","description":"The cluster is dominated by GO terms related to eye/retina biology and visual signaling (retina development, opsin-mediated signaling, visual perception) plus GPCR-related processes (GTPase activity regulation, GPCR internalization), indicating a cohesive retinal signaling theme. Some terms in the set are more general (DNA transcription, DNA repair, heart development) but do not override the visual system emphasis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0002031","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0007601","count":2}]},{"hash":"1043224409506960759","title":"RNA and protein methylation under stress","description":"This cluster is dominated by GO terms for RNA and protein methylation: RNA guanine-N7 methylation, rRNA modification, and 7-methylguanosine mRNA capping, plus N-terminal methylation of proteins. The presence of several stress-related terms (hyperosmotic, xenobiotic, immobilization) suggests a link between methylation processes and stress responses. Some metabolism terms (phosphatidylcholine biosynthesis, antibiotic biosynthetic process) are less central but do not override the core methylation/stress theme. Overall, a methylation-focused, stress-associated cluster best fits these terms.","confidence":"Medium","size":20,"edges":8,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006972","count":6},{"id":"GO:0035690","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0036265","count":5},{"id":"GO:0000154","count":5}]},{"hash":"2000157867366301460","title":"Cytoskeleton Dynamics and Trafficking","description":"The top terms cluster around spindle assembly and actin filament bundle assembly, plus ER-Golgi vesicle transport and GTPase regulation, which together point to cytoskeletal organization and intracellular trafficking as the shared theme. Some terms (mRNA processing, telomere maintenance) are less connected, so the overall signal is moderate.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0090501","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0006397","count":4}]},{"hash":"252367696963650641","title":"Calcium-Driven Neuronal Signaling","description":"The top GO terms are dominated by neuronal and calcium signaling concepts: calcium ion transport, excitatory postsynaptic potential, cellular response to electrical stimulus, and regulation of short-term synaptic plasticity, all indicating activity-dependent neuronal signaling and calcium dynamics. There are a few other terms (fungicide response, peptidoglycan catabolic process, macrophage cytokine regulation) that appear less central and at low counts, but they do not override the core neuronal signaling theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060992","count":2},{"id":"GO:0060907","count":2},{"id":"GO:0006816","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0065009","count":2}]},{"hash":"203151777771364842","title":"Unknown","description":"These GO terms describe diverse processes across tissues (heart development, skeletal muscle maintenance, hepatocyte homeostasis), general cellular processes (cell wall macromolecule catabolic process, ubiquitin-dependent protein catabolic process), transcription regulation, and DNA damage response. There is no clear common function or pathway linking them, and the proteins appear unconnected, so there is no coherent cluster theme to label confidently.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016998","count":2},{"id":"GO:0007368","count":2},{"id":"GO:0006511","count":1},{"id":"GO:0036333","count":1},{"id":"GO:2000616","count":1}]},{"hash":"407394154078762017","title":"Neural cell apoptotic signaling","description":"This cluster\u2019s top GO terms show clear enrichment for neuron and glial apoptotic processes (neuron apoptotic process, glial cell apoptotic process), with supporting neural-context terms like nerve growth factor production. While other terms (mitochondria-nucleus signaling, vacuolar protein catabolism, sporulation) are more peripheral, the neural apoptosis signals most strongly tie the proteins together, suggesting a theme of neural cell death pathways.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000920","count":3},{"id":"GO:0031930","count":3},{"id":"GO:0007039","count":3},{"id":"GO:0034349","count":3},{"id":"GO:0051402","count":3}]},{"hash":"213752851472433120","title":"Innate antiviral immunity and interferon signaling","description":"The top GO terms cluster around defense against viruses, innate immune responses, and interferon-beta production, with indications of NF-kappaB involvement. A few terms reflect general cellular processes (translation initiation, rRNA synthesis) that may be incidental background. Overall, the dominant theme is antiviral innate immunity and interferon signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0032728","count":1}]},{"hash":"313454380571141701","title":"Signaling and Translation Regulation","description":"This cluster combines GO terms spanning signaling (GTPase regulation, TGF-beta response, peptidyl-tyrosine phosphorylation), protein trafficking (ER-Golgi transport), cytoskeleton dynamics (actin filament capping), and translation control (initiation and reinitiation). The mix suggests a broader theme around coordination of signal transduction with protein synthesis and trafficking, rather than a single specific pathway, hence the label \u201cSignaling and Translation Regulation.\u201d","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0002043","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2276760969402779919","title":"RNA processing and translation initiation","description":"The top GO terms are dominated by RNA metabolism and control of translation, including mRNA splicing regulation, mRNA export from the nucleus, mRNA stabilization, and formation/assembly of translation preinitiation complexes and the eIF4F complex. These converge on RNA processing and the initiation of protein synthesis, suggesting the cluster centers on RNA maturation and translation regulation. A single term about antigen processing via MHC I stands out as a potential noise or peripheral link to broader cellular regulation rather than a core function of all proteins in this cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019885","count":2},{"id":"GO:0009089","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0097010","count":2}]},{"hash":"1395441983144670179","title":"Apoptosis and ubiquitin-regulated degradation","description":"The top GO terms point to cell death (cytolysis, cell death) and regulation of protein quality control via ubiquitin and ERAD-related processes (negative regulation of ERAD, ubiquitin-dependent ERAD, ubiquitin-specific protease activity). While some terms are less directly related or obsolete, the recurring theme is how proteostasis and ubiquitin-mediated degradation intersect with signals that govern apoptosis and immune signaling. This suggests a cohesive cluster centered on apoptosis coupled with proteostasis pathways and related regulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019835","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0002814","count":1},{"id":"GO:1904293","count":1},{"id":"GO:2000157","count":1}]},{"hash":"2210733302846709800","title":"Protein Synthesis and Fe-S Cluster Biogenesis","description":"This cluster shows strong signals for translation (cytoplasmic and mitochondrial) and iron-sulfur (Fe-S) cluster assembly/maturation, suggesting a core link to protein synthesis machinery and its maturation cofactors, with some additional metabolic and antibiotic-related associations.","confidence":"Medium","size":19,"edges":123,"triangles":547,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0032543","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0016226","count":2}]},{"hash":"1363017616806408980","title":"Stress-Linked Proteostasis and Organelle Import","description":"The terms cluster around protein quality control and turnover (proteasome-related processes, autophagosome maturation, ubiquitin-regulated steps), stress responses (cadmium stress, stress granule disassembly, DNA damage tolerance), and targeted protein import into organelles (mitochondrial intermembrane space, peroxisome matrix). Taken together, they point to a cohesive theme of maintaining protein homeostasis under stress and coordinating organelle protein targeting. ","confidence":"High","size":19,"edges":164,"triangles":855,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:1990171","count":6},{"id":"GO:0035617","count":6},{"id":"GO:1903007","count":6},{"id":"GO:0097352","count":6}]},{"hash":"696338046282070901","title":"Ribosome biogenesis and translation-related RNA processing","description":"The cluster is dominated by GO terms tied to ribosome biogenesis, rRNA maturation for SSU/LSU and 5.8S, and translation-related processes (translation, initiation, reinitiation), plus involvement in mRNA surveillance (NMD). This combination strongly points to a cohesive function in ribosome assembly and translation-associated RNA metabolism, with a possible link to transcription-coupled repair as a broader RNA-processing context. ","confidence":"High","size":19,"edges":112,"triangles":399,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006283","count":5},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0000463","count":3}]},{"hash":"345380746095872505","title":"Hormone and secondary metabolite biosynthesis","description":"The cluster is enriched for GO terms involving biosynthesis of steroids and hormone derivatives (glucocorticoids, estrogens, retinoic acid) as well as other secondary metabolites (fatty acids, alkaloids, antibiotics) and related metabolic processes, suggesting a shared theme around production of signaling molecules and secondary metabolites, with a peripheral membrane/transport component.","confidence":"Medium","size":19,"edges":10,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0071805","count":3},{"id":"GO:0006704","count":3},{"id":"GO:0006703","count":3},{"id":"GO:1902321","count":3}]},{"hash":"1679124574881345878","title":"Cell Division and Developmental Signaling","description":"The Top Terms show a focus on cell division-related processes (division septum assembly, cell septum assembly) along with embryonic development (spermatogenesis, regulation of embryonic cell shape). Mitochondrial fission and signaling pathways (TNF-mediated signaling, smoothened signaling) suggest broader coupling of organelle dynamics with developmental signaling. Taken together, the cluster appears to center on cellular remodeling during division and development, with integrated signaling. Confidence: Medium","confidence":"","size":19,"edges":29,"triangles":15,"max_degree":14,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0010950","count":3},{"id":"GO:0000266","count":3},{"id":"GO:0033209","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0016476","count":3}]},{"hash":"891266038620605188","title":"DNA replication and cell cycle machinery","description":"This cluster is dominated by GO terms for cell division and DNA replication (including viral genome replication), pointing to genome duplication and cell-cycle\u2013related processes as the core theme. The presence of proteasome regulatory particle assembly and SCF complex disassembly terms suggests coordinated protein turnover and regulation during replication. Some terms touch on stress responses and organelle function (ER polarization, stress granule disassembly, mitochondrial DNA replication and respiratory chain assembly), indicating additional layers of regulation under cellular stress. Overall, the cluster most plausibly represents DNA replication in the context of cell-cycle control, with supportive links to proteostasis and organelle regulation.","confidence":"Medium","size":19,"edges":35,"triangles":13,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0006260","count":7},{"id":"GO:0019079","count":7},{"id":"GO:0070682","count":6},{"id":"GO:1990171","count":6}]},{"hash":"1816670243624050144","title":"Multi-lineage cell differentiation","description":"This cluster's top GO terms cluster around differentiation into a wide range of tissues and lineages (ventricular septum development, enterocyte differentiation, nephron/ureteric bud nephrogenesis, pancreatic A cell differentiation, neuronal forebrain commitment, basophil differentiation, cardiac vascular smooth muscle differentiation), with DNA-templated transcription indicating developmental regulation. The diversity of tissues suggests a general differentiation theme rather than a single tissue-specific pathway, so the label reflects a broad developmental differentiation cluster.","confidence":"Medium","size":19,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0003281","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0021902","count":4},{"id":"GO:0072182","count":4},{"id":"GO:0030221","count":4}]},{"hash":"1483381649553624935","title":"Unknown","description":"The top GO terms span inflammation, GPCR/cAMP signaling, development (lung tissue, glomerulus), locomotion, and even bacterial peptidoglycan catabolism, with no clear single pathway or function tying these proteins together. The mix suggests either annotation noise or multi-functional proteins rather than a cohesive cluster core.","confidence":"","size":19,"edges":17,"triangles":0,"max_degree":17,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051930","count":3},{"id":"GO:0051482","count":3},{"id":"GO:0060427","count":3},{"id":"GO:0072224","count":3},{"id":"GO:0007626","count":3}]},{"hash":"946707234899273295","title":"Innate Immune Signaling and Cytokine Regulation","description":"The cluster shows strong enrichment for innate immune functions, including defense response to virus, innate immune response, TLR2 signaling, and NOD2 signaling, along with cytokine-related activities such as regulation and positive regulation of IL-6 production and dendritic cell cytokine production. The inclusion of cornea development and angiogenesis regulation hints at ocular immune privilege context, but the dominant pattern is innate immune sensing and cytokine modulation, justifying this label.","confidence":"Medium","size":19,"edges":17,"triangles":0,"max_degree":17,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0016525","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0002730","count":3}]},{"hash":"1046633046043168270","title":"Neural development and synaptic signaling","description":"The cluster shows several neural-specific terms, such as corpus callosum development, dopaminergic synaptic transmission, and positive regulation of synapse assembly, pointing to roles in neural development and synaptic function. Although other terms (redox homeostasis, apoptotic process) are present, they are less defining for the cluster\u2019s primary theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0022038","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0000902","count":3}]},{"hash":"13379988882909078","title":"Dendritic Spine Morphogenesis and Rac Signaling","description":"The cluster is dominated by terms related to actin cytoskeleton remodeling (ruffle and lamellipodium assembly) and neuronal spine development/morphogenesis, driven by Rac signaling, with hippocampus development supporting a neuronal maturation context. These together suggest Rac-mediated actin remodeling guiding dendritic spine formation in neurons.","confidence":"High","size":19,"edges":7,"triangles":0,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0097178","count":5},{"id":"GO:0010592","count":5},{"id":"GO:0061001","count":5},{"id":"GO:0016601","count":5},{"id":"GO:0045792","count":5}]},{"hash":"183767851788228922","title":"Mitochondrial Translation & tRNA Charging","description":"The most frequent terms point to translation and mitochondrial tRNA aminoacylation (valyl-, tryptophanyl-, and tyrosyl-), indicating a core role in mitochondrial protein synthesis. Other GO terms (xenobiotic transport, embryonic development, vasculogenesis) occur at low counts and are likely secondary or broader associations, but do not override the primary signal of mitochondrial translation machinery.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006855","count":2},{"id":"GO:0045910","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0001570","count":1}]},{"hash":"1513444808488423713","title":"Skeletal, cardiac, and neural development","description":"Most top GO terms cluster around developmental processes affecting the skeleton, heart, and nervous system (skeletal system development, heart development, embryonic cranial skeleton morphogenesis, nervous system development). The inclusion of axon fasciculation and Rho signaling supports a morphogenesis and neural development theme, with exocytosis regulation also aligning with developmental signaling. A few terms (DNA replication, amino acid starvation, pseudohyphal growth) appear as peripheral signals but do not override the central developmental theme.","confidence":"High","size":19,"edges":20,"triangles":5,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001501","count":17},{"id":"GO:0007507","count":16},{"id":"GO:0007399","count":16},{"id":"GO:0007124","count":16},{"id":"GO:0007266","count":16}]},{"hash":"1254874974710223395","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The cluster is strongly enriched for ubiquitin-dependent protein catabolic processes, SCF-dependent proteasomal degradation, and K48-linked ubiquitination, indicating a core function in proteolysis by the ubiquitin-proteasome system. A few terms related to transcription regulation and X chromosome inactivation appear less central but may reflect broader regulatory roles of ubiquitination. Overall, the shared theme is targeted protein degradation via ubiquitination.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0051865","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0070936","count":3}]},{"hash":"1782189195198095106","title":"Nutrient-starvation\u2013induced fungal pseudohyphal growth","description":"The top GO terms emphasize invasive and pseudohyphal growth triggered by glucose limitation, which is characteristic of nutrient-sensing morphogenesis in fungi. Although there are miscellaneous terms related to transcription and epigenetic marks, the core signal centers on a fungus undergoing filamentous growth under nutrient stress, supporting this label as representative of the cluster\u2019s function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001403","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007124","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0034729","count":2}]},{"hash":"1141249827797728939","title":"Motile cilium/axoneme assembly and left-right symmetry","description":"The top GO terms are dominated by motile cilium assembly and axonemal dynein complex assembly, plus determination of left/right symmetry, all pointing to ciliary/flagellar biogenesis and function. A few biosynthetic/process terms appear sporadic and don\u2019t align with the main ciliary theme, suggesting they are incidental annotations. Confidence that this label captures the cluster\u2019s core function is High.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044458","count":2},{"id":"GO:0070286","count":2},{"id":"GO:0007368","count":2},{"id":"GO:0052704","count":1},{"id":"GO:1903253","count":1}]},{"hash":"1440626690861774616","title":"Apoptosis and immune-vascular signaling","description":"This cluster shows enrichment for apoptotic regulation (neuron apoptosis, osmotic-stress\u2013induced apoptosis), immune-related terms (T cell homeostasis and regulation of T cell proliferation, I-kappaB phosphorylation), and vascular processes (negative regulation of angiogenesis and VEGF signaling) as well as wound healing and hypoxia response, suggesting a theme of stress-responsive signaling that links cell fate with immune and vascular remodeling. A few terms (e.g., flagellated sperm motility) appear as outliers. Overall, the label captures the dominant shared functions.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043525","count":2},{"id":"GO:0008627","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0046007","count":2}]},{"hash":"615036998378151692","title":"Unknown","description":"The top terms span a highly diverse set of processes\u2014from plant-specific traits like pollen hydration to nail development, alongside general metabolism and signaling terms (fatty acid biosynthesis, starch catabolism, signal transduction, protein kinase regulation, circadian rhythm). The lack of a unifying theme and the absence of connected edges make it unclear what common function ties this cluster together, so a single representative label isn\u2019t justifiable.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0009744","count":1},{"id":"GO:0009859","count":1},{"id":"GO:0035878","count":1},{"id":"GO:0006633","count":1}]},{"hash":"630599103520127368","title":"Neuronal signaling and axon regeneration","description":"Most GO terms point to nervous system processes, including synaptic vesicle endocytosis, peripheral nervous system axon regeneration, and pain response, with chloride transport supporting neuronal excitability. While there are some general cellular terms (DNA-templated transcription, ER protein folding), the neural-related terms predominate, suggesting the cluster centers on neuronal signaling and nerve repair functions.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0035212","count":1},{"id":"GO:0048488","count":1}]},{"hash":"171405118686433642","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":71,"triangles":103,"max_degree":16,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007568","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0006284","count":4},{"id":"GO:0006296","count":3},{"id":"GO:0006310","count":3}]},{"hash":"1739208524095958772","title":"Oxidative stress response and detoxification","description":"The top GO terms center on detoxification and redox balance (cellular oxidant detoxification, cellular redox homeostasis, glutathione metabolic process, toxin catabolic process), with additional signals pointing to stress responses and signaling (arsenic-containing substance response, EGFR-related signaling, prostaglandin biosynthesis, calcium-channel regulation) and differentiation cues. This combination suggests a core theme of antioxidant defense and detox pathways, modulated by signaling pathways that influence cell fate. Confidence: High","confidence":"","size":18,"edges":129,"triangles":508,"max_degree":17,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0098869","count":9},{"id":"GO:0045454","count":8},{"id":"GO:2000255","count":7},{"id":"GO:0001516","count":7},{"id":"GO:0071364","count":5}]},{"hash":"574040183756346983","title":"Mitochondrial respiration and Complex I assembly","description":"This cluster is best labeled by energy metabolism in mitochondria, since the strongest GO signals are electron transport chain and mitochondrial respiratory chain complex I assembly, indicating a core role in oxidative phosphorylation. Other terms (brain development, pantothenate biosynthesis, uracil catabolism) are less coherent with this theme, so the dominant pattern likely reflects mitochondrial respiration components.","confidence":"High","size":18,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0019556","count":2},{"id":"GO:0019557","count":2},{"id":"GO:0006212","count":1}]},{"hash":"1018248824026365935","title":"Neural development and synaptic regulation","description":"The GO terms cluster around neural development (spinal cord patterning, layer formation in cortex, motor neuron migration) and synaptic function (regulation of NMDA/AMPA receptor activity, PSD-95 clustering), suggesting a cohesive role in neural patterning and synaptic organization. A few terms (face morphogenesis, defense response) are peripheral noise but do not override the dominant neural theme.","confidence":"High","size":18,"edges":42,"triangles":40,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":1},{"id":"GO:0097477","count":1},{"id":"GO:2000310","count":1},{"id":"GO:0042832","count":1},{"id":"GO:0048265","count":1}]},{"hash":"289584756458956482","title":"Chromatin remodeling & transcription regulation","description":"These proteins are linked to chromatin remodeling and transcription control, with GO terms pointing to nucleosome mobilization/positioning, chromatin remodeling, and RNA Pol II\u2013related processes such as promoter start-site selection and transcription termination. Although some terms are obsolete, the common thread is nuclear chromatin modification/remodeling that influences transcription, rather than cytosolic functions.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":2},{"id":"GO:2000616","count":2},{"id":"GO:0001178","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0016584","count":2}]},{"hash":"2258574167147040287","title":"ER Stress Proteostasis","description":"The dominant GO terms point to protein quality control mechanisms activated by ER stress, including unfolded protein response, ER-associated degradation (ubiquitin-proteasome system), and protein refolding, plus regulation of translation under stress. These together indicate a cluster focused on maintaining protein homeostasis during ER stress, with some peripheral terms likely reflecting related cellular stress responses.","confidence":"High","size":18,"edges":61,"triangles":103,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0051259","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0035719","count":2}]},{"hash":"2038974363041659317","title":"Sterol and Fatty Acid Biosynthesis","description":"This cluster is dominated by GO terms for sterol and fatty acid production (ergosterol, cholesterol, unsaturated FAs, sphingolipid metabolism), plus lipid-rich tissue processes like myelin maintenance and sebaceous gland differentiation, suggesting a cohesive theme of lipid biosynthesis and membrane lipid metabolism. Some terms (nitric oxide, nitrate assimilation, mitochondrion inheritance) are less connected but do not override the lipid-centric pattern. ","confidence":"Medium","size":18,"edges":29,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":5},{"id":"GO:0006809","count":5},{"id":"GO:0006636","count":5},{"id":"GO:0032286","count":5},{"id":"GO:0001949","count":5}]},{"hash":"371332734577217788","title":"Germline Chromatin Remodeling and Dosage Compensation","description":"This cluster is dominated by GO terms tied to chromatin dynamics\u2014heterochromatin formation, chromatin remodeling and assembly, and localization to chromatin\u2014together with germline development processes like spermatogenesis and male gonad development, plus dosage compensation. The convergence on chromatin organization in germ cells and sex chromosome regulation suggests a cohesive role in chromatin state control during spermatogenesis and related developmental processes.","confidence":"High","size":18,"edges":85,"triangles":177,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":8},{"id":"GO:0007283","count":7},{"id":"GO:0051290","count":7},{"id":"GO:0008584","count":7},{"id":"GO:0000183","count":7}]},{"hash":"1692492214498565590","title":"Unknown","description":"The GO terms are highly heterogeneous, including plant meristem regulation, cerebellar neuronal development, neuronal response to glutamate, and various apoptotic/ER stress pathways, with no single cohesive function tying them together. This mix suggests the proteins in the cluster do not share a clear common biological role. Therefore, a specific, representative label cannot be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009934","count":2},{"id":"GO:1904721","count":1},{"id":"GO:0060702","count":1},{"id":"GO:1903298","count":1},{"id":"GO:1902236","count":1}]},{"hash":"2254630328497428258","title":"LDL receptor regulation","description":"The cluster\u2019s GO terms predominantly point to regulation and trafficking of LDL receptors and related lipoprotein receptor catabolic processes (negative/positive regulation of LDL particle receptor catabolic process, negative regulation of receptor recycling), suggesting a cohesive theme around lipoprotein receptor biology, with a few outliers like enkephalin processing and embryonic axis development that may be noise or cross-annotation.","confidence":"Medium","size":18,"edges":29,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":1},{"id":"GO:0010989","count":1},{"id":"GO:0032804","count":1},{"id":"GO:0030435","count":1},{"id":"GO:1905598","count":1}]},{"hash":"1719348740157227096","title":"DNA Repair and Damage Response","description":"The top terms point to DNA repair pathways (base-excision repair, nucleotide-excision repair, UV-damage excision repair) and DNA damage recognition, plus an apoptotic signaling pathway in response to DNA damage, indicating a DNA repair/damage-response module. Some transcription regulation and ubiquitin-proteasome\u2013related terms appear ancillary, but the dominant theme is DNA repair and damage signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":1},{"id":"GO:0070914","count":1},{"id":"GO:0000715","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0033683","count":1}]},{"hash":"1576642420144861693","title":"Embryogenesis with RA and PPAR Signaling","description":"The cluster's terms cluster around developmental processes (heart morphogenesis, lung saccule development, hemopoiesis) and signaling pathways involving retinoic acid and PPAR, suggesting a theme of embryonic development governed by RA and lipid signaling. While some terms (transposition, histone deubiquitination) are less directly related, the dominant signals point to developmental regulation via RA and PPAR pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032196","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0032526","count":1},{"id":"GO:0035359","count":1},{"id":"GO:0003007","count":1}]},{"hash":"685379018912930479","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning immune defense, chemokine/fractalkine production, general transcription regulation, tissue remodeling, several developmental processes (midbrain and exocrine pancreas), and multiple signaling pathways (Wnt and GPCR-PLC). There isn\u2019t a single clear functional theme linking most proteins, so a cohesive label isn\u2019t supported.