[{"hash":"1137029441640198478","title":"Unknown","description":"The top GO terms span very disparate biological themes (angiogenesis and leaf formation suggest development in plants/animals, while mycothiol, ectoine, melatonin biosynthesis, and polyamine acetylation point to diverse metabolic pathways). There isn\u2019t a cohesive single function that ties all terms together, so a precise, representative label isn\u2019t supported.","confidence":"","size":29,"edges":286,"triangles":2034,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":24},{"id":"GO:0032918","count":22},{"id":"GO:0010125","count":22},{"id":"GO:2000025","count":22},{"id":"GO:0046208","count":22}]},{"hash":"179673319453759775","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms for ubiquitination and ubiquitin-driven proteolysis (protein ubiquitination, ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, autoubiquitination) and ERAD, with a note on Wnt receptor turnover. The presence of these terms indicates proteins involved in tagging substrates for degradation and regulated proteostasis, potentially linked to growth regulation via Wnt signaling and dosage compensation contexts.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0038018","count":6},{"id":"GO:0060816","count":6},{"id":"GO:0033280","count":6}]},{"hash":"1268824118112269468","title":"Transcriptional Regulation and Chromatin Modification","description":"This cluster is dominated by GO terms related to DNA-templated transcription, protein methylation, and histone-related chromatin marks, suggesting a common theme of transcriptional control and epigenetic regulation. Several terms point to stress-responsive transcription (e.g., cellular response to xenobiotic stimulus, apoptosis, heat-stress transcription regulation). A few metabolic terms (antibiotic biosynthetic process, biotin biosynthesis) appear peripheral, likely reflecting annotation breadth rather than a central function. Overall, the data imply a focus on transcriptional regulation and chromatin state in response to stress rather than a single metabolic pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0061408","count":3},{"id":"GO:0055114","count":3}]},{"hash":"868882233477184656","title":"Rho/Ras GTPase Signaling and Actin Remodeling","description":"This cluster is dominated by GO terms tied to small GTPase signaling (Ras, Rho) and their regulation, alongside processes for actin cytoskeleton dynamics (microspike assembly, actin filament binding) and cell movement (neuron projection development, smooth muscle cell migration). The converging theme is signaling-driven remodeling of the actin cytoskeleton to drive cellular motility.","confidence":"High","size":29,"edges":24,"triangles":12,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046580","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0009395","count":4},{"id":"GO:0010976","count":4}]},{"hash":"2001566692611086835","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":5,"triangles":0,"max_degree":3,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000209","count":9},{"id":"GO:0048568","count":8},{"id":"GO:0006888","count":8},{"id":"GO:0000724","count":7},{"id":"GO:0000463","count":7}]},{"hash":"1312258809253453649","title":"Central carbon metabolism and amino acid catabolism","description":"The top GO terms are dominated by central metabolism: glycolysis, TCA cycle, pyruvate biosynthesis, and amino acid catabolic/ biosynthetic processes (L-alanine, L-serine, L-kynurenine). Although Notch signaling appears among the terms, it seems peripheral to the core metabolic theme that ties the majority of proteins in this cluster to energy production and amino-acid turnover. Therefore, the cluster is best described as central carbon metabolism and amino acid catabolism.","confidence":"Medium","size":29,"edges":405,"triangles":3627,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":11},{"id":"GO:0097053","count":11},{"id":"GO:0042853","count":11},{"id":"GO:0006564","count":10},{"id":"GO:0051591","count":10}]},{"hash":"1400364091072256933","title":"Unknown","description":"The top GO terms span diverse biological contexts (ROS generation, hydrogen peroxide biosynthesis, pH stress response, thyroid hormone generation, bone resorption, iron import, gravity detection, cuticle development, and hormone regulation) across different organisms, with no single coherent function dominating. This lack of a shared core theme across the proteins makes it unclear what common function ties the cluster together.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042554","count":4},{"id":"GO:0003081","count":4},{"id":"GO:0008365","count":4},{"id":"GO:0098706","count":4},{"id":"GO:1990451","count":4}]},{"hash":"185145633432263951","title":"Heavy metal detoxification and transport","description":"The GO terms cluster around detoxification and transport of metal ions (cadmium, zinc, copper), phytochelatin biosynthesis, and metal ion import/transport, pointing to plant metal-detox pathways. A peripheral term on indole glucosinolate catabolism fits plant metabolism but doesn\u2019t alter the core theme. This suggests a cohesive function in metal handling and transport.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":1},{"id":"GO:0098849","count":1},{"id":"GO:0010038","count":1},{"id":"GO:0010273","count":1},{"id":"GO:0042344","count":1}]},{"hash":"995823165025394084","title":"Neural development and axon guidance","description":"The top GO terms point to nervous system development (hippocampus, general nervous system, cochlea morphogenesis) and axon guidance (Roundabout signaling). Additional terms about vesicle trafficking and signaling (endosome transport, Rap signaling) fit neural development contexts where precise membrane trafficking and signaling regulate neurite outgrowth and guidance. Together, these terms suggest a cohesive cluster centered on neural development and axon guidance with supporting trafficking processes.","confidence":"High","size":29,"edges":76,"triangles":50,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021766","count":8},{"id":"GO:0007399","count":8},{"id":"GO:0050852","count":8},{"id":"GO:0032889","count":7},{"id":"GO:0031578","count":7}]},{"hash":"2079616414774319924","title":"Cardiac Muscle and Vascular Development","description":"The top terms cluster around muscle regeneration, heart-field cardioblast proliferation (a cardiac development process linked to Notch signaling), and sprouting angiogenesis with endothelial proliferation, pointing to a shared theme of muscle/heart development and vascular growth. While vitamin D response, ubiquitination, and mRNA processing are more general cellular processes present in many contexts, the strongest signals describe muscle and heart/vascular formation and remodeling. Therefore this label succinctly captures the main functional theme of the cluster.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033280","count":9},{"id":"GO:0016567","count":9},{"id":"GO:0006397","count":7},{"id":"GO:0035508","count":7},{"id":"GO:0043403","count":7}]},{"hash":"909710380987718146","title":"Calcium signaling in cardiac hypertrophy and vascular morphogenesis","description":"The cluster shows strong representation of calcium-related processes (detection of calcium ions, regulation of postsynaptic cytosolic calcium, and the calcineurin-NFAT signaling cascade) alongside cardiac hypertrophy in response to stress and its positive regulation. The presence of vascular morphogenesis terms (branching in blood vessel morphogenesis) suggests coordinated calcium-dependent signaling influencing cardiac and vascular remodeling. While there are some unrelated terms (e.g., ascospore formation), the dominant signal points to calcium-mediated control of heart hypertrophy and blood vessel remodeling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014898","count":5},{"id":"GO:0033173","count":4},{"id":"GO:0005513","count":4},{"id":"GO:0001837","count":4},{"id":"GO:0035562","count":4}]},{"hash":"101074914090441022","title":"Cell Division and Innate Immunity","description":"The cluster strongly features mitotic cell cycle terms (cell division, APC/C-dependent catabolic process, K11-linked ubiquitination) indicating roles in mitosis and protein turnover, plus innate immune terms (innate immune response, type I interferon, dsRNA response, antiviral defense). This mix suggests a group of proteins involved in both cell-cycle control and antiviral signaling, or shared regulation linking mitosis with immune pathways.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0000278","count":8},{"id":"GO:0070979","count":7},{"id":"GO:0031145","count":7},{"id":"GO:2001162","count":7}]},{"hash":"2240317349543855757","title":"Ubiquitin-mediated protein modification and turnover","description":"The cluster is dominated by GO terms related to ubiquitination (protein ubiquitination, ubiquitin-dependent protein catabolic process, and multiple ubiquitin linkage types like K48, K63, K6) including autoubiquitination, indicating a focus on ubiquitin-driven protein modification and degradation. Additional terms like histone catabolic process and maintenance of protein localization support roles in turnover and trafficking, with vitamin D response and TNF signaling aligning with ubiquitin-regulated signaling pathways. Confidence: High","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016567","count":10},{"id":"GO:0042787","count":8},{"id":"GO:0033280","count":7},{"id":"GO:0070936","count":7},{"id":"GO:0051865","count":7}]},{"hash":"1533851761284072809","title":"Telomere maintenance and cell-cycle regulation","description":"The cluster is dominated by telomere-related processes (positive regulation of telomere capping; positive regulation of telomere maintenance via telomerase) and cell-cycle control (negative regulation of cyclin-dependent protein serine/threonine kinase activity), with supporting signals from RNA processing, ubiquitination, differentiation, and signaling responses. This suggests a core theme around chromosome end maintenance and associated cell-cycle regulation, with broader regulatory processes represented, rather than a single tightly cohesive function.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1904355","count":11},{"id":"GO:0006397","count":11},{"id":"GO:0035994","count":11},{"id":"GO:0032212","count":11},{"id":"GO:0016477","count":11}]},{"hash":"1116698122675950088","title":"Fruit ripening and hormone-regulated biosynthesis","description":"This cluster centers on fruit ripening (ethylene) and hormone-linked biosynthesis, including auxin-related processes and production of secondary metabolites (proanthocyanidins, glucans), with transcriptional regulation implied by DNA-templated transcription terms. The GO terms collectively point to a plant developmental/metabolic program tied to ripening and hormone signaling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009835","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0006078","count":2},{"id":"GO:0009693","count":2}]},{"hash":"1874793685714186791","title":"Cell envelope glycan and capsule biosynthesis","description":"GO terms indicate biosynthesis of various surface polysaccharides and related glycan assembly steps (GPI anchors, capsule and hyaluronan, cellulose, mycolate layer) and the metabolism of sugar donors (UDP-glucose/galactose). The common thread is production of cell-surface glycans and envelope components, suggesting these proteins function in glycan/capsule biosynthesis and export rather than a single enzyme class.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:1903955","count":1},{"id":"GO:0030244","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0030213","count":1}]},{"hash":"2300998554070556733","title":"Unknown","description":"The proteins show a mix of GO terms spanning mitotic cytokinesis, histamine secretion, various biosynthetic processes (porphyrin/heme, chlorophyll, one-carbon metabolism), ion transport (cobalt and magnesium), mitochondrial transport, and insulin secretion regulation, with no clear shared function or pathway. There are no edges, suggesting a lack of cohesive functional connectivity, so there isn\u2019t a unifying theme to name a specific cluster; hence Unknown. ","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000281","count":2},{"id":"GO:1903595","count":2},{"id":"GO:0019353","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0015995","count":1}]},{"hash":"1030391196477511320","title":"Methylation and RNA modification","description":"This cluster is dominated by methylation-related processes: multiple GO terms describe methyltransferase activities on peptides (peptidyl-lysine/arginine methylation) and on RNA (rRNA, tRNA, and mRNA cap), plus chromatin-related effects (rDNA heterochromatin formation). An outlier term, nodulation, is less connected to the core theme. Overall, the proteins appear to be methyltransferases involved in RNA modification and chromatin regulation.","confidence":"High","size":28,"edges":376,"triangles":3225,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":8},{"id":"GO:0031167","count":8},{"id":"GO:0018013","count":7},{"id":"GO:0018023","count":7},{"id":"GO:0000183","count":7}]},{"hash":"783008729716645632","title":"Vacuolar amino acid transporters","description":"Top GO terms point to transmembrane transport of amino acids and related compounds, particularly into and out of the vacuole (arginine, tyrosine, histidine, proline, glutamine). A xenobiotic transport term is present but the dominant signal is vacuolar amino acid transport.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:1903070","count":2},{"id":"GO:0051365","count":2},{"id":"GO:0090514","count":2},{"id":"GO:0015824","count":2}]},{"hash":"2241419927377808053","title":"Male reproductive development and steroid signaling","description":"The cluster shows strong enrichment for cell division, male sex differentiation, prostate gland development, and steroid hormone receptor complex assembly, indicating a core theme of male reproductive development and hormone signaling. Immune-related terms like innate immune response and interferon response appear as secondary annotations, suggesting they are ancillary rather than the defining function of the cluster.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0046661","count":8},{"id":"GO:0006463","count":8},{"id":"GO:0030850","count":8},{"id":"GO:0071357","count":8}]},{"hash":"475988471310692067","title":"Endosomal trafficking and autophagy (Cvt)","description":"The top GO terms cluster around transport between endosomes, Golgi, and lysosomes, plus the cytoplasm-to-vacuole targeting (Cvt) pathway, indicating a cohesive group of proteins involved in endosomal maturation and autophagy-related trafficking. Some terms about plasma membrane localization and phosphorylation regulation appear, suggesting regulatory roles linked to trafficking processes. A few mitotic terms are present but likely reflect multifunctional proteins rather than a shared mitosis function. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045022","count":5},{"id":"GO:0032258","count":4},{"id":"GO:0034498","count":4},{"id":"GO:0008333","count":4},{"id":"GO:0090307","count":4}]},{"hash":"1898368811654191716","title":"Ubiquitin-Dependent Protein Turnover and Trafficking","description":"Most terms point to ubiquitin-dependent protein catabolism (ERAD, K48-linked ubiquitination, autoubiquitination) and vesicle trafficking (Golgi\u2013endosome transport, endosome organization). Peroxisomal matrix protein import and histone catabolic processes align with turnover and chromatin regulation linked to ubiquitin pathways; nodulation may reflect a plant-specific context. Overall, the cluster centers on ubiquitin-mediated protein turnover intertwined with trafficking.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0016558","count":4},{"id":"GO:0009877","count":3},{"id":"GO:0051301","count":3}]},{"hash":"320168541575334448","title":"RNA Methylation and Transcription Regulation","description":"This cluster is dominated by RNA modification and transcription-related terms, including mRNA capping (7-methylguanosine), various methylations (rRNA, guanine-N7) and DNA-templated transcription, plus negative regulation of RNA Pol II transcription. The presence of protein methylation/oxidation terms (peptidyl-lysine dimethylation, peptidyl-arginine hydroxylation) further supports a theme of transcriptional and post-translational regulation. The biosynthetic and xenobiotic response terms may reflect broader metabolic coordination with gene expression. Overall, the strongest signal ties to RNA processing and transcription control. ","confidence":"Medium","size":28,"edges":9,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":6},{"id":"GO:0006370","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0018027","count":5}]},{"hash":"1560229254643254058","title":"Developmental Regulation and Genome Maintenance","description":"This cluster centers on development-related functions (neuron and forebrain development; multicellular development; myoblast fusion) and gene expression and genome maintenance activities (DNA-templated transcription, DNA repair and replication) plus regulation of protein turnover and apoptosis, suggesting a cohesive theme of developmental programming with genome and proteome maintenance. The defense response to Gram-positive bacteria is present but secondary to the core developmental and regulatory signals.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048666","count":8},{"id":"GO:0032435","count":8},{"id":"GO:0050830","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0007275","count":8}]},{"hash":"256296269224434925","title":"Kinase-Regulated Signaling and Immune Pathways","description":"The cluster centers on regulation of signaling activities (positive regulation of GTPase activity, serine/threonine kinase activity, and autophosphorylation) with immune signaling components (NOD-like receptor pathway and NF-kappaB related regulation), plus links to cell proliferation, mitosis, and hypoxia response, suggesting a broad module of signaling control and associated stress/immune responses rather than a single enzymatic function; a few terms like xylan catabolic process may reflect annotation noise.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0071902","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0045493","count":4},{"id":"GO:0008284","count":4}]},{"hash":"170812872647456831","title":"Mechanosensory signaling and protein regulation","description":"This cluster is dominated by GO terms for detection and cellular response to mechanical stimuli (GO:0050966, GO:0071260), pointing to mechanotransduction. The presence of protein ubiquitination (GO:0016567) and processes related to membrane localization (GO:0072660) suggests regulation of signaling proteins at the plasma membrane. Some terms (e.g., vitamin D response, NOD2 signaling) are less central but do not override the core mechanosensory theme. Overall, the label reflects mechanosensory signaling with protein regulation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050966","count":8},{"id":"GO:0032088","count":8},{"id":"GO:0071260","count":8},{"id":"GO:0016567","count":8},{"id":"GO:0033280","count":8}]},{"hash":"357926746420915552","title":"Chloroplast metabolism and photoprotection","description":"The top GO terms cluster around plastid lipid biosynthesis (very long-chain fatty acid biosynthesis, fatty acid elongation), photoprotection (nonphotochemical quenching, photoreceptor maintenance), and photosynthetic components (cytochrome complex assembly, redox homeostasis), suggesting a cohesive role in chloroplast function and light stress responses. A few terms about nuclear regulation appear as noise rather than core to the cluster. Therefore, the label reflects the dominant chloroplast-related theme with moderate confidence.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042761","count":2},{"id":"GO:0030497","count":2},{"id":"GO:0045494","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0046826","count":2}]},{"hash":"1160189240087231243","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032782","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0030111","count":2},{"id":"GO:0098924","count":2},{"id":"GO:0007168","count":2}]},{"hash":"289846582723572530","title":"Nuclear chromatin remodeling and transcription control","description":"Most terms are about nuclear processes that regulate gene expression, including chromatin remodeling, histone modifications (acetylation/exchange), and regulation of DNA-templated transcription, plus DNA repair and ribosomal subunit export from the nucleus. The presence of obsolete histone-related terms and a few outliers suggests a broader set of chromatin/gene-expression regulators rather than a single cytoplasmic pathway. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0006338","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0042993","count":1},{"id":"GO:0043968","count":1}]},{"hash":"2194885646682830428","title":"Antiviral innate immune signaling","description":"The GO terms are centered on innate immune responses to viral infection, dsRNA sensing, interferon-beta production, TLR/MyD88 signaling, and macrophage activation, indicating a cohesive antiviral innate signaling module (TLR/NOD2 pathways driving inflammatory and interferon responses).","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":7},{"id":"GO:0051607","count":6},{"id":"GO:0032088","count":6},{"id":"GO:0070431","count":6},{"id":"GO:0045359","count":6}]},{"hash":"240635929687473850","title":"Lipid Metabolism and Hormone Response","description":"The top GO terms center on lipid metabolism (fatty acid oxidation, cholesterol biosynthetic process) and endocrine signaling (cellular response to peptide hormone stimulus, including FSH), suggesting proteins linked to lipid pathways and hormone-responsive signaling.","confidence":"Medium","size":27,"edges":9,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":11},{"id":"GO:0019395","count":8},{"id":"GO:0006695","count":8},{"id":"GO:0071375","count":8},{"id":"GO:0071372","count":8}]},{"hash":"544752766094703827","title":"Heat stress response and protein quality control","description":"This cluster centers on cellular stress handling, with recurrent terms for heat response and unfolded protein response, plus maintenance of protein localization, indicating a program of protein quality control; some RNA processing and growth-related terms are present but secondary, suggesting a cohesive theme around stress-induced protein management rather than a single specific pathway.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0072001","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0009736","count":2}]},{"hash":"1742224106965653495","title":"Endosome\u2013Vacuole Trafficking and Prospore Membrane Formation","description":"The top GO terms point to vesicle formation and trafficking within the endomembrane system, including intralumenal vesicle formation, endosome transport to late endosome and to the Golgi, and vacuole\u2013ER tethering, plus a specific fungal sporulation process (prospore membrane formation). Phosphatidic acid biosynthesis also ties to membrane biogenesis, supporting a membrane trafficking/assembly theme. Taken together, the cluster seems focused on endomembrane trafficking and membrane formation in yeast-like systems, with a nod to sporulation membranes. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070676","count":3},{"id":"GO:0032258","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0034498","count":2},{"id":"GO:2000769","count":2}]},{"hash":"1055325951908019404","title":"RNA processing and translation initiation","description":"The top GO terms center on RNA processing (mRNA splicing, polyadenylation), transcription, and translation initiation/regulation (preinitiation complex formation, IRES-dependent initiation, translation reinitiation). This suggests a cluster rich in gene expression machinery spanning transcription through translation, rather than a single pathway. Some terms about cellular responses or viral transcription may be incidental context, but the core theme is RNA processing and translation control.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0002188","count":2}]},{"hash":"791192173685958912","title":"Skeletal Development and Morphogenesis","description":"This cluster is dominated by terms related to multicellular development and cartilage condensation, with supporting themes of cell migration and tissue morphogenesis, suggesting roles in skeletal development. Additional terms point to gene regulation and mechanotransduction, which fit within developmental processes that shape tissues. Some outliers (pain perception, sperm capacitation) may reflect broader protein functions or annotation noise, but the core signal aligns with skeletal development. ","confidence":"Medium","size":27,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":13},{"id":"GO:0019233","count":13},{"id":"GO:0046827","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0048240","count":9}]},{"hash":"915471126529458201","title":"Cell signaling and polarity-driven migration","description":"This cluster centers on signaling pathways (Wnt, T cell receptor) and vesicle trafficking/polarity processes (endosome transport, Cvt pathway, cell polarity and shape), which together influence cell movement, morphology, and related functions. The terms are diverse but connect through signaling guiding trafficking and polarity to regulate migration and cell behavior; some terms are broad or tissue-specific, so confidence is moderate.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":4},{"id":"GO:0000186","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0032258","count":4},{"id":"GO:0050885","count":3}]},{"hash":"934677858936420329","title":"Chromatin organization and DNA repair","description":"The dominant GO terms point to chromatin maintenance processes (nucleosome assembly, heterochromatin formation, histone modification) and genome stability via replication-born double-strand break repair, suggesting a chromatin-centric cluster. A few terms related to muscle, olfactory nerve structure, and placenta morphogenesis appear peripheral or due to broader annotations. Overall, chromatin organization and DNA repair best captures the core theme of this cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010520","count":2},{"id":"GO:0016203","count":2},{"id":"GO:0014809","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0021629","count":2}]},{"hash":"1265518332569618527","title":"Cell Cycle, Growth Signaling, and RNA Processing","description":"This cluster centers on cell proliferation and growth control, including cell cycle and mitotic orientation, TORC1 nutrient signaling, telomere maintenance, and mRNA processing; a few outliers (skeletal development, cellular fusion) may reflect broad annotations, but the core theme links growth regulation and division.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":4},{"id":"GO:0001403","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0032212","count":3}]},{"hash":"1443933562731235565","title":"Cell cycle progression and proliferation signaling","description":"The top GO terms cluster around regulation of G2/M transition, cell division, and positively regulated CDK activity, all pointing to mitotic progression and proliferative signaling. The presence of canonical Wnt signaling further supports a role in growth and cell-cycle\u2013related processes, while transcription-related terms suggest coordinated gene expression during these events.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0032026","count":1},{"id":"GO:0046626","count":1},{"id":"GO:0030857","count":1}]},{"hash":"51561407109799296","title":"Unknown","description":"The GO terms are highly diverse, spanning neural signaling (potassium transport, excitatory postsynaptic potential, Schwann cell development, cocaine response) and core cell-cycle/DNA replication processes (G1/S transition, DNA replication, meiosis, kinetochore localization). With no edges and no clear single functional theme, there isn\u2019t a cohesive cluster function to label more specifically.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006813","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0009636","count":4},{"id":"GO:0042220","count":3},{"id":"GO:0000082","count":3}]},{"hash":"644722758821706940","title":"Unknown","description":"The GO terms attached to this cluster are highly diverse (immune signaling, nutrient response, vascular development/wound healing, cytolysis, metal ion homeostasis, neuromuscular processes, adiponectin signaling, etc.) with no single dominant function tying most proteins together. This makes it difficult to assign a specific cohesive biological role to the cluster; thus Unknown is most appropriate.","confidence":"","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901223","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0061042","count":1},{"id":"GO:0019835","count":1},{"id":"GO:0006882","count":1}]},{"hash":"1901222874901828199","title":"Cardiac and vascular development signaling","description":"This cluster\u2019s terms center on heart-field Notch signaling, angiogenesis and endothelial proliferation, and skeletal muscle regeneration, indicating a cardiovascular development and tissue regeneration signaling module; some entries are labeled obsolete, but the core theme is heart/vascular growth and muscle repair.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":12},{"id":"GO:0072660","count":11},{"id":"GO:0035508","count":11},{"id":"GO:0043403","count":11},{"id":"GO:0000083","count":11}]},{"hash":"1477485504900329475","title":"Cellular oxidative stress response","description":"The top GO terms cluster around cellular responses to diverse stressors, notably oxidative stress and toxin-related challenges (gamma radiation, diamide, sodium arsenite, singlet oxygen, cadmium). Despite a few obsolete terms, the common theme is a shared function in sensing and responding to cellular stress.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":2},{"id":"GO:1900462","count":2},{"id":"GO:0072738","count":2},{"id":"GO:1903936","count":2},{"id":"GO:0043497","count":2}]},{"hash":"439905064197127999","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900015","count":2},{"id":"GO:0003100","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0000973","count":2},{"id":"GO:0071039","count":2}]},{"hash":"1927341119222176769","title":"RNA Processing and Spliceosome Assembly","description":"Top GO terms are dominated by nuclear processes: spliceosomal snRNP assembly (GO:0000387), RNA processing (GO:0006396), and nucleosome assembly (GO:0006334). These indicate a core focus on RNA maturation and chromatin organization. Other terms point to vesicular trafficking and neural development, but they appear less represented, suggesting the cluster is primarily related to RNA metabolism with secondary roles in trafficking.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":2},{"id":"GO:2000616","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0006396","count":1},{"id":"GO:0006896","count":1}]},{"hash":"1351186490309383083","title":"Cytoskeletal Dynamics in Mitosis and Neurons","description":"The cluster is enriched for microtubule- and cytoskeleton-related processes (spindle assembly and dynamics, minus-end directed sliding, actomyosin ring formation) tied to cell division, along with neuron-specific terms (neuron projection maintenance, dendritic transport) and stress granule disassembly. This suggests a unifying theme of cytoskeletal regulation governing mitosis and neuronal transport/structure.","confidence":"High","size":26,"edges":90,"triangles":120,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":11},{"id":"GO:0045218","count":10},{"id":"GO:0032886","count":10},{"id":"GO:0051255","count":10},{"id":"GO:0000073","count":10}]},{"hash":"140165078459757670","title":"Wnt/PCP Signaling in Heart Morphogenesis","description":"The top GO terms center on Wnt signaling pathways (canonical and non-canonical) and planar cell polarity, with roles in morphogenesis such as outflow tract formation and neural/wing patterning. Terms about JNK activation, GTPase regulation, and microtubule localization further support PCP/JNK signaling as the core theme governing embryonic tissue morphogenesis represented by this cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0003151","count":3},{"id":"GO:0090179","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0043507","count":2}]},{"hash":"2079273561968091541","title":"Neural development and cytoskeletal dynamics","description":"This cluster is dominated by terms tied to central nervous system development, forebrain development, and neuron/axon formation (axonogenesis, axonal fasciculation), along with terms for cytoskeletal organization and signaling via small GTPases (Rho) and actin polarity. These collectively point to neural development driven by cytoskeletal remodeling and signaling. Some terms (e.g., mammary gland development, vascular permeability) are more general or peripheral noise but do not override the core theme.","confidence":"High","size":26,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007264","count":1},{"id":"GO:0035024","count":1},{"id":"GO:0007413","count":1},{"id":"GO:0030879","count":1},{"id":"GO:0030950","count":1}]},{"hash":"2030663603476147101","title":"DNA repair and telomere maintenance","description":"This cluster centers on genome stability, with GO terms about DNA ligation in repair, protection from NHEJ at telomeres, and subtelomeric heterochromatin formation. The presence of G-quadruplex DNA formation and telomere-associated chromatin hints further at telomere biology. PARP-related activities (poly-ADP-ribosylation) and energy-related terms suggest DNA damage response involvement, tying together repair and chromatin maintenance at chromosome ends.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0051103","count":2},{"id":"GO:0031848","count":2},{"id":"GO:0071919","count":2},{"id":"GO:0035390","count":2}]},{"hash":"484411189520864767","title":"RNA Methylation and Cofactor Biosynthesis","description":"The cluster is enriched in RNA modification (guanine-N7 methylation, tRNA methylation) and biosynthetic pathways for cofactors like biotin and cobalamin, along with related biosynthetic processes such as antibiotic biosynthesis. This pattern suggests a cohesive group of proteins involved in nucleotide modification and small-molecule cofactor production, with some broader metabolic roles. ","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0036265","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0009236","count":5},{"id":"GO:0030488","count":5}]},{"hash":"105361377281046437","title":"Unknown","description":"The top GO terms span diverse areas: hormone biosynthesis (prostaglandin, aldosterone, ecdysone), various tissue development (retina vasculature, mammary and prostate glands), and xenobiotic metabolism (carbazole and camphor catabolic processes) with no clear unifying function tying them together. This lack of a cohesive theme makes a precise, intuitive label difficult, so Unknown is appropriate.","confidence":"","size":26,"edges":30,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":11},{"id":"GO:0046232","count":11},{"id":"GO:0006697","count":10},{"id":"GO:0061298","count":10},{"id":"GO:0030879","count":10}]},{"hash":"1625149620115868358","title":"Unknown","description":"The terms are highly heterogeneous, including developmental signaling (mesoderm, smoothened pathway), stress responses (heat, cadmium), DNA replication, RNA processing, and cell cycle regulation. With no edges or cohesive functional theme tying the proteins together, there isn't a clear common function to label the cluster beyond an undefined, mixed set.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0006260","count":2}]},{"hash":"985017985521971877","title":"RNA Processing and Cytoskeletal Spindle Assembly","description":"Top GO terms show RNA metabolism (mRNA processing, regulation of mRNA stability) alongside cytoskeletal and mitotic processes (actin filament bundle assembly, spindle assembly), with additional signals for telomere maintenance and cell growth. This pattern suggests a cluster of proteins involved in coordinating RNA processing with cell division and cytoskeletal dynamics, rather than a single narrowly defined function.