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0050754","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0048771","count":1},{"id":"GO:0016055","count":1}]},{"hash":"1910197829821733526","title":"Ribosome Biogenesis and Translation Initiation","description":"The top GO terms cluster around ribosome and translation processes: maturation of LSU rRNA and formation of the translation preinitiation complex, with some regulation of translational frameshifting. The other terms appear more peripheral or annotation-noise, but the dominant theme ties to ribosome assembly and initiating translation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:2001125","count":6},{"id":"GO:0000463","count":6},{"id":"GO:0045143","count":6},{"id":"GO:0072520","count":6}]},{"hash":"1563332208661888703","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051568","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2}]},{"hash":"94431351370665750","title":"Golgi glycosylation and root development","description":"The top terms cluster around transport of sugar nucleotides into the Golgi lumen (UDP-glucose, GDP-fucose, phosphoenolpyruvate/triose phosphate transmembrane transport) and glycosylation processes (O-linked fucosylation, N-glycan fucosylation), with plant root development terms (lateral root development, root hair cell development) also represented. This suggests a theme of Golgi-associated glycosylation pathways that may influence root development in plants. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990536","count":1},{"id":"GO:0015786","count":1},{"id":"GO:0015713","count":1},{"id":"GO:0036085","count":1},{"id":"GO:0048527","count":1}]},{"hash":"951696056127411933","title":"Nuclear import and chromatin assembly","description":"The label reflects strong signals for nuclear import processes (NLS-bearing protein import into nucleus; ribosomal protein import into nucleus) and nuclear pore complex assembly, with a related emphasis on chromatin assembly during DNA replication. Additional terms hint at related regulatory and growth-related pathways (TORC1 signaling, GTPase regulation), suggesting a cluster focused on nuclear transport tied to chromatin and genome maintenance. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0060188","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0051292","count":2}]},{"hash":"190764010639143886","title":"Regulatory signaling pathways","description":"Top GO terms cluster around modulation and signaling cascades, including regulation of insulin receptor signaling, Rho/GTPase signaling, IP3/IP3 biosynthesis, PDGF response, and CDK activity, with additional links to innate immunity and development. This suggests the proteins act as regulators of diverse signaling pathways rather than a single, cohesive process, yielding a reasonable but not definitive label of regulatory signaling pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0032959","count":2}]},{"hash":"1494332180126524335","title":"Ribosome Biogenesis and Translation","description":"The cluster is enriched for translation-related GO terms across cytoplasmic and mitochondrial contexts, including translation, translational termination, and ribosomal large-subunit assembly, as well as preribosome maturation and positive regulation of ribosome biogenesis. This points to a cohesive theme centered on ribosome production and protein synthesis. The presence of antibiotic response and stringent response terms suggests adaptation to translational stress, which complements the core translation/biogenesis signal. A minor protein flavinylation term appears incidental to the main theme. Overall, the dominant function is ribosome assembly and translation machinery.","confidence":"High","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006415","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0032543","count":2}]},{"hash":"426517847077354878","title":"Mitochondrial translation and inner-membrane biogenesis","description":"The cluster shows strong enrichment for mitochondrial translation (GO:0006412) with several proteins linked to translation, plus related terms like cristae formation (GO:0042407), and protein insertion into the mitochondrial membrane (GO:0051204) as well as positive regulation of mitochondrial translation (GO:0070131). This combination points to a cohesive role in mitochondrial gene expression and inner-membrane assembly, rather than a general cytosolic translation or unrelated processes. Minor terms such as transcription regulation and phospholipid biosynthesis may reflect broader mitochondrial functions but do not override the core mitochondrial theme.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042407","count":1},{"id":"GO:0051204","count":1},{"id":"GO:0070131","count":1},{"id":"GO:0030007","count":1}]},{"hash":"1389424864298589667","title":"Redox Energy Metabolism","description":"Top GO terms in this cluster center on electron transfer and redox chemistry, including mitochondrial respiratory chain complex IV assembly, photosynthetic electron transport, methanogenesis, and cellular responses to hydrogen peroxide. While there are a few peripheral catabolic or biosynthetic terms, the dominant signal is energy production via redox reactions across diverse systems. Therefore, a concise and representative label is Redox Energy Metabolism.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0042426","count":1},{"id":"GO:0006214","count":1}]},{"hash":"222514900159712359","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":27,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0036444","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0051561","count":1},{"id":"GO:0006212","count":1}]},{"hash":"1165730259799854541","title":"Neuronal development and sensory signaling","description":"The cluster\u2019s top GO terms heavily emphasize neural structure and function\u2014dendrite morphogenesis, visual perception, and potassium ion transport\u2014suggesting a neuronal development and signaling theme. While cell cycle and DNA-related terms are present, they are common background processes in proliferating neural progenitors and do not outweigh the neuron-centric signals.","confidence":"Medium","size":17,"edges":108,"triangles":372,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":13},{"id":"GO:0007601","count":12},{"id":"GO:0006351","count":12},{"id":"GO:0043552","count":11},{"id":"GO:0048813","count":11}]},{"hash":"1768350397172777115","title":"Carbohydrate and Isoprenoid Metabolism","description":"The top GO terms combine carbohydrate-related processes (galactose, galactitol, galacturonate metabolism; carbohydrate phosphorylation) with isoprenoid/lipid biosynthesis (farnesyl diphosphate, mevalonate/MEP pathways, cholesterol). This suggests a cluster of proteins tied to general metabolism and synthesis of lipid precursors, with some regulatory elements linked to carbohydrate sensing. The theme is cohesive enough to justify a single label, though the set spans multiple related metabolic pathways rather than a single specific process.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":1},{"id":"GO:0042352","count":1},{"id":"GO:0010142","count":1},{"id":"GO:0000435","count":1},{"id":"GO:0046396","count":1}]},{"hash":"1293358499600647499","title":"RNA processing and ribosome biogenesis","description":"The cluster is dominated by terms linked to translation, ribosome biogenesis, and RNA maturation (rRNA and snRNA pseudouridine synthesis), suggesting a core theme around RNA metabolism and protein synthesis. A few outlier terms (innate immune response, antibacterial humoral response, cannabinoid biosynthesis) appear as single-term annotations, likely representing noise rather than a coherent functional module.","confidence":"Medium","size":17,"edges":18,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0019731","count":1},{"id":"GO:1901696","count":1},{"id":"GO:1901697","count":1}]},{"hash":"505283940524586935","title":"Neural development and neural tube formation","description":"The top GO terms emphasize neural and broader developmental processes, including neural tube closure, forebrain and spinal cord development, and skin development, indicating a neurodevelopmental/morphogenesis theme. Supporting terms like DNA-templated transcription and protein homooligomerization suggest transcriptional regulation and protein assembly typical of developmental programs, reinforcing a focus on neural development and tissue formation.","confidence":"High","size":17,"edges":12,"triangles":5,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":10},{"id":"GO:0051260","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0043588","count":8},{"id":"GO:0030900","count":6}]},{"hash":"1722575421057287059","title":"Transmembrane Transporters for Small Molecules","description":"The cluster is defined by GO terms that repeatedly point to transport across membranes for a variety of small molecules, including vitamins, sugars (arabinose, galactose), ions (sodium), nitrite, and xenobiotics, with an additional term related to neurotransmitter loading into synaptic vesicles. This pattern suggests proteins that function as membrane transporters or permeases handling diverse substrates. Although there are no observed protein-protein interactions in this cluster, the shared functional theme is clear.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0042891","count":3},{"id":"GO:1900754","count":2},{"id":"GO:0015739","count":2}]},{"hash":"238490163013309468","title":"DNA Damage Response and Cell Cycle Control","description":"The dominant GO terms point to DNA damage sensing and cell cycle regulation, including G1/S transition and mitotic intra-S checkpoint signaling, plus p53-mediated apoptotic signaling, suggesting the cluster centers on DNA damage response and cell cycle arrest. Related terms about ribosome rescue and ubiquitin-dependent degradation imply a proteostasis angle under stress. A few metabolic and differentiation terms are less clearly related and may reflect broader annotations, but the core theme is stress-induced control of the cell cycle and apoptosis.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0046256","count":1},{"id":"GO:1990116","count":1},{"id":"GO:0018937","count":1}]},{"hash":"1919237101305959665","title":"Plant developmental signaling and gene regulation","description":"The top GO terms point to plant-specific development and signaling (positive regulation of flower development; brassinosteroid-mediated signaling) with supporting roles in gene expression regulation (spliceosome-mediated splicing, histone methylation, ubiquitination). Despite some broader terms, the strongest coherence centers on plant development and transcriptional control, suggesting proteins involved in signaling and regulation during plant growth. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009911","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0045214","count":1}]},{"hash":"373868540429922440","title":"Unknown","description":"The GO terms span lipid receptor regulation (positive/negative regulation of LDL receptor\u2013related catabolic/recycling processes), neuropeptide processing (enkephalin), and more divergent developmental processes (zygotic axis) and sporulation. There isn\u2019t a single coherent functional theme tying all 17 proteins together, so a specific, representative label isn\u2019t justifiable.","confidence":"","size":17,"edges":19,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":2},{"id":"GO:0010989","count":2},{"id":"GO:0032804","count":2},{"id":"GO:0030435","count":2},{"id":"GO:1905598","count":2}]},{"hash":"2015093836170808491","title":"Lipid and Carbohydrate Catabolism","description":"This cluster is dominated by GO terms describing catabolic processes for multiple substrates, notably lipids (phosphatidylserine, diacylglycerol, monoacylglycerol) and carbohydrates (pectin, cellulose), suggesting a common theme of broad metabolic breakdown. A few terms touch signaling or autophagy, but the prevailing pattern is substrate-wide catabolism.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006660","count":1},{"id":"GO:0046340","count":1},{"id":"GO:2000124","count":1},{"id":"GO:0045490","count":1},{"id":"GO:0052651","count":1}]},{"hash":"1644221483372979930","title":"Innate Immune Ubiquitination and Proteasomal Regulation","description":"The top GO terms point to antiviral defense and innate immune signaling (defense response to virus, innate immune response) together with ubiquitin- and SUMO-related protein regulation (K63-linked ubiquitination, sumoylation, SCF-dependent proteasomal degradation, ERAD). This indicates a cohesive theme of ubiquitin-mediated control of immune signaling and protein turnover. The mitosis-related terms may reflect broader ubiquitin/SUMO roles across processes, but the primary signal here is immune defense linked to ubiquitin pathways. ","confidence":"High","size":17,"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:0031146","count":3},{"id":"GO:1903265","count":2},{"id":"GO:0070534","count":2}]},{"hash":"1918145740110707576","title":"Nuclear Gene Expression and Cell Cycle","description":"The top GO terms center on DNA-templated transcription, translation initiation, ribosome maturation, and mitotic processes (mitotic spindle assembly and chromosome segregation). This suggests the cluster reflects nuclear gene expression and cell division machinery, with some development/apoptosis signals as incidental terms.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0001731","count":2},{"id":"GO:2001125","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1555563267706034163","title":"Melanin biosynthesis and melanosome organization","description":"The cluster is dominated by pigmentation-related GO terms (pigmentation, melanosome organization, melanin biosynthetic process and its regulation), suggesting a pigment production/organization theme, with a few neural development terms present but less represented.","confidence":"High","size":17,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0002052","count":4},{"id":"GO:0032438","count":4},{"id":"GO:0006583","count":4}]},{"hash":"1805392097347787985","title":"Mammary gland development and epithelial proliferation","description":"Several terms indicate mammary gland biology, including mammary gland alveolus development and mammary gland epithelial cell proliferation, plus broader multicellular organism development terms. Wnt signaling and regulation of insulin receptor signaling suggest growth-regulatory pathways active during mammary development. Additionally, G1/S and G2/M cell cycle transitions and mitotic regulation align with proliferative expansion in developing mammary tissue. Collectively, the cluster seems to reflect a developmental program focused on mammary gland growth and epithelial proliferation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0060749","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0010389","count":2}]},{"hash":"3223235700794412","title":"Cytoskeletal dynamics and cell polarity","description":"Top terms point to cytoskeletal remodeling, Rho/GTPase signaling, cell shape and polarity, plus mitotic processes and vesicle transport, suggesting the proteins cluster around cytoskeleton-driven regulation of cell shape, division, and trafficking, with possible ties to neural development; the core theme is cytoskeleton regulation and polarity in cellular processes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031532","count":4},{"id":"GO:0043552","count":3},{"id":"GO:0071963","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006888","count":3}]},{"hash":"2184648070746144434","title":"Ubiquitin-Proteasome Response to Metal Stress","description":"This cluster is enriched for ubiquitin-dependent proteolysis and protein ubiquitination terms, including SCF-dependent proteasomal degradation, plus cellular responses to metals like arsenic, cadmium, and methylmercury. The common thread is activation of the ubiquitin-proteasome system and related stress signaling (including DNA damage and oxidative stress) under metal exposure, suggesting a cohesive proteolysis- and stress-centered function.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":7},{"id":"GO:0042787","count":4},{"id":"GO:0046685","count":4},{"id":"GO:1903378","count":4},{"id":"GO:1902916","count":4}]},{"hash":"889372172542194507","title":"Mitotic Division and Vesicle Trafficking","description":"The cluster shows strong signals for mitosis-related processes (cell division, mitotic cell cycle, mitotic spindle assembly, cell population proliferation) alongside membrane trafficking activities (COPII vesicle budding, Golgi-to-ER transport, vesicle docking) and protein ubiquitination, suggesting coordination between cell division and vesicle trafficking/regulation during mitosis.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0090114","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0008283","count":2}]},{"hash":"193547051542765187","title":"Riboflavin and flavin cofactor biosynthesis","description":"The top GO terms cluster around riboflavin, FMN, and FAD biosynthesis and related flavin metabolism, indicating a shared role in producing flavin cofactors. While other terms like various biosynthetic and regulatory processes appear, the flavin/cofactor biosynthesis theme is the strongest current signal. The lack of interactions among proteins also fits a collection of enzymes annotated with these biosynthetic functions rather than a single complex.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033864","count":1},{"id":"GO:0006747","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0009231","count":1},{"id":"GO:0009398","count":1}]},{"hash":"1754400728230603973","title":"Unknown","description":"The terms cover ribosome biogenesis and translation control, chromatin modification and chromosome segregation, development, cardiac apoptosis, and actin regulation, with no single cohesive function linking all proteins.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0001731","count":1},{"id":"GO:2001125","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0045143","count":1}]},{"hash":"921382290589035138","title":"Translational Regulation and Ribosome Biogenesis Under Stress","description":"The top GO terms cluster around translation and ribosome biogenesis (GO:0006412, GO:0042254, GO:0045903, GO:0045727) with related notes on translation regulation, ribosome export, and stress responses (UV, gamma radiation, antibiotic). This points to a coherent function group centered on protein synthesis machinery and its regulation, especially under cellular stress.","confidence":"High","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0045903","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006407","count":2}]},{"hash":"333285901568670740","title":"Amino acid and cofactor biosynthesis","description":"The top GO terms cluster around biosynthetic processes for amino acids (e.g., L-glutamate, beta-alanine) and cofactors (thiamine, lipoate), along with related central metabolism (2-oxoglutarate, dihydrolipoamide). This points to a metabolic biosynthesis theme rather than signaling or regulation, with redox homeostasis as a supporting context. ","confidence":"Medium","size":16,"edges":50,"triangles":73,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0043046","count":7},{"id":"GO:0045454","count":7},{"id":"GO:0009228","count":7},{"id":"GO:0019483","count":6}]},{"hash":"166438960045156633","title":"Amino acid catabolism and central carbon metabolism","description":"The cluster shows strong signals for amino acid breakdown (alanine and leucine catabolism, kynurenine catabolic process) and core energy pathways (pyruvate metabolism, TCA cycle, gluconeogenesis), plus liver development, which points to metabolism and liver function as the central theme. Notch signaling and antibiotic biosynthetic terms appear as outliers, but the dominant pattern supports a metabolic/energy-focused group. ","confidence":"Medium","size":16,"edges":115,"triangles":493,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":5},{"id":"GO:0007219","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0006099","count":3}]},{"hash":"1390924977551993086","title":"Mitochondrial Metabolism and Insulin Signaling","description":"This cluster is dominated by GO terms tied to mitochondrial function (alpha-ketoglutarate transport, malate-aspartate shuttle, mitochondrial nucleotide import, specific mitochondrial transport) and cellular responses to insulin/IGF stimuli, suggesting proteins that participate in mitochondrial metabolism and insulin-mediated growth/survival pathways. A couple of terms related to liver growth or pregnancy may reflect broader systemic roles but do not outweigh the mitochondrial/insulin theme. Confidence: Medium","confidence":"","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":13},{"id":"GO:0007565","count":12},{"id":"GO:0015742","count":12},{"id":"GO:1990314","count":12},{"id":"GO:0032869","count":12}]},{"hash":"1091655670705678683","title":"Cell Cycle and Chromosome Segregation","description":"The dominant GO terms point to DNA replication, centromere-associated chromatin assembly (CENP-A), and cell division, with supporting evidence from microtubule severing, all core to mitosis and chromosome segregation. Some vesicle trafficking terms are present but secondary to the main nuclear/cell-cycle signals. Therefore, label reflects the primary function of this cluster.","confidence":"High","size":16,"edges":74,"triangles":217,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0018279","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051301","count":4}]},{"hash":"1371449309848675817","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":26,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0019375","count":1},{"id":"GO:0015786","count":1},{"id":"GO:0034221","count":1},{"id":"GO:0036085","count":1},{"id":"GO:0046963","count":1}]},{"hash":"2199485542261991600","title":"Neuronal vesicle exocytosis and brain development","description":"The top GO terms are dominated by neural-related processes: regulation of synaptic vesicle exocytosis, brain development, and nervous system development, indicating the proteins are tied to neuronal signaling and brain formation. Other terms (ribosome biogenesis, mitotic cell cycle, GTPase regulation) are general cellular processes and do not override the neural theme. Overall, the cluster most consistently points to neuronal vesicle trafficking and brain development functions.","confidence":"High","size":16,"edges":41,"triangles":23,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:2000300","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0010796","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0006360","count":4}]},{"hash":"1710734931635873254","title":"Growth and membrane/cytoskeleton remodeling","description":"The Top Terms show a mix of cell growth-related processes (mitotic cell cycle, multicellular organism growth, ribosome biogenesis) and structural/trafficking activities (endosome-to-Golgi transport, plasma membrane tubulation, podosome assembly, cell morphogenesis, conjugation with cellular fusion, GTPase activity regulation). This suggests the cluster centers on growth-associated functions intertwined with membrane remodeling and cytoskeletal dynamics, rather than a single well-defined enzymatic pathway. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0035264","count":3}]},{"hash":"1979155497968261761","title":"Nucleolar rDNA Chromatin Organization","description":"The GO terms are dominated by nucleolar and rDNA-related processes: nucleolus organization, localization to nucleolar rDNA repeats, rDNA heterochromatin formation, and rDNA chromatin condensation, pointing to a role in nucleolar rDNA chromatin regulation. A few unrelated terms (fatty acid biosynthesis and courtship behavior) are present but sparse and do not define the cluster. ","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031030","count":1},{"id":"GO:0007000","count":1},{"id":"GO:1902543","count":1},{"id":"GO:0034503","count":1},{"id":"GO:0000183","count":1}]},{"hash":"1885684326003125272","title":"Membrane Protein Proteolysis and NFAT Signaling","description":"This cluster is driven by GO terms for membrane protein proteolysis in various contexts (ectodomain, intracellular domain, and ER-to-cytosol retrograde transport) and by positive regulation of the calcineurin-NFAT signaling cascade, plus general immune regulation. The presence of a spliceosome-related term and lithium response appears as noise, but the core theme centers on proteolytic processing of membrane proteins and downstream signaling relevant to immune pathways. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904211","count":1},{"id":"GO:0050776","count":1},{"id":"GO:0051533","count":1},{"id":"GO:0070886","count":1},{"id":"GO:0006509","count":1}]},{"hash":"731481313314657304","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms are dominated by ribosome biogenesis and rRNA processing (ITS1 cleavage, large subunit biogenesis), pointing to a shared role in ribosome assembly; the other terms are sparse and likely incidental noise.