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032212","count":6},{"id":"GO:0016049","count":6},{"id":"GO:0051225","count":6},{"id":"GO:0051017","count":6},{"id":"GO:0090501","count":6}]},{"hash":"393000189264377810","title":"Innate Immunity and Endomembrane Trafficking","description":"The cluster centers on innate immune responses (defense against virus, innate immunity) and endomembrane system processes (ER tubular network formation, Golgi protein retention, endomembrane organization) with ongoing vesicle dynamics like pinocytosis and cytoskeletal remodeling (microspike assembly). Some terms touch broader signaling (glucocorticoid signaling, SMAD assembly), but the dominant pattern links immune defense with intracellular trafficking and membrane organization.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":3},{"id":"GO:0051607","count":2},{"id":"GO:0042921","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0045842","count":2}]},{"hash":"511369139964201730","title":"Unknown","description":"The GO terms span diverse and seemingly unrelated processes, including lipid catabolism (monoacylglycerol, triglyceride, phosphatidylserine), biosynthesis in bacteria (antibiotic, menaquinone, biotin), plant-specific processes (secondary shoot formation, chlorophyll catabolic), and even regulation of endocannabinoid signaling. There isn\u2019t a single unifying function or pathway that ties these terms together, so a cohesive, intuitive cluster label cannot be confidently assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0052651","count":7},{"id":"GO:2000124","count":7},{"id":"GO:0006660","count":7},{"id":"GO:0019433","count":7}]},{"hash":"767367842411718556","title":"Ubiquitin-Dependent Protein Degradation","description":"Dominated by GO terms for protein ubiquitination and ubiquitin-dependent proteolysis (including autoubiquitination and ERAD), suggesting the cluster is enriched for components of the ubiquitin-proteasome system. Additional terms point to cell-cycle-related processes (spindle assembly, transcription regulation in G1/S) that are commonly regulated by ubiquitination. Overall, the function centers on tagging and degradation of proteins, with some cell-cycle regulatory connections.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0051865","count":7},{"id":"GO:0000083","count":6},{"id":"GO:0085020","count":6}]},{"hash":"1520625348133692012","title":"Amino acid and polyamine membrane transporters","description":"This cluster is enriched for GO terms describing transport of amino acids and related metabolites across the plasma membrane (L-lysine, L-arginine, ornithine, methionine, D-alanine, GABA, ammonium, polyamines) and includes transepithelial transport and import across membranes; the common theme is membrane transport of amino acids and related compounds.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070634","count":3},{"id":"GO:0002537","count":2},{"id":"GO:0042941","count":2},{"id":"GO:0097639","count":2},{"id":"GO:0015812","count":2}]},{"hash":"315715126225502022","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":29,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0097171","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0009244","count":4}]},{"hash":"344125702105816749","title":"Membrane transport and surface interactions","description":"The top GO terms point to membrane-related functions, including xenobiotic and transmembrane transport, brush border assembly, plasma membrane repair, and sperm-surface interactions (binding and motility). These indicate a cohesive theme of membrane dynamics and cell-surface processes, with a few terms like DNA repair serving as outliers. Overall, the cluster seems centered on membrane transport and surface organization.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0007339","count":2}]},{"hash":"1347234901622789376","title":"Transcriptional Regulation under Amino Acid Starvation","description":"Based on the enrichment of GO terms centered on DNA-templated transcription, negative regulation of transcription by RNA polymerase II, and cellular response to amino acid starvation, the cluster appears to comprise transcriptional regulators activated during nutrient stress, coordinating gene expression and stress responses. Some terms related to regeneration and mechanosensory detection are broader but likely reflect shared regulatory roles across tissues. ","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0060546","count":3},{"id":"GO:1903206","count":2},{"id":"GO:0043388","count":2}]},{"hash":"478555437218820815","title":"Wnt signaling and muscle regeneration","description":"The top GO terms point to Wnt signaling, cell growth/proliferation, and mitotic processes, with a notable connection to skeletal muscle tissue regeneration, suggesting these proteins jointly participate in Wnt-mediated growth and muscle repair. Some beyond-core terms (e.g., obsolete GPCR-related terms and cold response) appear as minor outliers, but the central theme remains Wnt-driven proliferation and muscle regeneration.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016055","count":5},{"id":"GO:0016049","count":5},{"id":"GO:0007205","count":5},{"id":"GO:0008284","count":4},{"id":"GO:0000278","count":4}]},{"hash":"1867155828551911016","title":"Skeletal muscle signaling and regeneration","description":"This cluster shows a strong representation of skeletal muscle tissue regeneration (GO:0043403) and intracellular signal transduction (GO:0035556), suggesting a muscle-centered signaling/regeneration theme. Additional terms related to basic cellular processes such as cell growth and vesicle trafficking (e.g., SNARE regulation) support muscle function and communication. Overall, the dominant muscle-related term combined with signaling components justifies a muscle regeneration and signaling label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":11},{"id":"GO:0035556","count":11},{"id":"GO:0006397","count":11},{"id":"GO:0072660","count":10},{"id":"GO:0035508","count":10}]},{"hash":"697810846271687784","title":"Wnt-Driven Growth and Muscle Development","description":"Dominant GO term is Wnt signaling (GO:0016055) with 8 proteins, backed by muscle- and growth-related terms (skeletal muscle tissue regeneration, multicellular organism growth, cell growth). This suggests a cluster enriched for Wnt-mediated control of growth and muscle development/regeneration. Protein localization in the plasma membrane hints at coordinated trafficking during these processes. Some terms are obsolete or tangential (SA node regulation, cold response), but the core theme is Wnt-driven growth and muscle biology.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016055","count":8},{"id":"GO:0098907","count":6},{"id":"GO:0007205","count":6},{"id":"GO:0035264","count":6},{"id":"GO:0072660","count":5}]},{"hash":"744496331362209068","title":"RNA Processing and Metabolism","description":"The top GO terms are dominated by post-transcriptional regulation: nonsense-mediated mRNA decay, mRNA stabilization, and methylation of rRNA and tRNA, indicating a core RNA processing/metabolism theme. Telomere-related terms appear but are less representative of the overall set; a few terms are general stress or growth signals. Thus, the label reflects the strongest, most consistent signal across the cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904354","count":2},{"id":"GO:0000184","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0048714","count":2},{"id":"GO:0007004","count":2}]},{"hash":"918904189821976068","title":"ECM Remodeling, Coagulation, and Innate Immunity","description":"The cluster is dominated by terms for extracellular matrix disassembly, blood coagulation, fibrinogen regulation, and proteolysis, all pointing to ECM turnover and coagulation. Concurrently, innate immune signaling (Toll) and defense responses to Gram-positive bacteria and fungus suggest immune activation, while Wnt signaling and growth relate to developmental or tissue growth processes; together these indicate a cohesive theme of tissue remodeling coordinated with immune and coagulation pathways.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0022617","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0050830","count":3}]},{"hash":"320321938591794350","title":"Muscle differentiation and motor neuron development","description":"Based on the GO terms, the proteins are enriched for skeletal muscle cell differentiation, spinal cord motor neuron differentiation, neuromuscular process controlling balance, and musculoskeletal movement, with supporting signals from IGF receptor signaling. This points to a shared function in muscle development and neuromuscular coordination, even though a few terms relate to general transcriptional regulation. Overall, a coherent theme around muscle and motor neuron biology emerges, with some noise from broader RNA processing terms.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016441","count":2},{"id":"GO:0061157","count":2},{"id":"GO:0051123","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1518733363205285209","title":"Dendritic Spine Morphogenesis and Synapse Organization","description":"The dominant GO terms center on neuronal synapse formation (dendritic spine morphogenesis, receptor clustering, protein localization to synapse) with Rho signaling shaping spine structure, suggesting a synaptic development theme; other terms reflect broad development or general transcription/cell cycle roles that are less central.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060997","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0008285","count":2}]},{"hash":"2293135771760590499","title":"Cell stress response and genome maintenance","description":"The terms cluster around cellular stress mechanisms and genome integrity: apoptosis, base-excision DNA repair, redox homeostasis, and regulation of mRNA stability, with additional hormone response. Although there are diverse terms like spermatogenesis and corneocyte development, the common thread is stress response and genome maintenance activities across cells, supporting this label.","confidence":"Medium","size":25,"edges":23,"triangles":12,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0080111","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0071375","count":2}]},{"hash":"2242096921504492329","title":"Unknown","description":"The top GO terms are scattered across neural development (cerebral cortex, in utero embryonic development, pituitary development), RNA processing (alternative mRNA splicing via spliceosome), stress/ xenobiotic responses, and a metabolic biosynthesis step, with several entries marked obsolete. This lack of a coherent, single-function signal suggests the proteins do not share a unified function or pathway, so an Unknown label is most appropriate.","confidence":"","size":25,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0016575","count":9},{"id":"GO:0021987","count":9},{"id":"GO:0021983","count":9},{"id":"GO:0000380","count":9}]},{"hash":"1116526722682648285","title":"Chromatin dynamics and DNA damage response","description":"Enriched terms point to chromatin organization and genome maintenance: heterochromatin formation, chromatin remodeling, telomere-related processes, and replication-associated double-strand break repair. Some RNA modification terms are present but likely peripheral; the dominant signal ties to chromatin dynamics coordinating genome stability and related cellular outcomes like growth and senescence.","confidence":"Medium","size":25,"edges":10,"triangles":0,"max_degree":5,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031167","count":7},{"id":"GO:0000183","count":6},{"id":"GO:0009236","count":5},{"id":"GO:0043044","count":5},{"id":"GO:0061820","count":5}]},{"hash":"1873814800327729615","title":"Drosophila embryonic morphogenesis and patterning","description":"This cluster is dominated by GO terms related to embryonic development across multiple tissues (foregut, hindgut, epidermis, wing disc) and key patterning axes (proximal/distal) plus signaling pathways (Torso and cell surface receptor signaling). The cohesive theme is early Drosophila morphogenesis and tissue patterning, suggesting these proteins participate in broad embryonic development rather than a single tissue. Confidence: High","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048617","count":1},{"id":"GO:0008544","count":1},{"id":"GO:0007362","count":1},{"id":"GO:0035220","count":1},{"id":"GO:0035277","count":1}]},{"hash":"930352105350171422","title":"Aromatic amino acid catabolism and detoxification","description":"This cluster is driven by GO terms for L-tyrosine and L-phenylalanine catabolic processes, glutathione metabolic/redox detoxification, and xenobiotic catabolic activity, with additional signals of antibiotic response and nucleotide salvage. Taken together, these terms point to a metabolic detoxification theme centered on aromatic amino acid breakdown and redox balance, rather than a single specialized pathway; a few outliers (transcription regulation, DNA replication) may reflect annotations or secondary associations. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0006572","count":3},{"id":"GO:0006559","count":3},{"id":"GO:0006749","count":3}]},{"hash":"2162514126743229955","title":"Oxylipin signaling and oxidative stress response","description":"The top GO terms are strongly centered on lipid-derived signaling: oxylipin biosynthesis and jasmonic acid biosynthesis, plus related fatty acid beta-oxidation. Supportive terms like response to ozone and response to toxic substances point to oxidative/chemical stress responses. Some other terms (developmental processes) seem incidental or cross-species, but the core theme across most terms supports lipid-based signaling and stress response. ","confidence":"Medium","size":25,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":4},{"id":"GO:0031408","count":4},{"id":"GO:0009695","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0061000","count":3}]},{"hash":"1514512616691450758","title":"Unknown","description":"The top terms are highly diverse (mitotic cell cycle, heme transport, mitochondrial ATP transport, insulin response, amino acid starvation, transcription) and there are no edges connecting the proteins, making it hard to identify a single cohesive function for the cluster. ","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0015886","count":4},{"id":"GO:0097274","count":4},{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1764365239618993170","title":"Membrane transporters for nutrients and xenobiotics","description":"The top GO terms are dominated by transmembrane transport of small molecules, including sialic acid, xenobiotics, methotrexate, 5-formyltetrahydrofolate, and UDP-N-acetylglucosamine. This indicates a shared role as membrane transporters rather than signaling or organelle-specific processes. Although a few terms relate to stress responses or centrosome cycle, the dominant pattern is transport across membranes, suggesting these proteins function mainly in importing/exporting nutrients and related compounds. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0051958","count":3},{"id":"GO:0015885","count":3},{"id":"GO:1990569","count":2}]},{"hash":"1668277236082783266","title":"Oxidative Stress and Xenobiotic Response","description":"The cluster is dominated by GO terms for responding to lipopolysaccharide, xenobiotic stimuli, and detoxification of oxidants, indicating a shared role in chemical and microbial stress defense. While there are also terms tied to RNA processing and chromatin modification that may reflect regulatory adjustments during stress, and a couple development terms likely reflect pleiotropic functions, the core signal points to oxidative/xenobiotic stress response as the main theme. ","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0032496","count":8},{"id":"GO:0042493","count":7},{"id":"GO:0051572","count":7},{"id":"GO:0098869","count":6}]},{"hash":"1116146357531033728","title":"Vertebrate developmental signaling and morphogenesis","description":"Top GO terms are dominated by developmental and signaling processes across multiple tissues (cranial skeleton morphogenesis, heart valve morphogenesis, orbitofrontal cortex development; FGFR signaling; STAT tyrosine phosphorylation; integrin-mediated adhesion), with some outliers like DNA replication and ovulation. This suggests a broad theme of developmental signaling and tissue morphogenesis in vertebrates rather than a single narrow function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":22},{"id":"GO:0061368","count":22},{"id":"GO:0048701","count":22},{"id":"GO:0035607","count":22},{"id":"GO:0003186","count":22}]},{"hash":"716800983881432827","title":"Actin-based protrusions and ciliogenesis","description":"These proteins prominently involve actin-driven structures (filopodia, microspikes) and regulators of GTPase activity that govern actin dynamics, along with components linked to cilium assembly and intraflagellar transport and related membrane organization. While a few terms lean toward nuclear processes, the dominant signal favors cytoskeletal remodeling and ciliogenesis, making this label a reasonable high-level description. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0010256","count":2},{"id":"GO:0030035","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0006355","count":2}]},{"hash":"215313654148833556","title":"Heart morphogenesis and mechanotransduction with ubiquitination","description":"The top GO terms point to cardiac development (cardiac right atrium morphogenesis, Notch signaling in heart field regulation) and mechanotransduction (cellular response to mechanical stimulus), along with protein ubiquitination, suggesting a cluster of proteins involved in heart formation and mechanosensitive regulation, with ubiquitin-related control. Some terms are obsolete, but the core theme remains focused on heart development and mechanical signaling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0003270","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0003213","count":5},{"id":"GO:0032088","count":5}]},{"hash":"774199868289215006","title":"Calcium-Dependent Signaling and Vesicle Trafficking","description":"The cluster is dominated by GO terms linked to calcium signaling and calcium-responsive processes: detection of calcium ion, calcineurin-NFAT signaling cascade, and ER-to-Golgi vesicle-mediated transport. These together suggest a theme of calcium-driven signaling that regulates vesicle trafficking and downstream transcriptional responses. Some other terms (EMT regulation, meiotic DNA processes, etc.) are more miscellaneous or context-dependent, but the recurring calcium signaling and vesicle transport terms provide a coherent core interpretation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0070940","count":6},{"id":"GO:0010719","count":6},{"id":"GO:2001241","count":6},{"id":"GO:0022011","count":6}]},{"hash":"205320836899210548","title":"Developmental signaling in heart, lung, and brain","description":"The top GO terms center on development across multiple tissues (cardiac right atrium morphogenesis, lung development, forebrain development) and include signaling pathways (Notch in heart field regulation, VEGF response) along with processes like cell adhesion and proteolysis. This pattern points to a cohesive theme of morphogenesis and signaling during embryonic development across cardiovascular and neural tissues, rather than a single organ-specific function.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0051919","count":2},{"id":"GO:0035924","count":2},{"id":"GO:0003270","count":2}]},{"hash":"755477867482979985","title":"Muscle differentiation and mechanotransduction","description":"This cluster centers on skeletal muscle cell differentiation and responses to mechanical stimulus, pointing to a muscle-specific signaling/differentiation program. Additional terms such as transcription regulation, ubiquitination, and oxidative stress-related processes appear to support regulatory and stress-response aspects within this muscle-related context.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0035914","count":3},{"id":"GO:0071260","count":3}]},{"hash":"2084041090559508793","title":"Autophagy and endosome-to-lysosome transport","description":"This cluster centers on autophagy/vacuolar transport (Cvt pathway) and endosome-to-lysosome trafficking, with additional support from stress responses to cadmium and gamma radiation and GTPase activity regulation, suggesting vesicle trafficking to the lysosome. Some obsolete terms are present, but the core theme remains autophagy-related vesicle transport.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0008333","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1133280611909052485","title":"Muscle development and membrane trafficking","description":"The top GO terms point to skeletal muscle regeneration and heart development signals (Notch pathway in heart field) alongside broad cell growth and cycle activity, complemented by membrane trafficking processes (pinocytosis, plasma membrane localization, SNARE regulation). This combination suggests a theme of muscle development tied to membrane dynamics and cellular growth, justifying the label.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":4},{"id":"GO:0072660","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0043403","count":3},{"id":"GO:0000083","count":3}]},{"hash":"1699137178227942304","title":"Mitotic spindle assembly and cytoskeletal regulation","description":"Reasoning: The top GO terms are strongly enriched for mitotic processes (mitotic cell cycle, mitotic spindle assembly, mitotic sister chromatid cohesion) and cytoskeletal regulation (actin filament depolymerization, Rho GTPase signaling, kinase activity). While some terms touch other cellular processes, the dominant signal points to roles in mitosis and cytoskeletal dynamics.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0051028","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0090307","count":3}]},{"hash":"2114475119514822700","title":"Muscle and vascular development signaling","description":"This cluster centers on processes tied to muscle tissue regeneration and vascular development, including skeletal muscle regeneration, endothelial cell proliferation and sprouting angiogenesis, Notch signaling in heart-field contexts, cell migration, and calcium-related signaling, suggesting coordinated muscle remodeling with vascular growth and tissue communication.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":6},{"id":"GO:0098703","count":5},{"id":"GO:0072660","count":4},{"id":"GO:0035508","count":4},{"id":"GO:0043403","count":4}]},{"hash":"1056328360198673206","title":"Heme and Chlorophyll Biosynthesis","description":"The top GO terms point to tetrapyrrole biosynthesis: heme biosynthetic process, protoporphyrinogen IX biosynthetic process, and chlorophyll biosynthetic process, which together suggest a common theme around porphyrin/tetrapyrrole production. Other terms like cell cycle, ER unfolded protein response, and growth signaling appear less cohesive with this core theme and may reflect annotation noise. Therefore, the label focuses on the central biosynthetic pathway suggested by the strongest signals.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0070584","count":2},{"id":"GO:0006783","count":1}]},{"hash":"1662394706514063942","title":"Ribosome dynamics and translational control","description":"The top GO terms overwhelmingly point to translation-related processes: formation of translation preinitiation complex, IRES-dependent initiation, regulation of translation, translation reinitiation, ribosome disassembly, and maintenance of translational fidelity. A few other terms touch on signaling or ubiquitination, but they are low in count and do not override the central theme of ribosome function and control of protein synthesis. This makes the label a concise and representative summary of the cluster\u2019s core function.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070433","count":2},{"id":"GO:0032790","count":1},{"id":"GO:0002192","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0009048","count":1}]},{"hash":"1078576808782219584","title":"NF-kappaB\u2013mediated inflammatory signaling","description":"Proteins in this cluster are enriched for inflammatory response and NF-kappaB pathway terms, including I-kappaB phosphorylation and non-canonical NF-kappaB signal transduction, indicating core involvement in NF-kB\u2013driven inflammation. While other terms touch on translation initiation and heart development, the dominant theme is inflammatory signaling via NF-kappaB, justifying this label as representative of the cluster.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0007252","count":3},{"id":"GO:0006954","count":3},{"id":"GO:0042346","count":3},{"id":"GO:0075522","count":2}]},{"hash":"1474419485704627378","title":"Unknown","description":"The top GO terms are highly diverse, ranging from vesicle trafficking and SNARE regulation to cell migration, muscle stretch response, cardiac action potential regulation, telomere maintenance, cell cycle kinase regulation, adipocyte differentiation, and even obsolete GO terms. This lack of a cohesive, dominant biological theme suggests the proteins do not cluster around a single shared function, making a meaningful, specific label inappropriate.","confidence":"","size":24,"edges":44,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0098907","count":3},{"id":"GO:1904355","count":3}]},{"hash":"1693737385498084838","title":"Transcriptional Regulation and Signaling","description":"The GO terms point to control of gene expression (DNA-templated transcription; negative regulation of transcription by RNA Pol II) and broad signaling/cell fate processes (Wnt signaling; Toll-like receptor signaling; regulation of necroptosis and apoptosis; cell cycle regulation; ubiquitination), suggesting a cluster of proteins that coordinately regulate transcription and multiple signaling pathways rather than a single pathway.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0000209","count":1},{"id":"GO:0000122","count":1}]},{"hash":"637861975380047389","title":"Nuclear import and meiotic chromosome cohesion","description":"The cluster is dominated by GO terms related to nuclear import (NLS-bearing and ribosomal protein import into the nucleus) and nuclear pore complex assembly, along with a clear meiotic chromosome cohesion term (meiotic sister chromatid cohesion, centromeric). These together point to a theme centered on nuclear transport machinery and meiotic chromosome organization, with additional regulatory terms (desumoylation, TORC1 signaling) that may modulate these core processes. This supports a concise label focusing on nuclear import combined with meiotic chromosome dynamics.","confidence":"High","size":24,"edges":6,"triangles":4,"max_degree":3,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0006607","count":10},{"id":"GO:0051754","count":10},{"id":"GO:0006610","count":10},{"id":"GO:0051292","count":9},{"id":"GO:0000060","count":9}]},{"hash":"777145428469041566","title":"Virus Entry and Immune Activation Signaling","description":"The terms cluster around viral process and receptor-mediated endocytosis, with accompanying immune signaling pathways (PKC and MAPK), monocyte activation, integrin-mediated cell adhesion, and T cell differentiation/chemotaxis. Together they suggest roles in virus entry and subsequent activation of innate and adaptive immune responses, rather than a single enzymatic function. While some terms are deprecated, the overall theme is coherent around virus uptake and immune signaling.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":4},{"id":"GO:0006898","count":2},{"id":"GO:0000186","count":2},{"id":"GO:0051088","count":2},{"id":"GO:0033089","count":2}]},{"hash":"1804272217933913635","title":"DNA Repair and Damage Response","description":"The top GO terms are centered on DNA repair pathways (double-strand break repair, alkylation repair) and cellular responses to ionizing radiation, indicating a cluster of proteins involved in DNA damage sensing/repair and genome maintenance. Some epigenetic terms appear but are likely ancillary; the main theme is DNA repair and damage response, despite no interaction edges in the network.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":1},{"id":"GO:0051593","count":1},{"id":"GO:0043281","count":1},{"id":"GO:0006306","count":1},{"id":"GO:2000781","count":1}]},{"hash":"1958143260026511398","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms point to chromatin-level control of gene expression (nucleosome assembly, histone H2A deubiquitination) and transcriptional regulation by RNA polymerase II, with additional signals of translational regulation and kinase activity modulation. A unifying theme is nuclear chromatin modification and transcriptional control, even though a couple terms reference heart development, which may reflect broader regulatory roles rather than tissue-specific function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0000272","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1403539403693178674","title":"Endomembrane vesicle trafficking","description":"The cluster is dominated by terms tied to vesicle formation and movement within the cell\u2014COPII budding (ER-to-Golgi), endosome-to-Golgi/lysosome transport, and CVT pathway transport to vacuoles\u2014indicating a cohesive function in intracellular trafficking among endomembrane compartments. A few growth-related terms appear, but the trafficking terms are the core signal.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032258","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0090114","count":5},{"id":"GO:0008283","count":5},{"id":"GO:0045022","count":4}]},{"hash":"2183096647165343379","title":"Ribosome Biogenesis and Translation","description":"This cluster is anchored by strong enrichment for ribosome biogenesis (GO:0042254) and translation (GO:0006412), with additional association to transcription-related term (GO:0006351). Together, these point to core protein synthesis and gene-expression machinery. The remaining terms (ER-stress\u2013related apoptosis, cell cycle, and developmental processes) likely reflect broader functional breadth or pleiotropy of the included proteins rather than a single coherent alternate function. Overall, the dominant signal is components and processes involved in assembling ribosomes and translating mRNA. ","confidence":"Medium","size":24,"edges":10,"triangles":0,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0006412","count":4},{"id":"GO:0006349","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1075401669574083949","title":"Golgi Vesicle Trafficking and Organization","description":"The top GO terms are all centered on Golgi apparatus trafficking and organization, including ER-to-Golgi transport, intra-Golgi and Golgi-to-vacuole transport, endosome-to-Golgi transport, and Golgi ribbon formation/regulation. This pattern points to a cohesive cluster of proteins involved in Golgi trafficking and the structural organization of the Golgi network.","confidence":"High","size":24,"edges":24,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":7},{"id":"GO:0048280","count":5},{"id":"GO:0034498","count":5},{"id":"GO:0090161","count":5},{"id":"GO:0006896","count":5}]},{"hash":"1107298669934596765","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0061820","count":3},{"id":"GO:1990414","count":3},{"id":"GO:0001701","count":3}]},{"hash":"974693253586404983","title":"Ribosome Biogenesis and RNA Processing","description":"Dominant GO terms center on ribosome biogenesis, ribosomal subunit export, and rRNA processing, indicating a cluster of proteins involved in ribosome assembly and maturation. Some unrelated terms (developmental and mitotic processes) are present but do not define the core function; the ribosome-related terms provide a coherent theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901998","count":2},{"id":"GO:0007369","count":1},{"id":"GO:0007095","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0000055","count":1}]},{"hash":"993703655845517375","title":"Unknown","description":"The top GO terms are highly heterogeneous, ranging from cellulose catabolism to transcription regulation, secretion, and various developmental processes, with no shared biological theme. There are no edges or triangles connecting proteins, and the ReCIPE result does not reveal a cohesive function, so a specific, representative label cannot be assigned.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0048096","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0046878","count":1},{"id":"GO:0042631","count":1}]},{"hash":"1123215939786254941","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006189","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0030416","count":3},{"id":"GO:0009097","count":3}]},{"hash":"1282154230944422521","title":"DNA Repair and Telomere Maintenance","description":"The set is dominated by terms on telomere maintenance, localization to DNA damage sites, and various DNA repair processes (nucleotide/strand break repair, including mitochondrial). A PARP-like auto-ADP-ribosylation term also points to genome-integrity roles. Together these indicate a cluster of DNA repair and telomere-related proteins.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904044","count":1},{"id":"GO:0070198","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0070213","count":1},{"id":"GO:1990166","count":1}]},{"hash":"1946965837075349336","title":"Unknown","description":"The GO terms are diverse, spanning immune response, reproductive development, nervous system morphogenesis, and metabolism, with no clear unifying function linking the cluster.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071357","count":5},{"id":"GO:0046661","count":4},{"id":"GO:0090526","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0030850","count":4}]},{"hash":"2208514567169899759","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":22,"triangles":0,"max_degree":10,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0000398","count":6},{"id":"GO:0000463","count":5},{"id":"GO:0000480","count":5}]},{"hash":"743870096400702174","title":"Meiosis and DNA replication proteins","description":"This cluster shows clear associations with meiotic processes and DNA replication, including DNA-templated DNA replication, meiotic heteroduplex formation, and meiotic spindle midzone assembly, suggesting a role in chromosome dynamics during meiosis. The presence of a few unrelated terms (protein folding, autophosphorylation, chemotaxis, tetrapyrrole linkage) likely reflects broad or incidental annotations, but the dominant signals point to meiosis/replication machinery.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0000713","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0051257","count":1}]},{"hash":"176036682568563068","title":"Chromatin-associated stress response regulators","description":"The cluster shows multiple terms tied to chromatin regulation (protein localization to chromatin, histone modification) and stress-responsive processes (regulation of mRNA stability in response to stress, response to heat), suggesting a set of proteins that modulate chromatin state and transcription under stress. A few terms relate to other processes (Rho signaling, endocytosis, IgA switching, hepatocyte homeostasis) that are more peripheral to this core theme, but the dominant signal is chromatin regulation in stress contexts.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071168","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1987877640703332217","title":"Unknown","description":"The top GO terms are highly diverse (proteolysis, spindle orientation, calcium release by Golgi, cell wall processes in fungi, FAD transport, adhesion, fibrinolysis, meiosis, ABA response) with no single shared function or pathway, and the cluster has no edges or connectivity, so it appears to be a mixed, non-cohesive set rather than a single functional module.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0061454","count":1},{"id":"GO:0071433","count":1},{"id":"GO:0015883","count":1}]},{"hash":"397583038542708965","title":"Developmental epigenetic regulation","description":"GO terms indicate chromatin remodeling, histone deacetylation, and spliceosome-mediated mRNA processing, with developmental contexts (cerebral cortex and embryonic development) and a link to 2-oxoglutarate\u2013dependent processes; together these suggest regulation of gene expression through chromatin state and RNA processing during development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043044","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0021987","count":3}]},{"hash":"2112403789544048060","title":"DNA-Templated Transcription Regulation","description":"This cluster is enriched for GO terms related to DNA-templated transcription and regulation of transcription by RNA polymerase II, including both positive and negative regulation, indicating that the proteins primarily function as transcription regulators. The presence of development-related terms such as intestinal epithelial cell differentiation and heart development supports a role in differentiation programs driven by transcription factors, while a few other terms (like xenobiotic transport) appear less central. Overall, the dominant theme is transcriptional control with links to development.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0043388","count":3},{"id":"GO:0060575","count":2},{"id":"GO:0006919","count":2}]},{"hash":"323600709348298337","title":"Cytoskeleton remodeling and vesicle trafficking","description":"The top GO terms point to actin-related dynamics (regulation of Rho signaling; microspike and filopodium assembly) combined with endomembrane system processes (ER tubular networks, Golgi-to-lysosome transport, lysosome targeting, and endomembrane organization), plus autophagic activity (aggrephagy). This pattern suggests a cohesive function linking cytoskeletal remodeling with membrane trafficking and lysosome-related pathways, rather than a single isolated process.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0007183","count":1},{"id":"GO:0071787","count":1},{"id":"GO:0045053","count":1},{"id":"GO:0010256","count":1}]},{"hash":"364743082331413854","title":"Cytokinesis and Autophagy-Linked Trafficking","description":"This cluster centers on cell division processes (cytokinesis, spindle/centriole regulation) and membrane trafficking/autophagy components (Cvt pathway, autophagosome assembly, MVB, Golgi retention), suggesting a shared theme of division-linked membrane remodeling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000920","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0090148","count":1}]},{"hash":"310627321054183792","title":"Membrane trafficking and signaling","description":"The terms cluster around processes at the cell membrane involving vesicle trafficking (positive regulation of pinocytosis, SNARE complex regulation, maintenance of protein location in the plasma membrane) and signaling pathways (Wnt signaling). Additional terms touch on growth and cell cycle, consistent with downstream effects of membrane signaling and trafficking. Overall, the cluster appears to represent membrane-associated signaling coupled with vesicle trafficking.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0072660","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0043403","count":2}]},{"hash":"517044453755888600","title":"Detox, Redox, and Lipid Metabolism","description":"This cluster\u2019s top GO terms center on defense against oxidative stress (response to toxic substance, cellular oxidant detoxification) and a variety of catabolic and biosynthetic lipid-related processes (phosphatidylserine and monoacylglycerol catabolism, menaquinone biosynthesis) along with pigment and secondary metabolism signals (chlorophyll catabolic process, antibiotic biosynthetic process). The common theme appears to be a broad metabolic module concerned with redox balance, detoxification, and lipid/pigment turnover, rather than a single specific pathway. Some terms reflect microbial secondary metabolism, but they fit within a general metabolism/redox context.","confidence":"Medium","size":24,"edges":11,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0009234","count":6}]},{"hash":"1373073578168570930","title":"Muscle development and regeneration signaling","description":"The presence of skeletal muscle tissue regeneration and heart-field Notch signaling terms, along with cell growth and cell-cycle terms, suggests a theme around muscle development and regenerative signaling. Some terms (xylan catabolic process, SNARE complex regulation) appear unrelated, which lowers specificity and confidence.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0072660","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0043403","count":2},{"id":"GO:0000083","count":2}]},{"hash":"1787088074472521078","title":"Cerebral cortex development and neuronal cytoskeleton regulation","description":"The top GO terms cluster around brain development, especially cerebral cortex development and neuron development, with strong signals for cortical actin cytoskeleton organization. This points to proteins involved in neuronal maturation and cytoskeletal remodeling during cortex formation. Additional terms like embryonic cranial skeleton morphogenesis and regulation of apoptotic signaling suggest broader craniofacial/brain morphogenesis and cell-survival coordination in developmental contexts. Some cell-cycle\u2013related terms (negative regulation of CDK activity, proteasomal protein turnover) align with proliferating neural progenitors during cortex formation. A few terms (kinetochore localization, trachea formation) are peripheral but do not negate the central brain-development theme. Overall, the cluster appears to center on cerebral cortex development with linked cytoskeletal dynamics and cell-cycle control.","confidence":"Medium","size":24,"edges":19,"triangles":3,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034501","count":23},{"id":"GO:0045736","count":23},{"id":"GO:0048666","count":23},{"id":"GO:0032435","count":23},{"id":"GO:0060440","count":22}]},{"hash":"149284648187417576","title":"Cardiac development and conduction system","description":"The top GO terms center on heart formation and function, including Notch signaling in the secondary heart field, right atrium morphogenesis, venous endothelial differentiation, and regulation of SA node action potentials, collectively signaling cardiac morphogenesis and the heart's conduction/pacemaker system, with some ancillary cellular processes.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003270","count":6},{"id":"GO:0003213","count":6},{"id":"GO:0060843","count":6},{"id":"GO:0098907","count":6},{"id":"GO:0048549","count":6}]},{"hash":"621510211417284452","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001942","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0035754","count":2},{"id":"GO:0042351","count":2},{"id":"GO:0097171","count":2}]},{"hash":"993342709035928952","title":"Gene Expression and ER-Golgi Transport","description":"The top GO terms point to transcription (DNA-templated transcription) and RNA processing (7-methylguanosine mRNA capping; RNA (guanine-N7)-methylation), plus protein homooligomerization and vesicle trafficking between the endoplasmic reticulum and Golgi (ER to Golgi and Golgi-to-ER transport). This suggests a cluster of proteins involved in core gene expression machinery and in the secretory pathway, rather than a single specialized function. The brain development term is less specific here and likely reflects tissue expression. Overall, the label reflects a combination of transcription-related and intracellular trafficking processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0036265","count":3}]},{"hash":"153526825089008750","title":"Unknown","description":"The GO terms cover a mix of unrelated processes (cell division, protein heterooligomerization, glucose transport across membranes, non-motile cilium assembly, interferon-alpha response, plant hormone signaling, and several obsolete terms), with no single dominant function binding the cluster together. Because there isn\u2019t a coherent, shared theme, a specific functional label cannot be confidently assigned.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0015758","count":2},{"id":"GO:1905515","count":1},{"id":"GO:0035457","count":1}]},{"hash":"2021998000944651739","title":"Intracellular trafficking and cytoskeleton remodeling","description":"This cluster centers on intracellular trafficking and cytoskeletal remodeling, as suggested by GO terms for endomembrane system organization, ER tubular network formation, Golgi-to-lysosome transport, and filopodium/microspike assembly, with autophagy-related turnover also reflected.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051096","count":1},{"id":"GO:0039021","count":1},{"id":"GO:0007183","count":1},{"id":"GO:0071787","count":1},{"id":"GO:0045053","count":1}]},{"hash":"518245555103834319","title":"Zinc homeostasis and ribosome biogenesis","description":"The cluster is strongly enriched for translation and ribosome biogenesis terms (translation, ribosome biogenesis, ribosomal large subunit assembly) and also features zinc-related processes (zinc import, zinc starvation response, detoxification). This points to a coordinated role where zinc availability influences protein synthesis and ribosome assembly, making the label Zinc homeostasis and ribosome biogenesis appropriate.","confidence":"High","size":23,"edges":103,"triangles":255,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0046677","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0010312","count":2}]},{"hash":"828925438142027355","title":"Lipid metabolism and immune signaling","description":"The set centers on lipid biosynthesis and remodeling (triglyceride biosynthesis, CDP-diacylglycerol biosynthetic process, cardiolipin remodeling, platelet activating factor biosynthesis) indicating lipid metabolism as the core theme. Immune-related terms (interleukin-2 production, negative regulation of activation-induced T cell death) suggest coupling between lipid signaling and immune regulation. A few terms related to development (glandular epithelial cell maturation, cerebellum morphogenesis) appear peripheral, but the dominant cluster theme is lipid metabolism with immune signaling connections.","confidence":"Medium","size":23,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":3},{"id":"GO:2001246","count":2},{"id":"GO:0070236","count":2},{"id":"GO:0006663","count":2},{"id":"GO:0070970","count":2}]},{"hash":"498533956737624253","title":"Innate antiviral immune response","description":"The term counts show two strong GO terms: defense response to virus and innate immune response, both indicating antiviral defense. Other annotations (RNA splicing, photoreceptor localization, and various \"obsolete\" terms) seem less representative and may reflect background noise or multifunctionality. Overall, the core theme appears to be innate antiviral immunity, supporting this label.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903546","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2}]},{"hash":"968707937248286026","title":"Mitochondrial energy metabolism and ribosome assembly","description":"The top terms are strongly centered on mitochondrial respiration (NADH to ubiquinone; complex II assembly), pointing to energy production, with additional terms related to cytoplasmic translation and ribosomal subunit assembly as peripheral signals. This suggests a cluster tied to basic biosynthetic energy metabolism, with some translation-related annotations present but less central. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0034553","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0000027","count":2}]},{"hash":"2252104620094318521","title":"Sporulation and amino acid biosynthesis in bacteria","description":"The cluster is driven by sporulation (cellular spore formation) and multiple amino acid biosynthetic processes (valine, proline), with accompanying stress-response signals (xenobiotic, hypoxia) and transcription activity. These together suggest a bacterial sporulation-associated metabolism cluster centered on spore formation and amino acid biosynthesis.","confidence":"Medium","size":23,"edges":32,"triangles":11,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0030435","count":3},{"id":"GO:0009097","count":2},{"id":"GO:0055129","count":2},{"id":"GO:0042493","count":2}]},{"hash":"736877516852044487","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0005978","count":6},{"id":"GO:0009103","count":6},{"id":"GO:0042619","count":6},{"id":"GO:0055007","count":5}]},{"hash":"100812033697653728","title":"Potassium Ion Transport and Membrane Potential Regulation","description":"This cluster is dominated by GO terms for potassium ion transport (import/export and transmembrane transport) and membrane hyperpolarization, pointing to a module that maintains membrane potential and K+ homeostasis. While a few terms touch on development or sensory processes, the strongest signal is ion movement across the membrane, especially potassium, which aligns with membrane potential regulation.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060081","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0098719","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0010754","count":3}]},{"hash":"1699069965930325776","title":"Chromatin modification & transcription regulation","description":"Top GO terms point to histone acetylation/deacetylation, histone methylation, and DNA-templated transcription, indicating a cohesive role in chromatin state control and gene expression regulation. While a few other terms touch on transport or metabolism, the dominant theme is chromatin modification linked to transcriptional control.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0016575","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0036265","count":2}]},{"hash":"717155107602177477","title":"Transmembrane Solute Transporters","description":"The top GO terms point to transport across membranes for a variety of substrates\u2014ions (sodium, potassium), sugars (galactose, arabinose, fucose), vitamins, and other metabolites, plus neurotransmitter vesicle loading\u2014indicating a cohesive theme of membrane transporter proteins handling diverse solutes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0006004","count":3},{"id":"GO:0015757","count":3}]},{"hash":"924414582582740948","title":"Membrane Transport of Ions and Small Molecules","description":"The top GO terms cluster around transmembrane transport: potassium and sodium ion transport, loading of neurotransmitters into vesicles, and transport of vitamins and various sugars (galactose, arabinose, fucose) as well as other small molecules. This indicates a cohesive function in moving diverse substrates across membranes, rather than a single specific substrate pathway. Therefore, a concise label reflecting membrane transport of ions and nutrients is appropriate.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0098700","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2}]},{"hash":"862754046422222035","title":"Cerebral cortex and hippocampus development","description":"Dominant GO terms point to neural development, especially cerebral cortex development and hippocampus development, with supporting signals from orbitofrontal cortex development and cortical actin organization. There are craniofacial morphogenesis terms (embryonic cranial skeleton morphogenesis) that tie in with cranial development, but the strongest and most recurrent themes are cortex- and hippocampus-focused development processes, making this label representative of the cluster\u2019s core function. ","confidence":"High","size":23,"edges":235,"triangles":1429,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":23},{"id":"GO:2001233","count":23},{"id":"GO:0061368","count":23},{"id":"GO:0030866","count":23},{"id":"GO:0048701","count":23}]},{"hash":"544111887774687228","title":"Cortex Development and Neural Morphogenesis","description":"This cluster is dominated by terms tied to brain development and cortical formation, including cerebral cortex, hippocampus, and orbitofrontal cortex development, plus FGFR signaling specifically involved in cortex development and actin cytoskeleton organization critical for neuronal morphogenesis. While there are a few craniofacial/developmental terms (trachea formation and embryonic cranial skeleton morphogenesis), these can be associated with neural crest\u2013driven craniofacial patterning that accompanies neural development. Overall, the shared theme is neural development with emphasis on cortex formation and structural remodeling. ","confidence":"High","size":23,"edges":208,"triangles":1031,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":23},{"id":"GO:2001233","count":23},{"id":"GO:0061368","count":23},{"id":"GO:0030866","count":23},{"id":"GO:0048701","count":23}]},{"hash":"1241930550225153978","title":"Calcium-Dependent Muscle and Heart Signaling","description":"The cluster\u2019s GO terms converge on calcium import into cells, regulation of cardiac action potentials (SA node), muscle-related regeneration, and membrane trafficking processes (protein localization, SNARE regulation). Together these suggest a theme of calcium-driven signaling that underpins muscle and cardiac function, with supporting roles in membrane dynamics. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":7},{"id":"GO:0007205","count":7},{"id":"GO:0098703","count":7},{"id":"GO:0072660","count":6},{"id":"GO:0035508","count":6}]},{"hash":"886954846482565841","title":"Neuronal signaling and cytoskeletal remodeling","description":"The top terms point to neural signaling processes, including synaptic vesicle budding and acetylcholine receptor\u2013mediated signaling, along with filopodium assembly indicating actin-based cytoskeletal remodeling relevant to neurite outgrowth and synapse formation. The presence of locomotory behavior hints at neural control of movement. Some terms appear obsolete or less relevant (toxin transport, immune cell processes), likely noise, but the core theme is neuronal signaling with cytoskeletal dynamics.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016185","count":3},{"id":"GO:0008344","count":3},{"id":"GO:1901998","count":3},{"id":"GO:0035924","count":2},{"id":"GO:0007213","count":2}]},{"hash":"2021773094081590200","title":"Regulation of developmental signaling and trafficking","description":"This cluster includes proteins tied to modulating signaling pathways (BMP/TGF-beta, NF-kappaB), including dephosphorylation events, as well as processes in nuclear export and vesicle/vacuole fusion, plus development-related functions like meristem identity. The common thread appears to be regulation of developmental signaling alongside intracellular trafficking, rather than a single, canonical pathway.","confidence":"Medium","size":23,"edges":199,"triangles":950,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0042006","count":20},{"id":"GO:0046827","count":20},{"id":"GO:0061191","count":20},{"id":"GO:0042347","count":20},{"id":"GO:0010991","count":20}]},{"hash":"932693597007107237","title":"DNA Repair and Lysosome Trafficking","description":"This cluster shows a mix of DNA replication/repair terms (TLS, nucleotide-excision repair, DNA repair, mitotic DNA replication) alongside lysosome-related terms (lysosome organization, N-glycan processing to lysosome, secretion of lysosomal enzymes). The proteins may participate in genome maintenance and lysosomal trafficking/biogenesis, or reflect a stress-response network linking nuclear maintenance to lysosomal pathways. The combination suggests two linked themes rather than a single narrow function, so the label captures both aspects without overstating a single function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042276","count":3},{"id":"GO:0007040","count":2},{"id":"GO:0016256","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0033299","count":2}]},{"hash":"1568278490239033687","title":"Fat and muscle differentiation signaling","description":"This cluster centers on differentiation processes in muscle and adipose tissues, supported by prominent terms for fat cell differentiation and skeletal muscle tissue regeneration, together with intracellular signal transduction. Additional terms indicate roles in cell growth, cell cycle, and membrane protein localization, suggesting broader growth and trafficking functions that accompany differentiation. Overall, the dominant theme is signaling and differentiation in fat and muscle contexts rather than a single, narrow pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":5},{"id":"GO:0045444","count":5},{"id":"GO:0072660","count":4},{"id":"GO:0035508","count":4},{"id":"GO:0043403","count":4}]},{"hash":"777658792503258750","title":"Ubiquitin-Proteasome in Antiviral Innate Immunity","description":"The dominant GO terms are ubiquitin-dependent proteolysis (SCF-dependent, ubiquitin-proteasome\u2013mediated), protein ubiquitination, and innate immune defense against viruses, along with NF-kB signaling regulation (I-kB phosphorylation) and NOD2 pathway signaling. This points to a functional module where ubiquitin-mediated protein turnover shapes antiviral innate immune responses, including NF-kB\u2013mediated transcription.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0045087","count":8},{"id":"GO:0051607","count":8},{"id":"GO:0016567","count":6},{"id":"GO:0042787","count":6}]},{"hash":"1314024033779261194","title":"Chromatin remodeling and cytoskeletal signaling","description":"This cluster combines chromatin-level processes (histone H3-K4 methylation regulation, nucleosome assembly, transcription regulation by RNA Pol II) with cytoskeletal dynamics and signaling (Rho pathway, filopodium assembly, cell migration) and developmental context (heart development), suggesting a link between chromatin regulation and morphogenesis/cell movement in development.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051569","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1133271948273122685","title":"Cellular stress signaling and metabolism","description":"This cluster shows a mix of GO terms tied to stress responses (oxidative stress, apoptotic process, DNA turnover) and metabolic regulation (heme and proline biosynthesis, nutrient and hormone signaling). While individual terms span different contexts, the common thread appears to be cellular signaling coordinating stress responses with metabolic processes.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006308","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0003085","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0006783","count":2}]},{"hash":"2136987161752002094","title":"Fungal Cell Wall Biosynthesis and Remodeling","description":"Most of the top terms cluster around fungal-type cell wall organization, beta-D-glucan and xyloglucan biosynthesis, chitin metabolism, and plant-type cell wall modification, indicating a group involved in cell wall production/remodeling in fungal and plant contexts, with a signal about detection of fungal origin supporting a host\u2013pathogen interaction theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006352","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0008202","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0009831","count":1}]},{"hash":"202999005591225890","title":"Rho-GTPase Signaling and Cytoskeleton","description":"The cluster centers on Rho and GTPase-related signaling with components of actin cytoskeleton organization (focal adhesion assembly, regulation of GTPase activity) and membrane dynamics (exocytosis, endocytic recycling), all pointing to cytoskeletal remodeling and vesicle trafficking. Some terms also touch on cell division (mitotic cell cycle, progenitor division), which often rely on cytoskeletal reorganization, supporting a cohesive theme around cytoskeletal signaling and membrane trafficking during adhesion and division.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0070493","count":3},{"id":"GO:0048041","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1684006141176420077","title":"Neuroinflammation and axon guidance","description":"The top terms point to inflammatory signaling (TLR2, I\u03baB phosphorylation, macrophage activation, inflammatory response) and neural development (axon guidance, nerve branching morphogenesis), as well as pain processing (formalin-induced pain). This suggests these proteins function at the interface of neuroimmune signaling and neural connectivity, such as microglial\u2013neuron interactions in pain and development. Therefore, the label captures the dominant themes.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061368","count":1},{"id":"GO:0034134","count":1},{"id":"GO:0090394","count":1},{"id":"GO:0042116","count":1},{"id":"GO:0007252","count":1}]},{"hash":"1824605399921148056","title":"Unknown","description":"The top GO terms are highly diverse (xylan catabolic process, DNA-templated transcription, T cell cytotoxicity, decidualization, thyroid hormone response, bradykinin catabolism, Wnt signaling-related regulation, etc.), with no clear common theme tying the cluster together. The cluster also shows very low connectivity (edges 2, max degree 1), suggesting a loose assembly rather than a cohesive functional module. Therefore no single, representative label can be confidently assigned.","confidence":"","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045493","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0014823","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0050790","count":3}]},{"hash":"1554922709629070939","title":"Amino acid metabolism and metabolic signaling","description":"The proteins are enriched for several amino acid\u2013related catabolic and biosynthetic processes (L-alanine catabolic, L-glutamate catabolic to aspartate, L-aspartate biosynthetic) along with related metabolic activities (heme biosynthesis, fatty acid homeostasis). Notch signaling and insulin stimulus responses also appear, implying integration of metabolism with signaling pathways. Some terms are obsolete, but the overall theme points to amino acid\u2013linked metabolism coordinated with regulatory signaling.","confidence":"Medium","size":22,"edges":147,"triangles":515,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":9},{"id":"GO:0007219","count":9},{"id":"GO:0097053","count":9},{"id":"GO:0042853","count":9},{"id":"GO:0032869","count":7}]},{"hash":"1019584251052306452","title":"Brain and craniofacial development","description":"This cluster is dominated by neural development terms (cerebral cortex development, hippocampus development, orbitofrontal cortex development) and craniofacial morphogenesis (embryonic cranial skeleton morphogenesis). Additional terms on cortical actin cytoskeleton organization and positive regulation of stem cell differentiation support neural progenitor dynamics and morphogenesis, suggesting a cohesive role in brain formation and associated cranial structures; a divergent term like trachea formation appears as a minor outlier. ","confidence":"High","size":22,"edges":201,"triangles":1021,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":22},{"id":"GO:2001233","count":22},{"id":"GO:0061368","count":22},{"id":"GO:0030866","count":22},{"id":"GO:0048701","count":22}]},{"hash":"1306013815470414222","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006189","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1332582886221145876","title":"Ribosome Biogenesis and Translation Machinery","description":"The cluster is dominated by translation-related GO terms (translation, initiation, termination) and ribosomal small subunit biogenesis, indicating a set of proteins involved in ribosome assembly and protein synthesis. Some terms about antibiotic response and bacterial cell division (conjugation, septum assembly) suggest additional linked processes in bacteria, but the core signal remains ribosome function.","confidence":"High","size":22,"edges":9,"triangles":1,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0046677","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0042274","count":3}]},{"hash":"630701666696536241","title":"Transcription and Ribosome Biogenesis","description":"These GO terms cluster around core gene-expression and protein-synthesis processes: transcription by RNA polymerases II and III, transcription-coupled nucleotide-excision repair, ribosome biogenesis, and eukaryotic translation initiation complex assembly. The combination suggests a functional module of transcriptional machinery and ribosome production. Some terms (cell division, meiosis I, Golgi retention, protein deneddylation, response to amine) are broader cellular processes that may accompany proliferative or signaling states, but they do not override the central theme of transcription and ribosome assembly.","confidence":"High","size":22,"edges":9,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006283","count":3},{"id":"GO:0045053","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0014075","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1774209288927989082","title":"Neuronal Purine Salvage and Nucleotide Metabolism","description":"This cluster shows strong representation of purine salvage pathways (IMP, GMP, guanine salvage) and PRPP biosynthesis, indicating nucleotide salvage/metabolism as the core function. A subset of terms also points to neuronal processes (dendrite morphogenesis, grooming) and signaling responses, suggesting these metabolism-related proteins may function in neuronal contexts.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":2},{"id":"GO:0032264","count":2},{"id":"GO:0032263","count":2},{"id":"GO:0046038","count":2},{"id":"GO:0032869","count":2}]},{"hash":"236789417392068704","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":16,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0046355","count":3},{"id":"GO:0070879","count":3},{"id":"GO:0044011","count":3},{"id":"GO:1904462","count":3}]},{"hash":"12359145458193612","title":"DNA replication initiation and S-phase control","description":"The cluster is enriched for GO terms tied to assembling the pre-replicative complex, DNA replication, DNA amplification, and regulation of the G1/S transition, as well as mitotic intra-S DNA damage checkpoint signaling. This points to a core function in initiating DNA replication and coordinating cell-cycle progression through S-phase and into mitosis. Some outlier terms (calcium and amino acid export) appear minor compared with replication-related terms, so the dominant theme remains replication initiation and S-phase control.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:1990034","count":1},{"id":"GO:0032973","count":1},{"id":"GO:0006267","count":1},{"id":"GO:0072428","count":1}]},{"hash":"688131978477937509","title":"Membrane Transporters and Ubiquitin Signaling","description":"This cluster is dominated by membrane transport GO terms, including calcium export, amino acid export, and UDP-N-acetylglucosamine transport, indicating a group of transporter proteins at the plasma membrane. A secondary pattern involves ubiquitination and signaling (protein ubiquitination, NOD2 pathway, NF-kappaB-related regulation), suggesting links to proteostasis and immune signaling. Some terms appear plant- or obsolete-specific or as noise, but the core theme centers on membrane transport with ubiquitin-related signaling.","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":2},{"id":"GO:0032973","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2}]},{"hash":"607777057365991531","title":"Membrane Transport and GTPase Signaling in Excitable Tissues","description":"This cluster is enriched for transmembrane transport terms (potassium and xenobiotic), combined with small GTPase\u2013mediated signaling and Ras regulation, along with heart-related processes (cardiac contraction, heart development, regulation of heart rate) and synaptic vesicle loading. Together, these indicate a theme of membrane transport linked to signaling in excitable cells such as cardiac and neuronal tissues.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0060048","count":2}]},{"hash":"431571397691388553","title":"Muscle development and regeneration signaling","description":"This cluster\u2019s top GO terms emphasize muscle-related biology\u2014skeletal muscle tissue regeneration, cell growth, and cell migration\u2014along with heart-associated signaling (SA node action potential regulation) and GPCR signaling. While some terms are obsolete or generic, the dominant themes point to muscle development, remodeling, and signaling processes maintaining muscle tissue function.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":6},{"id":"GO:0016477","count":5},{"id":"GO:0098907","count":5},{"id":"GO:2001275","count":5},{"id":"GO:0072660","count":4}]},{"hash":"399193142991875563","title":"Mitotic signaling and developmental regulation","description":"This cluster shows enrichment in mitotic cell cycle and signaling regulation (GTPase activity, serine/threonine kinase activity, autophosphorylation) and links to multicellular development and skin development, pointing to a coordinated control of cell division and tissue development. Additional terms on mRNA transport and ribosome maturation reflect supporting gene expression and RNA processing within the same network.","confidence":"Medium","size":22,"edges":89,"triangles":59,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0000278","count":6},{"id":"GO:0071902","count":5},{"id":"GO:0043588","count":5},{"id":"GO:0031954","count":5}]},{"hash":"616502039902430362","title":"Pain and mechanosensation with membrane signaling","description":"This cluster\u2019s top terms cluster around sensory responses to pain and mechanical stimuli (and cold), complemented by membrane-related processes (protein localization to plasma membrane, SNARE regulation) and signaling pathways (NOD1). The mix points to a theme of stimulus-triggered signaling and membrane dynamics, with a secondary note of excitability in cardiac tissue. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098907","count":10},{"id":"GO:0007205","count":9},{"id":"GO:0072660","count":8},{"id":"GO:0000083","count":8},{"id":"GO:0009409","count":8}]},{"hash":"280888369649977092","title":"Vacuolar amino acid transporters","description":"The top GO terms cluster around transport of various amino acids across the vacuolar membrane, including import and export of alanine, proline, glutamine, arginine, histidine, and tyrosine, suggesting a group of proteins functioning as vacuolar amino acid transporters involved in amino acid homeostasis and storage in plant cells; a couple terms touch on broader plant processes like root cap development and nutrient stress, but the dominant signal is vacuolar amino acid trafficking.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051365","count":2},{"id":"GO:0090514","count":2},{"id":"GO:0015824","count":2},{"id":"GO:1990818","count":2},{"id":"GO:0089708","count":2}]},{"hash":"1862295253592567664","title":"Proliferation, apoptosis, and differentiation signaling","description":"The top GO terms cluster around transcriptional control (DNA-templated transcription) and cell fate decisions (apoptotic process, autophagy regulation), linked with major growth-regulatory signaling (Hippo, Wnt) and events like keratinocyte differentiation, cell-cycle re-entry, and exocytosis. This suggests a network governing proliferation, survival, and differentiation, with connections to epithelial growth and secretion pathways.","confidence":"Medium","size":22,"edges":13,"triangles":2,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":18},{"id":"GO:0006915","count":17},{"id":"GO:0060044","count":16},{"id":"GO:0035329","count":16},{"id":"GO:0090263","count":16}]},{"hash":"1598897672734136654","title":"Endomembrane trafficking and lysosome targeting","description":"The cluster shows strong representation of endomembrane system organization, ER tubular network formation, Golgi-to-lysosome transport, protein targeting to lysosome, and endosomal vesicle fusion, indicating a cohesive group of proteins involved in vesicle trafficking within the secretory pathway and lysosome targeting.