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0060992","count":1},{"id":"GO:0060907","count":1}]},{"hash":"2189087766255873601","title":"Ribosome biogenesis and translation initiation","description":"Most terms point to ribosome production and the initiation of translation (ribosome biogenesis, cytosolic ribosome assembly, and formation of the translation preinitiation complex). A couple of outlier terms (megagametogenesis, presynapse assembly, energy homeostasis, GTPase activity regulation) are less central but may reflect broader regulatory roles. Overall, the cluster is best described as ribosome biogenesis and translation initiation.","confidence":"High","size":16,"edges":117,"triangles":520,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0009561","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0042256","count":2}]},{"hash":"27669166423085888","title":"Neural development and cell division","description":"This cluster shows strong signals for neural development and signaling (neuron differentiation, Schwann cell development, excitatory postsynaptic potential, response to cocaine) alongside cell cycle and mitosis-related terms (DNA replication, G1/S transition, meiotic cell cycle, kinetochore localization). The proteins appear involved in neural differentiation and function as well as cell division processes, suggesting a dual role in nervous system development and proliferation regulation. ","confidence":"Medium","size":16,"edges":61,"triangles":105,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030182","count":7},{"id":"GO:0051301","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0034501","count":5},{"id":"GO:0051321","count":5}]},{"hash":"2284200947447608023","title":"Mitochondrial tRNA aminoacylation and translation","description":"The cluster is enriched for mitochondrial tRNA charging events (threonyl-, prolyl-, glycyl-, and related tRNA biosynthesis) and for translation and translational fidelity regulation, indicating a cohesive role in mitochondrial protein synthesis rather than other processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035751","count":2},{"id":"GO:0043524","count":2},{"id":"GO:0070159","count":1},{"id":"GO:0006433","count":1},{"id":"GO:0097056","count":1}]},{"hash":"99749059158234102","title":"Neuronal Calcium Signaling and Memory","description":"The cluster is enriched for terms related to neuronal signaling and memory, including calcium ion transport, excitatory postsynaptic potential, and both long-term and short-term memory, suggesting a cohesive theme of synaptic activity and plasticity. NF-kappaB signaling and intracellular signal transduction further support a role in activity-dependent gene regulation in neurons. A few outliers (e.g., viral transport and obsolete terms) exist, but the dominant pattern is synaptic calcium signaling linked to memory processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007616","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0006816","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0035556","count":2}]},{"hash":"777642043571050465","title":"ER-Golgi Vesicle Trafficking","description":"The top GO terms point to ER-to-Golgi vesicle transport, intra-Golgi and retrograde transport, Golgi ribbon formation, and vesicle fusion with the Golgi, plus protein targeting to vacuole. This forms a coherent theme of Golgi- and ER-centered vesicle trafficking and Golgi organization, with axonogenesis and Wnt signaling terms present but less central. Confidence in this labeling is high. ","confidence":"High","size":16,"edges":16,"triangles":1,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0050771","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0048280","count":2},{"id":"GO:0006623","count":2}]},{"hash":"1863876757160217053","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0009103","count":6},{"id":"GO:0042619","count":5},{"id":"GO:0009243","count":4},{"id":"GO:0006564","count":3}]},{"hash":"364312757166980906","title":"Ubiquitin-regulated immune signaling and antigen presentation","description":"The cluster centers on ubiquitin-related processes (deubiquitination and SCF-proteasome\u2013dependent degradation) together with multiple immune pathways (T cell receptor signaling, TNF signaling, Fc receptor signaling) and MHC I antigen processing/presentation, suggesting a cohesive module in which ubiquitin turnover modulates immune signaling and antigen presentation.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":11},{"id":"GO:0050852","count":10},{"id":"GO:0051437","count":9},{"id":"GO:0090090","count":9},{"id":"GO:0033209","count":9}]},{"hash":"1593623396691120763","title":"Synaptic vesicle trafficking and Golgi-ER transport","description":"The top GO terms cluster around vesicle trafficking in neurons, including synaptic vesicle recycling/endocytosis, anterograde vesicle transport, and bidirectional Golgi-ER transport, plus Golgi localization. This points to a cohesive function in neuronal vesicle handling and synaptic cycling, with neural development/behavior terms suggesting a neural context. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036465","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0006896","count":1},{"id":"GO:0048490","count":1}]},{"hash":"680755861164381659","title":"Cytokinin signaling and transcription in plants","description":"The top GO terms emphasize a cytokinin-activated signaling pathway together with DNA-templated transcription and protein kinase activation, suggesting a cohesive plant-specific module where cytokinin signaling drives transcriptional regulation and kinase-mediated responses. While other terms touch on seed growth and nuclear processes, the strongest signal centers on cytokinin signaling linked to transcription and kinase activity in plants.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0032147","count":2},{"id":"GO:0001731","count":1}]},{"hash":"1061287262158935205","title":"Unknown","description":"The listed GO terms span cell division and chromosome segregation, RNA splicing regulation, and cell migration, with no single dominant function; and the cluster has no edges, suggesting there is no cohesive functional module to label.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007059","count":1},{"id":"GO:0051455","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0000381","count":1},{"id":"GO:0040039","count":1}]},{"hash":"2137009338913689656","title":"Ubiquitin-Proteasome Regulation of Cell Cycle","description":"The cluster\u2019s top GO terms repeatedly point to ubiquitin-dependent proteolysis (including SCF-mediated ubiquitination) and protein ubiquitination, along with regulation of DNA replication initiation and mitotic G1 DNA damage checkpoint signaling. This suggests a core function in ubiquitin-proteasome\u2013mediated control of cell cycle progression and replication initiation, with some stress-related terms (methylmercury response, oxidative stress\u2013induced apoptotic signaling) reflecting broader proteostasis and stress signaling context.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":6},{"id":"GO:0031146","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0032088","count":4}]},{"hash":"30297828286459920","title":"TLR-Driven Innate Immunity and Proteasomal Regulation","description":"This cluster centers on Toll-like receptor signaling (MyD88-dependent and MyD88-independent) linked to innate immune activation and inflammation, with strong representation of ubiquitin-proteasome\u2013dependent protein turnover (ERAD and SCF pathways). The terms also cover macrophage activation, dendritic cell cytokine regulation, and defense against virus, suggesting a cohesive module where TLR signaling is coupled to proteasomal degradation to control immune responses.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0006954","count":3}]},{"hash":"2268736643743207089","title":"Meiotic Telomere Tethering and Chromosome Pairing","description":"The proteins are best characterized by terms centered on meiosis, especially telomere attachment to the nuclear envelope, telomere tethering at the nuclear periphery, and homologous chromosome pairing, with supporting references to nuclear migration and centrosome localization during meiosis. Some unrelated terms (e.g., sarcomere organization, collagen remodeling) may reflect background annotations but do not define the main theme. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090286","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0051642","count":1},{"id":"GO:0034398","count":1},{"id":"GO:0031022","count":1}]},{"hash":"1554510533290195625","title":"Steroidogenesis and oxylipin biosynthesis","description":"The top GO terms cluster around steroid hormone production (testosterone biosynthetic process, androgen metabolic process, aldosterone biosynthetic process) and related female gonad development, with oxylipin biosynthesis supporting lipid signaling. This points to a coherent theme of steroid hormone biosynthesis and lipid-derived pathways, even though a few terms reflect stress responses or other biosynthetic activities. ","confidence":"Medium","size":15,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0008585","count":5},{"id":"GO:0010193","count":5},{"id":"GO:0061370","count":5},{"id":"GO:0031408","count":5}]},{"hash":"137581426641429796","title":"Unknown","description":"The Top Terms span diverse processes (translation initiation, rRNA maturation, chromosome segregation, histone modification, actin capping, and development/apoptosis) with no clear shared function, and the network has no connections, suggesting a heterogeneous, non-cohesive cluster. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:2001125","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0045143","count":2},{"id":"GO:0072520","count":2}]},{"hash":"438409518920242785","title":"Immune signaling and cytoskeletal remodeling","description":"This cluster is dominated by immune-related GO terms (B cell receptor signaling pathway, innate immune response, NK T cell differentiation) and cytoskeletal dynamics (actin filament binding, substrate adhesion-dependent cell spreading). The heart and skeletal muscle development terms suggest broader tissue contexts, but the core signal points to immune signaling tied to cytoskeletal changes.","confidence":"Medium","size":15,"edges":20,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0034446","count":2}]},{"hash":"1047411472476690784","title":"Cytoplasmic translation initiation and ribosome assembly","description":"The cluster is enriched for GO terms tied to translation and initiation, including translation (GO:0006412), formation of translation preinitiation complex (GO:0001731), formation of cytoplasmic translation initiation complex (GO:0001732), and cytosolic ribosome assembly (GO:0002256), indicating proteins involved in cytoplasmic translation machinery and ribosome assembly. Some related terms on stress responses and cell cycle regulation appear as ancillary connections, but the dominant theme is translation initiation and ribosome assembly.","confidence":"High","size":15,"edges":19,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0001731","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0046898","count":1},{"id":"GO:0046677","count":1}]},{"hash":"2161515956147154118","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":14,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0045007","count":1},{"id":"GO:1901291","count":1},{"id":"GO:0006296","count":1},{"id":"GO:0043066","count":1}]},{"hash":"519320475049961315","title":"Mitochondrial fatty acid oxidation","description":"The GO terms cluster around mitochondrial lipid metabolism: long-chain fatty acid catabolic processes and beta-oxidation via acyl-CoA dehydrogenase/oxidase, with related import into the mitochondrial matrix and carnitine biosynthesis, plus ancillary tissue development terms (heart, liver) and steroid biosynthesis. This suggests a cohesive function focused on mitochondria-driven fatty acid oxidation and associated lipid pathways.","confidence":"High","size":15,"edges":10,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042758","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0006809","count":1},{"id":"GO:0033539","count":1}]},{"hash":"2017509513730305168","title":"Epithelial polarity and junction assembly","description":"The top GO terms point to epithelial cell polarity establishment, tight/bicellular junction assembly, and cytoskeletal processes like filopodium formation and cell spreading, suggesting a core theme of epithelial polarity and cell\u2013cell adhesion. Some apoptosis and neuronal terms appear less central, likely reflecting multi-function proteins, but the dominant signal supports polarity and junction formation.","confidence":"Medium","size":15,"edges":100,"triangles":395,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090162","count":5},{"id":"GO:0046847","count":5},{"id":"GO:0031321","count":5},{"id":"GO:0070830","count":5},{"id":"GO:1900026","count":5}]},{"hash":"1087883737249388236","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0071031","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0034498","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0032258","count":2}]},{"hash":"1541711345673741707","title":"Multilineage cell differentiation","description":"Top GO terms indicate differentiation across multiple cell types (mast cells, basophils, enterocytes, nephron tubule cells, ureteric bud, cardiac vascular smooth muscle) along with general RNA processing terms. This pattern suggests proteins involved in directing or regulating lineage specification during development across tissues, rather than a single pathway, with estrogen response and neuronal commitment terms supporting a broad differentiation/regulatory role.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0060374","count":3},{"id":"GO:0043627","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006397","count":2},{"id":"GO:0021902","count":2}]},{"hash":"1328288747641133444","title":"Cell Division and Vesicle Trafficking","description":"The cluster centers on mitosis and cytokinesis together with vesicle trafficking pathways, including MVB\u2013lysosome fusion and exosomal secretion, supported by related cell-cycle terms (cell cycle, metaphase alignment, abscission). Developmental context terms (follicle cell stalk formation, lens maintenance) may reflect tissue-specific roles of these processes, while a viral life cycle term could reflect broader host\u2013pathogen interaction contexts within these cellular pathways.","confidence":"High","size":15,"edges":21,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030713","count":3},{"id":"GO:0000920","count":3},{"id":"GO:0061763","count":3},{"id":"GO:0036438","count":3},{"id":"GO:0030447","count":3}]},{"hash":"1930861050936477669","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0015786","count":1},{"id":"GO:0034221","count":1},{"id":"GO:0036085","count":1},{"id":"GO:0046963","count":1}]},{"hash":"617006161932870914","title":"Ubiquitin-Proteasome Degradation","description":"The top GO terms center on ubiquitin-dependent protein catabolism via ERAD and SCF-dependent proteasomal degradation, pointing to a proteostasis-focused cluster. While additional terms touch on cell cycle, vesicle transport, and transcriptional regulation, these can be linked to coordinated protein turnover and quality control roles. Overall, the shared theme is degradation of proteins through the ubiquitin-proteasome system.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0031146","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0050830","count":3}]},{"hash":"2241218061216041354","title":"Unknown","description":"The Top Terms are highly diverse, spanning oxidative stress response, ER-stress\u2013driven translation, mitotic cell cycle progression, snoRNP assembly, photoreceptor protein localization, morphine response, and histone-related processes; with zero edges and only single-term annotations, there is no clear shared function tying the proteins together, so a coherent label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":1},{"id":"GO:1901215","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0007091","count":1},{"id":"GO:1903546","count":1}]},{"hash":"2168590608600071272","title":"Synaptic Trafficking and Cytoskeletal Regulation","description":"Top GO terms indicate receptor recycling and endosome size control, along with glutamatergic synaptic transmission and cytoskeletal regulation via Rho signaling and tubulin deacetylation. This suggests a cohesive theme of neuronal receptor trafficking coordinated with cytoskeletal dynamics that influence synaptic signaling, despite some obsolete or unrelated terms present. Confidence in this label is Medium.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0034968","count":1},{"id":"GO:0035023","count":1}]},{"hash":"860040376357955776","title":"Developmental signaling and cell-cycle control","description":"This cluster is annotated with terms tied to developmental patterning and morphogenesis (anterior/posterior pattern specification, blood vessel development) and cell-cycle/cytoskeletal processes (regulation of Rho signaling, cytokinesis, negative regulation of G1/S transition). While a few mitochondrial-related terms appear, the predominant signals point to developmental signaling pathways and control of cell division, suggesting a role in coordinated growth and tissue development. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0009952","count":2},{"id":"GO:0001568","count":2},{"id":"GO:0010867","count":1}]},{"hash":"360811223471387894","title":"Unknown","description":"The GO terms are highly heterogeneous, ranging from ubiquitin-dependent ERAD and mRNA splicing to LDL receptor regulation, stomatal morphogenesis, and vacuolar protein catabolism, with several terms marked obsolete, giving no single coherent function for the cluster. Therefore, no interpretable label can be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0010989","count":3},{"id":"GO:1905598","count":3}]},{"hash":"828527614286993724","title":"Diverse Metabolite Biosynthesis","description":"This cluster shows enrichment across multiple biosynthetic processes, including steroid/retinoid pathways (glucocorticoids, estrogens, retinoic acid, retinal), alkaloids, antibiotics, and PHB, suggesting a general metabolite biosynthesis module rather than a single specific function. The presence of an unrelated term like lung development may reflect annotation noise. Overall, the common theme is diverse metabolite biosynthesis.","confidence":"Medium","size":15,"edges":38,"triangles":50,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030324","count":9},{"id":"GO:0042619","count":9},{"id":"GO:0055114","count":9},{"id":"GO:0006704","count":8},{"id":"GO:0006703","count":8}]},{"hash":"1846869141778772968","title":"Actin-based cell migration and morphogenesis","description":"The top GO terms point to actin-driven protrusions (lamellipodium and filopodium assembly), GTPase activation, and enhanced cell spreading and adhesion, all central to cytoskeletal remodeling and cell movement. Developmental processes like midbrain morphogenesis and blood vessel remodeling suggest a morphogenetic role, while membrane-related terms indicate associated trafficking and membrane dynamics. Together, these terms describe a cohesive theme of actin cytoskeleton dynamics guiding cell migration and tissue morphogenesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0046847","count":2},{"id":"GO:1900026","count":2}]},{"hash":"2250646535057416247","title":"Unknown","description":"The terms span several disparate processes, including ER-Golgi vesicle transport, retrograde Golgi-ER transport, pigmentation, translation initiation and translational frameshifting regulation, ribosomal RNA maturation, chromosome segregation, histone methylation, seminiferous tubule development, and cardiac muscle cell apoptosis, with no single cohesive function tying them together. Therefore there is no clear representative theme for this cluster. ","confidence":"","size":14,"edges":11,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0043473","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0001731","count":2},{"id":"GO:2001125","count":2}]},{"hash":"1510160314637321843","title":"Dopaminergic signaling and gut motility","description":"These proteins show recurring GO terms tied to dopamine regulation (uptake, receptor signaling, metabolism) and downstream signaling (ERK, IP3) alongside intestine-specific functions (posterior midgut development, intestinal smooth muscle contraction). The convergence of dopamine regulation with gut motility suggests a coherent role in dopaminergic control of intestinal function, hence this label.","confidence":"Medium","size":14,"edges":44,"triangles":45,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0051586","count":2},{"id":"GO:0010513","count":2},{"id":"GO:0060160","count":1}]},{"hash":"570208516028276623","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":32,"triangles":35,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":4},{"id":"GO:0033617","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0045039","count":3},{"id":"GO:0072321","count":3}]},{"hash":"1119023455583943648","title":"Innate antiviral signaling and interferon production","description":"This cluster is dominated by GO terms for antiviral and innate immune responses (defense response to virus, innate immune response, response to dsRNA, TLR2 signaling, and positive regulation of interferon-\u03b1/\u03b2 production, plus dendritic cell cytokine regulation). These collectively point to an innate antiviral immune program with interferon signaling; a single cell-cycle term appears as a minor outlier but does not define the group\u2019s core function.","confidence":"High","size":14,"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:0045842","count":2},{"id":"GO:0002730","count":2},{"id":"GO:0034134","count":2}]},{"hash":"210252094882966114","title":"Unknown","description":"The GO terms are highly heterogeneous (angiogenesis, transcription, nuclear export regulation, metabolism, chemotaxis, and cocaine response) with several obsolete terms, so no single cohesive function links the proteins; connectivity is minimal, supporting an Unknown cluster.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001525","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0046826","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0045150","count":4}]},{"hash":"326584223656523959","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000463","count":7},{"id":"GO:0000466","count":6},{"id":"GO:0036265","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0000472","count":5}]},{"hash":"2144164495478803736","title":"Unknown","description":"The top GO terms span telomere maintenance, organ and tissue development (lung, root meristem), plant hormone signaling (auxin transport, cytokinin pathways), cell polarity (neuroblast, pericentriolar material localization), and stress response (hypoxia). Their diversity and lack of a single shared process or pathway suggest there isn\u2019t a cohesive functional theme binding all proteins; the sparse network (one edge, zero triangles) further supports this being a mixed set rather than a distinct functional cluster.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1905323","count":2},{"id":"GO:0060430","count":1},{"id":"GO:0043947","count":1},{"id":"GO:0045201","count":1},{"id":"GO:0080037","count":1}]},{"hash":"1986825509796824379","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:1990022","count":1},{"id":"GO:0044376","count":1},{"id":"GO:0021552","count":1},{"id":"GO:0002244","count":1}]},{"hash":"1535324010377834467","title":"Unknown","description":"The GO terms span various processes\u2014parathyroid and heart development, cell fate specification, signaling pathway regulation, podosome assembly, IGF and nitric oxide responses, and NMDA receptor clustering\u2014covering developmental biology, signal transduction, and cytoskeletal/synaptic organization without a single coherent theme. ","confidence":"","size":14,"edges":16,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060017","count":2},{"id":"GO:0007507","count":1},{"id":"GO:0035156","count":1},{"id":"GO:1903753","count":1},{"id":"GO:0043552","count":1}]},{"hash":"1423775421734697401","title":"Telomere maintenance and DNA replication regulation","description":"This cluster is strongly enriched for telomere-related processes (telomere maintenance via telomerase, telomere capping) and initiation of DNA-templated DNA replication, with supporting signals from mRNA processing and regulation of gene expression, plus some development and stress-response terms. The core theme seems to be genome maintenance and cell-cycle control, with ancillary transcriptional/post-transcriptional regulation and developmental signals, making a name that centers on telomere maintenance and replication regulation appropriate.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032212","count":5},{"id":"GO:0006397","count":5},{"id":"GO:1904355","count":4},{"id":"GO:0045736","count":4},{"id":"GO:0032298","count":4}]},{"hash":"1821083306804230645","title":"Unknown","description":"The top GO terms cover dopamine signaling regulation, heart and intestinal smooth muscle processes, prostaglandin response, TNF regulation, and pain regulation, with no single dominant function tying them together. The absence of network connectivity and the diverse themes support labeling as Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060160","count":1},{"id":"GO:0007497","count":1},{"id":"GO:0032720","count":1},{"id":"GO:0032962","count":1},{"id":"GO:0042053","count":1}]},{"hash":"1754546626674026309","title":"Cardiac morphogenesis and pacemaker cell differentiation","description":"The cluster's top GO terms cluster around heart development and rhythm control: sinoatrial node cell differentiation, cardiac septum morphogenesis, regulation and circadian control of heart rate, and ascending aorta morphogenesis. While transcriptional regulation and some skeletal muscle differentiation appear as well, the dominant theme is heart morphogenesis and pacemaker cell formation, giving a cohesive interpretation for the cluster.","confidence":"High","size":14,"edges":12,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":6},{"id":"GO:0045064","count":5},{"id":"GO:2001016","count":5},{"id":"GO:0071353","count":4},{"id":"GO:0060411","count":4}]},{"hash":"1232622551443823634","title":"Drosophila Development and Apoptosis","description":"Contains several development-related GO terms (embryonic syncytial blastoderm, heart and hemocyte development, nurse cell apoptotic process) and apoptosis regulation (neuron and nurse cell apoptotic processes), suggesting a theme of developmental progression with programmed cell death in fly tissues. A few metabolic terms (mitochondrial ribosome assembly, ethanol metabolism) are present but do not define the main function of the cluster.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061668","count":2},{"id":"GO:0006067","count":2},{"id":"GO:0042060","count":1},{"id":"GO:0001700","count":1},{"id":"GO:0007605","count":1}]},{"hash":"577710464626108420","title":"Ubiquitin-Proteasome-Mediated Degradation","description":"This cluster centers on protein ubiquitination and degradation pathways, including SCF-dependent ubiquitination leading to proteasomal catabolism, ERAD, autoubiquitination, and diverse ubiquitin linkages (K6, K11) plus neddylation. The presence of NER and cell division terms suggests broader roles of ubiquitin signaling in DNA repair and the cell cycle, but the dominant theme is ubiquitin-proteasome\u2013driven protein turnover.","confidence":"High","size":14,"edges":81,"triangles":260,"max_degree":13,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0031146","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0070911","count":8},{"id":"GO:0016032","count":8},{"id":"GO:0051865","count":8}]},{"hash":"681277350229033922","title":"Actin Cytoskeleton Assembly and Phagocytosis","description":"This cluster is dominated by GO terms for actin filament polymerization, actin bundle assembly, and cortical patch assembly/localization, plus phagocytosis, pointing to a cohesive group of proteins involved in actin cytoskeleton remodeling and endocytic uptake. A couple of terms (subtelomeric heterochromatin formation and serine biosynthesis) appear less related and may reflect secondary roles or annotation noise, but the central theme is actin-driven cytoskeleton dynamics and phagocytic processes.","confidence":"Medium","size":14,"edges":23,"triangles":15,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009437","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0051666","count":2},{"id":"GO:0006348","count":2}]},{"hash":"207745130849201872","title":"TORC1-regulated translation initiation and ER\u2013Golgi trafficking","description":"This cluster centers on TORC1 signaling, formation of translation preinitiation complexes, mRNA transport, and vesicle trafficking between the ER and Golgi, with supporting roles in GTPase regulation and protein oligomerization. The combination suggests a cohesive module linking growth signaling to protein synthesis and intracellular trafficking, despite the proteins not showing direct interactions in this network. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0008283","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0051260","count":4}]},{"hash":"774517096771212166","title":"Innate antiviral and inflammatory signaling","description":"Proteins in this cluster are enriched for defense response to virus, innate immune response, inflammatory response, and IL-1\u03b2 production, with involvement in canonical and non-canonical NF-kappaB pathways as well as TLR and NOD2 signaling. This suggests a cohesive role in antiviral innate immunity and NF-kB\u2013mediated cytokine signaling, with dendritic cell cytokine regulation as a component.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0043124","count":1},{"id":"GO:0006954","count":1},{"id":"GO:0032611","count":1}]},{"hash":"11066325107657261","title":"RNA Processing and RNA Turnover","description":"The top GO terms are dominated by RNA-related processes (mRNA processing, snoRNA catabolic process, rRNA processing regulation, and RNA editing), indicating the proteins primarily function in RNA maturation and turnover, with only a few structural terms (spindle/actin assembly) that are less central. Overall, the cluster appears tied to RNA processing and metabolism.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0090501","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0006397","count":2}]},{"hash":"1518168706869442079","title":"Mitochondrial and plastid gene expression & import","description":"The cluster centers on organelle gene expression, including mitochondrial translation regulation and mRNA processing/modification, plus protein import and inner-membrane organization in mitochondria. The presence of chloroplast/plastid transcription and RNA processing terms suggests a shared module coordinating gene expression and protein targeting in both mitochondria and plastids. ","confidence":"High","size":13,"edges":62,"triangles":147,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0070131","count":2},{"id":"GO:0097033","count":1},{"id":"GO:0097034","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0007007","count":1}]},{"hash":"2012743391446945898","title":"Membrane Solute Transporters","description":"The top GO terms are dominated by transport across membranes for a variety of substrates (phosphate, nitrite/nitrate, sodium ions, trehalose, urate, 4-hydroxyphenylacetate, etc.), with a neuronal term related to neurotransmitter loading, indicating the cluster profiles as diverse membrane transport proteins. A single lactose biosynthetic process term is present but does not override the overall transport-centric theme.","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":3},{"id":"GO:0006817","count":3},{"id":"GO:0005989","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0015707","count":3}]},{"hash":"479521169871270645","title":"Golgi Vesicle Trafficking and SNARE-Mediated Exocytosis","description":"The cluster is dominated by GO terms describing Golgi apparatus processes (ribbon formation, vesicle transport to/from Golgi, intra-Golgi transport, and Golgi-to-vacuole transport), SNARE complex assembly, and exocytic insertion of receptors at the postsynaptic membrane, with a link to synaptic potentiation. This points to a cohesive role in Golgi-dependent vesicle trafficking and SNARE-driven exocytosis at synapses.","confidence":"High","size":13,"edges":53,"triangles":108,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":8},{"id":"GO:0006888","count":8},{"id":"GO:0006891","count":8},{"id":"GO:0048280","count":8},{"id":"GO:0035493","count":7}]},{"hash":"101184712182963689","title":"Unknown","description":"The GO terms for this cluster are highly diverse, including cellulose catabolic, diacylglycerol and acetylcholine/choline metabolism, proteolysis, detoxification, and various developmental/immune signaling processes (endothelial migration, T cell costimulation, neuroblast differentiation, fear behavior). There isn\u2019t a single clear function or pathway that ties all proteins together, making it difficult to assign a cohesive label beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030245","count":6},{"id":"GO:0098869","count":5},{"id":"GO:0006508","count":5},{"id":"GO:0046340","count":4},{"id":"GO:0043542","count":4}]},{"hash":"476629063836364722","title":"Glycan and lipid biosynthesis","description":"The top GO terms are largely biosynthetic processes for carbohydrates and lipids, including lipopolysaccharide, glycogen, glycolipid, and sucrose biosynthesis, plus mycothiol biosynthesis. This points to a core theme of carbohydrate- and lipid-building pathways for the cluster. A couple of terms about environmental stress (flooding, water deprivation) are present but less cohesive with the core biosynthetic theme, so the label reflects the dominant pattern with moderate confidence.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009744","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0000902","count":2},{"id":"GO:0009247","count":2}]},{"hash":"1977254392734850907","title":"Ribosome Biogenesis and Translation","description":"The cluster centers on ribosome assembly and ribosomal subunit biogenesis (both large and small), export of ribosomal subunits, and cytoplasmic translation, with additional links to cell cycle and cell division, suggesting coordination between ribosome production and cell proliferation.","confidence":"High","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0000055","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":3},{"id":"GO:1903833","count":3},{"id":"GO:0042254","count":3}]},{"hash":"882459815178209031","title":"Cell Cycle Control and Ubiquitin-Mediated Proteolysis","description":"GO terms show a strong emphasis on mitosis and ubiquitin-dependent protein degradation (APC- and SCF-mediated processes, K11-linked ubiquitination, mitotic cell cycle, chromatin organization, ERAD), indicating coordination of chromosome segregation with targeted proteolysis. RNA methylation and ribosome biogenesis appear as supporting themes related to growth and protein synthesis but do not dominate the cluster. This suggests the core function is regulation of cell division through ubiquitin-proteasome pathways.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0036265","count":4},{"id":"GO:0042254","count":4},{"id":"GO:1902426","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0031146","count":4}]},{"hash":"1591038728697131267","title":"Mitochondrial ATP synthase assembly and activity","description":"The top terms center on proton-motive-force-driven ATP synthesis, cristae formation, and assembly of the mitochondrial ATP synthase complex, pointing to a mitochondria-focused energy-production function. The remaining immune- and development-related terms are sparse and may reflect cross-species annotations or unrelated processes, but do not override the mitochondrial signature. Therefore the cluster best matches mitochondrial ATP synthase biology.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":2},{"id":"GO:0042407","count":1},{"id":"GO:0033615","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0042496","count":1}]},{"hash":"1243623951200704129","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0006362","count":2},{"id":"GO:0006296","count":2},{"id":"GO:0070911","count":2}]},{"hash":"241534721330676516","title":"Actin Cytoskeleton Remodeling and Endocytosis","description":"The cluster shows multiple actin-related terms (barbed-end actin filament capping, actin crosslink formation, microspike assembly, podosome assembly) and caveolin-mediated endocytosis, indicating a theme of actin-driven cytoskeletal remodeling linked to membrane trafficking. Some terms (e.g., heart development) appear tangential or noisy, but the core signal points to actin dynamics and endocytosis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":1},{"id":"GO:0051016","count":1},{"id":"GO:0043552","count":1},{"id":"GO:0051764","count":1},{"id":"GO:0030035","count":1}]},{"hash":"914416566523542927","title":"Developmental patterning and morphogenesis","description":"The top GO terms point to morphogenesis across multiple tissues (roof of mouth, heart, uterus, hair follicle, cartilage) and axis formation (anterior/posterior, left/right), with apoptosis sometimes involved in development, indicating a broad developmental program rather than a single pathway.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0009952","count":2},{"id":"GO:0006915","count":2}]},{"hash":"2228657314795752310","title":"Microtubule-driven spindle dynamics and transport","description":"The top GO terms are centered on microtubule-based processes: nuclear migration along microtubules, spindle orientation and kinetochore attachment, minus-end\u2013directed microtubule sliding, and microtubule depolymerization, with additional references to microtubule-dependent dendritic transport and stress granule disassembly. This points to a cohesive theme of microtubule network organization driving division, transport, and cellular positioning across contexts.","confidence":"High","size":13,"edges":14,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030473","count":13},{"id":"GO:0051296","count":13},{"id":"GO:0099607","count":13},{"id":"GO:0048364","count":13},{"id":"GO:0010938","count":13}]},{"hash":"2111268979501828055","title":"Megakaryocyte and Platelet Development","description":"The top GO terms are dominated by platelet formation and megakaryocyte development, pointing to a cluster of proteins involved in megakaryopoiesis and platelet biogenesis. Other terms (embryonic development, osmotic stress response, and signaling regulation) appear ancillary and do not override the platelet/megakaryocyte theme. This supports a cohesive platelet-development cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071470","count":2},{"id":"GO:0030220","count":2},{"id":"GO:0070445","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0035855","count":2}]},{"hash":"1739603194188112771","title":"Metabolism and Redox Regulation","description":"The top GO terms concentrate on metabolic processes involving NAD+/NADP+ and polyphosphate metabolism, plus redox-related activities like oxidation-reduction and deglutathionylation, suggesting a common theme of cellular energy metabolism and redox control. Some terms about phosphorylation and nuclear transport/DNA binding are present but appear ancillary to the central metabolism/redox signal. Overall, the cluster seems best described as metabo-redox regulatory functions.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019674","count":1},{"id":"GO:0006741","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0006797","count":1},{"id":"GO:0006662","count":1}]},{"hash":"1628070733215653738","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0006367","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0034402","count":1}]},{"hash":"455541176602071659","title":"Embryonic Development and Cellular Stress Response","description":"This cluster shows enrichment for embryonic development terms (placenta development; embryonic process in female pregnancy) alongside multiple cellular stress response and transcription-related terms (unfolded protein response, oxidative/chemical stress responses, DNA-templated transcription, chromatin remodeling). The mix suggests proteins involved in regulating gene expression during development and managing cellular stress, rather than a single narrow function.","confidence":"Medium","size":13,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0039702","count":2},{"id":"GO:0070207","count":2},{"id":"GO:0001892","count":2},{"id":"GO:0000304","count":2},{"id":"GO:1903936","count":2}]},{"hash":"1846037241705346872","title":"Diverse metabolite biosynthesis","description":"Most terms describe biosynthetic or catabolic processes for diverse metabolites (prostaglandins, aldosterone, vancomycin, alkaloids), with additional environmental and nutritional response terms (immobilization stress, vitamin D, ozone, food). This points to a grouping around broad metabolic biosynthesis rather than a single pathway, though one term (retina vasculature development) may reflect annotation noise. Therefore, a label like Diverse metabolite biosynthesis captures the main theme. ","confidence":"Medium","size":13,"edges":14,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":3},{"id":"GO:0035902","count":2},{"id":"GO:0032342","count":2},{"id":"GO:0090350","count":2},{"id":"GO:0033072","count":2}]},{"hash":"1126695432639461622","title":"Endomembrane trafficking and protein localization","description":"This cluster shows a strong bias toward endomembrane system processes: positive regulation of ER exit, protein localization to endosome, vacuole organization, and various membrane transport activities (phospholipid translocation, xenobiotic transport). The RNA-related and repair terms appear as outliers, but the dominant theme is intracellular trafficking and membrane dynamics.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0045332","count":1},{"id":"GO:0070863","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0036010","count":1}]},{"hash":"935123834302376281","title":"Unknown","description":"The terms point to ribosome biogenesis and translation control (translation initiation and rRNA maturation), but also to nuclear processes like chromatin modification, chromosome segregation, and various developmental/apoptotic processes. The mix of disparate functions, plus obsolete GO terms, suggests no single coherent theme tying all proteins together, so a precise label cannot be confidently assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:2001125","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0045143","count":2},{"id":"GO:0072520","count":2}]},{"hash":"1821603218825743773","title":"Translation Initiation and Nutrient Transport","description":"This cluster shows strong signals for translation-related processes (formation of translation preinitiation complex; translation reinitiation) alongside a range of transport-related terms (branched-chain amino acids, cobalt, taurine, mercury, doxorubicin transport) and cytochrome complex assembly. The combination suggests a loose grouping around components involved in translational machinery with accompanying transport/uptake activities rather than a single cohesive pathway. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0007584","count":5},{"id":"GO:0001731","count":4},{"id":"GO:0000132","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0006824","count":3}]},{"hash":"2196071998854462743","title":"Cytoskeletal remodeling and mitosis regulation","description":"I named it Cytoskeletal remodeling and mitosis regulation because the top GO terms center on actin filament dynamics, GTPase activity regulation, and mitotic spindle assembly/orientation, all pointing to cytoskeletal control during cell division and morphological changes. A developmental term appears, but the dominant signal is cytoskeletal/mitotic processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030042","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0090307","count":2}]},{"hash":"1304318593522303142","title":"Multi-Substrate Transmembrane Transporters","description":"Most GO terms here point to transmembrane transport of diverse substrates (cobalt ions, branched-chain amino acids, doxorubicin, mercury, taurine, xenobiotics, teichoic acid, long-chain fatty acids into peroxisomes, peptide pheromone export). This suggests a cluster of transporter proteins with broad substrate specificity rather than a single substrate class. The lone outlier term, cytochrome complex assembly, may reflect ancillary cellular processes or annotation overlap rather than a core function of the cluster. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006824","count":2},{"id":"GO:0015803","count":2},{"id":"GO:1900753","count":2},{"id":"GO:0046689","count":2},{"id":"GO:0015734","count":2}]},{"hash":"440126398778075313","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms tied to ubiquitination and proteolysis (ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, autoubiquitination, ERAD-related activity), suggesting a core function in tagging and degrading proteins. While there are a few broader or unrelated terms in the list, the central theme across most terms points to ubiquitin-mediated protein turnover and quality control.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0070936","count":1},{"id":"GO:0060816","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0046621","count":1}]},{"hash":"179325186775324076","title":"Cytokine and growth-factor signaling responses","description":"The top GO terms point to cellular responses to cytokine and growth-factor stimuli (GM-CSF, M-CSF, TGF-\u03b2) and regulation of related processes such as IL-2 production, plus a few ancillary signaling terms (PKA/cAMP, cGMP) and downstream effects like modulation of cardiac contraction. This suggests the cluster captures proteins involved in signaling pathways activated by cytokines and growth factors, i.e., immune-related or growth-factor\u2013driven signal transduction. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:0006198","count":1},{"id":"GO:0010738","count":1},{"id":"GO:0019934","count":1},{"id":"GO:0042053","count":1}]},{"hash":"1891511141617133650","title":"Unknown","description":"The top GO terms span ubiquitin-dependent protein catabolic processes, sarcomere organization, plant-specific metabolism and signaling, neuronal and immune pathways, and viral latency release, showing no single cohesive function across the cluster. A precise, representative label cannot be determined from these terms alone.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0045214","count":2},{"id":"GO:1990390","count":2},{"id":"GO:0019762","count":2},{"id":"GO:2000312","count":2}]},{"hash":"312588178067225829","title":"TLR signaling and inflammatory cytokine production","description":"The top GO terms point to Toll-like receptor signaling (including TLR8 and MyD88-independent pathways), NF-\u03baB regulation, inflammatory response, and cytokine production (notably IL-1\u03b2) with dendritic cell cytokine regulation, indicating a coherent theme of innate immune signaling and inflammation. Some cilium-related terms are present, which may reflect broader signaling roles or annotation noise, but the dominant signal is TLR-driven inflammatory responses.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044458","count":1},{"id":"GO:0070286","count":1},{"id":"GO:0007368","count":1},{"id":"GO:0043124","count":1},{"id":"GO:0006954","count":1}]},{"hash":"1035921300894770690","title":"Cell signaling in immune and neuroendocrine responses","description":"The top GO terms point to cellular responses to a variety of stimuli (xenobiotic, TGF-beta, M-CSF) and related signaling pathways (cAMP/PKA, dopamine metabolism), suggesting a theme of cells modulating signaling in response to immune, hormonal, and neurochemical cues. Although some terms are obsolete, the overall pattern indicates integrated signaling across immune and neuroendocrine contexts.","confidence":"Medium","size":12,"edges":19,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0006198","count":2},{"id":"GO:0010738","count":2},{"id":"GO:0019934","count":2},{"id":"GO:0042053","count":2}]},{"hash":"306521232758780824","title":"Mitochondrial Metabolite Transport and Insulin Signaling","description":"The top GO terms point to mitochondrial transport and metabolite shuttling (alpha-ketoglutarate transport, malate-aspartate shuttle, pyrimidine import into mitochondrion), coupled with cellular responses to insulin/IGF stimulus, suggesting a mitochondria-centered cluster coordinating energy/metabolite flux with growth-factor signaling. Some related terms (necroptosis regulation, mitochondrial genome maintenance) reinforce a mitochondrial role in cell survival and metabolism, rather than a single isolated pathway. Pregnancy-related annotation is less informative but does not override the mitochondria-centric pattern.","confidence":"High","size":12,"edges":54,"triangles":124,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":8},{"id":"GO:0015742","count":8},{"id":"GO:1990314","count":8},{"id":"GO:0032869","count":8},{"id":"GO:0000002","count":8}]},{"hash":"1912448363915664822","title":"Nucleotide salvage and isoprenoid biosynthesis","description":"The GO terms show strong signals for pyrimidine nucleotide salvage (CTP, UMP, CMP salvage) and multiple isoprenoid biosynthetic processes (geranylgeranyl, farnesyl diphosphate, cholesterol biosynthesis) plus coenzyme A biosynthesis, indicating a metabolic module centered on nucleotide recycling and lipid/isoprenoid production. Minor terms like phosphorylation and protein transport are less defining. This supports a cohesive label focused on nucleotides and isoprenoid metabolism.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:0044211","count":3},{"id":"GO:0044206","count":3},{"id":"GO:0006238","count":3},{"id":"GO:0006206","count":3}]},{"hash":"1527704004219116722","title":"Cardiac calcium signaling and morphogenesis","description":"The top terms center on calcium release from the sarcoplasmic reticulum and regulation of RyR channels, which are key to cardiac muscle function. Supporting terms point to left ventricular and Purkinje cell\u2013cardiac signaling and morphogenesis, suggesting a cardiac development theme, with a few additional organ-development terms (kidney) that imply broader morphogenesis contexts. Overall, the cluster seems best described by calcium-dependent cardiac signaling and development.","confidence":"Medium","size":12,"edges":12,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0014808","count":4},{"id":"GO:0060315","count":4},{"id":"GO:0003151","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0003220","count":3}]},{"hash":"1900286467546247277","title":"Actin-based protrusion assembly and remodeling","description":"The cluster\u2019s top GO terms center on actin cytoskeleton dynamics, including barbed-end capping, crosslink formation, microspike assembly, and podosome assembly, which collectively point to actin-driven protrusions and remodeling. While terms like heart development, neurotrophin signaling, and LPS response hint at broader developmental and immune roles, the strongest cohesive theme is cytoskeletal remodeling and protrusive structure formation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0048011","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0035156","count":1},{"id":"GO:1903753","count":1}]},{"hash":"1714070060865833046","title":"Sodium and potassium ion transport and homeostasis","description":"The cluster is enriched for potassium and sodium ion export/import across the plasma membrane and intracellular potassium ion homeostasis, with additional signals related to cell volume regulation and salt stress. This points to a shared function in maintaining ion gradients across membranes, i.e., Na+/K+ transport and homeostasis, which underlie cellular excitability, volume control, and related signaling contexts (including cardiac conduction and neurotrophic signaling). ","confidence":"High","size":12,"edges":17,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":8},{"id":"GO:0030007","count":8},{"id":"GO:0036376","count":6},{"id":"GO:0098719","count":6},{"id":"GO:0009651","count":4}]},{"hash":"1080253727232845870","title":"Hormone signaling and homeostasis","description":"The cluster is enriched for hormonal processes (C21-steroid hormone biosynthesis; regulation of retinoic acid receptor signaling; jasmonic acid response) alongside tissue and systemic homeostasis (tissue homeostasis; renal system development; regulation of urine volume; response to water deprivation). A redox-related stress response (cellular response to hydrogen peroxide) complements these themes, suggesting a cohesive role in hormonal control of tissue maintenance and organismal homeostasis with associated stress signaling.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":10},{"id":"GO:0048385","count":10},{"id":"GO:0001894","count":10},{"id":"GO:0006700","count":10},{"id":"GO:0019568","count":10}]},{"hash":"879470115187815831","title":"Muscle structure and calcium signaling","description":"Prominent terms include sarcomere organization and negative regulation of ryanodine-sensitive calcium-release channel activity, which point to muscle architecture and calcium signaling. While a few terms touch on spermatogenesis, coagulation, and oxidative stress, the strongest shared theme across the cluster is muscle-related processes, making this label a reasonable, though not exclusive, fit.","confidence":"Low","size":12,"edges":13,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0030194","count":2},{"id":"GO:0031214","count":2},{"id":"GO:0070301","count":1},{"id":"GO:0006662","count":1}]},{"hash":"338065662837580712","title":"Unknown","description":"The terms include actin cytoskeleton and cilium assembly signals, which suggest a cytoskeletal/ciliogenesis theme, but also translation initiation, rRNA maturation, and chromosome segregation, implying multiple unrelated cellular processes. There is no single coherent function tying all terms together, so the cluster is Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0060271","count":3},{"id":"GO:0030042","count":3},{"id":"GO:0035729","count":2},{"id":"GO:0033137","count":2}]},{"hash":"297145570010693383","title":"Motile cilium assembly and axon guidance","description":"GO terms cluster around motile cilium and dynein assembly (left-right symmetry), plus several neuron axon guidance terms, suggesting a theme of ciliary motility linked to neuronal pathfinding. Some growth factor receptor signaling terms (HGF, VEGF) may modulate development but are secondary. Overall, this cluster appears to collect proteins involved in ciliary structure and function with roles in neuronal projection guidance.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007368","count":3},{"id":"GO:0044458","count":2},{"id":"GO:0070286","count":2},{"id":"GO:0097374","count":1},{"id":"GO:0048012","count":1}]},{"hash":"940187274410954073","title":"Magnesium homeostasis and ER protein folding","description":"Based on GO terms, the cluster is enriched for magnesium ion transport and homeostasis (magnesium transmembrane transport, intracellular Mg2+ homeostasis, cellular response to magnesium ion) and ER-related protein processing (protein folding in the endoplasmic reticulum, ER calcium ion homeostasis). A secondary signal is the respiratory electron transport chain, which can be Mg2+-dependent, but the dominant theme is Mg2+ handling and ER protein folding. Therefore this label captures the primary shared function of the proteins.