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007183","count":2},{"id":"GO:0071787","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0010256","count":2},{"id":"GO:0030035","count":2}]},{"hash":"1523495535675656126","title":"Unknown","description":"The GO terms are spread across sensory perception (pain, touch), temperature-related responses, carbon dioxide detection, and various cardiac membrane potential processes (depolarization/repolarization in atrial tissue), with no clear unifying function. There are no edges tying the proteins into a single shared pathway, so a cohesive theme isn\u2019t evident.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0007275","count":11},{"id":"GO:0019233","count":11},{"id":"GO:0098914","count":10},{"id":"GO:0060081","count":10},{"id":"GO:0050976","count":10}]},{"hash":"1736228933698859245","title":"Pain and Cold Stress Signaling","description":"This cluster shows enrichment for sensory and cold-response terms (response to cold, detection of mechanical stimulus in pain, response to pain) plus an innate immune signaling component (NOD1 pathway) and various regulatory processes (SNARE regulation, mRNA stability). Together these suggest a theme of cellular stress\u2013driven signaling that integrates nociception, immune sensing, and regulatory control, rather than a single, tightly defined pathway. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0072660","count":4},{"id":"GO:0000083","count":4},{"id":"GO:0009409","count":4},{"id":"GO:0035544","count":4}]},{"hash":"1730958458563580465","title":"DNA replication and repair","description":"The cluster\u2019s proteins are enriched for DNA-centric processes: DNA repair (base excision, nucleotide excision), DNA replication, DNA-templated transcription, and related DNA biosynthetic activities, indicating a cohesive role in genome maintenance and replication. A few terms such as glycosylation and mannan biosynthesis are less related and may reflect annotation noise or multifunctionality, but the dominant theme is DNA replication/repair.","confidence":"High","size":22,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0006288","count":2},{"id":"GO:0006297","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1613247037472310457","title":"Unknown","description":"The top GO terms show a mix of plant-specific development and stress responses (root meristem regulation, osmotic stress, xylan/cellulose catabolic processes) and animal-related processes (endothelial tube lumen extension, glucocorticoid and progesterone metabolism) along with general cellular processes (ceramide transport, apoptosis). There is no clear shared function or pathway unifying these terms, and the cluster has no edges to suggest cohesive interactions. Therefore, a single, meaningful label cannot be inferred.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010082","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0097498","count":2}]},{"hash":"1877574038520227841","title":"Neural and Cardiac Excitability with Temperature Response","description":"This cluster mixes neural signaling and reflex terms (spinal cord development; GABA secretion; startle response) with cardiac electrical activity (membrane depolarization/repolarization in atrial and His bundle cells) and environmental stimuli responses (temperature, cold, CO2 detection). The common thread appears to be excitability and signaling in neural and cardiac contexts influenced by environmental cues, despite limited direct interactions among proteins.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":5},{"id":"GO:0021510","count":4},{"id":"GO:0060372","count":4},{"id":"GO:0003031","count":4},{"id":"GO:0071502","count":4}]},{"hash":"1805410764561883205","title":"Metanephric Kidney Development & Membrane Transport","description":"Two GO terms explicitly point to metanephric kidney formation: collecting duct development and ureteric bud development, suggesting a kidney-centric role. The presence of membrane-related processes (post-translational targeting to membrane, xenobiotic transmembrane transport) supports a theme of membrane proteins coordinating signaling or transport during kidney morphogenesis. While other terms indicate broader regulatory roles (kinase activity, calcium channel regulation, redox homeostasis), the kidney development signals provide the strongest cohesive thread for naming this cluster.","confidence":"Medium","size":22,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0042994","count":2},{"id":"GO:0072205","count":2}]},{"hash":"2062378746201923308","title":"Cell growth, trafficking, and protein turnover","description":"This cluster centers on processes that coordinate growth signaling with membrane trafficking and protein quality control, as evidenced by GO terms for cell migration, pinocytosis, TORC1 signaling, cell cycle, ubiquitination/ERAD, and mRNA transport, together with related transport and fusion interactions. The label captures the overarching theme of growth-associated signaling alongside intracellular trafficking and protein turnover.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0007205","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1544235546955023","title":"Neural development and synaptic organization","description":"This cluster is dominated by terms related to neural development and synaptic architecture, including formation of radial glial scaffolds, positive regulation of myelination, and NMDA glutamate receptor clustering, as well as cytoskeletal organization like sarcomere assembly. Lipid signaling terms (apolipoprotein A-I pathway and LDL response) suggest membrane-related processes that can influence neural cells, but the core theme remains neural development and synaptic organization. Overall, the label reflects the strongest, most coherent signal in the GO terms. ","confidence":"Medium","size":22,"edges":3,"triangles":0,"max_degree":3,"top_function":"wound healing","top_go_terms":[{"id":"GO:0021943","count":7},{"id":"GO:0070527","count":7},{"id":"GO:0071404","count":7},{"id":"GO:0050919","count":7},{"id":"GO:0045124","count":7}]},{"hash":"1461940012471591920","title":"Endomembrane trafficking and lysosome targeting","description":"GO terms point to endomembrane system organization, ER tubular network formation, Golgi-to-lysosome transport, protein targeting to lysosome, endosomal vesicle fusion, and aggrephagy, with additional emphasis on cytoskeletal elements involved in vesicle movement (filopodium/microspike assembly). This cohesive pattern centers on vesicle trafficking within the ER\u2013Golgi\u2013lysosome axis and associated autophagic processes, justifying a label focused on endomembrane trafficking to lysosomes.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007183","count":3},{"id":"GO:0071787","count":3},{"id":"GO:0045053","count":3},{"id":"GO:0010256","count":3},{"id":"GO:0030035","count":3}]},{"hash":"2121997711425884053","title":"TORC1 Growth and Trafficking","description":"The cluster features TORC1 signaling and trafficking-related processes (cytoskeletal organization, endosome transport, Golgi to plasma membrane transport) and growth-control terms (negative regulation of cell size). It also includes stress/aging signals (diapause entry, replicative senescence, DNA damage checkpoint) that tie growth signaling to cellular stress responses. This supports a cohesive theme of growth signaling linked with cytoskeletal dynamics and membrane trafficking, with stress-induced growth arrest.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":2},{"id":"GO:0030866","count":2},{"id":"GO:0045792","count":2},{"id":"GO:0015824","count":2},{"id":"GO:0045022","count":1}]},{"hash":"1960832493606530416","title":"Neuroimmune signaling and macrophage activation","description":"This cluster is dominated by innate immune terms: innate immune response, defense response to virus, Toll-like receptor 2 signaling, macrophage activation, and I-kappaB phosphorylation (NF-\u03baB pathway). While there are neural-related terms (axonogenesis, pain-related behavioral response, regulation of excitatory postsynaptic potential), the core signal centers on immune signaling and macrophage activation, suggesting neuroimmune cross-talk. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045842","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0045087","count":3}]},{"hash":"549581257021425251","title":"Cardiac Contractility and Heart Development","description":"The cluster shows strong representation of cardiac-related processes, including cardiac muscle contraction, regulation of SA node cell action potential, and heart development, suggesting involvement in cardiomyocyte function and cardiac maturation. While a few immune signaling terms appear, the cardiovascular terms dominate, supporting this label.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0098907","count":2}]},{"hash":"2251730096068571028","title":"Cardiac development and angiogenesis","description":"The top terms point to heart development (Notch signaling related to secondary heart field cardioblast proliferation) and vascular formation (endothelial cell proliferation in sprouting angiogenesis), along with muscle regeneration and general cell growth/migration. These together suggest a theme of cardiac/vascular developmental programs and associated proliferation, with some folate/metabolite transport terms likely reflecting proliferative cell biology. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":4},{"id":"GO:0051958","count":3},{"id":"GO:0015885","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0043403","count":3}]},{"hash":"149700484254228665","title":"Nuclear gene expression and growth signaling","description":"This cluster centers on nuclear processes\u2014DNA replication, transcription, and mRNA processing\u2014with inclusion of nuclear export, plus signaling pathways (Hippo and canonical Wnt) that regulate growth and proliferation. The presence of differentiation-related terms (keratinocyte differentiation) and morphogenesis (dendritic spine morphogenesis) suggests broader cellular development context, but the dominant theme remains nuclear gene expression tied to growth control. ","confidence":"High","size":21,"edges":115,"triangles":406,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0060044","count":12},{"id":"GO:0046827","count":12},{"id":"GO:0006397","count":12},{"id":"GO:0006351","count":12}]},{"hash":"2223835972540518902","title":"Unknown","description":"The top GO terms are very heterogeneous: cellular response to glucose stimulus, blood coagulation, Toll signaling regulation, defense response to fungus, proteolysis, multicellular growth, and other unrelated processes. There is no single dominant function linking these proteins, and the sparse connections suggest a mixed or incidental cluster rather than a cohesive biological module.","confidence":"","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071333","count":2},{"id":"GO:1900122","count":1},{"id":"GO:0030245","count":1},{"id":"GO:0044537","count":1},{"id":"GO:1904707","count":1}]},{"hash":"1712509025844632639","title":"Chromatin regulation and transcription","description":"This cluster is dominated by GO terms related to chromatin and gene expression, including establishment of protein localization to chromatin, DNA-templated transcription, histone methylation, and ubiquitin-proteasome\u2013mediated protein turnover. While there are a few peripheral terms (ribosome biogenesis, defense responses), the core signal points to nuclear chromatin-associated regulation of transcription. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0051568","count":2}]},{"hash":"889307190398514864","title":"Membrane transport and carbohydrate metabolism","description":"The top GO terms cluster around transmembrane transport of ions and nutrients (sodium, D-glucose, vitamin, fucose) and carbohydrate-related processes (lactose biosynthesis, carbohydrate metabolism), suggesting the proteins function collectively as nutrient transporters and carbohydrate-processing enzymes. While some terms are peripheral or obsolete, the dominant theme is membrane transport linked to sugar and nutrient metabolism, supporting a label focused on transport and carbohydrate pathways.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:1904728","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0042149","count":2}]},{"hash":"555616751977405459","title":"Metabolic Stress Response","description":"This cluster shows enrichment for stress-related and metabolic processes: responses to lipopolysaccharide and ethanol, cellular signaling via cAMP, glycolysis, and proton transport, suggesting proteins coordinating metabolism under stress. A few terms (tRNA wobble uridine modification, histone deacetylation) are more specialized and less directly tied to this theme, but do not override the overall pattern.","confidence":"Medium","size":21,"edges":139,"triangles":492,"max_degree":17,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0032496","count":11},{"id":"GO:0002098","count":9},{"id":"GO:0055114","count":9},{"id":"GO:0042853","count":8},{"id":"GO:0071320","count":7}]},{"hash":"2156632563986018502","title":"Cell Cycle and Transport Regulation","description":"This cluster highlights processes related to mitosis (sister chromatid cohesion, spindle checkpoint deactivation), intracellular transport (intraciliary transport, nuclear pore localization), actin dynamics, and neuronal development/plasticity, suggesting a shared theme of regulating movement and division within cells. The label reflects a broad coordination of cell cycle control, cytoskeleton, and transport functions.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":2},{"id":"GO:0035721","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0031915","count":2}]},{"hash":"595410423050303391","title":"Xenobiotic and metal ion membrane transport","description":"This cluster shows enrichment for xenobiotic transmembrane transport and cadmium/cobalt ion transport/homeostasis, plus guidance on protein localization to the plasma membrane, suggesting a shared function in moving foreign compounds and metal ions across membranes and maintaining membrane protein placement; some terms are obsolete but reinforce the metal/xenobiotic transport theme.","confidence":"Medium","size":21,"edges":22,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0006876","count":2},{"id":"GO:0006877","count":2},{"id":"GO:0072660","count":2}]},{"hash":"1449278661259904438","title":"Chloroplast and Endosome Trafficking","description":"Dominant GO terms cluster around plastid-related processes (amyloplast organization, phototropism, gravitropism, protein import into chloroplast stroma) and vesicle/endosome organization and transport, suggesting a coherent theme of chloroplast maintenance and intracellular trafficking in plant cells. A few terms appear unrelated (mitochondrial apoptotic regulation, uterine gland development) and may be noise or broader annotations, but the core signal supports a plastid\u2013trafficking theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009660","count":1},{"id":"GO:0009638","count":1},{"id":"GO:1902954","count":1},{"id":"GO:0009959","count":1},{"id":"GO:2000641","count":1}]},{"hash":"1809206523617337122","title":"Chloroplast photosynthesis and chlorophyll regulation","description":"The cluster is dominated by terms tied to photosynthesis and chlorophyll metabolism (photosynthesis; chlorophyll biosynthetic process), with additional support from protein heterooligomerization (common in photosystem complexes) and plant signaling (cytokinin signaling; GPCR signaling) as well as cell division. Although some terms are obsolete, the overall theme points to plant chloroplast function and regulation of chlorophyll-related processes, suggesting these proteins work together in photosynthetic machinery and related regulatory pathways.","confidence":"Medium","size":21,"edges":99,"triangles":156,"max_degree":18,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0051291","count":3},{"id":"GO:0055114","count":3},{"id":"GO:2000531","count":2},{"id":"GO:1903646","count":2}]},{"hash":"191302449915543579","title":"Membrane Transport and Targeting Regulation","description":"The cluster is dominated by membrane-associated processes: transmembrane transport of phosphate and xenobiotics, and post-translational targeting of proteins to membranes, suggesting roles in trafficking and membrane localization. There is also evidence of signaling regulation (negative regulation of kinase activity) near membranes, tying into membrane-embedded regulatory functions. While a few terms (redox homeostasis, tRNA import) are more general, the overall theme centers on membrane transport/targeting and related regulation.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0097274","count":4},{"id":"GO:0035435","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0051259","count":3}]},{"hash":"1402700249813884311","title":"Embryonic Development and Cell Proliferation","description":"This cluster combines GO terms tied to development and differentiation (embryonic cranial skeleton morphogenesis, fat cell differentiation, cell migration, response to muscle stretch) with core cellular and genome maintenance processes (DNA replication, mRNA processing, telomere maintenance/capping, and regulation of cyclin-dependent kinase activity). The co-occurrence of developmental cues with proliferation and genome maintenance suggests genes coordinating growth and differentiation during embryogenesis, hence the combined label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":17},{"id":"GO:0006260","count":17},{"id":"GO:1904355","count":17},{"id":"GO:0006397","count":17},{"id":"GO:0045736","count":17}]},{"hash":"1072421768544389153","title":"Developmental and Immune Signaling","description":"The top GO terms indicate involvement in developmental processes (lung and cartilage development) alongside immune/inflammatory pathways (leukocyte migration, response to IL-6, NF-kappaB activation) and apoptosis, suggesting these proteins participate in broader regulatory programs that couple development with immune signaling, even though there are no apparent network connections here.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":5},{"id":"GO:0006915","count":4},{"id":"GO:0050900","count":3},{"id":"GO:0017038","count":3},{"id":"GO:0070741","count":3}]},{"hash":"1437468433625103844","title":"Neural and embryonic development","description":"The top GO terms are dominated by neural and broader embryonic development processes (neural tube closure, forebrain development, multicellular organism development, skeletal system development) with supporting signals for mitotic cell cycle and transcription, suggesting a developmental program with a neural emphasis rather than a single metabolic or immune function.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":13},{"id":"GO:0006349","count":12},{"id":"GO:0050830","count":12},{"id":"GO:0006351","count":12},{"id":"GO:0070059","count":12}]},{"hash":"888082709928049214","title":"Ubiquitin-Proteasome\u2013Innate Immune Signaling","description":"The top GO terms show strong enrichment for ubiquitin-dependent protein degradation (SCF-mediated) alongside innate immune functions (defense response to virus, NOD2 signaling, NF-\u03baB-related regulation). This suggests the cluster centers on proteostasis in the context of antiviral/immune signaling, with vitamin D\u2013related immune modulation as a secondary link. Some terms seem incidental or deprecated, but the core theme is proteolysis coupled to immune pathways.","confidence":"Medium","size":21,"edges":10,"triangles":0,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0032088","count":7},{"id":"GO:0070431","count":7},{"id":"GO:0042787","count":6},{"id":"GO:0033280","count":5}]},{"hash":"2214773187743435197","title":"Membrane Transporters for Ions and Sugars","description":"Most frequent GO terms relate to transmembrane transport of ions (sodium, potassium), and various sugars (galactose, arabinose, fucose), plus vitamin transport and nitrate assimilation. This pattern points to a cluster enriched in membrane transport activities and nutrient uptake; the few outliers (regulation of Rho signaling and neurotransmitter loading) do not override the dominant transport theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0098700","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2}]},{"hash":"1470001101367794115","title":"Cardiac membrane potential regulation with sensory detection","description":"This cluster is dominated by GO terms related to atrial cardiac muscle cell membrane repolarization and ion transport (K+ export, Na+ import), plus regulation of atrial repolarization, pointing to cardiac electrophysiology as the core theme. The presence of sensory perception terms (touch, pain) and gas/temperature sensing suggests accompanying environmental sensing signals, but the strongest and most coherent signal remains membrane potential regulation in cardiac cells. ","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098914","count":13},{"id":"GO:0050976","count":13},{"id":"GO:0034465","count":12},{"id":"GO:0007275","count":12},{"id":"GO:0019233","count":12}]},{"hash":"515897761544851237","title":"Antiviral defense and proteostasis","description":"The cluster is enriched for innate immune response, defense against virus, and ubiquitin-proteasome\u2013dependent protein degradation, indicating a shared function in antiviral defense and protein turnover. Some terms about development and meiosis appear peripheral, so the core theme remains immune defense with proteostasis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042769","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0060378","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0045087","count":2}]},{"hash":"2134681189440619418","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms for ubiquitin-mediated protein turnover (ubiquitin-dependent protein catabolic process, protein ubiquitination, polyubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, K63-linked ubiquitination). The strong representation of these terms suggests a shared role in tagging proteins for degradation via the ubiquitin\u2013proteasome system. Additional terms such as innate immune response and vitamin D response may reflect regulatory connections between ubiquitination and signaling pathways, though the core theme remains protein degradation via ubiquitination.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0033280","count":5},{"id":"GO:0032088","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0070534","count":4}]},{"hash":"221897467889868112","title":"Cardiac and Neural Transport and Calcium Signaling","description":"Top GO terms indicate membrane transport of xenobiotics, vitamins, and antifolate compounds, along with cardiac functions (heart development, cardiac muscle contraction) and calcium-mediated signaling (release of sequestered calcium into cytosol) plus neural vesicle loading. This mix suggests a cluster of membrane transport and signaling processes linked to heart and nervous system function, with palmitoylation implying membrane association. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0051958","count":2},{"id":"GO:0015885","count":2},{"id":"GO:0018230","count":2},{"id":"GO:0060048","count":2}]},{"hash":"1970152042390987845","title":"Cerebral cortex development and actin remodeling","description":"These proteins are enriched for neural development and cytoskeletal terms, especially cerebral cortex development and cortical actin cytoskeleton organization, along with embryonic cranial morphogenesis and regulation of stem cell differentiation. Although some terms (sperm capacitation, pain behavior) seem unrelated, the dominant pattern ties to brain development and actin-driven morphogenesis, supporting this label.","confidence":"High","size":21,"edges":126,"triangles":302,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":9},{"id":"GO:0048240","count":9},{"id":"GO:0060440","count":8},{"id":"GO:2001233","count":8},{"id":"GO:0061368","count":8}]},{"hash":"23453312525027158","title":"Developmental growth and stress signaling","description":"The cluster shows enrichment for core growth and development processes (mitotic cell cycle, multicellular organism development, DNA-templated transcription, translation initiation) alongside cellular stress responses (ER stress\u2013related apoptotic signaling, cadmium ion response), suggesting a coordinated role in developmental growth and stress signaling pathways.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0001501","count":5},{"id":"GO:0001403","count":5},{"id":"GO:0006351","count":5}]},{"hash":"1148203897984830106","title":"Serine/Threonine Kinase Regulation and Mitosis","description":"The cluster is dominated by GO terms for positive regulation of Ser/Thr kinase activity and autophosphorylation, plus cell-cycle and G2/M transition terms, suggesting a functional focus on phosphorylation-driven signaling that governs mitotic progression. Some terms (like bioluminescence) appear as outliers, but the core pattern supports kinase-regulated mitosis as the main theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0008218","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0043547","count":4}]},{"hash":"433568646243643826","title":"Unknown","description":"The terms span plant development (pollen exine formation, shoot apical meristem regulation) and glycan transport, plus neural/immune signaling (pain response, TLR2 signaling, inhibitory synaptic activity), with no single cohesive function tying all proteins together. Therefore there is no clear unifying theme for this cluster.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010584","count":1},{"id":"GO:1990569","count":1},{"id":"GO:1903857","count":1},{"id":"GO:1903070","count":1},{"id":"GO:1902183","count":1}]},{"hash":"929802806351040971","title":"RNA Processing and Mitotic Cell Cycle","description":"The Top Terms show a strong emphasis on RNA processing steps (spliceosomal complex assembly, mRNA splicing, SSU-rRNA maturation, tRNA methylation) along with basic cell division and mitotic cycle activities (mitotic cell cycle, cell division, intra-S DNA damage checkpoint signaling). There are also mitochondrial gene expression connections (regulation of mitochondrial transcription, transcription initiation at mitochondrial promoter), which frame the cluster as involving both nuclear RNA processing and mitochondrial transcription. Taken together, the proteins appear to participate in core RNA processing pathways linked to cell cycle regulation, with an additional mitochondrial transcription facet.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031573","count":2},{"id":"GO:0000278","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0051301","count":1}]},{"hash":"302019988414085232","title":"Mitotic progression and chromosome segregation","description":"The cluster is dominated by mitosis- and cell division-related terms, including mitotic cell cycle, cell division, chromosome passenger complex localization to kinetochore, and Ran-mediated signal transduction, suggesting a coherent role in spindle dynamics and chromosome segregation. Positive regulation of GTPase activity supports regulation of mitotic signaling, while a few terms (e.g., visual perception, endosome size) may reflect ancillary roles or annotation noise. ","confidence":"High","size":21,"edges":156,"triangles":670,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":20},{"id":"GO:0007601","count":19},{"id":"GO:0000278","count":19},{"id":"GO:0042068","count":18},{"id":"GO:0051301","count":18}]},{"hash":"2208904817619109791","title":"NOD1/2 Signaling with Thermal and Mechanical Stress Response","description":"The dominant GO terms point to NOD1 and NOD2 signaling pathways, indicating NOD-like receptor\u2013mediated innate immune signaling. Coupled with several terms for responses to heat, cold, temperature sensing, and mechanical stimulus, the cluster appears to combine innate immune signaling with environmental stress sensing. Confidence: High","confidence":"","size":21,"edges":21,"triangles":0,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032088","count":9},{"id":"GO:0070431","count":9},{"id":"GO:0035508","count":7},{"id":"GO:0009409","count":7},{"id":"GO:0033280","count":7}]},{"hash":"1877396088045660057","title":"Ubiquitin-Dependent Proteolysis and NF-kB Signaling","description":"This cluster centers on ubiquitin-mediated protein degradation (SCF-dependent and K48-linked ubiquitination, autoubiquitination) and NF-kB pathway regulation (I\u03baB phosphorylation, NIK activation). Additional terms reflect receptor turnover and immune-related processes (Wnt receptor catabolism, V(D)J recombination), which are commonly controlled by ubiquitination and proteasomal degradation. Some terms about X-chromosome inactivation appear peripheral but can relate to broader ubiquitin-regulated chromatin dynamics, supporting a unifying theme of ubiquitin-dependent signaling and protein turnover.","confidence":"Medium","size":21,"edges":11,"triangles":3,"max_degree":8,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0042787","count":11},{"id":"GO:0038018","count":10},{"id":"GO:0070936","count":10},{"id":"GO:0051865","count":10}]},{"hash":"996330205530593154","title":"Innate Immune Signaling and Xenophagy","description":"This cluster centers on innate immune sensing and response, highlighted by MyD88-dependent TLR signaling, NOD2 pathway activity, and defense against virus, along with ubiquitin-proteasome\u2013mediated protein turnover and positive regulation of xenophagy, suggesting coordinated pathogen detection and autophagic defense. There is also a link to inflammatory cytokine production and Th17 differentiation, reinforcing an immune-activation theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0002755","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0032088","count":4},{"id":"GO:0070431","count":4}]},{"hash":"2022086471388959565","title":"Cell Migration and Cytoskeletal Signaling","description":"The cluster centers on cytoskeletal dynamics and cell movement, with lamellipodium assembly and cell migration, plus regulation of Rho/Ras signaling and thrombin GPCR signaling, suggesting coordinated cytoskeletal remodeling and motility; accompanying terms on vesicle priming and degranulation/regulation of exocytosis support a theme of regulated vesicle trafficking linked to movement.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043314","count":7},{"id":"GO:0046580","count":7},{"id":"GO:0030032","count":7},{"id":"GO:0016477","count":7},{"id":"GO:0035023","count":7}]},{"hash":"386924010081135126","title":"TLR-Driven Innate Immunity","description":"The cluster shows strong enrichment for innate immune response, antiviral defense, TLR signaling (MyD88-dependent), and macrophage activation, indicating proteins involved in TLR-driven innate immunity and inflammatory regulation. A single neuronal signaling term appears as noise.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0034134","count":3},{"id":"GO:0090394","count":3}]},{"hash":"176045038383086796","title":"Skeletal muscle growth and regeneration","description":"This cluster shows a notable enrichment for muscle-related processes, including response to muscle stretch, skeletal muscle tissue regeneration, and cell growth, suggesting a focus on muscle maintenance, growth, and repair. A cardiac-related term (regulation of SA node action potential) hints at muscle physiology more broadly but does not override the skeletal muscle emphasis; other terms are more general (membrane protein localization, cold response, SNARE regulation) and do not define a different primary theme. Overall, the core signal points to muscle growth and regeneration processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035994","count":5},{"id":"GO:0098907","count":5},{"id":"GO:0007205","count":5},{"id":"GO:0072660","count":4},{"id":"GO:0035508","count":4}]},{"hash":"278558865352331427","title":"Unknown","description":"The GO terms span fungal cell wall biogenesis, general cell wall biogenesis, diverse developmental processes (spermatid and pollen sperm differentiation, multicellular growth regulation, brown fat differentiation), kinase activity regulation, neurotransmitter loading, and vitamin transport. There is no single coherent function tying these across species, so a specific label cannot be meaningfully assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032995","count":1},{"id":"GO:0042546","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0033674","count":1},{"id":"GO:0007286","count":1}]},{"hash":"1091738251408036049","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0001193","count":1},{"id":"GO:0042797","count":1},{"id":"GO:2001253","count":1}]},{"hash":"1603332616824877866","title":"Endomembrane vesicle trafficking","description":"GO terms indicate transport between ER-Golgi, endosomes, lysosome, and vacuole, pointing to proteins coordinating intracellular membrane trafficking within the endomembrane system. While a couple of terms relate to other processes, the dominant pattern is vesicle transport between organelles.","confidence":"High","size":20,"edges":73,"triangles":95,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0033138","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0031274","count":2},{"id":"GO:0000278","count":2}]},{"hash":"2226894090586983385","title":"Plant hormone signaling and chromatin/telomere regulation","description":"The cluster heavily features plant hormone responses (abscisic acid, salicylic acid, cytokinin signaling) alongside chromatin-level processes (nucleosome assembly) and telomere-related regulation (shelterin assembly, protein localization to telomeres), with some meiosis and senescence references, suggesting a theme where hormonal signaling interacts with chromatin and telomere dynamics in plants.","confidence":"Medium","size":20,"edges":14,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":3},{"id":"GO:0010520","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1904792","count":2}]},{"hash":"1950892712933153187","title":"Unknown","description":"The GO terms are highly diverse, spanning RNA processing, DNA replication, protein quality control (ERAD), transcriptional regulation and immune cell differentiation, with a few unrelated signals (EGF response, erythrocyte differentiation, viral transcription). There isn\u2019t a single coherent function or pathway that ties the proteins together, so a unified functional label is not evident.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0008033","count":1},{"id":"GO:0071364","count":1},{"id":"GO:0045657","count":1},{"id":"GO:0046782","count":1}]},{"hash":"2087476512583510748","title":"Chromosome dynamics in gametogenesis and development","description":"The cluster centers on chromosome maintenance and segregation (CENP-A chromatin assembly, spindle assembly, DNA integration) and germline-related processes (spermatogenesis, male gonad development, single fertilization), with broader developmental signals (brain development, multicellular growth) suggesting a shared role in developmental programs involving chromatin and cell division. A defense term is present but less coherent with the main theme. ","confidence":"Medium","size":20,"edges":12,"triangles":1,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0007283","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0035264","count":2}]},{"hash":"129713320111664741","title":"Vitamin and Steroid Metabolism and Secondary Metabolites","description":"The cluster is enriched for retinol/retinal and phylloquinone metabolism, C21-steroid hormone metabolism and steroid catabolism, and tropane alkaloid biosynthesis, with supporting antibiotic biosynthetic processes and responses. Some terms (sporulation, obsolete oxidation-reduction) are outliers and do not drive the overall theme.","confidence":"Medium","size":20,"edges":116,"triangles":272,"max_degree":15,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0030435","count":6},{"id":"GO:0042574","count":6},{"id":"GO:0042572","count":6}]},{"hash":"1003829327692359793","title":"Mitochondrial metabolism and redox stress response","description":"This cluster is dominated by GO terms related to mitochondrial processes, redox balance, and metabolic responses (oxidation-reduction, redox homeostasis, membrane fission, starvation response, valine catabolism). While there are some broader terms, the prevailing theme centers on mitochondria-driven metabolism and stress signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006574","count":3},{"id":"GO:0000002","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0007507","count":3}]},{"hash":"1317686882253608959","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":13,"triangles":0,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0042273","count":3},{"id":"GO:1902416","count":3},{"id":"GO:0002188","count":3}]},{"hash":"2051671479112727013","title":"Post-transcriptional RNA processing and translation regulation","description":"The cluster's GO terms converge on RNA metabolism: mRNA export, splicing and spliceosomal regulation, mRNA modification and poly(A) tail dynamics, and regulation of cytoplasmic translation. Together these indicate a group of proteins involved in post-transcriptional control of gene expression, especially processing and export of transcripts and modulation of translation under various stimuli.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031990","count":2},{"id":"GO:0032869","count":2},{"id":"GO:1900248","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0031047","count":2}]},{"hash":"691664815067239129","title":"Cerebral cortex and hippocampus development","description":"The top GO terms are strongly centered on brain development, notably cerebral cortex development and hippocampus development, plus related cortical morphogenesis and neural differentiation signals (e.g., cortex-related signaling and actin cytoskeleton organization). While some terms touch broader embryonic morphogenesis (cranial structures, trachea), the dominant pattern points to cortical/hippocampal formation and neural patterning. This justifies a label focused on brain region development.","confidence":"High","size":20,"edges":147,"triangles":574,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":20},{"id":"GO:2001233","count":20},{"id":"GO:0061368","count":20},{"id":"GO:0030866","count":20},{"id":"GO:0048701","count":20}]},{"hash":"268503875245461800","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The cluster is dominated by GO terms tied to protein ubiquitination and ubiquitin-dependent proteasomal degradation, including autoubiquitination, general ubiquitination, and SCF-dependent proteasomal pathways. This points to a cohesive role in tagging proteins for destruction and turnover (proteostasis), with ERAD involvement indicating endoplasmic reticulum quality control. A subset of terms also touches on signaling regulation via NF-kB/TNF pathways and receptor turnover (e.g., Wnt receptor catabolic process), consistent with downstream consequences of ubiquitin-mediated degradation. Overall, the clearest shared function is ubiquitin-proteasome\u2013driven protein catabolism.","confidence":"High","size":20,"edges":11,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0070911","count":8},{"id":"GO:1903265","count":8}]},{"hash":"449269622646180020","title":"Brush border microvilli and endomembrane organization","description":"GO terms center on intestinal apical surface structures (microvilli, terminal web, microspike assembly, microvillus length) and trafficking/endomembrane processes (endomembrane system organization, glucose absorption, antigen processing via MHC II, pinocytosis, autophagy). This pattern suggests a cluster of proteins coordinating brush border assembly and vesicular trafficking in intestinal epithelial cells, with supporting roles in nutrient uptake and immune processing. A few terms such as myelin assembly may be incidental, but the dominant theme is epithelial surface organization and endomembrane dynamics.","confidence":"High","size":20,"edges":130,"triangles":416,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:1902896","count":2},{"id":"GO:0001951","count":2},{"id":"GO:0016236","count":2},{"id":"GO:0032532","count":2}]},{"hash":"930352627498985859","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0061641","count":3},{"id":"GO:0000132","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0051013","count":3}]},{"hash":"1619791142524000214","title":"Developmental signaling and morphogenesis","description":"This cluster centers on GO terms related to development and signaling across multiple tissues: morphogenesis of cranial structures and heart valves, brain development, and FGFR- and STAT-mediated signaling, along with integrin-regulated adhesion and mast cell differentiation. These together point to a shared theme of signaling pathways guiding development and tissue remodeling. The inclusion of a pain-behavior term may reflect annotation pleiotropy rather than a core function of the cluster. Confidence: Medium","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061368","count":19},{"id":"GO:0048701","count":19},{"id":"GO:0035607","count":19},{"id":"GO:0003186","count":19},{"id":"GO:0042698","count":19}]},{"hash":"1812638207923008262","title":"Cranial skeletogenesis and cell-cycle regulation","description":"This cluster centers on embryonic cranial skeleton morphogenesis and core cell-cycle/DNA replication processes (centrosome cycle, DNA replication, spindle assembly, chromatid cohesion regulation), with supporting signals from Wnt pathway regulation and transcriptional control, suggesting proteins coordinating skull development with cell proliferation and mitosis.","confidence":"Medium","size":20,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":7},{"id":"GO:0007098","count":7},{"id":"GO:0010571","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0090263","count":5}]},{"hash":"389237979507755869","title":"Mitochondrial energy metabolism and stress response","description":"It centers on mitochondrial energy production, transport, and dynamics, with links to stress responses (ROS/superoxide) and nutrient signaling (insulin, amino acid starvation, adaptive thermogenesis).","confidence":"Medium","size":20,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":14},{"id":"GO:0034198","count":14},{"id":"GO:0032869","count":14},{"id":"GO:1990845","count":14},{"id":"GO:0035349","count":14}]},{"hash":"2247794505145280503","title":"Epigenetic Chromatin Regulation","description":"The terms focus on histone modifications (H3K23 acetylation, H3K27 trimethylation, H3K4 trimethylation) and DNA methylation\u2013dependent heterochromatin formation, pointing to regulation of chromatin state and gene expression; a few items relate to autophagy and drug response, but the dominant theme is epigenetic control of chromatin.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0090308","count":2},{"id":"GO:2000791","count":2},{"id":"GO:0043972","count":2},{"id":"GO:1901097","count":2}]},{"hash":"1503675364856936658","title":"Calcium-Dependent Synaptic Signaling and Membrane Repair","description":"This cluster is dominated by terms of calcium signaling, neuronal communication, and synaptic plasticity (cellular response to calcium, neurotransmitter secretion, long-term potentiation), plus calcium-triggered lysosome exocytosis and plasma membrane repair. These together point to calcium-dependent exocytic processes underlying synaptic function, with a membrane repair aspect. Peripheral terms like angiogenesis or neutrophil degranulation are less central to the core theme.","confidence":"High","size":20,"edges":173,"triangles":870,"max_degree":19,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0016525","count":8},{"id":"GO:0071277","count":8},{"id":"GO:0048015","count":8},{"id":"GO:0007269","count":8},{"id":"GO:0043065","count":8}]},{"hash":"1898537552895532426","title":"Central metabolism and stress response cluster","description":"Dominant signals are metabolic processes (TCA cycle, 2-oxoglutarate, amino acid biosynthesis) and cellular stress responses (oxidative stress, starvation), suggesting an energy-production and adaptive-response theme. Some terms (liver development, non-motile cilium assembly) appear as less connected or incidental. Confidence: Medium","confidence":"","size":20,"edges":117,"triangles":297,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0019878","count":4},{"id":"GO:0070301","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0043278","count":4}]},{"hash":"1600242893925025522","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":140,"triangles":466,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:0031425","count":1},{"id":"GO:0042793","count":1},{"id":"GO:0000961","count":1},{"id":"GO:0031426","count":1}]},{"hash":"1818539133960789321","title":"Mitochondrial Protein Import and Energy Metabolism","description":"The dominant GO terms reference mitochondrial import into the matrix and inner membrane, assembly of the cytochrome complex, TCA cycle, and aerobic respiration, which together point to mitochondrial energy production and the machinery that imports and assembles respiratory components. A couple of terms mentioning chloroplast stroma import and ergosterol biosynthesis suggest some cross-compartment or annotation noise, but the core signal is mitochondria-focused energy metabolism.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0045037","count":2},{"id":"GO:0032094","count":2}]},{"hash":"1662429528111965455","title":"Muscle development and signaling","description":"This cluster centers on proteins linked to skeletal muscle regeneration and developmental signaling (Wnt and Notch). The presence of ubiquitination and membrane trafficking terms suggests regulatory control of protein turnover and localization in muscle cells, tying the proteins to muscle development and related pathways, even though no direct interactions are observed here.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0072660","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0043403","count":2}]},{"hash":"724077979156853766","title":"Mitotic regulation and cytoskeletal dynamics","description":"The cluster is enriched for cell-cycle and mitosis-related terms (cell cycle, spindle assembly, cohesion regulation) and proteins involved in ubiquitination and GTPase signaling, which are key to mitotic control and chromosome segregation. Additional terms for cell migration and kinase activity modulation suggest coordinated signaling and cytoskeletal remodeling that support division and movement.","confidence":"High","size":20,"edges":17,"triangles":10,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0007049","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0051225","count":4}]},{"hash":"2247994938207858952","title":"Unknown","description":"The GO terms are highly diverse, spanning sensory perception, reproduction, ion transport, pH regulation, angiogenesis, detoxification, centrosome maintenance, vesicle docking, and tissue identity. There is no clear single function tying all proteins together, so a coherent label cannot be justified.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":3},{"id":"GO:0048240","count":3},{"id":"GO:1902476","count":3},{"id":"GO:0051454","count":3},{"id":"GO:0060055","count":3}]},{"hash":"2175774651597477710","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":180,"triangles":990,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0045218","count":20},{"id":"GO:0032886","count":20},{"id":"GO:0051255","count":20},{"id":"GO:0000073","count":20},{"id":"GO:1990535","count":20}]},{"hash":"575441640808162354","title":"Amino acid biosynthesis and catabolism","description":"This cluster is dominated by GO terms for the biosynthesis of branched-chain amino acids (leucine, isoleucine, valine) and for D-/amino acid catabolic/biosynthetic processes, suggesting a shared function in amino acid metabolism. There are a few outliers related to cell cycle regulation and mRNA stability, but they are low in frequency and do not override the main metabolic theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900087","count":2},{"id":"GO:0009097","count":1},{"id":"GO:0009098","count":1},{"id":"GO:0019478","count":1},{"id":"GO:0010817","count":1}]},{"hash":"2001435652926203548","title":"Regulated Kinase Signaling and Proliferation","description":"The terms cluster around positive regulation of kinase activity and GTPase signaling, autophosphorylation, and cell proliferation, with supporting hints from mitotic cycle, development, and hypoxia responses. This suggests a group of proteins that broadly promote signaling pathways driving growth and development, rather than a single specific pathway, justifying a label focused on kinase-driven signaling and proliferation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0071902","count":6},{"id":"GO:0031954","count":6},{"id":"GO:0008284","count":6},{"id":"GO:0000278","count":6}]},{"hash":"1570169556023645637","title":"Membrane ion transport and hyperpolarization","description":"The top GO terms include sodium ion import across the plasma membrane, potassium ion transmembrane transport, and membrane hyperpolarization, which together point to a core function in regulating ion flux and membrane potential. While other terms (DNA replication, SOS response, development, pain) appear in the list, they are less coherent with the membrane/ion signaling theme, suggesting some functional noise but a strong underlying signal for ion transport activity.","confidence":"Medium","size":20,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0060081","count":5},{"id":"GO:0098719","count":5},{"id":"GO:0007275","count":4},{"id":"GO:0019233","count":4}]},{"hash":"2124545436191908897","title":"Developmental kinase signaling and proliferation","description":"The cluster includes terms tied to regulation of kinase activity and autophosphorylation, cell cycle progression, and broad development processes (multicellular, skin development), with a consistent theme of controlling cell proliferation and tissue development. While there are also terms on hypoxia response and mRNA transport, the dominant signal points to developmental signaling pathways that govern growth, differentiation, and proliferation, including cardiac-related assembly as a tissue-specific aspect. ","confidence":"Medium","size":20,"edges":8,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":5},{"id":"GO:0043588","count":5},{"id":"GO:0031954","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0008284","count":5}]},{"hash":"989518920805608184","title":"Unknown","description":"The cluster's terms span very different biological themes\u2014from proteolysis and carbohydrate catabolism (proteolysis, xylan, cellulose catabolic processes) to neural development (neuron differentiation, substantia nigra development), toxin response, calcineurin-NFAT signaling, and meiotic DNA repair terms\u2014offering no single cohesive function or pathway to name succinctly. ","confidence":"","size":20,"edges":19,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0045493","count":3},{"id":"GO:0030182","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0009636","count":2}]},{"hash":"364960015320155901","title":"ER-Golgi and Endosome Vesicle Trafficking","description":"This cluster is dominated by GO terms describing intracellular transport through the ER-Golgi pathway, including ER-to-Golgi vesicle transport, Golgi-to-ER retrograde transport, endosome-to-Golgi transport, and general intracellular protein transport, plus vesicle fusion. A brain development term appears but the strongest signal is secretory pathway trafficking, indicating a coherent vesicle trafficking function for the proteins. ","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0042147","count":3},{"id":"GO:0006906","count":3}]},{"hash":"1149369385164363602","title":"Endomembrane trafficking and cell polarity","description":"This cluster centers on vesicle transport and membrane organization among key organelles (endosomes, Golgi, vacuole) and associated processes like vacuole-ER tethering, Cvt/autophagy-related pathways, and membrane formation during cytokinesis and sporulation. The recurring GO terms point to endomembrane trafficking and lipid/membrane dynamics as a unifying theme, with a secondary emphasis on cell polarity and shape maintenance.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032258","count":3},{"id":"GO:0045022","count":3},{"id":"GO:0034498","count":3},{"id":"GO:2000769","count":3},{"id":"GO:1990854","count":3}]},{"hash":"1787424210491452007","title":"Neural development with lipid signaling","description":"The cluster is enriched for neural development terms (mesodermal differentiation, radial glial scaffold formation, myelination, NMDA receptor clustering) and lipid-related signaling (apolipoprotein A-I pathway, LDL particle response), suggesting CNS maturation influenced by lipid pathways. Peripheral terms like platelet aggregation and bone resorption likely reflect broader remodeling but do not define the main theme.","confidence":"Medium","size":20,"edges":16,"triangles":1,"max_degree":5,"top_function":"wound healing","top_go_terms":[{"id":"GO:0048333","count":9},{"id":"GO:0021943","count":8},{"id":"GO:0070527","count":8},{"id":"GO:0071404","count":8},{"id":"GO:0050919","count":8}]},{"hash":"19144164015022864","title":"Neuroimmune Signaling and Axonogenesis","description":"The top terms show strong signals for immune and stress responses (lipopolysaccharide signaling, dsRNA response, interferon-beta production, defense against bacteria) alongside neural development processes (axonogenesis, corpus callosum development). This suggests a cluster of proteins involved in neuroimmune interactions during brain development, with some broader cellular stress responses as ancillary signals.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031663","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0022038","count":2}]},{"hash":"1317658872586744632","title":"Mechanotransduction and Cytoskeletal Signaling","description":"Based on the dominant terms, this cluster centers on cells sensing and responding to mechanical cues (cellular response to mechanical stimulus, response to muscle stretch) and remodeling the cytoskeleton (regulation of Rho signaling, cell migration). Other terms such as transcription and immune signaling appear as peripheral associations, but the core theme is mechanosensitive signaling and cytoskeletal dynamics.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0035249","count":3},{"id":"GO:0016477","count":2},{"id":"GO:0035994","count":2}]},{"hash":"670268475453657264","title":"Vitamin, antibiotic, and lipid biosynthesis","description":"The top GO terms point to multiple biosynthetic pathways: antibiotic biosynthesis, cobalamin (B12) and biotin biosynthesis, polyamine biosynthesis, and phosphatidylcholine biosynthesis, plus nodulation, which can relate to plant-associated metabolism. A few terms (transcription regulation and mRNA capping) are less directly tied to biosynthesis and may reflect multifunctional proteins or annotation overlap. Overall, the cluster centers on metabolic biosynthetic processes, though with some peripheral functions. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0009236","count":4},{"id":"GO:0006596","count":4},{"id":"GO:0035690","count":4},{"id":"GO:0009102","count":4}]},{"hash":"1049823776771225969","title":"Unknown","description":"The GO terms span very different biological contexts (DNA-templated transcription, bacterial lipopolysaccharide and antibiotic biosynthesis, steroid and alkaloid metabolism, and even epigenetic histone demethylation), with no single cohesive function tying the proteins together. Several terms are also obsolete in current GO, and the sparse network (Edges: 2, Triangles: 0) suggests weak functional cohesion. Therefore there isn\u2019t a clear, representative label for this cluster.","confidence":"","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0034720","count":4},{"id":"GO:0070544","count":4}]},{"hash":"787357601125585226","title":"Zinc Ion Transport and Homeostasis","description":"The top GO terms centre on zinc ion import across the plasma membrane, zinc ion homeostasis, cellular response to zinc ion starvation, and cadmium transport, plus xenobiotic transmembrane transport. This cohesive set points to membrane transporters dedicated to zinc and related metal detoxification and regulation, so the cluster likely represents zinc uptake and metal homeostasis pathways.","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:0008360","count":2},{"id":"GO:0010312","count":2},{"id":"GO:1903615","count":2},{"id":"GO:0006831","count":2}]},{"hash":"1155667705720208756","title":"Cardiac development and mechanotransduction","description":"The cluster is enriched for heart-related developmental processes (cardiac right atrium morphogenesis; venous endothelial differentiation; Notch signaling in heart-field cardioblast regulation) and for cellular responses to mechanical stimulus and cell migration, indicating proteins involved in heart morphogenesis and mechanosensitive signaling. Telomere maintenance and mRNA processing terms are present but less representative of the dominant theme. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":9},{"id":"GO:0035994","count":9},{"id":"GO:1904355","count":9},{"id":"GO:0032212","count":9},{"id":"GO:0045736","count":9}]},{"hash":"1678100985497622428","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is enriched for GO terms related to ubiquitination and proteasome-mediated protein catabolism (including ubiquitin-dependent degradation, SCF-dependent pathways, and autoubiquitination) and protein quality-control processes like aggrephagy, indicating a common role in tagging and removing proteins to regulate turnover and proteostasis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0070431","count":3}]},{"hash":"1830217378428994499","title":"Muscle mechanotransduction and innate immune signaling","description":"This cluster is enriched for GO terms linking cellular response to mechanical stimulus (mechanotransduction), protein ubiquitination, NOD-like receptor signaling, defense response to Gram-positive bacteria, and skeletal muscle regeneration, suggesting proteins that integrate mechanical stress signals with ubiquitin-regulated signaling and innate immune pathways to drive muscle remodeling. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":8},{"id":"GO:0016567","count":6},{"id":"GO:0032088","count":6},{"id":"GO:0070431","count":6},{"id":"GO:0050830","count":5}]},{"hash":"1533526992741739531","title":"Unknown","description":"The GO terms are highly heterogeneous (xylan catabolic process, redox homeostasis, spore wall assembly, lipid A biosynthesis, allantoin biosynthesis, etc.), spanning plant cell-wall degradation, fungal spore wall formation, bacterial envelope biosynthesis, and general metabolism, with no single coherent function tying the proteins together. Thus no clear theme emerges to name the cluster meaningfully.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006879","count":2},{"id":"GO:0042244","count":1}]},{"hash":"571977950786700702","title":"Developmental Differentiation Regulation","description":"The top GO terms point to regulatory control of cell differentiation and development across multiple tissues (muscle, eye, lung, and nervous system) and include notes on signaling and growth regulation. This suggests a general theme of controlling developmental differentiation rather than a single tissue-specific pathway, making a label around developmental differentiation regulation appropriate.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000721","count":1},{"id":"GO:2000587","count":1},{"id":"GO:2001015","count":1},{"id":"GO:2001045","count":1},{"id":"GO:1900239","count":1}]},{"hash":"373412538148928497","title":"Small GTPase signaling and vesicle trafficking","description":"Based on the Top Terms, the most represented functions are small GTPase\u2013mediated signaling and regulation of GTPase activity, together with vesicle trafficking processes such as endocytosis and Golgi-to-ER transport. Although there are some terms tied to pigmentation and whole-organism development (heart, spinal cord) those seem less central to the cluster's core GO signals. Therefore, the label reflects the core shared role in GTPase-driven signaling and vesicle trafficking.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007264","count":3},{"id":"GO:0043473","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0007507","count":3}]},{"hash":"99117725146230159","title":"tRNA charging and translation","description":"The cluster is dominated by translation-related terms, especially multiple tRNA aminoacylation processes (glycyl-, histidyl-, prolyl-, selenocysteinyl-tRNA) and regulation of translational fidelity, indicating involvement in the protein synthesis machinery and tRNA charging. A few other terms (DNA biosynthesis, embryonic development) are less cohesive with this theme and may reflect annotation noise. Overall, the key theme is tRNA charging and translation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0006407","count":1},{"id":"GO:0097056","count":1},{"id":"GO:0070150","count":1}]},{"hash":"165607972438933959","title":"TLR signaling and innate immune activation","description":"The GO terms cluster around innate immunity, with TLR2 signaling, MyD88-dependent pathways, macrophage activation, dendritic cell cytokine production, and inflammatory responses, all pointing to defense against Gram-positive bacteria. A few outlier terms exist, but the dominant theme is innate immune recognition and response.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0048549","count":4},{"id":"GO:0034134","count":3},{"id":"GO:0042116","count":3},{"id":"GO:0050729","count":3}]},{"hash":"687700968484261690","title":"Epigenetic chromatin silencing and cell cycle control","description":"This cluster is dominated by GO terms related to chromatin organization and epigenetic regulation (DNA methylation\u2013dependent heterochromatin formation, chromatin silencing) and cell cycle-related processes (sister chromatid cohesion, transcription regulation linked to cell cycle), with additional context from nucleolar rDNA localization. A secondary signal for translation appears, but the core theme centers on chromatin state and chromosome maintenance.","confidence":"Medium","size":19,"edges":69,"triangles":153,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0034503","count":8},{"id":"GO:0010870","count":8},{"id":"GO:0006346","count":8},{"id":"GO:1901300","count":8}]},{"hash":"936366620598219179","title":"Triglyceride catabolism and phospholipid remodeling","description":"The cluster is dominated by GO terms tied to lipid breakdown and membrane lipid turnover, including triglyceride catabolic process, triglyceride mobilization, triglyceride catabolic process, triglyceride acyl-chain remodeling, and phosphatidylcholine/phosphatidylethanolamine catabolic processes. This points to a core function in lipid metabolism and remodeling of membrane lipids. A few terms (receptor internalization, receptor-mediated virion attachment, and retina vasculature development) appear as minor outliers, possibly reflecting multifunctional proteins or annotation cross-talk. Overall, the cluster represents lipid metabolism and membrane lipid remodeling.","confidence":"Medium","size":19,"edges":20,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034638","count":3},{"id":"GO:0036153","count":3},{"id":"GO:0046338","count":3},{"id":"GO:0006642","count":3},{"id":"GO:2000480","count":3}]},{"hash":"2103620467784441019","title":"RNA Splicing and Post-Transcriptional Regulation","description":"The top GO terms point to RNA-level processing, with multiple entries for RNA splicing and regulation of alternative splicing, plus chloroplast mRNA modification, suggesting a cluster centered on RNA processing and its regulatory layers. Additional terms touch on ubiquitin-related regulation and stress responses, indicating possible co-regulation, but the core signal is RNA processing/splicing. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071600","count":1},{"id":"GO:0070536","count":1},{"id":"GO:1900871","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0043066","count":1}]},{"hash":"1162613241132495441","title":"RNA processing and splicing machinery","description":"Dominant GO terms cluster around RNA maturation and processing\u2014spliceosome-related functions (snRNP assembly, mRNA splicing via spliceosome), rRNA and tRNA processing, and P-body assembly\u2014indicating a core role in RNA metabolism. A few terms (hair cycle, water deprivation, heterochromatin formation) are less directly related but do not override the overarching theme. Confidence: Medium","confidence":"","size":19,"edges":125,"triangles":425,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000387","count":11},{"id":"GO:0008033","count":10},{"id":"GO:0033962","count":10},{"id":"GO:0008334","count":10},{"id":"GO:0009414","count":10}]},{"hash":"1165014323679507695","title":"Membrane transporters for nutrients and xenobiotics","description":"The cluster is dominated by transmembrane transport GO terms (vitamin, xenobiotic, sodium ion transport) with supporting metabolic and stress-response terms (fucose metabolism, glucose starvation, antibiotic response). While translation and cell division appear as broader cellular processes, the strongest shared function among members is transporting small molecules across membranes, especially nutrients and xenobiotics. This makes a membrane transport module the most representative label.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0042891","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0051301","count":3}]},{"hash":"963977406101174411","title":"Membrane Transport and Signaling","description":"The top GO terms show enrichment for transmembrane transport (sodium and vitamin transport) together with GPCR signaling, suggesting proteins linked to membrane transporters and related signaling roles. Some terms on metabolism and stress or tissue maintenance are more peripheral but fit within a broader membrane-associated functional theme, so this label captures the main shared function without overfitting to any single pathway.","confidence":"Medium","size":19,"edges":31,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0098907","count":2},{"id":"GO:1904728","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0035725","count":1}]},{"hash":"1041768957894642363","title":"Kidney and vascular metabolic signaling","description":"This cluster centers on metabolism-related GO terms (fructose, pyridoxal, retinol) along with kidney/renal system development and tissue homeostasis, plus growth-factor\u2013related signaling (PI3K/AKT) and endothelial cell apoptosis regulation, suggesting coordinated metabolic signaling affecting kidney and vascular tissue homeostasis and development.","confidence":"Medium","size":19,"edges":139,"triangles":633,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0097238","count":7},{"id":"GO:0051897","count":7},{"id":"GO:0046370","count":7},{"id":"GO:0042572","count":7}]},{"hash":"339328206319734384","title":"Developmental signaling and morphogenesis","description":"These proteins cluster around developmental signaling and tissue formation. The top GO terms cover regulation of transcription, Wnt signaling, neural development (cerebral cortex migration, neural tube patterning), and morphogenesis of cochlea and epidermis, as well as cytoskeleton polarity and protein complex assembly, suggesting a module coordinating signaling pathways and morphogenetic processes across multiple tissues.","confidence":"High","size":19,"edges":129,"triangles":440,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0021799","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0030950","count":2}]},{"hash":"513183500142852223","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":127,"triangles":439,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0000462","count":4}]},{"hash":"558087512300578616","title":"DNA replication and telomere maintenance","description":"The cluster is centered on replication and telomere biology, with GO terms for DNA replication (GO:0006260), mitotic leading-strand elongation (GO:1903460), telomere capping (GO:1904355), and telomere maintenance via telomerase (GO:0032212). Additional terms for mRNA processing and CDK-related regulation suggest ancillary links to gene expression and cell-cycle control, with a few differentiation/migration signals that may reflect broader cellular contexts. Overall, the core theme appears to be DNA replication and telomere maintenance.","confidence":"Medium","size":19,"edges":67,"triangles":86,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0045444","count":2}]},{"hash":"1850784617749274738","title":"Ribosome Biogenesis and rRNA Maturation","description":"This cluster is strongly enriched for GO terms related to ribosomal RNA maturation (SSU and LSU) and ribosome biogenesis, indicating a group focused on ribosome assembly and processing; a few terms about protein interactions are present but secondary.","confidence":"High","size":19,"edges":21,"triangles":3,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000747","count":3},{"id":"GO:0042273","count":3}]},{"hash":"1179237024808072854","title":"Unknown","description":"The top GO terms span immune cytotoxicity, hormone response, reproductive development, matrix remodeling, and signaling, spanning diverse areas with no clear unifying function. Therefore no single theme; label Unknown.","confidence":"","size":19,"edges":125,"triangles":415,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":6},{"id":"GO:0001913","count":6},{"id":"GO:0097067","count":6},{"id":"GO:0010815","count":6},{"id":"GO:0046697","count":6}]},{"hash":"37540537003518814","title":"Chloroplast RNA processing and plastid biosynthesis","description":"This cluster centers on chloroplast/plastid RNA processing, plastid transcription, RNA modification, and related biosynthetic processes (protoporphyrinogen IX and thiamine biosynthesis), with additional organellar RNA regulation terms (mitochondrial). The common theme is plastid gene expression and metabolism.","confidence":"Medium","size":19,"edges":169,"triangles":935,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006782","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0031425","count":2}]},{"hash":"540585284591193893","title":"Mitochondrial Assembly and Dynamics","description":"Most of the top GO terms point to mitochondrial processes (complex IV assembly, regulation of mitochondrial translation, mitochondrial fission, and magnesium ion transport), indicating a theme of mitochondrial biogenesis and morphology. Some immune/hormonal terms appear but do not define the cluster's core function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0070130","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0002377","count":1},{"id":"GO:0000266","count":1}]},{"hash":"1813903415899424574","title":"Antiviral innate immune response","description":"The cluster is dominated by terms related to antiviral defense and interferon signaling (innate immune response; cellular response to type I interferon; cellular response to dsRNA; negative regulation of defense response to virus by host), indicating a coherent antiviral innate immune theme; a few metabolism/division terms appear but do not define the main function.","confidence":"High","size":19,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0009097","count":3},{"id":"GO:0009099","count":3}]},{"hash":"1372779077055471985","title":"Cellular Excitability and Signaling","description":"The cluster centers on processes involving electrical excitability and signaling across multiple tissues: membrane depolarization/repolarization in cardiac muscle, GABA secretion and startle responses in neurons, and various environmental and chemical stimulus responses (cAMP signaling, temperature/cold responses, CO2 detection, and regulation of gastric acid secretion). This combination suggests a cohesive theme around rapid signaling and excitability rather than a single narrow pathway, justifying a label like Cellular Excitability and Signaling.","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":3},{"id":"GO:0060372","count":2},{"id":"GO:0003031","count":2},{"id":"GO:0071502","count":2},{"id":"GO:0086048","count":2}]},{"hash":"1561381418459395384","title":"Endosome Trafficking and Cardiac Signaling","description":"The top terms emphasize endosomal transport and recycling alongside heart-related functions, suggesting a cluster of proteins involved in endocytic trafficking that modulates signaling relevant to cardiac muscle development and contraction. While immune signaling terms are present, the most coherent theme is endocytic trafficking linked to cardiac signaling pathways.