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903830","count":1},{"id":"GO:0010961","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0032469","count":1}]},{"hash":"102887836381180861","title":"Ribosome Biogenesis and Transcription Regulation","description":"This cluster centers on translation and rRNA maturation (SSU/LSU rRNA processing) and on transcriptional regulation and chromatin remodeling, implying a shared theme of nuclear gene expression and ribosome assembly. Some terms (e.g., DNA restriction-modification, associative learning, and obsolete terms) may reflect annotation noise or cross-annotation, but the core signals point to ribosome biogenesis paired with transcriptional control.","confidence":"Medium","size":11,"edges":40,"triangles":72,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0045944","count":2}]},{"hash":"2166745890599284973","title":"Acetylation and Biosynthesis Pathways","description":"The top GO terms cluster around acetylation events (N-terminal serine/glutamic acid acetylation, spermine acetylation, histone H4 acetylation) alongside several biosynthetic processes (mycothiol, ectoine, glucosamine, melatonin). This suggests the proteins are linked to acetyl transfer and related metabolite biosynthesis, rather than a single fixed pathway. Some terms are obsolete, but the overall theme remains acetylation-linked metabolism.","confidence":"Medium","size":11,"edges":12,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0017198","count":7},{"id":"GO:0010125","count":5},{"id":"GO:0043967","count":5},{"id":"GO:0019491","count":5},{"id":"GO:0006041","count":5}]},{"hash":"2280070551119585482","title":"Protein catabolism and mitochondrial processing","description":"The terms show a strong emphasis on protein catabolic processes (protein catabolic process, hormone catabolic process, insulin catabolic process, bradykinin catabolic process) and regulation of proteolysis, with supporting signals of mitochondrial involvement (protein processing involved in protein targeting to mitochondrion, mitochondrial electron transport) and protein complex formation (homotetramerization/heterooligomerization). This points to a cohesive theme of protein turnover and mitochondrial handling.","confidence":"High","size":11,"edges":31,"triangles":53,"max_degree":8,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0042447","count":4},{"id":"GO:0045861","count":4},{"id":"GO:0018189","count":4},{"id":"GO:0006627","count":4},{"id":"GO:1901143","count":4}]},{"hash":"1085289367672006959","title":"Neuronal development and synaptic signaling","description":"This cluster is enriched for nervous system\u2013related terms: nervous system development, dendrite morphogenesis, regulation of synapse structural plasticity, and signaling pathways such as ephrin receptor signaling and canonical Wnt signaling. Although immune signaling terms appear, the dominant theme centers on neuronal development and synaptic connectivity and plasticity.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043552","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0048013","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0048813","count":3}]},{"hash":"5606938927518114","title":"Amino acid and carnitine transporters","description":"GO-term pattern is dominated by transmembrane transport of amino acids and carnitine (methionine, D-serine, D-alanine, L-lysine, L-arginine, and carnitine). Additional terms related to nitric oxide, macrophage activation, and osmotic/volume regulation appear as contextual associations but do not alter the clear transport-focused theme. Thus, labeling this cluster as amino acid and carnitine transporters captures the core function represented.","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044690","count":3},{"id":"GO:0006809","count":3},{"id":"GO:0006884","count":3},{"id":"GO:0042116","count":3},{"id":"GO:0042942","count":3}]},{"hash":"1361714463909939903","title":"Unknown","description":"The GO terms are heterogeneous, including muscle development/regeneration, stress response, axon growth regulation, phagocytosis, and vesicle transport, with no single cohesive function dominating. This makes it unclear what representative theme best groups these proteins together.","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006950","count":1},{"id":"GO:0034605","count":1},{"id":"GO:0042692","count":1},{"id":"GO:0048671","count":1},{"id":"GO:0030517","count":1}]},{"hash":"1181788937625163678","title":"ER Stress and Protein Quality Control","description":"The top GO terms cluster around ubiquitin-proteasome\u2013mediated handling of misfolded proteins, especially in the ER (ERAD, unfolded protein response), plus nuclear quality control and translation regulation in response to ER stress, indicating a shared role in proteostasis under stress. Some residual terms (e.g., DNA replication, hormone signaling) are ancillary annotations and do not define the main theme.","confidence":"High","size":11,"edges":42,"triangles":91,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0051259","count":4},{"id":"GO:0036494","count":4},{"id":"GO:0071374","count":4},{"id":"GO:0035719","count":4}]},{"hash":"21420680967410746","title":"Retinoid signaling and eye development","description":"This cluster is notably enriched for retinoic acid catabolic processes and retina vasculature development, which together point to a theme of retinoid metabolism influencing eye development. Other terms reflect broader hormonal and stress-responsive pathways, but the strongest direct link is to retinoid signaling and ocular development.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":3},{"id":"GO:0032342","count":3},{"id":"GO:0090350","count":3},{"id":"GO:0033072","count":3},{"id":"GO:0033280","count":3}]},{"hash":"2022871319774120644","title":"Mitochondrial Metabolism and Insulin Response","description":"This cluster is enriched for GO terms related to insulin and IGF signaling (cellular response to insulin stimulus; cellular response to IGF stimulus) alongside several mitochondrial metabolite transport and energy metabolism processes (alpha-ketoglutarate transport; malate-aspartate shuttle; pyrimidine nucleotide import into mitochondrion; mitochondrial L-ornithine transport). The convergence on mitochondrial transport/metabolism and insulin signaling strongly suggests a coherent theme around mitochondrial energy metabolism linked to insulin response, making the label appropriate.","confidence":"High","size":11,"edges":15,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":5},{"id":"GO:0015742","count":5},{"id":"GO:1990314","count":5},{"id":"GO:0032869","count":5},{"id":"GO:0000002","count":5}]},{"hash":"2170519815482230253","title":"Mitophagy Regulation","description":"The cluster shows strong representation of autophagy-related terms specifically targeting mitochondria, including autophagy of mitochondrion and positive regulation of mitophagy, indicating a coherent focus on mitochondrial autophagy processes. Other terms present (stress response, cell-cycle regulation) appear secondary and do not overshadow the mitophagy theme.","confidence":"High","size":11,"edges":41,"triangles":76,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":2},{"id":"GO:0010610","count":2},{"id":"GO:1903204","count":1},{"id":"GO:1903599","count":1},{"id":"GO:0000422","count":1}]},{"hash":"1132133648204763190","title":"Synaptic vesicle exocytosis and brain development","description":"The top GO terms are dominated by synaptic vesicle exocytosis, docking, and budding, along with brain development, indicating these proteins cluster around neuronal vesicle trafficking and neural development. While there are some bone-related terms and a few obsolete or unrelated categories, the strongest signal centers on synaptic vesicle dynamics in neurons.","confidence":"Medium","size":11,"edges":16,"triangles":7,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0007420","count":6},{"id":"GO:2000300","count":6},{"id":"GO:0006904","count":3}]},{"hash":"1012689891825776537","title":"Ribosome biogenesis and cell division","description":"The majority of top GO terms point to ribosome maturation and translation initiation (formation of translation preinitiation complex, rRNA maturation) and core mitotic processes (mitotic cell cycle, chromosome segregation), indicating a cluster centered on protein synthesis machinery linked to cell division. Some apoptosis terms in neural/glial contexts appear but do not define the main theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034349","count":3},{"id":"GO:0051402","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001731","count":2}]},{"hash":"1813336148653222306","title":"Diverse substrate membrane transporters","description":"GO terms cluster around transmembrane transport for xenobiotics, vitamins, sugars, nitrite, sodium, and neurotransmitter loading into synaptic vesicles, indicating a set of membrane transport proteins with broad substrate specificity and possible vesicular transport roles. This cohesion around membrane transport across diverse substrates supports a label of diverse substrate membrane transporters. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":5},{"id":"GO:1900754","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0015739","count":4},{"id":"GO:0035725","count":4}]},{"hash":"1379023938857554446","title":"Pseudouridine Synthesis Enzymes","description":"The strongest shared signal is RNA modification via pseudouridine synthesis, spanning mRNA, tRNA, and snRNA, suggesting the cluster comprises pseudouridine synthases or related RNA-modifying enzymes. Other terms (ubiquitination and learned behavioral responses) are present but far less representative of the core function, so the RNA modification theme best explains the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990481","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0051568","count":1}]},{"hash":"2176340440277591336","title":"Synaptic Vesicle Cycling and Spine Morphogenesis","description":"These proteins show strong signals for presynaptic vesicle exocytosis/endocytosis regulation, postsynaptic excitatory signaling, and dendritic spine morphogenesis, pointing to a neuronal synapse and spine remodeling theme. Membrane transport and actin-associated ruffle assembly further support synapse-related trafficking and structural changes; the substantia nigra development term suggests a brain-region context, while one term on mitotic cell cycle may be incidental. Overall, the cluster centers on neuronal synaptic function and spine dynamics.","confidence":"High","size":11,"edges":12,"triangles":1,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":4},{"id":"GO:0000060","count":3},{"id":"GO:0071806","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0060079","count":3}]},{"hash":"2268026543763619691","title":"Ribosome Biogenesis and Translation","description":"Based on the top GO terms, the cluster is dominated by translation-related processes (translation, tRNA aminoacylation, translational fidelity) and ribosome biogenesis and related nuclear export, pointing to a cohesive set of ribosome assembly and protein-synthesis machinery proteins. Other terms (cell cycle, stress responses, iron transport) are less represented and likely secondary. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0006435","count":1},{"id":"GO:0000055","count":1}]},{"hash":"1640604081824911057","title":"Protein and metabolite acetylation","description":"The top terms are dominated by acetylation processes (peptidyl-lysine, N-terminal acetylation, histone acetylation, and spermine acetylation), suggesting acetyltransferase activity as a unifying theme. Additionally, several biosynthetic terms (mycothiol, ectoine, glucosamine, melatonin) often involve acetylation steps, indicating broader acetylation-related metabolism across both proteins and small molecules.","confidence":"Medium","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":10},{"id":"GO:0017198","count":9},{"id":"GO:0010125","count":9},{"id":"GO:0043967","count":9},{"id":"GO:0019491","count":9}]},{"hash":"1495183610074043119","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0042176","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0090394","count":2}]},{"hash":"1274067808337173339","title":"Midbrain dopaminergic neuron differentiation","description":"This cluster shows explicit enrichment for midbrain dopaminergic neuron differentiation, with the GO term GO:1904948 appearing among the top terms. Additional terms point to neuronal maturation, signaling, and cytoskeletal organization (e.g., actin bundle assembly), suggesting a cohesive theme around neuronal differentiation and maturation in the dopaminergic lineage, supported by signals and calcium-related trafficking in neurons. The combination of a specific differentiation term plus related neuronal development processes makes this label representative of the cluster\u2019s function.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035751","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0014041","count":2},{"id":"GO:1904948","count":2},{"id":"GO:0051017","count":2}]},{"hash":"574109397379355218","title":"Multi-substrate membrane transporters","description":"The top GO terms point to transport activities across diverse substrates, including ions (sodium, nitrite/nitrate), small molecules (urate, trehalose, hydroxyphenylacetate), and even neurotransmitter loading into synaptic vesicles. While there is one biosynthetic term (lactose biosynthetic process) among the set, the dominant pattern is membrane transport. This suggests the cluster represents a group of various solute transporters at membranes.","confidence":"Medium","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":1},{"id":"GO:0006817","count":1},{"id":"GO:0005989","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0015707","count":1}]},{"hash":"2185104435281573399","title":"Vesicle trafficking in organ morphogenesis","description":"The cluster's GO terms cluster around intracellular protein transport and COPII vesicle coating regulation, along with lumen formation and morphogenesis of lung, trachea, and cardiovascular structures. The presence of antigen processing via MHC II also ties into endosomal/vesicular pathways, supporting a membrane-traffic\u2013centered function. Collectively, these terms suggest a shared role in vesicle trafficking processes that drive organ development and related cellular remodeling.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":3},{"id":"GO:0060982","count":2},{"id":"GO:0060463","count":2},{"id":"GO:2000189","count":2},{"id":"GO:0003400","count":2}]},{"hash":"1017023436223088738","title":"Unknown","description":"Top terms are spread across diverse processes (glycosylation, multiple transport and homeostasis terms, antibiotic biosynthesis, transcription regulation, development, and behavior) with no clear single function linking the proteins, and there are no edges or shared pathways to define a coherent theme. Confidence: None","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006488","count":1},{"id":"GO:0015811","count":1},{"id":"GO:0034488","count":1},{"id":"GO:0007625","count":1},{"id":"GO:0060905","count":1}]},{"hash":"2228406936901647509","title":"Dopamine metabolism and neural development","description":"The cluster contains dopamine catabolic process and cortical/neuron projection development terms, pointing to neural functions. It also includes metabolic and redox-related processes (2-oxoglutarate, beta-alanine, mitochondrial complex III assembly) that support neuronal energy and neurotransmitter biology.","confidence":"Medium","size":10,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042420","count":2},{"id":"GO:0034551","count":1},{"id":"GO:0060992","count":1}]},{"hash":"1628164543834568994","title":"Nucleotide Sugar Metabolism and N-linked Glycosylation","description":"This cluster is dominated by GO terms for the catabolism of nucleotide sugars (CDP, UDP, GDP, ADP) and the key process of protein N-linked glycosylation, pointing to a glycoprotein biosynthesis/processing theme. Other terms like pollen exine formation and sarcomere organization seem less connected and may reflect noise. Confidence: Medium","confidence":"","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0046706","count":2},{"id":"GO:0046032","count":2},{"id":"GO:0006487","count":2},{"id":"GO:0006256","count":2},{"id":"GO:0046712","count":2}]},{"hash":"1677379514822432761","title":"Transmembrane Transport of Diverse Substrates","description":"The GO terms show a clear enrichment for membrane transport processes across a variety of substrates (cobalt, branched-chain amino acids, xenobiotics, taurine, long-chain fatty acids into peroxisomes, teichoic acids) and related secretion, with few non-transport terms. This suggests the proteins function broadly as membrane transporters or components of transport pathways, rather than a single substrate-specific activity. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006824","count":2},{"id":"GO:0015803","count":2},{"id":"GO:1900753","count":2},{"id":"GO:0046689","count":2},{"id":"GO:0015734","count":2}]},{"hash":"1867585591440273890","title":"ER Stress Response and Proteostasis","description":"This cluster shows multiple GO terms tied to the unfolded protein response, translation regulation under ER stress, and nuclear/ubiquitin-proteasome\u2013related proteostasis. While there are other functions like RNA transport and DNA replication present, the strongest cohesive theme centers on ER stress signaling and protein quality control, suggesting a proteostasis-focused cluster with auxiliary cell cycle/nuclear functions.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0051259","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0035719","count":1}]},{"hash":"1753015521940101754","title":"Developmental signaling and centrosome regulation","description":"The cluster shows strong enrichment for broad development terms (heart, nervous system, skeletal) alongside centrosome/centriole-related processes (centrosome duplication, centriole replication) and DNA replication, suggesting a group of proteins involved in developmental signaling coupled with cell cycle and centrosome dynamics, with additional links to Rho signaling and exocytosis. This combination points to a theme of development-associated signaling intersecting with cell division machinery.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007507","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0007124","count":6},{"id":"GO:0007266","count":6},{"id":"GO:0045956","count":6}]},{"hash":"1512360225195005183","title":"Gene expression regulation and DNA replication","description":"This cluster shows enrichment for transcriptional regulation (negative regulation of RNA Pol II), epigenetic control (histone methylation), translation initiation/reinitiation, DNA replication, and ubiquitination, pointing to a group of proteins involved in coordinating gene expression control with genome maintenance and cell-cycle-related processes rather than a single, tight functional module.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000209","count":2}]},{"hash":"783988503117750327","title":"Glycosphingolipid biosynthesis and development signaling","description":"The top GO terms cluster around glycosphingolipid biosynthetic processes (globoside and mannosyl-inositol phosphorylceramide biosynthesis). A few terms touch on development- and signaling-related processes (embryonic cell shape regulation, hepatocyte growth factor receptor signaling, tissue remodeling), which can be linked to lipid-mediated modulation of signaling during development. Some terms are obsolete, which lowers certainty, but the dominant theme remains lipid biosynthesis with developmental signaling context.","confidence":"Medium","size":10,"edges":10,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0051999","count":1},{"id":"GO:0016267","count":1},{"id":"GO:0016476","count":1}]},{"hash":"698863989524686156","title":"Memory-Linked Synaptic Signaling","description":"The Top Terms center on memory (short-term and long-term memory) and neuronal signaling (excitatory postsynaptic potential, calcium ion transport), which together suggest proteins involved in synaptic transmission and memory formation. Supporting terms like regulation of GTPase activity and histone deacetylation point to regulatory layers that modulate signaling and gene expression relevant to plasticity. Some terms (gastrulation, mitotic cell cycle, aging) are less aligned and may reflect multifunctional proteins or annotation noise, but the core theme is memory-associated synaptic signaling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007614","count":3},{"id":"GO:0006816","count":2},{"id":"GO:0007616","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0016575","count":2}]},{"hash":"644256318473318987","title":"Vascular and GI development signaling","description":"The GO terms cluster around signaling pathways that govern development and function of vascular and digestive tissues (vascular permeability, heart and midgut development, intestinal smooth muscle contraction) and prostaglandin- and GTPase-mediated signaling, with minor ties to dopamine-related regulation in enteric contexts. This suggests a cohesive theme of cardiovascular\u2013gastrointestinal developmental signaling rather than a single enzymatic function. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0043114","count":2},{"id":"GO:0060160","count":1},{"id":"GO:0007497","count":1},{"id":"GO:0032720","count":1}]},{"hash":"1699788940844154829","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045492","count":1},{"id":"GO:0052889","count":1},{"id":"GO:0016042","count":1},{"id":"GO:2000344","count":1},{"id":"GO:0051292","count":1}]},{"hash":"741203414075521407","title":"Neural anti-inflammatory and oxidative detoxification","description":"This cluster shows strong enrichment for anti-inflammatory regulators (negative NF-kB, TNF, IL-1\u03b2), prostaglandin/COX pathway activity, nitric oxide aspects, and oxidative detoxification, with an additional signal for oligodendrocyte development. The common theme is neural/glial contexts where inflammatory signaling is dampened and oxidative defense is emphasized.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":6},{"id":"GO:0001516","count":5},{"id":"GO:0043124","count":4},{"id":"GO:0032720","count":4},{"id":"GO:0035732","count":4}]},{"hash":"1869427561567144586","title":"Nutrient-responsive transcription regulation","description":"The dominant terms describe RNA polymerase II\u2013mediated transcription and its regulation, especially in response to nutrients and metabolic signals (carbon source, oleic acid, nitrogen catabolite). Some metabolism-related processes appear, but the core theme is transcriptional control linked to nutrient status.","confidence":"Medium","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035948","count":3},{"id":"GO:0060947","count":3},{"id":"GO:0061415","count":2},{"id":"GO:0035961","count":2}]},{"hash":"739923571504466247","title":"Mitochondrial Translation and Respiratory Complex Assembly","description":"The top GO terms cluster around mitochondrial protein synthesis (mitochondrial translation, cytoplasmic translation, ribosomal large subunit assembly) and mitochondrial respiratory chain complex II assembly, suggesting proteins involved in ribosome biogenesis and mitochondrial translation as well as assembly of mitochondrial respiratory complexes. Some obsolete or development-related terms appear, but the dominant signal is mitochondrial translation and complex assembly.","confidence":"Medium","size":9,"edges":17,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0034553","count":1},{"id":"GO:0010259","count":1}]},{"hash":"2227615196353970261","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by translation and ribosomal large subunit biogenesis/assembly terms, indicating a core role in protein synthesis. A few cell cycle and neural development terms are present but substantially less represented, so the primary function aligns with ribosome-related processes.","confidence":"High","size":9,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042273","count":2},{"id":"GO:0010458","count":1},{"id":"GO:0060041","count":1},{"id":"GO:0021554","count":1}]},{"hash":"1206364804851983834","title":"Spliceosome-Mediated RNA Processing","description":"The top terms center on mRNA splicing via the spliceosome, spliceosomal complex and snRNP assembly, plus related RNA processing steps (tRNA processing, decapping/deadenylation). This points to a cohesive cluster of proteins involved in RNA maturation and splicing rather than other pathways; the ABA response term appears ancillary to the main theme.","confidence":"High","size":9,"edges":31,"triangles":59,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0000245","count":4},{"id":"GO:0006369","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4}]},{"hash":"1878767257138785301","title":"Cytoskeletal Dynamics and Vesicle Trafficking in Morphogenesis","description":"Top GO terms point to tubulin complex assembly and vesicle trafficking (exocytosis, synaptic vesicle budding), with several morphogenesis-related processes (dendrite morphogenesis, trabecula morphogenesis, osteoclast development). This suggests a core theme of cytoskeletal organization and membrane trafficking driving cell shape and development, with some broader cellular infrastructure signals (nuclear envelope organization, ribosomal export). The label captures the central function of coordinating cytoskeletal dynamics and vesicle trafficking in morphogenesis.","confidence":"Medium","size":9,"edges":12,"triangles":3,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007021","count":4},{"id":"GO:0006904","count":3},{"id":"GO:0070142","count":3},{"id":"GO:0036035","count":3},{"id":"GO:0043552","count":3}]},{"hash":"74728035539597165","title":"Unknown","description":"The top GO terms are diverse and largely unrelated (protein stabilization, proteolysis, collagen catabolic process, chromatin organization, various methylation processes, glomerular filtration, etc.), with no shared biological pathway or process tying the 9 proteins together. The lack of edges or coherent functional theme makes it impossible to assign a meaningful, specific label.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050821","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0035551","count":1}]},{"hash":"1788235710699993859","title":"Bacterial transcription-translation coupling under stress","description":"The cluster is dominated by GO terms for translation (initiation) and transcription-related processes (DNA-templated termination and transcription antitermination), which point to bacterial transcription-translation coupling. Additional terms for antibiotic and metal ion/amino acid transport suggest a stress response context, aligning with regulation of gene expression under chemical stress. Dendrite morphogenesis appears incidental. Overall, the set coherently highlights bacterial gene expression control under stress conditions.","confidence":"Medium","size":9,"edges":9,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0048813","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0031564","count":2}]},{"hash":"1988637116399525002","title":"Histone deacetylation and transcriptional repression","description":"The GO terms cluster around deacetylation processes (histone H3, peptidyl-lysine, Hsp90) and negative regulation of transcription, pointing to a chromatin-modifying, HDAC-driven repression module; a few terms are obsolete but the core theme is consistent.","confidence":"High","size":9,"edges":16,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":4},{"id":"GO:0060766","count":4},{"id":"GO:0032204","count":2},{"id":"GO:0010621","count":2},{"id":"GO:0051038","count":2}]},{"hash":"141998918500718117","title":"Mitotic Exit and Proteasomal Regulation","description":"These proteins are annotated with mitosis-related terms such as exit from mitosis, G2/M transition, and chromosome segregation, and they are linked to SCF-dependent ubiquitin-proteasome\u2013mediated protein degradation, suggesting a role in mitotic control and proteostasis. While there are also terms for DNA repair and other processes, the strongest signals point to mitotic progression and targeted proteolysis.