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045022","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0001782","count":2}]},{"hash":"1334937964468558790","title":"Beta-lactam antibiotic response and beta-lactamase regulation","description":"The top GO terms are dominated by antibiotic-related processes: response to antibiotic, regulation of beta-lactamase activity, and beta-lactam antibiotic catabolic process, suggesting a core theme of antibiotic resistance/metabolic handling in these proteins. Nylon catabolic process also appears, indicating broader biodegradation potential. Other terms (transcription, protein folding, secretion, lipid droplet organization, viral release, leukocyte migration) seem less central. Overall, the cluster centers on antibiotic response and beta-lactamase regulation with ancillary metabolic processes, making this label representative.","confidence":"High","size":19,"edges":42,"triangles":94,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":9},{"id":"GO:0033252","count":8},{"id":"GO:0019876","count":8},{"id":"GO:0030655","count":8},{"id":"GO:0006351","count":2}]},{"hash":"711045317523210979","title":"Neural and endocrine signaling","description":"The terms cluster around signaling and hormonal regulation: GPCR signaling, cAMP/cGMP pathways, ROS-related signaling, thyroid hormone metabolism, and adenohypophysis morphogenesis, with related neural functions like memory and drug responses. Some terms (e.g., insect cuticle development) are less aligned and may reflect annotation noise, but the prevailing theme is signaling and endocrine control across neural and endocrine systems.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050665","count":5},{"id":"GO:0031284","count":5},{"id":"GO:0042554","count":5},{"id":"GO:0008365","count":5},{"id":"GO:0007613","count":5}]},{"hash":"1743113345851140841","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":2},{"id":"GO:0000494","count":1},{"id":"GO:0032211","count":1},{"id":"GO:0000390","count":1},{"id":"GO:1904876","count":1}]},{"hash":"1906041122826389601","title":"Vacuolar amino acid transporters","description":"Most terms point to transport of amino acids and related folates across the vacuolar membrane, especially L-tyrosine import into vacuole and L-arginine/histidine export. A few terms (polyubiquitination, GTPase regulation, root cap development) are less connected, but the dominant theme is vacuolar amino acid transport.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051958","count":2},{"id":"GO:0015885","count":2},{"id":"GO:0051365","count":2}]},{"hash":"1188298202816761394","title":"Sugar transport and redox detoxification","description":"The top terms emphasize sugar transport (D-glucose and D-xylose transmembrane transport; lactose biosynthetic process) and redox-related detoxification (oxidation-reduction process; cellular oxidant detoxification). Some terms are obsolete or less related, but the strongest signal centers on carbohydrate handling and redox management, suggesting a cluster of proteins involved in sugar transport and oxidative stress responses.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0006626","count":2},{"id":"GO:1904728","count":1},{"id":"GO:0042149","count":1}]},{"hash":"1087027788519295167","title":"Glutamatergic synapse regulation","description":"The most represented GO terms cluster around excitatory synaptic function: positive regulation of glutamatergic neurotransmission, AMPA receptor activity, and PSD-95 clustering, with receptor internalization pointing to receptor trafficking at the synapse. While some terms are broader (transcription, retina development, fertilization, ribosome biogenesis), the dominant signal is modulation of glutamatergic signaling at the synapse.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050731","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0007338","count":3},{"id":"GO:0060041","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1463510764967636821","title":"Light-sensing signaling and transcription","description":"The top GO terms cluster around transcriptional activity (DNA-templated transcription) and various signaling pathways, including phosphorelay systems and light- or hypoxia-detection processes (detection of hypoxia, detection of visible light, red light signaling). This suggests a theme where environmental signals, especially light, regulate gene expression. Some terms appear as legacy or metabolic outliers (phosphorelay, tetrapyrrole linkage, obsolete regulatory terms), but the dominant pattern ties light-responsive signaling to transcription. ","confidence":"Medium","size":19,"edges":101,"triangles":247,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0000160","count":10},{"id":"GO:0017006","count":9},{"id":"GO:0009401","count":9},{"id":"GO:0030823","count":9}]},{"hash":"1767970450194790009","title":"Developmental Transcriptional Regulation","description":"This cluster is dominated by GO terms for DNA-templated transcription and regulation of gene expression (including imprinting) and a suite of developmental processes (forebrain and neural tube development, skeletal system development, multicellular organism development). Together these suggest co-regulated gene expression guiding development, with some stress- or immune-related terms appearing as contextual responses. Thus, a developmental transcriptional regulatory theme best fits the cluster.","confidence":"High","size":19,"edges":31,"triangles":53,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":12},{"id":"GO:0006349","count":11},{"id":"GO:0050830","count":11},{"id":"GO:0070059","count":11},{"id":"GO:0000278","count":11}]},{"hash":"425040520127852105","title":"Diverse biosynthetic pathways","description":"This cluster's top GO terms point to biosynthetic processes across a wide range of metabolites, from antibiotics and plant alkaloids to lipopolysaccharides and lipid-derived molecules, plus related hormone and catabolic processes; the shared thread is production of diverse small molecules rather than a single, specific function. Given the heterogeneity, the label captures the overarching theme but with moderate confidence.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0009103","count":4},{"id":"GO:0006564","count":4},{"id":"GO:0008207","count":4}]},{"hash":"1987461290602515531","title":"Glycosylation and cell-wall biosynthesis","description":"The top GO terms cluster around glycan-related processes: protein O-linked glycosylation via GalNAc, mannan biosynthesis, and cell wall organization, pointing to a set of proteins involved in glycosylation and building/modifying cell walls. Other terms (xenobiotic response/transport, cell growth, mRNA processing) are more peripheral but may reflect broader cellular roles. Overall, the dominant theme is glycosylation-related modification and cell-wall biosynthesis.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0043403","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0046354","count":2}]},{"hash":"465875439873057493","title":"Unknown","description":"The top GO terms are diverse, covering transcription, VEGF signaling, heart development, immune processes (IL-4 production, B cell maturation), cell cycle, apoptosis, and synapse localization. There isn\u2019t a single coherent biological theme tying these proteins together, making a concise, specific label unlikely. ","confidence":"","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035924","count":7},{"id":"GO:0006351","count":7},{"id":"GO:2001275","count":7},{"id":"GO:0007118","count":6},{"id":"GO:0000320","count":6}]},{"hash":"2113475677355271707","title":"Immune cell activation and migration","description":"This cluster is dominated by GO terms related to immune function: positive regulation of T cell differentiation, T cell chemotaxis, and monocyte activation, plus integrin-mediated adhesion. These point to immune cell activation and trafficking as the core theme. Some terms (xenobiotic transmembrane transport, spliceosome/mRNA splicing) are less coherent with the immune signal and may reflect housekeeping roles or annotation noise.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0000186","count":1}]},{"hash":"570034155919045972","title":"Sphingolipid and phospholipid metabolism","description":"The cluster is driven by lipid-related processes, including sphinganine-1-phosphate metabolic process (sphingolipid metabolism) and various phospholipid pathways (phospholipid dephosphorylation, phospholipid catabolic process, phosphatidylglycerol biosynthesis). While a few terms are unrelated (germ cell repulsion, obsolete Wnt terms) and one relates to detoxification, the core signal points to lipid biosynthesis and remodeling, particularly sphingolipid and membrane phospholipid metabolism.","confidence":"Medium","size":19,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0006668","count":1},{"id":"GO:0044329","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0035233","count":1}]},{"hash":"8876082901245705","title":"Vesicle trafficking and endosome transport","description":"This cluster is dominated by GO terms describing vesicle formation and movement within the endomembrane system: COPII budding, endosome transport between early/late endosomes, endosome-to-Golgi and endosome-to-lysosome routes, and Golgi-associated transport, plus related autophagy-like cargo delivery (Cvt pathway). These converge on a common theme of intracellular trafficking and routing of cargo, with ancillary links to Wnt signaling via trafficking of pathway components. Some terms about cell cycle and neuromuscular/neuronal processes appear ancillary to the main trafficking theme. ","confidence":"High","size":19,"edges":13,"triangles":5,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0090114","count":9},{"id":"GO:0045022","count":8},{"id":"GO:0008333","count":8},{"id":"GO:0090263","count":8}]},{"hash":"1634229509354594102","title":"Ubiquitination-Driven Protein Regulation","description":"This cluster is dominated by GO terms tied to ubiquitination: protein autoubiquitination and protein K63-linked ubiquitination, with a related note on ubiquitin-dependent modulation of SMAD signaling. These indicate a theme of ubiquitin-mediated regulation of protein function and signaling. Other terms in the set touch on translation or lipid/hormone metabolism that appear as less cohesive outliers, but the strongest signal centers on ubiquitin-based regulation of proteins and signaling pathways.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006431","count":3},{"id":"GO:0043651","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0030579","count":3}]},{"hash":"108144583578146485","title":"Neuro-immune inflammatory signaling","description":"GO terms suggest innate immune pathways and inflammatory signaling (TLR2 signaling, NF-kappaB/I-kappaB phosphorylation, macrophage activation, response to triacyl lipopeptide, pain behavior) together with neural development/remodeling processes (nerve branching morphogenesis, regulation of excitatory postsynaptic potential). This points to a theme of immune signaling influencing neural function and inflammation, i.e., neuro-immune cross-talk.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0060348","count":3},{"id":"GO:0061368","count":2},{"id":"GO:0034134","count":2},{"id":"GO:0090394","count":2}]},{"hash":"1482667149854474473","title":"Muscle development and regeneration signaling","description":"The top GO terms point to muscle-related biology, notably skeletal muscle tissue regeneration and Notch signaling in heart-field cardioblast proliferation, suggesting a muscle development/regeneration theme. Supporting terms on cell growth and cell cycle indicate growth signaling, while membrane trafficking terms (pinocytosis, membrane protein localization, SNARE regulation) reflect related cellular processes essential for muscle cell function. Overall, the cluster appears representative of muscle development and associated signaling pathways, with some broader cellular processes attached.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":4},{"id":"GO:0072660","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0043403","count":3},{"id":"GO:0000083","count":3}]},{"hash":"169261029110001364","title":"Unknown","description":"The GO terms in this cluster span telomere regulation, RNA processing, cell migration, differentiation, and signaling, showing no single dominant function. With this heterogeneity, there isn\u2019t a clear, cohesive theme to name the cluster beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1904355","count":7},{"id":"GO:0006397","count":7},{"id":"GO:0035994","count":7},{"id":"GO:0032212","count":7},{"id":"GO:0016477","count":7}]},{"hash":"68265540321367274","title":"Neural development and synaptic vesicle exocytosis","description":"This cluster is enriched for brain and nervous system development terms, alongside several GO terms related to synaptic vesicle exocytosis and calcium-dependent exocytosis, pointing to neuronal differentiation and synaptic signaling processes as the primary theme. Some cell cycle terms are present but appear less central to the main neural/synaptic pattern, and a couple of older/obsolete terms can be ignored for the core interpretation.","confidence":"Medium","size":19,"edges":66,"triangles":55,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":9},{"id":"GO:0007399","count":8},{"id":"GO:0051301","count":8},{"id":"GO:0045956","count":7},{"id":"GO:0000278","count":7}]},{"hash":"1188965825044335538","title":"Neural Drug-Response Signaling","description":"This cluster shows multiple GO terms tied to neuronal signaling and pharmacological responses, such as excitatory postsynaptic potential, response to morphine, response to cocaine, and regulation of endocannabinoid signaling. While it also contains unrelated terms (e.g., antibiotic biosynthesis, triglyceride catabolism), the dominant pattern points to neural signal transduction and drug-response processes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0000082","count":3},{"id":"GO:2000124","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0060079","count":3}]},{"hash":"1464956994890178381","title":"Neuronal Development and Microtubule Transport","description":"The top GO terms cluster around nervous system development, neuron projection morphogenesis, and microtubule-based movement/transport, with support from regulation of cytoskeleton organization and GTPase activity. Together they point to proteins that coordinate cytoskeletal dynamics and intracellular transport in neurons, linking development with microtubule-mediated movement. Some terms reflect broader developmental roles, but the dominant theme is neuronal cytoskeleton\u2013driven morphogenesis and transport.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":3},{"id":"GO:0007286","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0051493","count":2},{"id":"GO:0048812","count":2}]},{"hash":"684605445881167106","title":"Ribosome Biogenesis and Translation","description":"The strongest GO signals are ribosome biogenesis, ribosomal large subunit export from the nucleus, and tRNA modification, all pointing to ribosome assembly and protein synthesis. Additional terms related to cell cycle and stress responses are less central to the cluster's main theme, suggesting a primary focus on ribosome-related machinery.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0070212","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0006400","count":2}]},{"hash":"1607469325149970530","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006311","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0045087","count":2}]},{"hash":"64527134168993660","title":"Vesicle trafficking and Golgi transport","description":"The proteins in this cluster are tied to multiple vesicle trafficking processes, especially Golgi-to-vacuole transport, intracellular protein transport, Golgi inheritance, and retrograde Golgi-to-ER transport, along with synaptic vesicle endocytosis, recycling, and budding. These recurring themes indicate a cohesive role in vesicle trafficking and secretory pathway dynamics, centered on the Golgi and vesicle handling rather than other cellular processes.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006896","count":3},{"id":"GO:0048488","count":3},{"id":"GO:0021691","count":3},{"id":"GO:0048313","count":3},{"id":"GO:0036465","count":3}]},{"hash":"1695267803028776971","title":"Inflammation and eicosanoid biosynthesis","description":"The top GO terms point to inflammatory responses (chronic inflammatory response, response to LPS, inflammatory signaling) and lipid mediator production (leukotriene and prostaglandin biosynthesis), with additional oxidative stress-related detoxification. This suggests a cohesive role in inflammatory signaling and eicosanoid biosynthesis, with some supporting oxidative stress components.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0006401","count":1},{"id":"GO:0008285","count":1},{"id":"GO:0002544","count":1},{"id":"GO:0032496","count":1}]},{"hash":"2270247699348413380","title":"Innate Immune Signaling and Macrophage Activation","description":"The cluster centers on pattern-recognition receptor pathways (NOD2 and TLRs such as TLR2 and TLR9), with downstream NF-kappaB regulation, IL-1 production, and macrophage activation. Additional terms like positive xenophagy and Th17 differentiation support a microbe-response and autophagic clearance program typical of innate immune cells, making this a cohesive group of innate immune sensing and inflammatory signaling proteins.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0070431","count":5},{"id":"GO:1904417","count":4},{"id":"GO:0050701","count":4},{"id":"GO:2000321","count":4}]},{"hash":"1690821679685019311","title":"Immune signaling and transcriptional regulation under stress","description":"The terms point to immune signaling (innate immune response, LPS response, T cell receptor signaling) alongside transcriptional regulation (DNA-templated transcription, regulation of nuclear export), with additional stress- and cell fate-related processes (cadmium response, mitotic cycle, apoptosis). This suggests a cluster themed around immune response coordination with transcriptional control under cellular stress, though the mix includes broader stress-related processes, tempering confidence. ","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:0071276","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0097194","count":2}]},{"hash":"115277129635551106","title":"Calcium-Dependent Signaling and Kinase Regulation","description":"The Top Terms point to calcium ion detection, phototransduction, and regulation of serine/threonine phosphorylation (including kinase activity and peptidyl-threonine phosphorylation), suggesting a core theme of signaling modulation via calcium sensing and phosphorylation. Some other terms (e.g., medial cortex localization, terminal web assembly, cardiac contraction) are less cohesive with the main theme, but overall the cluster appears to reflect signaling and regulatory processes driven by calcium signaling and phosphorylation rather than a single tight pathway. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043950","count":1},{"id":"GO:0071574","count":1},{"id":"GO:0086004","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0007602","count":1}]},{"hash":"1678706778350826137","title":"Polarity and Signaling Regulation","description":"The cluster is enriched for GO terms about regulating cell polarity and Rho-mediated signaling, plus regulation of stress-related pathways (p38 MAPK cascade, hydrogen peroxide metabolism, respiratory burst). This points to proteins that modulate signaling and cytoskeletal organization rather than a single, specific process. Some terms (e.g., conjugation with cellular fusion, certain developmental terms) may reflect broader regulatory roles or annotation noise, but the core theme is regulatory control of polarity and signaling.","confidence":"Medium","size":18,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000769","count":2},{"id":"GO:0031139","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0032005","count":2},{"id":"GO:0030433","count":2}]},{"hash":"719865470703322490","title":"Endomembrane trafficking and cytoskeleton assembly","description":"The proteins cluster around endomembrane system organization and vesicle trafficking (Golgi to lysosome transport, lysosomal targeting, protein retention in Golgi, ER tubular network formation) and also participate in actin-based protrusions (filopodium/microspike assembly) and autophagy (aggrephagy), suggesting a shared role in vesicle movement and cytoskeletal dynamics.","confidence":"High","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":4},{"id":"GO:0007183","count":2},{"id":"GO:0071787","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0010256","count":2}]},{"hash":"2030115706225060523","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms tied to ribosome assembly and function, including ribosome biogenesis, maturation and export of ribosomal subunits, and initiation/termination of translation, indicating a cohesive ribosome/translation-focused group.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006415","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0060702","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0032790","count":1}]},{"hash":"1405720992517495020","title":"Nuclear transport and RNA processing","description":"This cluster is driven by terms tied to the nucleus and nucleocytoplasmic transport (nuclear pore complex assembly, pre-miRNA export from nucleus, tRNA processing, protein import), with additional signals of vesicle trafficking regulation (retrograde Golgi-ER transport, GTPase activity) and cell-cycle related processes (cell division, chromatid cohesion). These together suggest a coherent theme around nuclear transport, RNA processing, and coordination with cell cycle and trafficking.","confidence":"Medium","size":18,"edges":17,"triangles":4,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042176","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0006890","count":3},{"id":"GO:0070262","count":3}]},{"hash":"1209359873919230747","title":"Cilium Assembly and Trafficking in Development","description":"The top GO terms cluster around ciliogenesis (cilium assembly; protein localization to cilium) and ciliary trafficking (protein localization to endosome; retrograde transport ER to cytosol; endosome localization). Added developmental terms (forebrain-midbrain boundary formation, pronephros development, muscle organ development, fat cell differentiation, renal filtration) suggest these proteins function in ciliary biology during organ development and differentiation. This combination points to a cohesive theme of cilium-related assembly/trafficking linked to developmental processes.","confidence":"High","size":18,"edges":23,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0021905","count":2},{"id":"GO:0007517","count":2},{"id":"GO:0048793","count":2}]},{"hash":"1915547347448540394","title":"Genome maintenance and ER quality control","description":"The top GO terms cluster around genome maintenance (DNA replication, transcription, sister chromatid cohesion, trinucleotide repeat maintenance) alongside endoplasmic reticulum protein handling (ER folding and ubiquitin-dependent ERAD). This suggests a group of proteins involved in both genome integrity and ER-associated protein quality control, with a few immune-related terms appearing as possible outliers. Confidence: Medium","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":2}]},{"hash":"921044030702447370","title":"Proteolysis-Driven Tissue Remodeling","description":"The cluster\u2019s GO terms cluster around proteolytic and catabolic processes (bradykinin catabolic, collagen catabolic, proteolysis in protein catabolic process) and tissue remodeling activities (decidualization), with several terms tied to hormonal signaling (thyroid hormone stimulus, response to fatty acid) and reproductive context. This suggests proteins involved in hormone-regulated extracellular matrix turnover and tissue remodeling, though a few immune-related terms (T cell mediated cytotoxicity) appear less central. Overall, a cohesive theme of proteolysis linked to remodeling under hormonal influence.","confidence":"Medium","size":18,"edges":13,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":4},{"id":"GO:0070542","count":3},{"id":"GO:0050790","count":3},{"id":"GO:0001913","count":3},{"id":"GO:0097067","count":3}]},{"hash":"1093496387237795610","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":42,"triangles":28,"max_degree":12,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0051301","count":4}]},{"hash":"910401285831422349","title":"Mitotic spindle assembly and microtubule regulation","description":"Dominant GO terms cluster around mitosis and microtubule dynamics (metaphase alignment, spindle pole separation, midzone assembly, and regulation of microtubule-based processes), indicating a core theme of chromosome segregation and cytoskeletal organization. While there are related terms on cell adhesion and migration that reflect cytoskeletal remodeling in movement contexts, the central function appears to be spindle organization during cell division.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":4},{"id":"GO:0007080","count":4},{"id":"GO:0046580","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0045218","count":3}]},{"hash":"508866573318674715","title":"Neural development and synaptic vesicle trafficking","description":"The proteins cluster around neural development themes, with GO terms for brain development, radial glial scaffolds, Hedgehog signaling, and synaptic vesicle processes (exocytosis, maturation, and intracellular transport). This suggests a coherent focus on neural formation and synaptic machinery, with a minor presence of non-neural terms that may be incidental. ","confidence":"High","size":18,"edges":12,"triangles":0,"max_degree":3,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0010796","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0031384","count":3}]},{"hash":"2022951052286429312","title":"Intracellular trafficking and cell division","description":"This cluster is enriched for processes tied to the intracellular logistics machinery, including ER-Golgi vesicle transport, actin filament bundle assembly, exocytosis, spindle assembly, and overall cell division. Additional terms like mRNA processing and telomere maintenance hint at broader nuclear/cell-cycle functions, and brain development reflects developmental context. Taken together, the major theme appears to be the cellular machinery governing trafficking and division.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0090501","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0051225","count":2}]},{"hash":"1490881417396780301","title":"Ribosome biogenesis and ER-Golgi trafficking","description":"The top GO terms point to ribosomal large subunit biogenesis and rRNA maturation, along with multiple vesicle trafficking processes between the ER and Golgi (including COPII budding and retrograde transport). This suggests a cluster centered on fundamental ribosome assembly combined with secretory pathway functions, with growth-related terms (TORC1 signaling, multicellular growth) providing context for their broader roles in cellular growth and development.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2074959723649011184","title":"Ubiquitin-Mediated Proteolysis and Innate Immunity","description":"Proteins in this cluster are enriched for ubiquitin-dependent protein catabolic processes, autoubiquitination, and related ubiquitination terms, indicating a core role in protein degradation. The inclusion of innate immune response and dsRNA-related terms suggests immune signaling is intertwined with ubiquitin regulation, with some transcription and signaling terms present as secondary associations.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":4},{"id":"GO:0000083","count":3},{"id":"GO:1903265","count":3},{"id":"GO:0085020","count":3}]},{"hash":"1870323662775529280","title":"Membrane Transport of Xenobiotics, Nutrients, and Peptides","description":"Most top GO terms point to transmembrane transport of diverse substrates: xenobiotics and drugs (xenobiotic transport; doxorubicin/daunorubicin transport), vitamins and other nutrients (vitamin, taurine transport; cholesterol absorption regulation), and peptide/antigen movement (peptide antigen transport; antigen processing via MHC I). This suggests a cluster of membrane transporters handling small molecules and peptide antigens, with an additional plant ABA signaling term reflecting broader transport/signal roles. Therefore, Membrane Transport of Xenobiotics, Nutrients, and Peptides is an appropriate label.","confidence":"High","size":18,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":5},{"id":"GO:0019885","count":4},{"id":"GO:1900753","count":4},{"id":"GO:0046968","count":4},{"id":"GO:1901527","count":4}]},{"hash":"1143299477515049617","title":"RNA processing regulation under stress","description":"The cluster is dominated by GO terms on RNA metabolism and gene expression control, such as regulation of mRNA splicing via the spliceosome, regulation of mRNA stability in response to stress, and regulatory ncRNA\u2013mediated gene silencing, with some terms related to polyadenylation. While a few entries touch on cell division, lipid droplets, viral release, and secretion, the common thread is RNA processing regulation influenced by stress/host-pathogen context.","confidence":"Medium","size":18,"edges":46,"triangles":38,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":6},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0010610","count":4}]},{"hash":"196071416676234899","title":"Mitotic spindle assembly and microtubule dynamics","description":"The cluster is enriched for terms related to microtubule organization and spindle dynamics (microtubule nucleation, spindle pole body duplication, kinetochore localization) and cell cycle control, pointing to a core function in mitosis and microtubule regulation. Tyrosine dephosphorylation may reflect regulatory phosphatases that modulate mitotic signaling, with additional but secondary signals related to neuronal differentiation and stress/cytokine responses. Overall, the dominant theme ties to mitotic spindle assembly and microtubule-based cell division.","confidence":"High","size":18,"edges":126,"triangles":484,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":8},{"id":"GO:0030182","count":5},{"id":"GO:0007020","count":4},{"id":"GO:1903087","count":4},{"id":"GO:0034599","count":4}]},{"hash":"1049357875944968069","title":"Cytoskeleton remodeling and endosomal trafficking","description":"The dominant GO terms point to cytoskeleton dynamics (cellular response to mechanical stimulus, positive regulation of stress fiber and ruffle assembly) and vesicle trafficking between endosomes, Golgi, ER, and lysosomes/melanosomes, suggesting a cohesive role in mechanical response coupled with membrane transport, despite some noisy or obsolete terms present.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":3},{"id":"GO:1903215","count":3},{"id":"GO:0051496","count":3},{"id":"GO:0097178","count":3},{"id":"GO:0045493","count":3}]},{"hash":"55734754889243869","title":"Ribosome Biogenesis and mRNA Surveillance","description":"The GO terms point to ribosome lifecycle processes (large subunit export from the nucleus, ribosome disassembly, translation termination) and mRNA quality control (nonsense-mediated decay), with supporting themes in ER organization and cell-cycle-related nuclear membrane changes. These collectively suggest a cluster centered on ribosome biogenesis/ turnover and mRNA surveillance rather than a single signaling pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015768","count":1},{"id":"GO:1904751","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0002184","count":1}]},{"hash":"1919965399783617614","title":"Transmembrane drug and nutrient transporters","description":"This cluster is driven mainly by GO terms for transport across membranes, including drug (doxorubicin/daunorubicin) and nutrient (taurine, vitamins) transport, as well as peptide antigen transport and related membrane potential processes. While there are a few outliers (mercury response, ABA signaling), the overarching theme is membrane transport activity and associated regulation.","confidence":"Medium","size":18,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0046689","count":4},{"id":"GO:0019885","count":3},{"id":"GO:1900753","count":3},{"id":"GO:0046968","count":3},{"id":"GO:1901527","count":3}]},{"hash":"1839914895361897395","title":"Brain Development and Cortical Morphogenesis","description":"This cluster centers on neural development, with strong signals for cerebral cortex and hippocampus development, embryonic cranial skeleton morphogenesis, and cortical actin cytoskeleton organization, indicating a core program of brain morphogenesis and neuronal differentiation. Additional terms related to transcriptional regulation and signaling (DNA-templated transcription, phosphorylation, and apoptotic signaling) support a coherent theme of development and structural organization in the brain, with some craniofacial/head-patterning context reflected by trachea formation and cranial skeleton morphogenesis.","confidence":"High","size":18,"edges":97,"triangles":266,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":18},{"id":"GO:0060440","count":17},{"id":"GO:2001233","count":17},{"id":"GO:0061368","count":17},{"id":"GO:0030866","count":17}]},{"hash":"1451488324232699252","title":"Membrane Trafficking and Signaling Regulation","description":"The Top Terms mix signaling pathway regulation (NF-kappaB, NOD2, Notch) with membrane-related processes such as maintaining protein location in the plasma membrane and SNARE complex regulation, plus related growth and muscle regeneration terms. This suggests a cluster of proteins involved in controlling signaling at membranes and vesicle trafficking, rather than a single narrow function. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":7},{"id":"GO:0070431","count":7},{"id":"GO:0072660","count":6},{"id":"GO:0035508","count":6},{"id":"GO:0043403","count":6}]},{"hash":"1936595078681463213","title":"Neural development and signaling regulation","description":"This cluster centers on neural development terms (cerebellar cortex formation, Bergmann glial differentiation) and on the regulation of signaling pathways (insulin receptor signaling, T cell receptor signaling, and negative regulation of cyclin-dependent kinase activity), alongside related cell proliferation controls and kinetochore-related localization. This suggests proteins that coordinate growth, metabolism, and neural development through various signaling controls.","confidence":"Medium","size":18,"edges":109,"triangles":342,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034501","count":16},{"id":"GO:0045736","count":16},{"id":"GO:2001275","count":16},{"id":"GO:0050852","count":16},{"id":"GO:0008286","count":16}]},{"hash":"2171289985959664274","title":"Vacuolar amino acid transporters","description":"The cluster\u2019s top GO terms center on transport of multiple amino acids across the vacuolar membrane (e.g., L-tyrosine import, L-arginine/histidine import/export, proline, alanine, and glutamine transport), indicating a common function as vacuolar amino acid transporters in plants. A related term on root cap development suggests a plant-specific context, but the cohesive theme remains vacuolar amino acid transport.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051365","count":1},{"id":"GO:0090514","count":1},{"id":"GO:0015824","count":1},{"id":"GO:1990818","count":1},{"id":"GO:0089708","count":1}]},{"hash":"1981257612886985984","title":"Unknown","description":"The listed GO terms are highly heterogeneous, spanning photosystem regulation (plant/chloroplast), vacuole fusion, general phosphorylation/dephosphorylation, MAPK signaling, BMP/TGF-beta/SMAD signaling, meristem maintenance, germ-line masculinization, and nuclear export. There is no single cohesive biological process or function that ties these terms together across species and contexts, so a concise, representative label cannot be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080005","count":2},{"id":"GO:0061191","count":2},{"id":"GO:0035970","count":2},{"id":"GO:0000173","count":2},{"id":"GO:0030514","count":2}]},{"hash":"1594392203575535197","title":"Xenobiotic Response and Biosynthesis Pathways","description":"The top GO terms cluster around responses to xenobiotic stimuli and antibiotic-related processes, accompanied by several biosynthetic pathways (biotin, menaquinone, phosphatidylcholine) and some RNA-processing activities. This suggests a broad theme of metabolism and detox/defense against external compounds, despite some outliers like nodulation and mRNA capping. The label captures the central tendency without overfitting to a single precise function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0009234","count":3}]},{"hash":"263897687210057169","title":"Coagulation and innate immune signaling","description":"The top GO terms show a strong emphasis on blood coagulation, regulation of fibrinogen/fibrinolysis, and innate immune responses (Toll signaling and defense against fungus). Although a few terms touch on growth or transcription, the dominant pattern links hemostasis with immune signaling, suggesting a module that integrates coagulation with innate defense mechanisms.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0044537","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0045752","count":3}]},{"hash":"520789563778841924","title":"Unknown","description":"The terms span spindle organization, GTPase regulation, heart development, RNA silencing, circadian/sleep regulation, starvation behavior, jump response, spermatogenesis, and anoikis, with no clear single theme tying the cluster together. With no edges and diverse functions, a coherent, specific label isn\u2019t supported.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007051","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0016246","count":1},{"id":"GO:0042321","count":1}]},{"hash":"207267532852744794","title":"Skeletal Muscle Regeneration and Growth Signaling","description":"The most specific GO term is skeletal muscle tissue regeneration, with supporting terms for cell growth and cell cycle, indicating a muscle growth/regeneration program. Other terms point to immune signaling (NOD2 pathway and NF-kappaB regulation) that can influence muscle remodeling, and trafficking-related terms (membrane localization maintenance, SNARE regulation) suggesting signaling dynamics in muscle cells. Together, these imply a muscle-focused regeneration and growth signaling cluster with ancillary immune and trafficking components.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0072660","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0043403","count":3}]},{"hash":"1666299375726689298","title":"Unknown","description":"The GO terms cover diverse processes\u2014from telomere maintenance and DNA replication to immune signaling, GPCR pathways, and even plant hormone signaling\u2014showing no single cohesive function for the cluster. Therefore, there isn\u2019t a clear, representative theme to name the group.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:0032088","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0009738","count":3}]},{"hash":"773971358509255929","title":"Cardiovascular and skeletal muscle regeneration","description":"The top GO terms cluster around muscle and heart development and growth, including skeletal muscle tissue regeneration, Notch signaling in heart field regulation, and endothelial proliferation during sprouting angiogenesis, plus general cell growth and membrane localization. While a couple terms (telomere maintenance regulation, SNARE assembly regulation) are less directly related, the dominant theme is signaling and processes tied to cardiovascular and muscular tissue formation and regeneration.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904357","count":8},{"id":"GO:0072660","count":7},{"id":"GO:0035508","count":7},{"id":"GO:0043403","count":7},{"id":"GO:0000083","count":7}]},{"hash":"868621272592844941","title":"Transcription, chromatin, and DNA damage response","description":"The top GO terms indicate a nuclear regulatory program involving transcription, chromatin modification (H3-K4 methylation), DNA damage signaling via p53, and cell cycle regulation, plus RNA processing and ubiquitination, suggesting a cohesive theme of genome maintenance and expression control.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:2000134","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0030330","count":2},{"id":"GO:0032466","count":2}]},{"hash":"2046870465096643231","title":"Nuclear transcriptional stress response","description":"Top GO terms indicate DNA-templated transcription and nuclear import, with multiple cellular stress responses (cadmium ion, gamma radiation, diamide, sodium arsenite) also enriched. This pattern supports a theme of transcriptional regulation in the nucleus under stress, potentially involving import/export and stress-activated signaling that modulates GTPase activity. Placenta development and obsolete terms are likely noise, not central to the cluster\u2019s core function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071480","count":2}]},{"hash":"1795401573702430863","title":"Cellular stress response and secretory pathway","description":"This cluster centers on cellular stress signaling and protein processing in the secretory pathway, as evidenced by terms like unfolded protein response, ER-to-Golgi transport, and cardiac hypertrophy in response to stress. Additional signals of glucocorticoid signaling and toxin-related responses (morphine, lead ion) support a stress- and signaling-focused theme, though a few terms (DNA replication, dephosphorylation) may reflect broader cell-cycle regulation. Overall, the dominant theme is stress response linked to protein handling and trafficking.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0016311","count":3},{"id":"GO:2000324","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0010288","count":2}]},{"hash":"497800982752584993","title":"Innate Immune Response and Pathogen Sensing","description":"The cluster is enriched for innate immunity terms: defense against virus, innate immune response, macrophage activation, detection of bacterium, and TLR2 signaling, with NF-kappaB regulation; additional terms like ubiquitin-dependent proteolysis and peroxisome import may relate to antigen processing and antiviral responses. This points to a cohesive theme of immune sensing and response to pathogens.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:0051607","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0016558","count":3},{"id":"GO:0034134","count":3}]},{"hash":"393170529814237512","title":"Meiosis, chromatin remodeling, and telomere maintenance","description":"The top terms cluster around nuclear genome maintenance and meiotic processes: chromatin remodeling, DNA-templated transcription, replication-related double-strand break repair, and regulation of meiotic recombination, plus shelterin assembly and telomere localization. The inclusion of ascospore formation reinforces a fungal meiosis context, while hormone-response terms appear peripheral. Overall, this suggests a module focused on meiosis-associated chromatin dynamics and telomere protection.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990414","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0030437","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010520","count":2}]},{"hash":"566765344308478594","title":"Endomembrane trafficking and phosphate metabolism","description":"The GO terms cluster around intracellular membrane dynamics (endosome organization, phagosome handling, vacuole fusion) and phosphate-related metabolism (phosphate ion homeostasis, polyphosphate biosynthesis) with a note on membrane lipid turnover (glycerophospholipid catabolic process). This suggests a cohesive theme of vesicle trafficking within the endomembrane system coupled to phosphate and lipid metabolism.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007032","count":1},{"id":"GO:0044655","count":1},{"id":"GO:0016237","count":1},{"id":"GO:0016036","count":1},{"id":"GO:0070417","count":1}]},{"hash":"1890228443282850637","title":"Unknown","description":"The terms span very different biology: autophagy regulation, proteolysis, enzymatic activity regulation, plant phytochelatin biosynthesis, Rho signaling, ion transport, host-symbiont/virus interactions, mRNA capping, and viral replication/attachment. With no edges and only scattered terms, there is no clear shared function tying all proteins together, so a single coherent label cannot be inferred.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904715","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0043085","count":2},{"id":"GO:0046938","count":2},{"id":"GO:0035023","count":2}]},{"hash":"677556126821855428","title":"Unknown","description":"The GO terms span diverse processes (blood coagulation, development of multiple organs like gonad and lung, muscle regeneration, general cell growth, cold response, membrane localization maintenance, and SNARE regulation), with no clear shared pathway or function linking them. This suggests the cluster does not represent a coherent single theme, hence the Unknown label.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007596","count":3},{"id":"GO:0008584","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0072660","count":2},{"id":"GO:0035508","count":2}]},{"hash":"1661077391434170384","title":"Membrane lipid biosynthesis and remodeling","description":"The cluster is enriched for lipid-related processes (triglyceride biosynthesis, CDP-diacylglycerol biosynthetic process, cardiolipin acyl-chain remodeling) with additional, but less cohesive, mentions of potassium ion transport. This suggests a core theme of membrane lipid metabolism, with some related transport annotations.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":2},{"id":"GO:0010107","count":2},{"id":"GO:2001246","count":1},{"id":"GO:0070236","count":1},{"id":"GO:0006663","count":1}]},{"hash":"1638381784513269853","title":"Vesicle Trafficking and Vacuolar Targeting","description":"This cluster centers on endosome transport, Cvt-mediated targeting to the vacuole, vacuole-ER tethering, and prospore membrane formation, suggesting a core vesicle trafficking/vacuolar organization theme in yeast; a few terms like spliceosome assembly and GPCR regulation appear as outliers due to multifunctional proteins.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000244","count":2},{"id":"GO:0070536","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0045022","count":1},{"id":"GO:0034498","count":1}]},{"hash":"1767014697842147196","title":"RNA Processing and Translation Initiation","description":"This cluster centers on post-transcriptional RNA processing, especially mRNA splicing and spliceosome regulation, plus components involved in translation initiation, such as translation reinitiation and preinitiation complex formation. The mix of splicing-related GO terms and translation initiation terms suggests a cohesive module coordinating RNA processing with the onset of translation.","confidence":"High","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0016556","count":2}]},{"hash":"81747405230983254","title":"Neuronal Development and Signaling Regulation","description":"Primarily driven by brain and hippocampus development and dendrite morphogenesis, with several entries involving regulation of calcium-dependent exocytosis, phosphorylation (peptidyl-serine), and signaling cascades (ERK/JNK). This points to a cohesive theme of proteins coordinating neuronal development and the modulation of intracellular signaling, despite the occasional cell-cycle term that may reflect neurogenic proliferation contexts.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021766","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0045956","count":4},{"id":"GO:0043366","count":4},{"id":"GO:0033138","count":4}]},{"hash":"110667634258568959","title":"Nucleic acid and protein methylation","description":"The top GO terms are dominated by methylation-related processes across RNA (rRNA methylation), DNA (obsolete gamete-related methylation), histone (H4-R3 methylation), and protein arginine methylation, suggesting a cluster centered on methyltransferase functions and methylation regulation; other terms appear ancillary or legacy annotations.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0031167","count":4},{"id":"GO:0043046","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0043985","count":3}]},{"hash":"451001883911726214","title":"Actin-driven cell migration and polarity in osteogenesis","description":"Top GO terms point to actin cytoskeleton remodeling (actin filament bundle assembly, podosome assembly), cell movement (cell migration), and polarity establishment/regulation (establishment of epithelial cell polarity, regulation of cell shape). Also features cleavage furrow formation and plasma membrane tubulation, consistent with dynamic membrane\u2013cytoskeleton remodeling. Bone development and osteoblast fate commitment indicate a bone formation context. Collectively, the cluster likely comprises proteins coordinating actin dynamics, polarity, and migration in bone-related cells.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0051017","count":2},{"id":"GO:2000769","count":2},{"id":"GO:0036089","count":2}]},{"hash":"257956563274924819","title":"Muscle regeneration and signaling regulation","description":"This cluster is characterized by terms linked to skeletal muscle regeneration, cell growth, and regulation of signaling via ubiquitination and kinase activity, suggesting a theme of muscle growth signaling and protein turnover. While some terms touch on broader stress responses (vitamin D, cold) or general protein localization, the strongest signals are the muscle regeneration and regulatory processes, which makes the label representative of the core functional theme. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071901","count":7},{"id":"GO:0000083","count":7},{"id":"GO:0033280","count":7},{"id":"GO:0048549","count":7},{"id":"GO:0016567","count":7}]},{"hash":"2205453282828609922","title":"Neuronal excitability and synaptic plasticity","description":"The cluster is dominated by neural signaling terms\u2014neuronal action potential, membrane hyperpolarization, and regulation of potassium channels\u2014with emphasis on synaptic modulation (long-term synaptic depression), indicating roles in neuronal excitability and synaptic plasticity. Brain-related GO terms such as optic nerve organization and globus pallidus development support a neural context, while a few terms touch on general membrane potential regulation.","confidence":"High","size":17,"edges":14,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":2},{"id":"GO:0021633","count":1},{"id":"GO:0060372","count":1},{"id":"GO:0035024","count":1},{"id":"GO:0060081","count":1}]},{"hash":"604516393530035326","title":"Cell cycle and growth with stress response","description":"The cluster centers on mitotic cell cycle, cell division, and multicellular organism growth, with supporting signals from development (brain, spermatid) and metabolism (glycolytic process) and proteostasis/stress responses (unfolded protein response, redox homeostasis). This suggests a cohesive theme of coordinating cell proliferation and organismal growth while managing cellular stress, rather than a single precise pathway.","confidence":"Medium","size":17,"edges":10,"triangles":3,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051572","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0006986","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0007286","count":3}]},{"hash":"194708772994753170","title":"Protein quality control and ER-Golgi trafficking","description":"This cluster centers on protein quality control and trafficking: multiple terms point to protein unfolding and misfolded protein response, stress granule dynamics, and ER-to-Golgi vesicle transport, suggesting a theme of managing protein folding stress and secretory pathway traffic; the presence of cell cycle-related terms may reflect broader cellular processes linked to these activities.","confidence":"Medium","size":17,"edges":21,"triangles":13,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":7},{"id":"GO:0043335","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0035617","count":6},{"id":"GO:0051301","count":6}]},{"hash":"1699488295775494695","title":"Proteostasis and signaling regulation","description":"The cluster\u2019s top GO terms center on protein handling and modification: proteolysis, regulation of chaperone-mediated autophagy, ubiquitination, and regulation of catalytic/kinase activities. These point to a theme of protein quality control and modulation of signaling via post-translational processes. Some terms (e.g., phytochelatin biosynthesis, terminal web assembly, cardiac contraction regulation) are less central and may reflect broader context or annotation noise, but the core signals support a proteostasis- and regulation-focused cluster.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904715","count":4},{"id":"GO:0006508","count":4},{"id":"GO:0043085","count":4},{"id":"GO:0046938","count":4},{"id":"GO:0043950","count":1}]},{"hash":"1023258901757467573","title":"Unknown","description":"The top terms are highly diverse (transcription, placenta development, ER-Golgi transport, synapse and kinetochore localization, immune defense, mRNA processing, angiogenesis, and response to cocaine), with no single functional theme connecting them all. Therefore a cohesive label isn\u2019t supported.","confidence":"","size":17,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001893","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0035418","count":2},{"id":"GO:0014068","count":2}]},{"hash":"659922254979475343","title":"Neuronal lipid metabolism and myelin maintenance","description":"The top GO terms point to neural membrane and myelin-related processes (CNS myelin maintenance; positive regulation of neuron projections), suggesting a neuronal function theme. Coupled with lipid biosynthesis terms (unsaturated fatty acid biosynthesis; sphingolipid metabolism) this indicates membrane lipid homeostasis supporting neurons and myelin. Some terms about ergosterol regulation and fungal sphingolipids align with lipid membrane biogenesis, reinforcing a lipid-centric cluster with neural relevance. A few terms (nitrate assimilation, nitric oxide biosynthesis) are broader metabolic signals and seem less directly tied but do not negate the lipid-neural pattern.","confidence":"Medium","size":17,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0010976","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1902019088353368803","title":"Mitochondrial protein import and respiration","description":"This cluster centers on mitochondrial functions: import into the intermembrane space, components of the respiratory chain and Complex II assembly, and related tRNA processing/translation activities, suggesting a cohesive mitochondrial protein\u2013handling and oxidative phosphorylation theme.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0090116","count":1},{"id":"GO:1901485","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0016567","count":1}]},{"hash":"1408044584358422781","title":"ER stress and redox homeostasis","description":"These proteins cluster around endoplasmic reticulum\u2013associated processes (protein folding in ER; ER stress response) and redox/oxidative stress regulation (cell redox homeostasis; deglutathionylation). The transcription-related terms may reflect stress-induced transcriptional changes that accompany ER and redox stress responses, making this a coherent ER stress\u2013redox cluster.","confidence":"High","size":17,"edges":22,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0080058","count":1},{"id":"GO:1903206","count":1},{"id":"GO:0016032","count":1}]},{"hash":"152837376011472557","title":"Diverse Metabolic Biosynthesis and Catabolism","description":"The top terms span multiple biosynthetic pathways (antibiotic, biotin, cobalamin, chlorophyll) as well as several lipid- and lipid-related catabolic processes, plus cellular oxidant detoxification and tRNA modification. This indicates a cluster of proteins involved in general metabolism with both synthesis and breakdown roles rather than a single functional module. Therefore the label \"Diverse Metabolic Biosynthesis and Catabolism\" reflects the broad metabolic theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":5},{"id":"GO:0098869","count":5},{"id":"GO:2000124","count":4},{"id":"GO:0006660","count":4}]},{"hash":"119220056306747806","title":"Neural development and cytoskeletal signaling","description":"The top GO terms suggest a theme around nervous system development (spinal cord development, sensory perception of sound) and cytoskeletal regulation (regulation of Rho signaling, microtubule-based movement), pointing to neural signaling and cytoskeletal dynamics as a cohesive function of this cluster. Some terms (like glucose transport) appear less related, indicating partial noise, but the central signal remains neural development with cytoskeletal control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0070493","count":6},{"id":"GO:0021510","count":6},{"id":"GO:0007018","count":6},{"id":"GO:0007605","count":6}]},{"hash":"2077710009371641717","title":"Cerebral cortex and hippocampus development","description":"The top GO terms are strongly centered on brain development and cortical morphogenesis (cerebral cortex development, hippocampus development, orbitofrontal cortex development), plus related processes like cortical actin cytoskeleton organization and embryonic cranial morphogenesis. A single outlier term (trachea formation) does not negate the prevalent neural-development theme, so the cluster likely reflects proteins involved in brain development and cortical formation.","confidence":"High","size":17,"edges":22,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":17},{"id":"GO:2001233","count":17},{"id":"GO:0061368","count":17},{"id":"GO:0030866","count":17},{"id":"GO:0048701","count":17}]},{"hash":"660009441737327763","title":"Oxidative stress response and redox homeostasis","description":"Dominant signals are cellular response to oxidative stress, oxidation-reduction processes, and redox homeostasis, pointing to a core role in managing oxidative balance and detoxification. Some unrelated terms (collagen catabolic process, neural crest migration) may reflect secondary processes or annotation noise.","confidence":"Medium","size":17,"edges":16,"triangles":2,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034599","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0030574","count":4},{"id":"GO:0030416","count":3},{"id":"GO:0045454","count":3}]},{"hash":"102833594613318486","title":"Membrane Transporters and Related Metabolism","description":"The top GO terms are dominated by transmembrane transport activities for diverse substrates (taurine, thiamine, heme, cysteine, monoatomic anions) and peptide export, plus regulation of ion channels, suggesting a shared theme of membrane transport. Supporting signals include cytochrome complex assembly and very long-chain fatty acid catabolism, which tie to energy metabolism and mitochondrial/peroxisomal function. While ABA signaling and stomatal movement appear less central, they can connect to ion transport and membrane regulation. Overall, the cluster seems to reflect membrane transport and linked metabolic processes rather than a single pathway. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901527","count":3},{"id":"GO:0015734","count":3},{"id":"GO:0042760","count":3},{"id":"GO:0099133","count":3},{"id":"GO:1902943","count":3}]},{"hash":"424445613295364266","title":"Cytokine signaling and macrophage activation","description":"The top GO terms are dominated by immune-related processes: macrophage activation, regulation of cytokine production, and positive regulation of IL-8 production, plus general cytokine signaling; actin filament severing complements immune cell migration. While a couple of terms refer to development (imaginal disc polarity, meristem organization) and a deprecated lysosomal pH term, the cluster mainly reflects immune/cytokine regulation, supporting a label focused on cytokine signaling and macrophage activity.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":2},{"id":"GO:0016336","count":2},{"id":"GO:0035751","count":2},{"id":"GO:0051014","count":2},{"id":"GO:0090394","count":2}]},{"hash":"1217640497846931120","title":"Neural development and cytoskeletal dynamics","description":"The cluster is driven by GO terms such as spinal cord development, microtubule-based movement, and filopodium assembly, all central to neural development and cytoskeletal remodeling. Additional terms like regulation of Rho signaling, acetylcholine GPCR signaling, and cellular responses to VEGF support neuronal signaling and morphogenesis. Some terms are less directly connected (lipid glycosylation, T cell death, basement membrane assembly), but the dominant theme points to neurite outgrowth and cytoskeletal regulation in development.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0021510","count":5},{"id":"GO:0007018","count":5},{"id":"GO:0051260","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0035924","count":3}]},{"hash":"695892566148735819","title":"Vertebrate Development and Neural Tissue Formation","description":"The cluster is enriched for vertebrate developmental processes, especially neural structures (neural tube and spinal cord development) and tissue formation (skin, cartilage condensation). The presence of DNA-templated transcription points to regulatory programs driving these developmental pathways, with additional signals related to immune homeostasis and osmotic stress, but the dominant theme centers on vertebrate embryonic development and neural tissue formation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0001502","count":3},{"id":"GO:0043588","count":3}]},{"hash":"972764096223077116","title":"Plant Hormone Signaling and Senescence Regulation","description":"The cluster is enriched for plant hormone response and signaling terms (ABA, cytokinin, salicylic acid) and developmental regulation (negative regulation of leaf senescence, trichome patterning), suggesting a cohesive role in hormone-mediated growth and aging in plants. Some telomere- and meiosis-related terms appear but do not define the main theme.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010520","count":4},{"id":"GO:0009737","count":4},{"id":"GO:0009736","count":4},{"id":"GO:1904792","count":4},{"id":"GO:1903086","count":4}]},{"hash":"726712670718685663","title":"Plant cell wall polysaccharide degradation","description":"The top GO terms are dominated by catabolic processes for plant cell wall components (xylan, cellulose, arabinan, L-arabinose), indicating the proteins in this cluster are involved in polysaccharide breakdown. Some entries like extracellular matrix secretion and immunoglobulin production appear as noise/obsolete annotations, but the core signal points to plant cell wall polysaccharide catabolism. Confidence: High","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":3},{"id":"GO:0007565","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0030245","count":2}]},{"hash":"1366329396323892500","title":"Muscle-Bone Remodeling and Innate Immunity","description":"This cluster combines terms tied to musculoskeletal remodeling\u2014skeletal muscle regeneration and bone development\u2014with mechanotransduction (response to mechanical stimulus) and vitamin D signaling, plus innate immune defenses, consistent with a coordinated musculoskeletal-immune remodeling theme; ubiquitination and membrane protein localization support dynamic signaling and trafficking in these processes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0033280","count":4},{"id":"GO:0051607","count":3},{"id":"GO:0060348","count":3}]},{"hash":"757483026656050139","title":"Bacterial sugar transporters","description":"Most of the GO terms point to carbohydrate transport and metabolism in bacteria, including transmembrane transport of glucose and xylose, lactose biosynthesis, and related sugar-related transport processes (e.g., dehydroascorbic acid and organic cation transport), with an additional note on enterobacterial common antigen biosynthesis. Taken together, the cluster seems to group proteins involved in sugar uptake and cell-surface carbohydrate biosynthesis in bacteria, rather than a single specific function. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009246","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0052106","count":1},{"id":"GO:0060731","count":1}]},{"hash":"2036539551508027761","title":"Redox stress response and protein quality control","description":"The cluster centers on oxidative-reduction processes, cellular response to oxidative stress, and redox homeostasis, with supporting roles in protein repair, deglutathionylation, and ER-associated protein folding and quality control. Transcription-related GO terms may reflect stress-responsive regulation, but the dominant theme is redox balance and proteostasis under stress.","confidence":"Medium","size":17,"edges":6,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0030091","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0034599","count":2},{"id":"GO:0080058","count":2}]},{"hash":"2135048500036749352","title":"Cytoskeleton remodeling and membrane trafficking","description":"This cluster centers on actin/cytoskeleton dynamics (filopodium assembly; Rho signaling) and intracellular transport pathways (endosomal transport; ER tubular networks; Golgi protein retention), indicating a theme of coordinated cytoskeletal remodeling with vesicular trafficking and organelle morphology. While some terms touch on signaling pathways, the dominant pattern points to actin-related remodeling coupled with membrane trafficking processes.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046847","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0016197","count":3},{"id":"GO:0035924","count":2},{"id":"GO:0007213","count":2}]},{"hash":"1416967839464077047","title":"Nociception and Thermoception","description":"Most terms point to sensing and responding to temperature and pain (response to cold, detection of temperature stimulus in thermoception, detection of mechanical and chemical stimuli involved in sensory perception of pain, and general response to pain), indicating a nociceptive/thermoceptive module. A few terms relate to vasopressin secretion and endothelial processes, which are less central to the theme and may reflect broader or secondary roles in the gene set. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":4},{"id":"GO:0048265","count":4},{"id":"GO:0050960","count":4},{"id":"GO:0050966","count":4},{"id":"GO:0098907","count":4}]},{"hash":"2012991328557178621","title":"Development and Membrane Trafficking","description":"The GO terms show a mix of developmental processes (morphogenesis, embryo axis specification, sporulation) and membrane trafficking/processing (receptor recycling regulation, endocytosis related to cholesterol transport, LDL receptor catabolic process) with some peptide/protein maturation. There isn't a single cohesive pathway, but the cluster centers on signaling-linked development intertwined with membrane trafficking and protein processing.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0007354","count":2},{"id":"GO:0001920","count":2}]},{"hash":"279793958796263148","title":"Inflammatory eicosanoid biosynthesis","description":"The GO terms point to an inflammatory state with lipid mediator production, notably prostaglandins and leukotrienes via the lipoxygenase pathway (GO:0001516, GO:0002540, GO:0019372). Additional terms like response to LPS and chronic inflammatory response reinforce this theme, while lipid hydroperoxide and oxidant detoxification relate to inflammatory redox environments. Together, these suggest a cohesive cluster centered on inflammatory signaling and eicosanoid biosynthesis.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":1},{"id":"GO:0002544","count":1},{"id":"GO:0032496","count":1},{"id":"GO:0071277","count":1},{"id":"GO:0032526","count":1}]},{"hash":"898930765819758278","title":"Mitochondrial translation and ribosome assembly","description":"The GO terms cluster around mitochondrial protein synthesis and ribosome function: translation and mitochondrial translation, protein import into the mitochondrial matrix, and maturation of LSU-rRNA, which together indicate a mitochondria-centered translation/ribosome biosynthesis theme. Some unrelated terms (e.g., plant development or interferon response) may reflect cross-species annotations or noise, but the mitochondrial core is clear.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0030150","count":2},{"id":"GO:2000122","count":1},{"id":"GO:0015976","count":1},{"id":"GO:0071244","count":1}]},{"hash":"1288180649192641123","title":"Unknown","description":"The top terms cover a mix of photosynthesis-related processes (photosynthesis, bacteriochlorophyll biosynthetic process, gas vesicle organization) alongside general cellular functions (DNA-templated transcription, DNA replication, ribosomal subunit assembly, protein catabolic process) and some eukaryote-specific processes (cilium movement, anterograde neuronal dense core vesicle transport). Because there isn\u2019t a single cohesive function linking these terms, a concise, meaningful label cannot be confidently assigned beyond Unknown.","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0015979","count":5},{"id":"GO:0031412","count":4},{"id":"GO:0030494","count":4},{"id":"GO:1990048","count":4}]},{"hash":"30686539291444156","title":"RNA Processing and Gene Expression Regulation","description":"The top GO terms cluster around RNA metabolism and gene expression control: regulatory ncRNA-mediated gene silencing, positive regulation of mRNA splicing via spliceosome, transcription termination, rRNA maturation, and mRNA export. This points to a coordinated role in RNA processing, maturation, and export, with some additional development- or signaling-related terms that may reflect broader regulatory contexts. Overall, the cluster appears linked to RNA processing and gene expression regulation rather than a single enzymatic function.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0006369","count":8},{"id":"GO:0042766","count":7},{"id":"GO:0000463","count":7}]},{"hash":"792096806763219785","title":"Meiotic DSB Formation and Repair","description":"The cluster is dominated by terms related to meiotic double-strand break formation, subsequent DSB processing for repair (including SDSA), and related meiotic transcription regulation, plus at least one mitochondrial HR repair term. This points to a cohesive theme of meiosis-associated DNA damage response and repair, with some additional calcium signaling and developmental terms that may reflect broader or pleiotropic roles. Overall, the shared function appears to center on meiotic DSB formation and repair.","confidence":"Medium","size":16,"edges":36,"triangles":10,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010780","count":2},{"id":"GO:0051037","count":2},{"id":"GO:0010791","count":2},{"id":"GO:0033173","count":2},{"id":"GO:0005513","count":2}]},{"hash":"861403938343459515","title":"Diverse differentiation programs","description":"The top GO terms cluster around differentiation events across tissues and species (hematopoietic progenitor differentiation, hematopoietic stem cell proliferation, pollen sperm cell differentiation, sieve element differentiation, brown fat cell differentiation, face morphogenesis, acetylcholine biosynthetic/secretion processes). This suggests a shared theme of cell fate specification and development, despite cross-kingdom diversity. Thus, a concise label like \u201cDiverse differentiation programs\u201d best captures the cluster\u2019s common function.