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010458","count":1},{"id":"GO:0070911","count":1},{"id":"GO:0007275","count":1},{"id":"GO:0007059","count":1},{"id":"GO:0045910","count":1}]},{"hash":"1333505609375163245","title":"Developmental transcription and nuclear transport","description":"The top GO terms point to regulation of transcription and nucleocytoplasmic transport (DNA-templated transcription; positive regulation of protein export from the nucleus) and cell-cycle-related processes (centrosome cycle; spindle checkpoint\u2013related regulation), with links to development (heart development; dendrite morphogenesis) and prostaglandin signaling. This suggests a cluster of proteins coordinating gene expression and nuclear transport in a developmental context, with supporting mitotic and signaling roles.","confidence":"Medium","size":9,"edges":17,"triangles":9,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0036290","count":3},{"id":"GO:0071380","count":3},{"id":"GO:0007507","count":3}]},{"hash":"632731387269325881","title":"Cardiovascular and neuromuscular development","description":"The cluster's top GO terms center on heart development, angiogenesis, and myoblast fusion, with axonogenesis and neural plasticity (long-term potentiation) alongside responses to muscle activity, indicating a coordinated set of processes governing muscle/heart tissue development and neural connectivity.","confidence":"High","size":9,"edges":28,"triangles":50,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0007520","count":5},{"id":"GO:0060291","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0010800","count":5}]},{"hash":"398561849096206567","title":"RNA processing and translation initiation regulation","description":"The top terms cluster around mRNA splicing, mRNA export, preinitiation complex formation, and eIF4F assembly, all pointing to post-transcriptional RNA processing and control of translation initiation. This suggests a coherent role in RNA maturation and initiation of protein synthesis, justifying a combined label.","confidence":"High","size":9,"edges":33,"triangles":66,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":7},{"id":"GO:0048026","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0097010","count":4},{"id":"GO:1905663","count":4}]},{"hash":"2141993352887071052","title":"Nuclear RNA and ribosome export","description":"The top GO terms cluster around nuclear-cytoplasmic transport: mRNA export, ribosomal subunit export, and import of snRNPs into the nucleus, suggesting a shared theme of nucleocytoplasmic trafficking and processing with links to transcription regulation and mitosis/ciliogenesis. A divergent term like phosphatidylcholine biosynthesis may be an annotation artifact rather than indicating a different core function. ","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":8},{"id":"GO:0006656","count":6},{"id":"GO:0006608","count":6},{"id":"GO:0060188","count":6},{"id":"GO:0000122","count":6}]},{"hash":"1170310088349516982","title":"Detox and Catabolic Metabolism","description":"The top GO terms cluster around detoxification and catabolic degradation, with multiple entries for toxic-substance response, redox processes, and various catabolic pathways (triglyceride, uracil, nicotine) as well as proteolysis. Although a few terms relate to signaling or migration, the dominant pattern is metabolic breakdown and xenobiotic response, suggesting a functional theme of detox and catabolic metabolism.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0019433","count":3},{"id":"GO:0006212","count":2},{"id":"GO:0060244","count":2}]},{"hash":"1505380234629229559","title":"Cross-Organ Morphogenesis","description":"The top terms show heart development, dendrite morphogenesis, and bronchus morphogenesis, pointing to morphogenesis across multiple tissues. Supporting signaling terms (protein trans-autophosphorylation; prostaglandin response) suggest developmental signaling accompanying tissue remodeling. Some cell-cycle/spindle-check terms appear but don\u2019t define a single organ, so the overarching theme is tissue morphogenesis with associated signaling across organs.","confidence":"Medium","size":9,"edges":26,"triangles":33,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036290","count":9},{"id":"GO:0071380","count":9},{"id":"GO:0007507","count":9},{"id":"GO:0043552","count":9},{"id":"GO:0007098","count":9}]},{"hash":"477214302320563899","title":"Amino acid and osmolyte transporters","description":"The top GO terms are dominated by specific transporter activities: taurine, choline, glycine betaine, and general amino acid transport, plus related processes like protein complex oligomerization, all pointing to transporter proteins handling osmolytes and amino acids. While a few other terms (ER stress translation initiation, tRNA import, DNA replication) are more general cellular processes, the strongest theme across the cluster is transport of amino acids and osmolytes, justifying this label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032781","count":3},{"id":"GO:0015734","count":2},{"id":"GO:0006865","count":2},{"id":"GO:0015871","count":2},{"id":"GO:0031460","count":2}]},{"hash":"1766233416915797724","title":"Golgi\u2013Endosome Vesicle Trafficking","description":"The top GO terms are dominated by intracellular transport, vesicle docking/fusion, Golgi ribbon formation, endosome-to-Golgi retrograde transport, endocytic recycling, and Golgi vesicle transport, indicating a cohesive role in Golgi/endosome\u2013associated vesicular trafficking. A single outlier term about neuroblast proliferation does not disrupt this core theme.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0006906","count":1},{"id":"GO:0090161","count":1},{"id":"GO:0048278","count":1},{"id":"GO:0042147","count":1}]},{"hash":"1545825252557587189","title":"Neuronal development and oxidative stress response","description":"This cluster shows enrichment for nervous system-related terms, including nervous system development and positive regulation of neuron projection development, suggesting a neuronal context. It also includes cellular responses to hydrogen peroxide, indicating an oxidative stress dimension. While other terms touch on endocytosis and immune regulation, the strongest cohesive signal is neuronal development paired with oxidative stress response, hence the label. ","confidence":"Medium","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0070301","count":3},{"id":"GO:0010976","count":2},{"id":"GO:0002762","count":2},{"id":"GO:0051259","count":2}]},{"hash":"1984005413780459817","title":"LDL receptor trafficking and neuropeptide processing","description":"The terms cluster around regulation of LDL receptor\u2013related processes (lipid receptor catabolic activity, receptor recycling) and neuropeptide-related functions (enkephalin processing, nerve growth factor production), suggesting a theme of receptor trafficking coupled with neuropeptide signaling. A few development-related terms appear but seem incidental to the main signal. ","confidence":"Low","size":8,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":1},{"id":"GO:0010989","count":1},{"id":"GO:0032804","count":1},{"id":"GO:0030435","count":1},{"id":"GO:1905598","count":1}]},{"hash":"2301289723921125914","title":"Central metabolism and nucleotide catabolism","description":"The GO terms cluster around core energy metabolism and nucleotide turnover: glycolysis, 2-oxoglutarate and lipoate/dihydrolipoamide metabolism, beta-alanine biosynthesis (CoA-related), and uracil/thymidine catabolism, suggesting proteins focused on energy metabolism and nucleotide degradation. A few terms on membrane potential regulation or mercury detox are peripheral and do not override the main metabolic theme.","confidence":"High","size":8,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042391","count":3},{"id":"GO:0050787","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0006214","count":2}]},{"hash":"282224907007614165","title":"Methylation-Regulated Developmental Chromatin","description":"This cluster shows a strong emphasis on methylation processes (N-terminal glycine methylation, rRNA methylation, and peptidyl-lysine methylation/dimethylation) and chromatin-related activity (rDNA heterochromatin formation), alongside several vertebrate developmental terms (floor plate development, somitogenesis, amacrine cell differentiation, lung vasculature development) and transcription. The combination suggests proteins involved in methylation-based regulation of chromatin and gene expression during development, rather than a single, narrow function.","confidence":"Medium","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0018023","count":3},{"id":"GO:0018027","count":3},{"id":"GO:0000183","count":3}]},{"hash":"1130713989435018763","title":"Ribosome and Translation Regulation","description":"The top terms are dominated by translation-related processes, including general translation, cytoplasmic and mitochondrial translation, ribosome disassembly, and various steps of elongation and termination. Several terms point to regulatory roles in translation fidelity and efficiency (positive regulation of translation/elongation, selenocysteine incorporation). Together they indicate a cluster of proteins involved in ribosome function and control of protein synthesis, with a possible annotation artifact for antibiotic response.","confidence":"High","size":8,"edges":24,"triangles":34,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0002184","count":2},{"id":"GO:0014009","count":2},{"id":"GO:2000767","count":2}]},{"hash":"113003644202741723","title":"Unknown","description":"The terms are highly heterogeneous, spanning apoptotic signaling, stress responses, transcription regulation, immune defense, and several organism- and tissue-specific development terms (insects and mammals), with no connecting pathway or shared function evident and no edges linking proteins. This makes a coherent, specific label unlikely.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":3},{"id":"GO:1904576","count":2},{"id":"GO:0010691","count":2},{"id":"GO:0061614","count":2},{"id":"GO:0042832","count":2}]},{"hash":"2000106472611368615","title":"Insulin signaling and energy metabolism with redox balance","description":"This cluster is enriched for insulin-related processes (negative regulation of insulin secretion; response to insulin) together with core energy pathways (glycolysis; fatty acid beta-oxidation; carnitine catabolic process). The inclusion of cell redox homeostasis and xenobiotic response suggests a link between energy metabolism and cellular stress/redox balance. Taken together, the proteins likely function in insulin-regulated metabolic control, coupling glucose and lipid metabolism with redox status. ","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046676","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0032868","count":2},{"id":"GO:0006096","count":2}]},{"hash":"583010966755404999","title":"Metabolism and Signaling Regulation","description":"The proteins cluster around multiple metabolic processes (fatty acid, retinol/retinoic acid, and D-xylulose 5-phosphate biosynthesis) while also showing regulatory terms (extracellular negative regulation of signal transduction, response to lipopolysaccharide, and blood pressure regulation). This points to a group of metabolic enzymes with broader roles in signaling and immune-related regulation, rather than a single, cohesive pathway.","confidence":"Medium","size":8,"edges":11,"triangles":4,"max_degree":5,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:1901159","count":4},{"id":"GO:0006633","count":4},{"id":"GO:0045777","count":4},{"id":"GO:0033859","count":4},{"id":"GO:0006069","count":4}]},{"hash":"701543558695577610","title":"Immune and muscle signaling regulation","description":"The top GO terms point to modulation of multiple signaling pathways (Rho/Ras, IP3) together with immune-related processes (B cell differentiation and BCR signaling) and muscle-related events (myoblast fusion), plus calcium-dependent lysosome exocytosis. This suggests a cohesive theme of signaling regulation across immune and muscle contexts, despite some functional diversity. ","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0009395","count":3},{"id":"GO:0032959","count":3},{"id":"GO:0034351","count":3},{"id":"GO:0046580","count":3}]},{"hash":"447347718559266666","title":"Unknown","description":"The Top Terms are highly diverse, including insecticide response, TNF signaling regulation, protein deglycosylation, spindle pole body duplication, rRNA maturation, regulation of neurotransmitter secretion, and cellular responses to toxins, plus obsolete terms. This mix does not converge on a single clear function or pathway, suggesting either noisy annotations, multi-functional proteins, or multiple unrelated processes grouped together. Without a cohesive theme, a concise functional label cannot be assigned beyond Unknown.","confidence":"","size":8,"edges":22,"triangles":31,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0017085","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0006517","count":4},{"id":"GO:0030474","count":4},{"id":"GO:0014070","count":4}]},{"hash":"293800724680299758","title":"mRNA processing and translation initiation","description":"This cluster centers on mRNA maturation and expression initiation, with repeated signals for mRNA export from the nucleus, regulation of mRNA splicing and splice-site recognition, formation of the translation preinitiation complex, and assembly of eukaryotic translation initiation factor 4F. Additional terms about mRNA stabilization and regulation of translational initiation reinforce a cohesive theme around post-transcriptional processing and the start of translation, despite a couple of noisy obsolete terms. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0048026","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0097010","count":2},{"id":"GO:1905663","count":2}]},{"hash":"806897213168412159","title":"Neural Calcium Signaling and Synaptic Plasticity","description":"The top GO terms cluster around neuronal signaling: calcium ion transport, excitatory postsynaptic potential, intracellular signal transduction, cellular response to electrical stimulus, and regulation of short-term neuronal synaptic plasticity, all pointing to calcium-dependent signaling and synaptic modulation in neurons. While a couple of terms (oocyte maturation, osteoclast proliferation, fungicide response) are less related, the dominant themes support a neural signaling/plasticity role.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060992","count":2},{"id":"GO:0006816","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0065009","count":2},{"id":"GO:0051930","count":2}]},{"hash":"937748040127350650","title":"RNA Pol III Transcription Machinery","description":"Most terms point to RNA polymerase III transcription and its preinitiation complex assembly, plus 5S rRNA transcription by Pol III, which suggests the cluster centers on Pol III transcriptional machinery. The remaining terms reference hormonal signaling and muscle differentiation, which may reflect broader cellular responses or annotation noise; however the Pol III transcription theme is the strongest signal.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000999","count":1},{"id":"GO:0042791","count":1},{"id":"GO:0035914","count":1},{"id":"GO:0001041","count":1},{"id":"GO:0001009","count":1}]},{"hash":"1330445473092194552","title":"Thymus morphogenesis and T cell tolerance","description":"Based on the GO terms, the cluster is most clearly tied to thymus epithelium morphogenesis and peripheral T cell tolerance induction, indicating a focus on thymus-related development and T cell immune regulation. Additional terms related to organ development and transcriptional regulation suggest broader developmental control in these tissues, with a few general cell-cycle/chromatin terms reflecting common regulatory processes in development. Therefore, the cluster best represents thymus development and T cell tolerance, with a moderate level of confidence given some terms are non-specific. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":2},{"id":"GO:0048513","count":1},{"id":"GO:2000791","count":1},{"id":"GO:0070562","count":1},{"id":"GO:0097536","count":1}]},{"hash":"422893429119477424","title":"Fungal carbon-source transcription regulation","description":"This cluster is dominated by GO terms describing regulation of transcription from the RNA polymerase II promoter in response to carbon sources (nonfermentable carbon source, oleic acid, nitrogen catabolite activation, etc.), along with fungal-specific metabolic processes such as ergosterol biosynthesis, sterol import, and aflatoxin biosynthetic process. The convergence on transcriptional regulation in response to nutrients, especially in a fungal context (ergosterol and aflatoxin pathways), suggests a cohesive theme of nutrient-responsive transcription control in fungi.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061415","count":1},{"id":"GO:0035961","count":1},{"id":"GO:0035969","count":1},{"id":"GO:2001158","count":1},{"id":"GO:0045122","count":1}]},{"hash":"2118302941240198759","title":"Unknown","description":"The top GO terms are highly disparate (lipid A biosynthesis, mitochondrial DNA repair, glycogen regulation, myelination, meiotic DSB formation, kinetochore-microtubule attachment, extrinsic apoptotic signaling, cardiac hypertrophy, blood vessel branching, and cocaine response), with no clear shared function or pathway. There are no edges linking the proteins, so a cohesive, specific label cannot be inferred.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":3},{"id":"GO:0097552","count":3},{"id":"GO:0005979","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0010780","count":2}]},{"hash":"2087943675238048461","title":"Sterol and lipid biosynthesis regulation","description":"This cluster centers on lipid and membrane metabolism, with multiple terms for ergosterol/sterol biosynthesis (including regulation), unsaturated fatty acid and sphingolipid metabolism, and lipid-related tissue differentiation (myelin maintenance, sebaceous gland differentiation). These cohesive themes point to membrane lipid biosynthesis and homeostasis as the core function, though a couple of terms (nitrate assimilation, mitochondrial inheritance) are less tightly connected and may reflect broader metabolic links.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":2},{"id":"GO:0006809","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0001949","count":2}]},{"hash":"2143487127732878753","title":"Metabolic and cell-cycle signaling proteins","description":"This cluster mixes core metabolic processes (carbohydrate metabolism, fatty acid biosynthesis, gluconeogenesis, transsulfuration, hydrogen sulfide production) with regulatory/interaction features (protein kinase activation, protein tetramerization, regulation of mitotic transition, nuclear import). The co-occurrence of metabolism-centric terms with signaling and cell-cycle related terms suggests proteins that participate in metabolism while also engaging in regulatory or signaling roles, justifying a combined label.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0032147","count":6},{"id":"GO:0005975","count":6},{"id":"GO:0019346","count":6},{"id":"GO:0051289","count":6},{"id":"GO:0030071","count":6}]},{"hash":"1241628759640177367","title":"Proteostasis and Stress Response","description":"The terms point to protein quality control and turnover (stress granule disassembly, proteasome assembly, SCF complex disassembly, autophagosome maturation) and linked stress adaptations, including ubiquitin-related processes and mitochondrial/autophagy-related regulation (ER polarization, mitochondrial complex III assembly, mtDNA replication, respiration). This cohesive theme fits a cluster centered on how cells manage damaged/misfolded proteins and adapt metabolism under stress.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":3},{"id":"GO:0070682","count":2},{"id":"GO:1990171","count":2},{"id":"GO:1903715","count":2},{"id":"GO:0061166","count":2}]},{"hash":"913937334102829725","title":"Neurodevelopment and auditory function","description":"These proteins show enrichment for neural development terms (brain development, heart development, sensory perception of sound, neuron apoptotic regulation) with supporting cellular processes (ribosome biogenesis, ER-Golgi transport, GTPase regulation, protein homooligomerization, cell division, glucocorticoid response). The prominent neural and auditory-related themes suggest a neurodevelopmental/sensory function cluster, with non-neural terms likely reflecting general cellular machinery active during development.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043525","count":2},{"id":"GO:0006888","count":2}]},{"hash":"261532964845141497","title":"Flower and Inflorescence Development Regulation","description":"The cluster is dominated by GO terms related to plant development, especially flower development, inflorescence development, and regulation of flowering timing (vegetative-to-reproductive transition), indicating a cohesive theme around flowering processes. A few non-plant terms appear, but the overarching signal is clearly about floral development.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000160","count":2},{"id":"GO:0009911","count":1},{"id":"GO:0060409","count":1},{"id":"GO:0010951","count":1},{"id":"GO:0009910","count":1}]},{"hash":"1351389509203281581","title":"Biosynthesis and metabolic stress response","description":"Top terms indicate a common theme of biosynthesis and metabolism, including galactose metabolism, phenylpropanoid and anthocyanin biosynthesis, and colanic acid biosynthesis, along with related oxidation-reduction processes and nitrogen utilization regulation. There are a couple of outliers (vasculogenesis/angiogenesis and valyl-tRNA aminoacylation), but the dominant signal points to biosynthetic metabolism and stress-related responses. ","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006808","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006012","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009718","count":2}]},{"hash":"1306945535429493100","title":"Mitochondrial protein import and respiration","description":"The dominant GO terms point to protein import into the mitochondrial matrix and inner membrane, insertion into the inner membrane, and components of the electron transport chain and respiration (including respirasome assembly and aerobic respiration). A chloroplast stromal import term appears, but the core pattern centers on mitochondrial protein handling and energy production, with translation also aligning to mitochondrial function. Overall, the cluster reflects mitochondrial protein import/assembly coupled to respiration.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":3},{"id":"GO:0045039","count":3},{"id":"GO:0030150","count":3},{"id":"GO:0045037","count":2},{"id":"GO:0032094","count":2}]},{"hash":"2012142079570317260","title":"Retinoic acid signaling and nose development","description":"The strongest terms point to retinoic acid signaling (GO:0048384; GO:0071300) and nose development (GO:0043584), with related patterning, suggesting a theme of RA-driven craniofacial development. While other metabolic terms appear, the RA/nose-related terms provide a coherent, specific functional context for the cluster.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0015976","count":7},{"id":"GO:0006537","count":7},{"id":"GO:0048384","count":7},{"id":"GO:0009450","count":7},{"id":"GO:0019544","count":7}]},{"hash":"664534583332698061","title":"Nuclear proteostasis and replication","description":"The terms cluster around nuclear functions: unfolded protein response and heat-related stress, nuclear protein quality control by the ubiquitin-proteasome system, tRNA import into the nucleus, and DNA replication, with supporting roles for protein complex oligomerization and ATP-dependent activity regulation. Although some terms are obsolete, the dominant theme is nuclear proteostasis coupled with genome maintenance. ","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032781","count":3},{"id":"GO:0097428","count":3},{"id":"GO:0051259","count":3},{"id":"GO:0035719","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1061745165401805302","title":"Fatty acid and sphingolipid metabolism and adipogenesis","description":"The majority of top GO terms point to lipid metabolism\u2014monounsaturated fatty acid biosynthesis, sphinganine/sphingosine and cholesterol esterification\u2014and one term indicates adipocyte differentiation (white fat cell differentiation). While a couple terms are less related (e.g., tarsal gland development, photoinhibition), the shared theme is lipid biosynthesis/metabolism coupled with fat cell development, supporting this label.","confidence":"High","size":7,"edges":8,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903699","count":3},{"id":"GO:0034435","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0010205","count":3},{"id":"GO:0033561","count":3}]},{"hash":"1248630701611538893","title":"Ribosome biogenesis and translation initiation","description":"The top GO terms are dominated by rRNA maturation for both small and large subunits and formation of the translation preinitiation complex, plus negative regulation of translational frameshifting. This points to a coherent theme of ribosome assembly and early translation control. A few other terms (chromatin modification and some developmental processes) appear less consistently and may reflect broader cellular roles or annotation noise, but the strongest signal centers on ribosome biogenesis and translation initiation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0001731","count":2},{"id":"GO:2001125","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0045143","count":2}]},{"hash":"320746484254375420","title":"Cardiolipin Regulation and Lipid Trafficking","description":"Most of the top GO terms point to mitochondria and lipid biology: positive regulation of cardiolipin metabolic process, lipid localization, and SREBP signaling, along with positive regulation of mitochondrial DNA replication and membrane raft localization. This suggests a coherent theme of mitochondrial lipid regulation and lipid trafficking within membranes, with some additional terms like toll-like receptor signaling and podocyte development likely reflecting broader regulatory connections or dataset noise rather than a distinct functional module.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1900210","count":7},{"id":"GO:0045861","count":7},{"id":"GO:0052547","count":7},{"id":"GO:0034141","count":7},{"id":"GO:0032933","count":7}]},{"hash":"1561685640598902615","title":"Nervous system development and dendrite morphogenesis","description":"The top GO terms are strongly centered on nervous system development and dendrite morphogenesis, with supporting signals like Wnt signaling and centrosome/cell cycle processes, suggesting these proteins contribute to neuronal development and related cellular remodeling.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":2},{"id":"GO:0010571","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0048701","count":2}]},{"hash":"58355419636015436","title":"Unknown","description":"The top GO terms are scattered across metabolism (phosphatidylcholine, sterol, cobalamin, resorcinol biosynthesis) and various stress/immune-related responses (immobilization stress, interleukin-1 response, cellular senescence, tumor cell response), plus protein modification terms, with no clear unifying function or interactions (no edges). This makes it difficult to assign a coherent, representative label for the cluster.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018012","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0006656","count":1},{"id":"GO:0030961","count":1},{"id":"GO:0009236","count":1}]},{"hash":"252183902198539525","title":"Genome integrity and chromatin regulation","description":"The represented terms cluster around genome maintenance and chromatin dynamics: nucleotide-excision repair, error-free translesion synthesis, mitotic exit, ubiquitin-dependent protein turnover, and heterochromatin formation, including meiotic telomere clustering. These point to a cohesive theme of maintaining genome stability and regulating chromatin structure, with some outlier terms (e.g., peroxisome import) that are less central to nuclear genome maintenance but do not override the core pattern.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0045141","count":7},{"id":"GO:1901487","count":7},{"id":"GO:0016558","count":7},{"id":"GO:0070911","count":7},{"id":"GO:0070987","count":7}]},{"hash":"2005257288221114299","title":"Vesicle Trafficking and Endosome-Golgi Transport","description":"Based on the dominant GO terms, the cluster centers on vesicle docking/exocytosis, regulation of vesicle size, and transport between endosomes and the Golgi, indicating a core vesicle trafficking module. Other terms (development, migration, immune response, gene regulation) appear less cohesive with the main theme, suggesting peripheral or context-dependent roles. Therefore, the label reflects the primary shared function of these proteins.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006904","count":1},{"id":"GO:0010738","count":1},{"id":"GO:0097494","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0036035","count":1}]},{"hash":"1875361493831352591","title":"Ubiquitin-Dependent TNF-NF-\u03baB Signaling","description":"These proteins show a pattern of ubiquitination-related processes (protein ubiquitination, K6-linked ubiquitination, histone ubiquitination) together with immune signaling pathways (adaptive immune response, TNF-mediated signaling, I\u03baB phosphorylation leading to NF-\u03baB activation) and regulation of RIG-I signaling. The common theme is ubiquitin-mediated control of TNF/NF-\u03baB\u2013driven immune responses, with supportive hints from histone-related ubiquitination.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090073","count":3},{"id":"GO:0002250","count":2},{"id":"GO:0039536","count":2},{"id":"GO:0016567","count":2},{"id":"GO:1903265","count":2}]},{"hash":"1178719094895660614","title":"Plant defense responses and ER secretory trafficking","description":"These proteins are tied to plant immune responses (systemic acquired resistance; defense against fungi and bacteria; response to herbivore) and to the secretory pathway (ER localization and COPII vesicle budding), suggesting a role in producing and trafficking defense-related proteins within the plant secretory system.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009627","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0042742","count":1},{"id":"GO:0080027","count":1},{"id":"GO:0070972","count":1}]},{"hash":"1337815204142185487","title":"Post-translational modifications in immune signaling","description":"Enriched terms center on protein ubiquitination and sumoylation, with immune-related regulatory processes such as T-helper cell differentiation and RIG-I signaling, suggesting a theme of PTMs modulating immune pathways. Although several terms are obsolete and a few are unrelated, the core pattern ties ubiquitin/SUMO modification to immune signaling regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0045623","count":1},{"id":"GO:0060157","count":1},{"id":"GO:0033280","count":1},{"id":"GO:0039536","count":1}]},{"hash":"1158571147394259078","title":"Adaptive Immune Regulation","description":"Based on the top GO terms, the cluster centers on regulation of adaptive immune functions, including negative regulation of interleukin-4 production, T cell proliferation, and antibody isotype switching (IgG/IgE). The presence of positive regulation of NF-kappaB signaling and protein ubiquitination suggests modulation of immune signaling pathways. A couple of transport-related terms appear, but the dominant theme is immune response tuning.","confidence":"Medium","size":7,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030001","count":1},{"id":"GO:0048302","count":1},{"id":"GO:0007034","count":1},{"id":"GO:0032713","count":1},{"id":"GO:0032410","count":1}]},{"hash":"1336911342254983946","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000389","count":1},{"id":"GO:0035196","count":1},{"id":"GO:0048024","count":1},{"id":"GO:0051533","count":1},{"id":"GO:0030422","count":1}]},{"hash":"671430378610557616","title":"Unknown","description":"The top GO terms span highly diverse functions, including neuronal vesicle transport, cilium movement, ribosome assembly, gas vesicle organization, ubiquitin-proteasome protein turnover, various metabolic processes (acetyl-CoA, fatty acids), nonribosomal peptide biosynthesis, and fermentation. With no clear, single coherent function or pathway linking these terms, the cluster appears to be multi-functional or non-specific, so a definitive, representative label cannot be assigned.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990048","count":3},{"id":"GO:0003341","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0031412","count":3},{"id":"GO:0031146","count":2}]},{"hash":"1403320222836968090","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000463","count":1},{"id":"GO:0070475","count":1}]},{"hash":"1830527602644512122","title":"Heart and retinal vascular development","description":"The top GO terms prominently feature retina vasculature development and heart development, suggesting a cluster focused on developmental processes governing vascularization in cardiac and ocular tissues. Additional terms indicate transcriptional regulation and signaling, as well as cellular stress/turnover processes that can accompany development, supporting a broader developmental signaling context. Taken together, the dominant tissue- and process-specific terms justify labeling this cluster as heart and retinal vascular development, with secondary ties to developmental signaling pathways.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061298","count":3},{"id":"GO:0043433","count":3},{"id":"GO:0032436","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0006351","count":3}]},{"hash":"403452556395316851","title":"Transcription and signaling regulators","description":"This cluster centers on regulatory processes spanning transcription (DNA-templated transcription, mRNA splicing), post-translational modification (protein ubiquitination), telomere maintenance regulation, and multiple signaling pathways and stimulus responses, suggesting proteins that modulate gene expression and signal transduction.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0016055","count":2}]},{"hash":"1448914936961111694","title":"Plant meiosis, pollen development, and cytoskeleton","description":"The terms show plant reproductive development (embryo sac and pollen development) plus meiotic processes (meiotic recombination, double-strand break repair), with clear links to cytoskeletal organization (cortical microtubule organization, tubulin complex assembly). Proteostasis-related terms (protein folding, ubiquitin-proteasome quality control) also appear to support these developmental and meiotic activities. Together, they suggest a cluster centered on plant meiosis and gametogenesis coupled with cytoskeletal dynamics and proteostasis.","confidence":"Medium","size":7,"edges":11,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006302","count":1},{"id":"GO:0009553","count":1},{"id":"GO:0007131","count":1},{"id":"GO:0009555","count":1},{"id":"GO:0071629","count":1}]},{"hash":"442940257000912411","title":"Mitochondrial energy and viral DNA response","description":"The top GO terms include mitochondrial electron transport and Complex II assembly, plus several nucleic acid\u2013related and viral processing terms (DNA repair via homologous recombination, clearance of intracellular DNA, viral RNA genome replication, and viral protein processing). This suggests a theme around cellular energy production paired with nucleic acid handling and antiviral responses. The connection is plausible but not tight, pointing to a cluster about mitochondrial energy metabolism linked to DNA repair and viral defense processes. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0000724","count":1},{"id":"GO:0019082","count":1}]},{"hash":"277195715510038376","title":"Drosophila follicle development and chitin synthesis","description":"The top GO terms point to insect development, especially follicle epithelium polarity and adhesion (which are key for egg chamber formation) and chitin biosynthesis, consistent with Drosophila ovarian tissue development and cuticle/eggshell matrix production. Although some terms are less specific (e.g., infection structure, teichoic/hyaluronan biosynthesis), the dominant signals converge on insect developmental processes tied to follicle cells and chitin-containing structures.","confidence":"Medium","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001744","count":2},{"id":"GO:0042248","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0075015","count":2},{"id":"GO:0006031","count":1}]},{"hash":"2054937116305051533","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0006189","count":2},{"id":"GO:0042594","count":2},{"id":"GO:0033512","count":2},{"id":"GO:0006541","count":2}]},{"hash":"653228211602771598","title":"Unknown","description":"The terms span mitochondrial import and lipid/quinone metabolism, plus several neuronal and light-stress related functions; with only a single connection and no cohesive theme, there isn\u2019t a clear single function tying the proteins together. A concise, representative label cannot be confidently assigned.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":1},{"id":"GO:1901006","count":1},{"id":"GO:0055088","count":1},{"id":"GO:1902171","count":1},{"id":"GO:0021692","count":1}]},{"hash":"234930878836078220","title":"Mitochondrial phospholipid biosynthesis and respiration","description":"This cluster's GO terms cluster around mitochondrial processes: biosynthesis of phospholipids such as phosphatidylethanolamine, phosphatidylserine, and phosphatidylglycerol, and the assembly of the mitochondrial respiratory chain complexes, including NADH to ubiquinone and complex II assembly. Together these imply a module focused on mitochondrial membrane biogenesis and energy metabolism. Some terms (negative regulation of G0 to G1 transition and DNA topological change) appear less directly related and may reflect broader cellular context or annotation noise, but the dominant theme is mitochondrial lipid synthesis and respiration.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":1},{"id":"GO:0010512","count":1},{"id":"GO:0006655","count":1},{"id":"GO:0006663","count":1},{"id":"GO:1905711","count":1}]},{"hash":"297036235425635306","title":"Innate antiviral response and translation regulation","description":"These proteins show strong signals for innate immune defense against viruses and for regulation of protein synthesis, including translation initiation and ribosome biogenesis, particularly under stress (ER) conditions. While a few terms are peripheral (e.g., neural crest differentiation, photoreceptor localization), the dominant pattern points to antiviral defense coupled to translation control. Confidence: Medium","confidence":"","size":6,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0032147","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0014033","count":1}]},{"hash":"1573358086364602485","title":"Unknown","description":"The top GO terms are highly diverse, including LDL receptor\u2013related processes, neuropeptide processing, nerve growth factor production, and developmental/sporulation terms. There is no single coherent biological theme tying these terms together, suggesting the cluster does not reflect a unified function. Confidence is None.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":1},{"id":"GO:0010989","count":1},{"id":"GO:0032804","count":1},{"id":"GO:0030435","count":1},{"id":"GO:1905598","count":1}]},{"hash":"1284704110367586066","title":"Ubiquitin-Dependent Degradation and Mitophagy","description":"The cluster shows dominant ubiquitin-related processes: K48- and K63-linked ubiquitination, ubiquitin-dependent protein catabolic process, and autoubiquitination, indicating a core role in tagging proteins for degradation. It also includes mitophagy (type 2) and signals that regulate JNK cascade and GTPase activity, suggesting a link between ubiquitin signaling, proteostasis, and mitochondrial quality control.","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0070936","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0051865","count":2}]},{"hash":"1718323806784194150","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0071051","count":2},{"id":"GO:0071038","count":2},{"id":"GO:0034476","count":2},{"id":"GO:0071042","count":2}]},{"hash":"108341990842935598","title":"Unknown","description":"The proteins in this cluster map to a highly diverse set of GO terms (chromatin/epigenetic processes, development, ribosome assembly, tRNA modification, metabolism, signaling regulation) with no clear shared function. The terms include obsolete annotations and several unrelated biological contexts, and there are no network connections (edges/triangles) linking them, suggesting the cluster does not represent a cohesive biological function.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904802","count":1},{"id":"GO:0016578","count":1},{"id":"GO:0043569","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0000028","count":1}]},{"hash":"1895645315110598634","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0002940","count":1}]},{"hash":"970420292359379105","title":"Synaptic vesicle exocytosis and trafficking","description":"This cluster is defined by GO terms centered on synaptic vesicle priming and neurotransmitter release, SNARE complex assembly, and exocytic insertion of receptors, pointing to a shared role in vesicle trafficking and neurotransmitter secretion at synapses, with related Golgi/endo/lysosome transport and autophagy processes as broader trafficking contexts. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001916","count":1},{"id":"GO:0035493","count":1},{"id":"GO:0098967","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0006896","count":1}]},{"hash":"2140349900638813705","title":"Ubiquitin-Dependent TNF/NF-\u03baB Signaling","description":"The top GO terms center on ubiquitin-dependent protein catabolic processes and various ubiquitin linkages (K63, K6), coupled with positive regulation of TNF-mediated signaling and I-kappaB phosphorylation. This points to a cohesive function where ubiquitination modulates TNF/NF-\u03baB signaling, with additional hints of chromatin-level regulation via histone ubiquitination. Overall, the cluster seems to represent ubiquitin-mediated control of inflammatory signaling and related chromatin processes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:1903265","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0070535","count":2},{"id":"GO:0085020","count":2}]},{"hash":"230085734336792626","title":"Genome Maintenance: mtDNA Repair and Telomere Maintenance","description":"GO terms converge on genome integrity, spanning mtDNA repair, mitochondrial genome maintenance, telomere maintenance, and replication dynamics, suggesting a cohesive cluster of genome-stability functions.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1902455","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0043504","count":1},{"id":"GO:0097046","count":1},{"id":"GO:0032211","count":1}]},{"hash":"2273829040147786223","title":"Ribosome Biogenesis and Translation Control","description":"This cluster is best characterized by terms tied to translation initiation and rRNA maturation (formation of translation preinitiation complex; maturation of LSU rRNA) and regulation of translational frameshifting, suggesting a shared function in ribosome biogenesis and translation control. Other terms (chromosome segregation, seminiferous tubule development, histone modifications) appear incidental and do not align with the main signal, making the translation-focused theme only moderately supported.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":1},{"id":"GO:2001125","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0045143","count":1},{"id":"GO:0072520","count":1}]},{"hash":"719509193586851268","title":"DNA replication and genome maintenance","description":"The top GO terms cluster around DNA replication, repair, and genome stability: replication processes, transcription-coupled nucleotide-excision repair, telomere maintenance via recombination, and meiotic recombination, with an additional signal for centrosome cycle. While a developmental term appears, the dominant theme is genome maintenance and DNA synthesis/repair pathways, suggesting these proteins form a replication/repair module.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":3},{"id":"GO:0045003","count":3},{"id":"GO:0010571","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006283","count":3}]},{"hash":"572752684494253286","title":"DNA replication and RNA Pol II transcription regulation","description":"The cluster centers on DNA replication and transcription control by RNA polymerase II, with chromatin-related terms (nucleosome mobilization/positioning, histone acetylation) and transcription-start-site regulation, suggesting a shared theme of genome replication linked to transcriptional regulation and chromatin state, despite some obsolete terms and odd entries like associative learning.","confidence":"Medium","size":6,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0019079","count":6},{"id":"GO:0000463","count":5},{"id":"GO:0042766","count":5},{"id":"GO:0045944","count":5}]},{"hash":"1289952629038948022","title":"Vertebrate Neural and Skeletal Development","description":"The top GO terms cluster around vertebrate development, notably neural/forebrain development and neural tube closure, along with skeletal system development and general DNA-templated transcription. This points to a set of proteins involved in developmental gene regulation in vertebrates. Some terms are unrelated (cadmium response, Gram-positive defense), but the dominant theme is developmental regulation in neural and skeletal contexts.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0001403","count":5},{"id":"GO:0071276","count":5}]},{"hash":"2016406439186895974","title":"Unknown","description":"The top GO terms cover metabolism (cholesterol, glucose), neural development (dendrite morphogenesis, cerebral cortex development), transcription, apoptosis, ion transport, and sperm capacitation, with no single unifying function. Because the cluster lacks a cohesive theme, a confident, representative label cannot be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006695","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0048813","count":3},{"id":"GO:0006351","count":3}]},{"hash":"415117534288736814","title":"Proteostasis and ER stress response","description":"Most terms point to protein quality control and handling, including response to unfolded protein, ER stress signaling with regulation of translation, and nuclear ubiquitin-proteasome quality control; plus terms about post-translational targeting to membranes and protein complex oligomerization. A few terms like DNA replication or hormone response appear as outliers, but the dominant theme is proteostasis and protein trafficking.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051259","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0035719","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1831672544526517158","title":"Synaptic vesicle trafficking and spine morphogenesis","description":"Based on the GO terms, the cluster centers on neuronal membrane trafficking and spine development: Golgi to plasma membrane transport and synaptic vesicle budding point to vesicle delivery to the neuronal surface, while dendritic spine development/morphogenesis and nervous system development suggest roles in forming and maintaining synaptic contacts. Additional terms like ruffle assembly and organelle organization likely reflect broader cellular functions in these neural proteins. Overall, the data point to a module coordinating synaptic vesicle trafficking with spine morphogenesis.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":3},{"id":"GO:0060999","count":3},{"id":"GO:0070142","count":2},{"id":"GO:0006998","count":2},{"id":"GO:0007399","count":2}]},{"hash":"1323498165628775276","title":"Cardiac muscle development and calcium signaling","description":"This cluster is driven by cardiac-related terms (heart development, cardiac muscle contraction, hypertrophy) and calcium-centric processes (calcium ion transport, calcium-regulated lysosome exocytosis), with supporting evidence from myoblast fusion and actin organization that reflect muscle formation. Some terms such as myelination and bioluminescence appear less connected and may be noise. Overall, the theme points to cardiac muscle function and calcium signaling.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901841","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0007520","count":1},{"id":"GO:0022011","count":1},{"id":"GO:0006816","count":1}]},{"hash":"2287957556768025887","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to translation and ribosome biogenesis (translation, cytoplasmic translation, ribosome biogenesis), with these functions appearing twice each. This suggests the proteins largely participate in the protein synthesis machinery. The other single-count terms (muscle response, sensory perception, etc.) appear only once and do not define the cluster\u2019s core function. Therefore, the label Ribosome Biogenesis and Translation captures the primary theme.","confidence":"High","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0014873","count":1},{"id":"GO:1903833","count":1}]},{"hash":"953975146887414474","title":"Glycan and cell-wall biosynthesis","description":"The top GO terms point to biosynthesis of diverse glycans and cell-surface polymers (chitin, teichoic acid, cellulose, hyaluronan) plus related sugar metabolism, glycosylation, and cell division envelope processes, suggesting a cohesive theme of glycan production and cell-wall assembly.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006031","count":1},{"id":"GO:0016266","count":1},{"id":"GO:0000920","count":1},{"id":"GO:0001744","count":1},{"id":"GO:0070592","count":1}]},{"hash":"2183482041394205107","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0000028","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0042273","count":1}]},{"hash":"569008461191493143","title":"Amino acid biosynthesis and nutrient metabolism","description":"The GO terms point mainly to biosynthetic pathways for amino acids (valine, isoleucine) and the shikimate pathway, indicating a focus on amino acid production. Additional terms about nutrient response and stress support the idea of metabolic adaptation under nutrient conditions, though some terms are peripheral or obsolete. This supports a cohesive label centered on amino acid biosynthesis and related metabolism.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0000002","count":1},{"id":"GO:0001887","count":1},{"id":"GO:0007584","count":1},{"id":"GO:0019632","count":1}]},{"hash":"106219376782177960","title":"Amino acid biosynthesis and nitrogen metabolism","description":"The top GO terms cluster around amino acid biosynthesis (L-histidine, L-tryptophan) and related nitrogen metabolism (carbamoyl phosphate biosynthesis, cellular response to ammonium ion), as well as nutrient-related stress (response to starvation). Developmental terms (liver, midgut) and dexamethasone response appear but are less central, suggesting a core theme of metabolic and nutrient sensing rather than a single signaling pathway.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0071548","count":1},{"id":"GO:0032094","count":1},{"id":"GO:1903718","count":1}]},{"hash":"557823353707516825","title":"Neural and Muscular Development","description":"These proteins are linked to developmental and functional processes across nervous, muscular, and cardiac tissues, with terms including nervous system development, axonogenesis, myoblast fusion, heart development, and long-term synaptic potentiation. A common theme is the orchestration of neuron\u2013muscle interactions and synaptic activity during organismal development and maturation, supported by calcium-dependent exocytosis and signal phosphorylation.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0060291","count":2}]},{"hash":"200825643365999735","title":"Ketone body and amino acid metabolism","description":"The proteins are aligned with ketone body biosynthesis/catabolism, propionyl-CoA biosynthesis, and isoleucine catabolism, pointing to energy-yielding metabolic pathways. Although a few development terms appear, the dominant signal is metabolic catabolic processes, justifying this label as representative of the cluster\u2019s function.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019619","count":4},{"id":"GO:0001889","count":4},{"id":"GO:0014070","count":4},{"id":"GO:0046951","count":4},{"id":"GO:0032385","count":4}]},{"hash":"394565602541114868","title":"Developmental Chromatin Regulation","description":"The cluster includes GO terms spanning tissue differentiation (osteoblast differentiation, spermatogenesis, spermatid development, muscle cell differentiation, vitellogenesis) and chromatin/transcription control (establishment of protein localization to chromatin, negative regulation of transcription by RNA Pol II, negative regulation of chromosome condensation), suggesting a shared theme of developmental regulation via chromatin mechanisms.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":3},{"id":"GO:0007283","count":2},{"id":"GO:0007549","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0007286","count":2}]},{"hash":"1947791496252549499","title":"Neuronal stress response and proteostasis","description":"The GO terms point to neuron-specific stress signaling (e.g., negative regulation of excitatory postsynaptic potential, oxidative stress-induced neuronal apoptotic signaling), changes in mitochondrial dynamics (positive regulation of mitochondrial fission), and protein quality control pathways (ubiquitin-dependent proteolysis/ERAD). Together they suggest a cohesive role in neuronal stress response and proteostasis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0071287","count":2},{"id":"GO:0090141","count":2},{"id":"GO:1903378","count":2},{"id":"GO:0042787","count":2}]},{"hash":"545536313258703687","title":"Ciliary assembly and Hedgehog signaling","description":"The Top Terms point to non-motile cilium assembly and Smoothened signaling, both central to primary cilium function and Hedgehog pathway activity, suggesting the proteins cluster around ciliogenesis and ciliary signaling rather than other processes.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1905515","count":1},{"id":"GO:0007224","count":1}]},{"hash":"1555125106619474555","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0042766","count":5},{"id":"GO:0045944","count":5},{"id":"GO:0000716","count":5},{"id":"GO:2000616","count":5}]},{"hash":"237188851981519487","title":"Unknown","description":"There are no top GO terms provided to define a shared function; with five proteins and no functional terms, there is insufficient information to assign a meaningful label.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"4560491099501184","title":"mRNA Splicing and Translation Initiation","description":"GO terms emphasize mRNA splicing and splice-site recognition, formation of the translation preinitiation complex, eIF4F assembly, and mRNA export/stability, indicating a coordinated role in RNA processing that primes transcripts for translation. This label captures the combined emphasis on splicing and translation initiation in the cluster.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0097010","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0006406","count":1}]},{"hash":"2245761272596691643","title":"Unknown","description":"The terms span meiosis-specific processes, chromatin silencing, cell cycle exit, multiple DNA repair pathways, ubiquitin-proteasome\u2013mediated turnover, and even peroxisomal import, with no single cohesive function linking them all. This heterogeneity suggests no clear, unified theme for the cluster.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0045141","count":5},{"id":"GO:1901487","count":5},{"id":"GO:0016558","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0070987","count":5}]},{"hash":"1882280431069798751","title":"Microtubule-driven spindle dynamics and transport","description":"Based on the GO terms, the cluster is dominated by microtubule-related processes: nuclear migration along microtubules, spindle orientation and kinetochore attachment, minus-end directed microtubule sliding, and cytoplasmic transport along microtubules (e.g., dendritic transport). Additional terms point to cytoskeletal roles in cell junction maintenance and development, suggesting a broader theme of microtubule dynamics coordinating division, transport, and cell architecture. ","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030473","count":2},{"id":"GO:0051296","count":2},{"id":"GO:0099607","count":2},{"id":"GO:0048364","count":2},{"id":"GO:0010938","count":2}]},{"hash":"2183602904803283012","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019243","count":2},{"id":"GO:0010197","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0034414","count":2},{"id":"GO:0006398","count":2}]},{"hash":"918482387692621843","title":"Embryonic organogenesis and proliferation","description":"These terms point to broad developmental programs across multiple organs (heart morphogenesis, lung septation, kidney branching, neural precursor growth, hematopoietic differentiation) and associated control of transcription and DNA replication, indicating an embryonic organogenesis and proliferative process rather than a specific signaling pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0035470","count":2},{"id":"GO:1902257","count":1},{"id":"GO:0061144","count":1},{"id":"GO:0060038","count":1}]},{"hash":"1998294920630408864","title":"Ubiquitin-Proteasome Proteolysis in Mitosis","description":"The top GO terms emphasize ubiquitin-dependent protein degradation (SCF-dependent proteasomal process) and the mitotic cell cycle, suggesting this cluster centers on regulated proteolysis during mitosis, with supporting links to DNA repair and stress response processes.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0070301","count":1},{"id":"GO:0007507","count":1}]},{"hash":"1216714681440887749","title":"Unknown","description":"No shared GO terms or connections are reported (no edges, no enriched terms), so there is no clear functional theme to label this cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1346410223451168882","title":"Acetyl-CoA Metabolism and Fatty Acid Biosynthesis","description":"Most GO terms cluster around acetyl-CoA production and use: pyruvate decarboxylation to acetyl-CoA, 2-oxoglutarate metabolism feeding the TCA cycle, leucine catabolism to acetyl-CoA via saccharopine, malonyl-CoA biosynthesis, and long-chain fatty acid biosynthesis. A translation term appears ancillary and not central to this theme, but the dominant pattern points to an acetyl-CoA\u2013driven energy and lipid metabolism cluster.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000002","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0033512","count":1},{"id":"GO:0042759","count":1}]},{"hash":"647722037307163223","title":"Phosphate Transport and Homeostasis","description":"This cluster centers on phosphate handling, with GO terms for phosphate ion transmembrane transport and intracellular phosphate ion homeostasis; the obsolete signaling term is likely a historical artifact, but the core function relates to phosphate transport and regulation.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":1},{"id":"GO:0048016","count":1},{"id":"GO:0030643","count":1}]},{"hash":"1615686155588514542","title":"Actin Cytoskeleton Remodeling in Muscle and Cell Division","description":"The cluster\u2019s GO terms center on sarcomere organization, muscle fiber adaptation, Arp2/3-mediated actin nucleation, mitotic contractile ring assembly, and cytokinesis, with a calcium-response component. These collectively point to actin cytoskeleton remodeling and contractile machinery used in both muscle function and cell division, justifying this label.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":4},{"id":"GO:0045214","count":4},{"id":"GO:0043486","count":4},{"id":"GO:0043982","count":4},{"id":"GO:0051592","count":4}]},{"hash":"2210387906390633136","title":"Transmembrane Transporters","description":"GO terms indicate diverse substrates moved across membranes (sugar, vitamin, nitrite, sodium, xenobiotics, neurotransmitter loading into vesicles, etc.), pointing to a shared function in transmembrane transport rather than substrate-specific roles. This clustering of transporter-related GO terms supports naming the group as membrane transport proteins that mediate various transmembrane exports/imports. Confidence: High","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0015739","count":4},{"id":"GO:0035725","count":4},{"id":"GO:0006855","count":4}]},{"hash":"1315722078320890048","title":"Unknown","description":"The top GO terms are highly diverse, including protein ubiquitination, fatty acid metabolism, meiosis-related processes, adaptive immune response, RIG-I signaling regulation, photomorphogenesis, and organelle tethering. With only 4 proteins and no clear shared function beyond a couple of ubiquitination terms, there isn't a cohesive biological theme to name this cluster. Therefore, label as Unknown.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006513","count":1},{"id":"GO:0000038","count":1},{"id":"GO:0007112","count":1},{"id":"GO:0002250","count":1},{"id":"GO:0039536","count":1}]},{"hash":"646074489682190163","title":"Nuclear transcription and cell cycle regulation","description":"The cluster\u2019s top GO terms cluster around nuclear processes: DNA-templated transcription and transcription regulation (GO:0006351, GO:0060567, GO:0031564) and cell cycle/DNA replication components (GO:0007049, GO:0006267). Supporting signals from RNA processing (pre-miRNA processing, miRNA catabolic process) and mRNA stabilization indicate broader regulation of gene expression tied to the nucleus. A few terms related to stress responses and kidney development are present but less central. Overall, this set points to a cohesive role in nuclear transcriptional control coupled with cell cycle regulation.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901724","count":1},{"id":"GO:0070934","count":1},{"id":"GO:0031054","count":1},{"id":"GO:0010587","count":1},{"id":"GO:1902219","count":1}]},{"hash":"1032077674978271291","title":"Ribosome Biogenesis and Translational Regulation","description":"This cluster centers on ribosome assembly and control of protein synthesis, as reflected by dominant GO terms for ribosome biogenesis, cytoplasmic translation, and regulation of translational elongation and fidelity. The terms indicate involvement in the production of ribosomes and modulation of translation rather than a single, one-off process. A few terms touch on RNA-templated transcription or chromatin-related regulation, but the prevailing signal is translation machinery and its regulation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1},{"id":"GO:2000767","count":1},{"id":"GO:0045901","count":1},{"id":"GO:0045903","count":1}]},{"hash":"2062035296512233569","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0006369","count":2},{"id":"GO:0048026","count":1},{"id":"GO:0006265","count":1},{"id":"GO:0045944","count":1}]},{"hash":"2275370792500534157","title":"Actin cytoskeleton remodeling and membrane repair","description":"This cluster centers on actin dynamics, with terms for barbed-end capping, lamellipodium assembly, stress fiber regulation, and actin network formation, plus plasma membrane repair. The presence of megakaryocyte and oligodendrocyte development terms may reflect broader cytoskeletal roles in differentiation or tissue-specific contexts, and a BDNF-related response suggests neuronal signaling involvement. Overall, the dominant theme is actin-driven structural remodeling and membrane repair.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":2},{"id":"GO:0051016","count":1},{"id":"GO:0035855","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0051497","count":1}]},{"hash":"75177054666922443","title":"Unknown","description":"The cluster's top GO terms span diverse processes: spindle assembly, actin filament bundle assembly, mRNA processing, telomere maintenance via telomerase, TNF signaling, chiasma assembly, and K63-linked ubiquitination. These represent cytoskeletal, nuclear, signaling, and post-translational modification activities with little overlap, and there are no edges linking the proteins, so there is no coherent, single theme to label; thus Unknown with None. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0090501","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0006397","count":1}]},{"hash":"1142797874249325329","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning glycogen and lipid biosynthesis, nervous system myelination, meiotic recombination, mitotic spindle attachment, apoptosis, cardiac hypertrophy, vascular branching, cocaine response, and fungal ascospore formation. This scattered set provides no single cohesive biological theme for a meaningful label.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0005979","count":4},{"id":"GO:0009245","count":4},{"id":"GO:0022011","count":4},{"id":"GO:0010780","count":4},{"id":"GO:0051315","count":4}]},{"hash":"952925979292694074","title":"Unknown","description":"The terms include organelle fission and various biosynthetic processes (lactose, lipid A, peptidoglycan, UDP-GlcNAc, glycogen, cell wall mannoprotein) and cell morphogenesis, with no clear single function tying them together.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016559","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0005989","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0009252","count":2}]},{"hash":"1149737590312016548","title":"Unknown","description":"No shared GO terms or interaction signals are available for this cluster (Top Terms empty, no edges/triangles). Without a detectable common function, it cannot be confidently labeled.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1786930800381058923","title":"Actin Cytoskeleton and Cell Polarity","description":"The top GO terms point to actin cytoskeleton assembly/organization (cardiac myofibril assembly, actin cortical patch assembly), vesicle docking/exocytosis, and cell polarity/migration (T cell polarity, uropod organization, axon choice point recognition). Together they suggest a coherent theme of cytoskeletal dynamics guiding cell shape, movement, secretion, and polarization, rather than a single tissue-specific function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":2},{"id":"GO:0000147","count":2},{"id":"GO:0006904","count":1},{"id":"GO:0070493","count":1},{"id":"GO:0001768","count":1}]},{"hash":"1065756162402867878","title":"Unknown","description":"The terms span neural growth factor production, LDL receptor regulation, sporulation, stomatal morphogenesis, receptor recycling, and enkephalin processing, with no clear shared function or pathway linking the four proteins. The mix and lack of connectivity (no edges) suggest no coherent single theme for this cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":1},{"id":"GO:0010989","count":1},{"id":"GO:0032804","count":1},{"id":"GO:0030435","count":1},{"id":"GO:1905598","count":1}]},{"hash":"693667149033084966","title":"Muscle development and sarcomere assembly","description":"This cluster is driven by terms related to heart development, myoblast fusion, and cardiac myofibril assembly, along with calcium handling and actin organization, pointing to proteins involved in muscle formation and the assembly of the contractile apparatus, despite a few unrelated annotations. ","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901841","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0007520","count":1},{"id":"GO:0006816","count":1}]},{"hash":"1194566326732672359","title":"Neuronal development and axon guidance","description":"This cluster centers on nervous system development, dendrite morphogenesis, and Robo-roundabout signaling, indicating roles in neuron connectivity and axon guidance; endocytosis and vesicle docking terms reflect synaptic trafficking supporting these processes.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0035385","count":3},{"id":"GO:0006897","count":3},{"id":"GO:0034260","count":3}]},{"hash":"1775977229315176174","title":"ER Stress and Unfolded Protein Response","description":"This cluster\u2019s terms cluster around cellular stress handling, notably unfolded protein response and ER stress-related translation regulation, along with oxidative and antiviral defense responses. A few terms (e.g., photoreceptor localization and mitotic transition) are less connected, but the core signals point to stress response and protein folding management.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":1},{"id":"GO:1901215","count":1},{"id":"GO:0043278","count":1},{"id":"GO:0036494","count":1},{"id":"GO:1903546","count":1}]},{"hash":"1792155374438672691","title":"Follicle Epithelium Polarity and Chitin Biosynthesis","description":"GOs indicate insect egg chamber follicle cell biology: adhesion, maintenance of polarity in the follicular epithelium, and chitin/biosynthetic cell wall processes, with supporting terms on cytoskeletal dynamics during cytokinesis. This combination suggests a cohesive theme of follicle epithelium development and chitin-containing matrix formation in insects.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007299","count":1},{"id":"GO:0006031","count":1},{"id":"GO:0075015","count":1},{"id":"GO:0000920","count":1},{"id":"GO:0000918","count":1}]},{"hash":"249342226837042823","title":"Unknown","description":"The GO terms are scattered across development, morphogenesis, centrosome cycle, and stress responses, with no clear shared function for all three proteins. Because there isn't a unifying theme, a precise label can't be formed.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036290","count":1},{"id":"GO:0071380","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0043552","count":1},{"id":"GO:0007098","count":1}]},{"hash":"316388492196835320","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":1},{"id":"GO:0035606","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0042823","count":1},{"id":"GO:0009089","count":1}]},{"hash":"168727084779896819","title":"Proteostasis and Stress Response","description":"Dominant terms point to protein quality control and stress responses: ubiquitin-dependent degradation and protein isomerization; plus responses to cadmium and hydrogen peroxide and ER stress\u2013driven translation. A few terms involve mitosis or photoreceptor localization, but the core theme is proteostasis under cellular stress.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0000413","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0070301","count":1},{"id":"GO:1901215","count":1}]},{"hash":"668312071798842182","title":"Unknown","description":"There are 3 proteins and no GO terms listed to indicate a common function, so no coherent theme emerges. The cluster therefore cannot be confidently labeled.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"2101645755363130365","title":"Nuclear RNA Splicing and Processing","description":"These proteins show strong representation of spliceosome-related terms (snRNP assembly, spliceosomal complex assembly, mRNA splicing via spliceosome) and other RNA maturation steps (tRNA processing, rRNA maturation, import into nucleus, deadenylation-dependent decapping). This points to a cohesive role in nuclear RNA processing and splicing machinery, with supporting signals from RNA maturation pathways. High","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000290","count":3},{"id":"GO:0008334","count":3},{"id":"GO:0009737","count":3},{"id":"GO:0000387","count":3},{"id":"GO:0008033","count":3}]},{"hash":"153049273398625372","title":"Unknown","description":"The top GO terms cover a broad and unrelated set of processes\u2014from pore complex assembly and cell cycle to immune functions like B cell cytokine production and isotype switching, as well as RNA localization and mitochondrial import. There is no single cohesive function or pathway linking these terms, suggesting the cluster is not functionally cohesive. ","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046931","count":3},{"id":"GO:0032212","count":3},{"id":"GO:1904469","count":3},{"id":"GO:0090666","count":3},{"id":"GO:0002368","count":3}]},{"hash":"1899965856833523405","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009845","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0080188","count":1},{"id":"GO:0000395","count":1},{"id":"GO:0000398","count":1}]},{"hash":"312460002823652711","title":"mRNA processing and translation initiation","description":"It centers on mRNA life-cycle processes: splicing and splice-site recognition, mRNA export and stability, and the initiation of translation via preinitiation complex formation and EIF4F assembly. The shared GO terms suggest a cohesive cluster of factors regulating mRNA maturation and translation initiation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0097010","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1282257469937579263","title":"Unknown","description":"Top terms include translation initiation components (GO:0001731, GO:0097010) and a mix of calcium transport, immune/cytokine regulation, pain regulation, neuronal plasticity, and other disparate processes. The terms do not converge on a single biological function, and with zero edges among the three proteins, there is no cohesive theme. Therefore Unknown with None confidence.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":1},{"id":"GO:0060907","count":1},{"id":"GO:0006816","count":1},{"id":"GO:0097010","count":1},{"id":"GO:0051930","count":1}]},{"hash":"1122923023476825421","title":"Fungal pseudohyphal and invasive growth under glucose limitation","description":"The presence of pseudohyphal growth and invasive growth in response to glucose limitation strongly points to a fungal differentiation program triggered by nutrient stress, often coupled with transcriptional reprogramming (RNA polymerase II transcription and preinitiation complex assembly). Despite a couple obsolete terms, the core theme is nutrient-stress\u2013induced morphological changes in fungi.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0016578","count":1},{"id":"GO:0009960","count":1}]},{"hash":"148953725976194210","title":"Diverse Transmembrane Transport","description":"The top GO terms are dominated by transmembrane transport activities across a wide range of substrates (sodium ions, nitrite, arabinose, sialic acid, vitamins, xenobiotics, and even neurotransmitter loading into synaptic vesicles). Although a single steroid biosynthetic process term appears, the recurring theme is membrane transport and substrate translocation, suggesting these proteins function as transporters or transport regulators.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006694","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0015739","count":1},{"id":"GO:0035725","count":1}]},{"hash":"1998700498647433481","title":"RNA Processing & Modification","description":"The top GO terms are dominated by RNA-related processes: endonucleolytic ITS1 cleavage to separate rRNA components, RNA guanine-N7 methylation, and 7-methylguanosine mRNA capping, indicating a core theme of RNA maturation/modification. The remaining terms are diverse (e.g., lipid biosynthesis, retinal development) and likely represent annotation noise or multifunctionality, so the label is cautiously representative but not definitive.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0018012","count":1},{"id":"GO:0006656","count":1}]},{"hash":"1669717095928080343","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0048026","count":2},{"id":"GO:0006265","count":2},{"id":"GO:0000463","count":2}]},{"hash":"552051044749672038","title":"Ribosome biogenesis and translation regulation","description":"Based on the top GO terms, the cluster centers on ribosome-related processes: formation of translation preinitiation complex, negative regulation of translational frameshifting, and maturation of LSU rRNA. While other terms in the list are unrelated or obsolete, these translation/ribosome biogenesis terms suggest a common functional theme among the cluster's proteins. The lack of edges and small size adds some uncertainty, but the core appears to involve ribosome assembly and translation control.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":1},{"id":"GO:2001125","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0045143","count":1},{"id":"GO:0072520","count":1}]},{"hash":"576103898893981966","title":"Unknown","description":"The listed GO terms span a wide mix of processes from metabolism (glycogen and lipid A biosynthesis) to neural development (myelination), cell division and spindle attachment, apoptosis signaling, cardiac stress responses, blood vessel branching, and even fungal sporulation and a drug-response phenotype. This lack of a coherent, single functional theme across the terms suggests there isn\u2019t a clear common function tying these proteins together, so a generic Unknown label is most appropriate.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0005979","count":3},{"id":"GO:0009245","count":3},{"id":"GO:0022011","count":3},{"id":"GO:0010780","count":3},{"id":"GO:0051315","count":3}]},{"hash":"115339112246100116","title":"Unknown","description":"The top GO terms cover disparate areas\u2014stress response, hormone biosynthesis, vitamin/retinoid metabolism, and various metabolic processes\u2014without a unifying biological theme or interactions among the proteins (Edges: 0, Triangles: 0).","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":3},{"id":"GO:0032342","count":3},{"id":"GO:0090350","count":3},{"id":"GO:0033072","count":3},{"id":"GO:0033280","count":3}]},{"hash":"152821982928473034","title":"mRNA processing and translation initiation regulation","description":"The top GO terms cluster around mRNA processing, splicing, export, and stability, as well as components and steps of translation initiation (preinitiation complex formation, eIF4F assembly). This suggests a coordinated role in regulating mRNA maturation and the initiation of translation, particularly under stress. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":3},{"id":"GO:0048026","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0097010","count":2},{"id":"GO:1905663","count":2}]},{"hash":"1677634908166989335","title":"Meiosis and Gamete Development","description":"The top terms cluster around meiotic recombination, meiotic double-strand break repair, and gamete development (spermatid and ovarian follicle development), with supporting roles in DNA damage response and transcription. This points to a cohesive theme of meiosis and gamete formation, with DNA repair as a key mechanism.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007131","count":2},{"id":"GO:0090267","count":2},{"id":"GO:0072711","count":2},{"id":"GO:0051106","count":2}]},{"hash":"350501947487854430","title":"Sarcomere organization and actin dynamics","description":"The terms cluster around sarcomere organization, skeletal muscle fiber adaptation, and actin-myosin dynamics (including Arp2/3-mediated actin nucleation and contractile-ring/cytokinesis processes) with a calcium response component, suggesting a muscle cytoskeleton theme; some histone-related terms appear unrelated, lowering confidence somewhat.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":1},{"id":"GO:0045214","count":1},{"id":"GO:0043486","count":1},{"id":"GO:0043982","count":1},{"id":"GO:0051592","count":1}]},{"hash":"936553849782325710","title":"Unknown","description":"The Top Terms span many unrelated processes (nuclear receptor signaling, estrogen signaling regulation, mRNA processing, sex differentiation, ncRNA-mediated silencing, cytokine signaling, mitotic chromatid separation, lipid biosynthesis, snRNP import, kinase regulation) with no clear shared function. There are no edges or coherent clustering signals, so no single biological theme emerges to name the cluster confidently.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000327","count":1},{"id":"GO:0033147","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0007548","count":1},{"id":"GO:0031047","count":1}]},{"hash":"960007309967634190","title":"Proteostasis and Autophagy under Stress","description":"The top GO terms point to protein quality control and turnover (proteasome assembly, SCF complex dynamics, ubiquitin-related activity) together with autophagy (autophagosome maturation) and stress-related organelle functions (ER polarization, mitochondrial assembly/mtDNA regulation, stress granule disassembly). Taken together, the cluster appears to reflect cellular stress responses that maintain proteome integrity via proteasomal degradation and autophagy, with linked mitochondrial/ER involvement. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":1},{"id":"GO:1990171","count":1},{"id":"GO:1903715","count":1},{"id":"GO:0061166","count":1},{"id":"GO:0035617","count":1}]},{"hash":"1446358653790638948","title":"Synaptic vesicle trafficking","description":"The top GO terms point to vesicle docking in exocytosis and synaptic vesicle budding, with dendrite morphogenesis supporting a neuronal context. Other terms (bone morphogenesis, nuclear processes) appear peripheral, so the strongest coherent theme is neuronal vesicle trafficking, though the signal is not strong across all terms.","confidence":"Low","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006904","count":1},{"id":"GO:0070142","count":1},{"id":"GO:0036035","count":1},{"id":"GO:0043552","count":1},{"id":"GO:0006998","count":1}]},{"hash":"1627572937376601356","title":"SCF-mediated ubiquitination in mitosis","description":"The top terms are dominated by ubiquitin-proteasome\u2013related processes (SCF-dependent ubiquitination, protein polyubiquitination, ubiquitin-protein ligase activity) and mitotic cell cycle regulation (mitotic G1 checkpoint signaling, negative regulation of cell proliferation). This suggests a coherent cluster of proteins involved in ubiquitin-mediated proteolysis that controls mitosis and DNA damage responses, with a few outliers that may reflect ancillary or noisy associations. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051436","count":2},{"id":"GO:0031571","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0021678","count":1}]}]