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901532","count":1},{"id":"GO:1902035","count":1},{"id":"GO:0006919","count":1},{"id":"GO:0060325","count":1},{"id":"GO:0008292","count":1}]},{"hash":"1399721444475771773","title":"Mitochondrial energy metabolism and insulin signaling","description":"This cluster centers on mitochondrial processes and energy-related pathways, including mitochondrial ATP transport, membrane fission, CoA transport, and adaptive thermogenesis, along with GO terms tied to insulin signaling and glucose response, oxidative stress, and amino acid starvation. The convergent theme is mitochondrial energy production and its regulation in metabolic and stress contexts.","confidence":"High","size":16,"edges":28,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061179","count":9},{"id":"GO:1990544","count":8},{"id":"GO:0034198","count":8},{"id":"GO:0032869","count":8},{"id":"GO:1990845","count":8}]},{"hash":"431242877295349930","title":"Meiosis and Germ Cell Development","description":"Dominant terms revolve around meiosis and germ cell development (homologous chromosome pairing at meiosis; DNA recombination; oogenesis; spermatid development), suggesting a cluster enriched for meiotic and gametogenic functions. Additional transcription regulation terms hint at coordinated gene expression during meiosis, while metabolism terms (mycothiol, glycogen, glucose) appear as ancillary or housekeeping annotations. Overall, \"Meiosis and Germ Cell Development\" best summarizes the main theme.","confidence":"High","size":16,"edges":8,"triangles":0,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007129","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0010125","count":3},{"id":"GO:0005978","count":3}]},{"hash":"897052001605817948","title":"Xenobiotic/drug response and macrophage activation","description":"The cluster features GO terms for response to cocaine, cellular response to xenobiotic stimulus, antibiotic response, and macrophage activation, suggesting a xenobiotic/drug response linked to immune activation. While RNA-processing terms like spliceosome conformational change and ribosomal biogenesis appear, the dominant pattern centers on xenobiotic/immune responses.","confidence":"Medium","size":16,"edges":33,"triangles":17,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0042274","count":2},{"id":"GO:0032516","count":2},{"id":"GO:0042116","count":2}]},{"hash":"657428917710676597","title":"RNA processing and splicing machinery","description":"The cluster is dominated by RNA-centric processes: tRNA processing, mRNA splicing via the spliceosome, spliceosomal snRNP assembly, termination of RNA Pol II transcription, and maturation of SSU-rRNA, plus P-body assembly, all pointing to post-transcriptional RNA metabolism and processing. Some co-occurring terms (histone mRNA metabolism, pericentric heterochromatin formation, stress response, and cell cycle regulation) likely reflect broader cellular roles or indirect associations rather than core function of the group. ","confidence":"High","size":16,"edges":40,"triangles":77,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":5},{"id":"GO:0045292","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0033962","count":2},{"id":"GO:0008334","count":2}]},{"hash":"1865279527492225910","title":"Vesicle trafficking and Golgi-ER transport","description":"The cluster\u2019s GO terms cluster around intracellular transport, especially vesicle movement and Golgi-ER dynamics, including vesicle fusion with the Golgi, retrograde Golgi-to-ER transport, and general protein transport. A few terms (xylan catabolic process, lung development, hindgut contraction, dendrite morphogenesis) are less related and may reflect broader annotations or cross-species context, but the strongest signal is vesicle trafficking and secretory pathway processes.","confidence":"Medium","size":16,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0048280","count":1},{"id":"GO:0043134","count":1}]},{"hash":"1432739973988117747","title":"Developmental regulation and mitosis","description":"The cluster shows strong representation of developmental processes (multicellular development, skeletal system development, neural tube closure) alongside mitotic functions (mitotic cell cycle, sister chromatid cohesion). Additional GO terms touch on transcriptional regulation and stress responses, suggesting a broad program that coordinates development with cell division and gene expression control.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007064","count":6},{"id":"GO:0001501","count":6},{"id":"GO:0001403","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0070059","count":6}]},{"hash":"251180114524943294","title":"Organelle trafficking and mitochondrial dynamics in development","description":"This cluster is driven by ER-to-Golgi transport and Golgi retention terms, protein complex assembly (tetramerization), and mitochondrial dynamics terms (fusion and apoptotic fragmentation), with development-related terms (lung and cardiac muscle development). Together these suggest a cohesive function in membrane trafficking and mitochondrial remodeling during development, despite some noisy annotations.","confidence":"High","size":16,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":3},{"id":"GO:0030324","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0043653","count":2}]},{"hash":"1040818680371258720","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":2},{"id":"GO:0048254","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0071166","count":2},{"id":"GO:0000244","count":2}]},{"hash":"1480697880413418453","title":"Neural development and spine morphogenesis","description":"The top GO terms point to neuronal development, neural crest specification, forebrain-midbrain boundary formation, and regulation of dendritic spine development, indicating a cluster of proteins involved in neural development and synaptic maturation. A few terms highlight post-transcriptional regulation (mRNA binding, miRNA silencing, splicing), which may reflect auxiliary regulatory roles supporting neural differentiation. Overall, a coherent theme around neural development and synaptic morphology emerges.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098908","count":1},{"id":"GO:0048755","count":1},{"id":"GO:0002092","count":1},{"id":"GO:2000637","count":1},{"id":"GO:0060998","count":1}]},{"hash":"589687623056437356","title":"Synapse assembly and postsynaptic organization","description":"Top GO terms strongly point to synapse formation and postsynaptic organization (positive regulation of synapse assembly; postsynaptic membrane assembly; neuroligin clustering; excitatory postsynaptic potential). Additional terms involve vesicle trafficking and hair-cell mechanosensory connections, which fit neuronal communication and membrane targeting. Overall, the cluster centers on neural synapse assembly and postsynaptic organization, with some developmental/behavioral associations.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042060","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0042297","count":1},{"id":"GO:2000463","count":1},{"id":"GO:0060122","count":1}]},{"hash":"2005517983306047947","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0000448","count":1},{"id":"GO:0042255","count":1}]},{"hash":"1392837235353879230","title":"Chromatin Regulation and Splicing","description":"The top GO terms cluster around regulation of chromatin state (histone methylation/deacetylation, chromatin binding) and mRNA processing via the spliceosome, with some development-related terms; this points to proteins that control gene expression through chromatin dynamics and RNA processing, potentially impacting differentiation and immune-related responses.","confidence":"High","size":16,"edges":54,"triangles":54,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":5},{"id":"GO:0051572","count":5},{"id":"GO:0030851","count":5},{"id":"GO:0016575","count":5},{"id":"GO:0021987","count":5}]},{"hash":"1554042343177809087","title":"Unknown","description":"The Top Terms are diverse (viral release, Tat transport, cell wall and peptidoglycan catabolism, defense response to bacteria, cytolysis, intracellular transport, mitochondrial respiration, and insulin secretion), with no clear unifying function. This cluster does not suggest a single coherent biological theme, so an Unknown label with no confidence is appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":1},{"id":"GO:0043953","count":1},{"id":"GO:0016998","count":1},{"id":"GO:0042742","count":1},{"id":"GO:0019835","count":1}]},{"hash":"1556685831724285532","title":"Immune and vascular regulation","description":"This cluster includes immune signaling terms (positive regulation of IL-2 and IL-5 production; T cell receptor signaling) together with vascular/cardiac functions (regulation of cardiac muscle cell contraction; vascular permeability) and stress responses (xenobiotic stimulus, TGF-beta stimulus), suggesting a theme of immune activity interacting with vascular and heart-related regulation rather than a single isolated pathway.","confidence":"Medium","size":16,"edges":9,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0032754","count":2},{"id":"GO:0032743","count":2},{"id":"GO:0086004","count":2},{"id":"GO:0010753","count":2}]},{"hash":"1231708454492388355","title":"Oxidative Detoxification and Signaling Modulation","description":"This cluster centers on cellular oxidant detoxification and various stimulus-responsive pathways, including prostaglandin biosynthesis and responses to EGF, insulin, ethanol, and ascorbic acid. The presence of nitric oxide storage and negative regulation of ERK/MAPK signaling and MCP-1 production suggests a coupling of redox homeostasis with modulation of signaling and inflammatory responses.","confidence":"High","size":16,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":14},{"id":"GO:0001516","count":11},{"id":"GO:2000255","count":11},{"id":"GO:0045471","count":10},{"id":"GO:0071364","count":10}]},{"hash":"899511814627917181","title":"Muscle, adipose, and heart development","description":"The top GO terms cluster around adipocyte differentiation (fat cell differentiation), skeletal muscle tissue regeneration, and Notch signaling in heart-field cardioblasts, suggesting a developmental/regenerative program in mesoderm-derived tissues. Additional terms related to cell growth and cell cycle point to proliferation during tissue formation, while membrane localization and SNARE regulation hint at intracellular trafficking required for differentiation. Overall, the terms imply mesodermal lineage differentiation and regeneration rather than a single enzymatic function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":4},{"id":"GO:0072660","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0043403","count":3},{"id":"GO:0000083","count":3}]},{"hash":"2116029453210644916","title":"Translation Initiation and Cell Cycle Regulation","description":"This cluster is dominated by GO terms related to translation initiation (formation of cytoplasmic translation initiation complex, eIF2 complex assembly, and positive regulation of translational initiation), with additional emphasis on cell cycle processes (cell cycle, regulation of cell cycle, cell division). A few terms point to stress responses (heat) and redox homeostasis, suggesting the proteins may coordinate protein synthesis with cell-cycle progression and stress responses. Overall, translation initiation appears to be the core theme, with cell cycle as a secondary, linked function.","confidence":"High","size":16,"edges":15,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001732","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0009408","count":2},{"id":"GO:1905143","count":1},{"id":"GO:0045948","count":1}]},{"hash":"828751097294410915","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":58,"triangles":105,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0000463","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0000209","count":5},{"id":"GO:0030433","count":5}]},{"hash":"879704147780775585","title":"Unknown","description":"The top GO terms are spread across coagulation, immune signaling, development, and sensory responses, with no clear, single functional theme tying the proteins together. This suggests the cluster is functionally heterogeneous rather than representing a cohesive pathway or process.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051919","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0044537","count":1},{"id":"GO:0035264","count":1}]},{"hash":"781692731488538467","title":"Selective autophagy and vacuolar targeting","description":"The GO terms are centered on autophagy-related processes (glycophagy, autophagosome assembly, Cvt pathway, nucleophagy, PMN) and vesicle/membrane targeting, pointing to a shared function in intracellular degradation and organelle turnover via autophagy pathways, including mitophagic aspects.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061723","count":1},{"id":"GO:0006501","count":1},{"id":"GO:0043653","count":1},{"id":"GO:0044805","count":1},{"id":"GO:0032258","count":1}]},{"hash":"1668663070253974190","title":"Neural development and transcriptional regulation","description":"The terms cluster around brain development (midbrain development, cerebral cortex regionalization), axon extension regulation, and transcriptional control (DNA-templated transcription, negative regulation of RNA Pol II), with Wnt signaling regulation linking to neural patterning. While there are a few broader or divergent terms (multicellular development, hepatoblast differentiation), the dominant theme is neural development coupled with transcriptional regulation.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0030901","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0030111","count":2}]},{"hash":"1202768897194929911","title":"Cytoskeletal dynamics in mitosis and neurons","description":"This cluster centers on microtubule- and actin-based remodeling: spindle assembly, spindle pole separation, minus-end\u2013directed microtubule sliding, and actomyosin ring formation, alongside zonula adherens maintenance. It also includes neuron-focused terms such as neuron projection maintenance and anterograde dendritic transport, indicating shared cytoskeletal machinery governing both cell division and neuronal maintenance/transport. The common theme is overarching cytoskeletal organization and intracellular transport bridging mitotic and neuronal contexts.","confidence":"Medium","size":16,"edges":104,"triangles":386,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0045218","count":16},{"id":"GO:0032886","count":16},{"id":"GO:0051255","count":16},{"id":"GO:0000073","count":16},{"id":"GO:1990535","count":16}]},{"hash":"858849536528824411","title":"Endosome trafficking and ubiquitination","description":"The top GO terms are dominated by endosomal transport pathways (early to late endosome, endosome to lysosome, endosome to Golgi, and Cvt pathway targeting to the vacuole), with ubiquitination potentially regulating these trafficking events. While there are a couple of other terms (cell cycle, mechanosensitive response), the clear majority points to vesicular trafficking through the endomembrane system, justifying this label.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045022","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0033028","count":2},{"id":"GO:2000171","count":2}]},{"hash":"510640538269305148","title":"RNA Methylation and Cap Formation","description":"This cluster is dominated by GO terms related to RNA modifications: RNA (guanine-N7)-methylation, tRNA methylation, rRNA methylation, and 7-methylguanosine mRNA capping, suggesting a core grouping around RNA methyltransferases and cap-forming activities. Some additional terms (phosphatidylcholine biosynthesis, nodulation, antibiotic biosynthesis, cobalamin biosynthesis, and histone methylation) may reflect broader or pleiotropic annotations, but the strongest signal points to RNA modification/methylation functions.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0030961","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0006656","count":2}]},{"hash":"1370752632430153712","title":"Ubiquitin-Dependent Proteostasis and Signaling","description":"The top GO terms highlight ubiquitination and ubiquitin-dependent degradation (ubiquitin-dependent protein catabolic process, ERAD, protein ubiquitination) as central to the cluster, suggesting a core theme of protein quality control. Additional terms point to signaling roles (NOD2 signaling and NF-kappaB regulation) and membrane/trafficking processes (SNARE regulation, maintenance of protein location in plasma membrane), with some cell-cycle-related terms (spindle assembly) and mechanotransduction. Together, these indicate a cohesive group centered on ubiquitin-mediated proteostasis linked to signaling and trafficking functions.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0035544","count":4},{"id":"GO:0051225","count":4}]},{"hash":"1332252302124003856","title":"Neuronal development and signaling regulation","description":"This cluster is dominated by GO terms related to neuron development and morphogenesis (neuron development, dendritic spine morphogenesis) and several signaling pathways (Wnt, Hippo, Rho) as well as components of signaling cascades (NFAT/CaN). While there are a few terms from other tissues (keratinocyte differentiation), the prevailing theme ties neuronal development to coordinated regulation of signaling and cellular growth, suggesting proteins that influence neural development through multiple signaling routes and proteostasis balance.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048666","count":11},{"id":"GO:0032435","count":11},{"id":"GO:0051534","count":10},{"id":"GO:0060997","count":9},{"id":"GO:0060044","count":9}]},{"hash":"1121078369900422692","title":"Plant chloroplast photosynthesis and stress responses","description":"Top GO terms are dominated by plant-centric core processes: photosynthesis and chlorophyll biosynthesis, together with stress-related responses such as hydrogen peroxide signaling and cadmium ion exposure. There are also terms related to ubiquitination and cell cycle, but the strongest signals point to chloroplast-associated metabolism and regulation of defense/stress pathways in plants. The presence of cellular response to type I interferon may reflect cross-ontology annotation noise, but does not override the chloroplast-focused theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071357","count":8},{"id":"GO:0009938","count":8},{"id":"GO:1902325","count":7},{"id":"GO:0007091","count":7},{"id":"GO:0090526","count":7}]},{"hash":"1001877767868263708","title":"Unknown","description":"The top GO terms span diverse metabolic and signaling processes (beta-ketoadipate, menaquinone, antibiotic and alkaloid biosynthesis, endocannabinoid signaling, strigolactone response) with no single shared function or interaction linking the 16 proteins, and there are no edges connecting them, so a cohesive cluster function cannot be inferred.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990577","count":2},{"id":"GO:0042952","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009820","count":2}]},{"hash":"1714115129543524574","title":"Muscle development and membrane trafficking","description":"The top GO terms cluster around muscle biology and membrane processes: skeletal muscle tissue regeneration, Notch signaling in heart-field cardioblast proliferation, and regulation of myosin-light-chain-phosphatase activity, along with maintenance of protein localization at the plasma membrane and negative regulation of SNARE complex assembly. This suggests a theme of muscle development/regeneration coupled with membrane trafficking or protein localization control, with ubiquitination reflecting protein turnover. Some terms (cold, vitamin D response) are broader, but they do not override the dominant muscle/trafficking signal.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":15},{"id":"GO:0016567","count":15},{"id":"GO:0072660","count":14},{"id":"GO:0035508","count":14},{"id":"GO:0043403","count":14}]},{"hash":"1055735722260673054","title":"Cardiac pacing and heart-rate regulation","description":"This cluster is dominated by GO terms tied to heart rate regulation and SA node action potential, pointing to cardiac pacing and electrophysiology as the central theme. Additional terms reflect general intracellular signaling (e.g., GTPase activity) that could modulate pacemaker activity, though several terms are obsolete, suggesting annotation artifacts. Overall, the shared function appears to be signaling pathways involved in controlling heart rhythm.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002027","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007205","count":2}]},{"hash":"1765272847407352256","title":"Epithelial Growth Signaling and Keratinocyte Migration","description":"This cluster centers on signaling pathways that govern growth, differentiation, and movement in epithelial cells: Wnt and Hippo signaling, PI3K-AKT signaling, keratinocyte differentiation, and cell migration, with associated responses to VEGF and GM-CSF. The presence of apoptotic process and cardiac proliferation regulation suggests broader growth-control context, but the predominant theme is signaling networks coordinating epithelial development, survival, and motility.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060044","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0030216","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0035329","count":4}]},{"hash":"2052333533257512026","title":"Membrane trafficking and cortical remodeling","description":"The top GO terms emphasize vesicle docking/exocytosis, plasma membrane repair, brush border/microvilli assembly, pigment granule transport, and polarized growth at the apical membrane. Together they point to a shared function in coordinating membrane trafficking and remodeling at the cell cortex, rather than a single organ-specific pathway. Some terms are unrelated or obsolete, but the core theme remains membrane-cytoskeleton dynamics.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007339","count":2},{"id":"GO:1903478","count":2},{"id":"GO:1904970","count":2},{"id":"GO:0031585","count":2},{"id":"GO:0060474","count":2}]},{"hash":"1516618761949573608","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042245","count":1},{"id":"GO:1990180","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0001680","count":1},{"id":"GO:0039022","count":1}]},{"hash":"1034395384366541612","title":"Presynaptic Vesicle Exocytosis and Neurotransmitter Release","description":"The top terms are dominated by presynaptic functions: calcium-dependent exocytosis, synaptic vesicle maturation, presynaptic dense core vesicle exocytosis, and neurotransmitter secretion, indicating a focus on vesicle trafficking and release at the nerve terminal. Also, small GTPase\u2013mediated signaling (Rho, Ras) and related regulatory pathways point to modulation of vesicle dynamics and cytoskeletal processes, consistent with presynaptic neurotransmitter release; a glucose transporter term is peripheral but does not outweigh the central theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0015758","count":2},{"id":"GO:0016188","count":2},{"id":"GO:0099525","count":2},{"id":"GO:0007269","count":2}]},{"hash":"1645908455822397068","title":"Unknown","description":"The top GO terms cover diverse processes: GTPase signaling, mitotic cell cycle, epithelial cell polarity, hepatocyte and myeloid apoptosis, cell migration, telomere localization, DNA repair, and tRNA aminoacylation. This broad mix lacks a single cohesive function, so a precise label is not supported.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1253245793538703159","title":"Innate Immune Signaling and Inflammatory Response","description":"The cluster centers on innate immune recognition and signaling (TLR2 pathway, detection of bacteria, response to triacyl lipoprotein), NF-\u03baB activation (I-kappaB phosphorylation and non-canonical NF-\u03baB regulation), and macrophage activation, with actin remodeling and migration supporting immune cell movement. A formalin-induced pain behavioral term suggests a downstream inflammatory/pain response. Together, these terms point to an inflammation-associated immune module.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061368","count":2},{"id":"GO:0034134","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0042116","count":2},{"id":"GO:0051638","count":2}]},{"hash":"141967075976955712","title":"Transcriptional Regulation and Cell Cycle Control","description":"The top GO terms center on transcription initiation at RNA polymerase II promoters and regulation of the G2/M transition, suggesting these proteins commonly regulate gene expression and cell cycle progression. Other terms point to broader signaling and stress-response roles (Wnt signaling, insulin receptor signaling, response to magnesium and water deprivation), implying these proteins act as regulators that connect transcription with signaling pathways. Overall, the strongest common theme is transcriptional control linked to cell cycle regulation, with ancillary signaling associations.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2000070","count":1},{"id":"GO:0032026","count":1},{"id":"GO:0046626","count":1}]},{"hash":"1400819118532639009","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1075943784356853550","title":"Negative Regulators of Signaling Pathways","description":"The top GO terms show strong enrichment for negative regulation of multiple signaling cascades (MAPK/ERK, PI3K-AKT) and immune signaling (T cell receptor), plus terms related to synaptic architecture (postsynaptic density assembly, synaptic vesicle clustering) and focal adhesion. This pattern points to proteins whose primary function is suppressing or modulating signaling and associated adhesion/synaptic processes, rather than performing a single enzymatic task. Therefore the label 'Negative Regulators of Signaling Pathways' captures the central theme across the majority of terms.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":13},{"id":"GO:0070373","count":12},{"id":"GO:0050860","count":12},{"id":"GO:0000200","count":12},{"id":"GO:0051898","count":11}]},{"hash":"1239934672185991918","title":"T cell differentiation and proliferation regulation","description":"The cluster is dominated by GO terms related to T cell differentiation (including T follicular helper cells) and regulation of T cell proliferation and homeostasis, indicating an immune T cell\u2013centered functional theme. A few unrelated terms (e.g., monocyte differentiation, EGFR-related response) are present but do not override the main T cell signal.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":2},{"id":"GO:0045657","count":2},{"id":"GO:0046782","count":2},{"id":"GO:0061470","count":2},{"id":"GO:0043029","count":2}]},{"hash":"681230358885745311","title":"RNA Processing and Translation Initiation","description":"The cluster is enriched for translation initiation and reinitiation terms (formation of translation preinitiation complex, regulation of translational initiation, translation reinitiation, IRES-dependent viral translational initiation), indicating regulation of how mRNA is engaged by ribosomes. It also includes spliceosome-mediated mRNA processing and regulatory ncRNA-mediated gene silencing terms, suggesting a broader RNA metabolism theme that can influence translation.","confidence":"High","size":15,"edges":92,"triangles":321,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0006446","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0002188","count":3}]},{"hash":"995788311624739222","title":"Metabolic versatility","description":"The Top Terms include several biosynthetic and catabolic pathways (antibiotic biosynthesis, menaquinone biosynthesis, alkaloid metabolism, beta-ketoadipate pathway, cellulose and uracil catabolism) as well as proteolysis, suggesting enzymes involved in a variety of metabolic reactions rather than a single pathway. Some terms like regulation of endocannabinoid signaling and strigolactone response appear peripheral or cross-kingdom annotations, but the core signal points to broad metabolic capabilities. Therefore, a concise label is Metabolic versatility.","confidence":"Medium","size":15,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0006212","count":3},{"id":"GO:1990577","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0042952","count":2}]},{"hash":"1558950711705939356","title":"SRP-dependent cotranslational ER targeting","description":"These terms are dominated by SRP-dependent cotranslational protein targeting to membranes and translocation, including signal sequence recognition, indicating proteins that guide nascent peptides to the ER membrane during translation. The presence of cytoplasmic translation and ribosomal RNA maturation terms supports a ribosome/translation-focused cluster, with additional entries related to mitochondrial membrane insertion and cytochrome c release that may reflect broader coordination of protein targeting and stress responses. Overall, the cluster likely represents components of the SRP-mediated ER targeting pathway and related translation machinery.","confidence":"High","size":15,"edges":23,"triangles":14,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0006617","count":1},{"id":"GO:1903645","count":1},{"id":"GO:0010421","count":1}]},{"hash":"764589595051199023","title":"Ribosome Biogenesis and rRNA Processing","description":"The majority of terms point to ribosome assembly, LSU/5.8S rRNA maturation, and RNA methylation, indicating a ribosome biogenesis module; the accompanying chromatin organization and cell-cycle terms likely reflect coordinated growth and development contexts.","confidence":"High","size":15,"edges":89,"triangles":303,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0031497","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0036265","count":2}]},{"hash":"1635867336991026341","title":"Mitochondrial respiration and protein complex assembly","description":"The top GO terms center on aerobic respiration and proton transmembrane transport, which are hallmarks of mitochondrial energy production via oxidative phosphorylation. Supporting signals include protein oligomerization terms (homotetramerization, heterooligomerization), suggesting assembly of mitochondrial protein complexes. Some terms appear noisy or obsolete (e.g., viral process, lifespan, certain archaic terms), but the core theme points to mitochondrial metabolism and complex formation.","confidence":"Medium","size":15,"edges":16,"triangles":7,"max_degree":10,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0010815","count":4},{"id":"GO:0009060","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0006627","count":3},{"id":"GO:0071432","count":3}]},{"hash":"118998182300212936","title":"Mitochondrial Complex II & Flavoproteins","description":"The cluster shows enrichment for mitochondrial respiration and flavin-related terms, notably succinate to ubiquinone (Complex II) and the assembly of mitochondrial respiratory chain Complex II, along with protein-FAD linkage and flavinylation. These indicate a cohesive theme around Complex II\u2013related oxidative metabolism and flavoprotein biology. Some translation/transcription terms appear more generic, but they do not override the dominant mitochondrial signal. Thus, the cluster is best described as mitochondrial Complex II\u2013related flavoproteins.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0006121","count":1},{"id":"GO:0017013","count":1}]},{"hash":"1907522629797377318","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0009751","count":2},{"id":"GO:0009723","count":2}]},{"hash":"1394538158613662411","title":"Actin remodeling and endosomal transport","description":"This cluster is strongly enriched for cytoskeletal dynamics: filopodium and microspike assembly, and regulation of Rho signaling, which drive actin remodeling. Endosomal transport aligns with vesicle movement linked to the cytoskeleton. Other terms like transcription or sensors (hypoxia/light) are less central and may reflect broader regulatory connections or annotation noise. Overall, the common theme is actin-driven motility and associated vesicle trafficking.","confidence":"Medium","size":15,"edges":29,"triangles":12,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0046847","count":8},{"id":"GO:0035023","count":8},{"id":"GO:0030035","count":7},{"id":"GO:0016197","count":7}]},{"hash":"1800740557233501406","title":"Neural development and cerebral cortex morphogenesis","description":"This cluster is enriched for terms tied to brain development, notably cerebral cortex development and cortical actin cytoskeleton organization, alongside embryonic cranial skeleton morphogenesis, suggesting a set of proteins involved in neural differentiation and cortical morphogenesis. Some other terms indicate broader developmental and transcriptional regulation, but the strongest signal points to neural development and cytoskeletal remodeling of the cortex.","confidence":"Medium","size":15,"edges":48,"triangles":103,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0019551","count":2},{"id":"GO:0060440","count":2},{"id":"GO:2001233","count":2},{"id":"GO:0061368","count":2}]},{"hash":"1402660799090506563","title":"Diverse metabolite biosynthesis","description":"This cluster is enriched for a variety of biosynthetic processes, including antibiotic and alkaloid biosynthesis, steroid and phylloquinone metabolism, mycolic acid and PHB biosynthesis, and related metabolic steps. While there is a standout emphasis on biosynthesis of diverse secondary metabolites and lipids, there isn\u2019t a single unified pathway, suggesting a functionally broad biosynthetic cluster.","confidence":"Medium","size":15,"edges":51,"triangles":66,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0017000","count":8},{"id":"GO:0030435","count":6},{"id":"GO:0042619","count":6},{"id":"GO:0008207","count":5}]},{"hash":"1174521827341627833","title":"Cysteine and sulfur amino acid metabolism","description":"This cluster shows proteins enriched for cysteine-related biosynthesis and transsulfuration (L-cysteine biosynthesis, transsulfuration, D-serine biosynthesis) and related amino acid metabolism terms, with additional links to general amine catabolism and central carbon metabolism (pyruvate). The strongest shared theme is sulfur-containing amino acid biology, particularly cysteine metabolism. Medium","confidence":"","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009097","count":7},{"id":"GO:0019343","count":7},{"id":"GO:0006535","count":7},{"id":"GO:0042866","count":7},{"id":"GO:0019346","count":7}]},{"hash":"1660664136505836448","title":"Nucleotide Biosynthesis and Salvage in Development","description":"The top GO terms cluster around nucleotide metabolism (purine ribonucleotide interconversion, CDP/ADP biosynthesis, AMP salvage), indicating a core role in nucleotide generation and maintenance. The presence of brain and liver development terms suggests developmental or tissue-specific expression, though other terms appear noisy or obsolete. Overall, the primary signal is nucleotide metabolism with developmental associations.","confidence":"Medium","size":15,"edges":28,"triangles":7,"max_degree":8,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0046041","count":2},{"id":"GO:0046939","count":2}]},{"hash":"196324607326090388","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0014075","count":3},{"id":"GO:0071548","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0060416","count":2},{"id":"GO:0008153","count":2}]},{"hash":"1013870656037145482","title":"Ciliary and Flagellar Axoneme with Tubulin Modifications","description":"The top GO terms cluster around cilium/flagellum structure and movement (axoneme assembly, cilium movement, flagellated sperm motility, epithelial cilium movement) and tubulin post-translational modifications (polyglycylation, polyglutamylation) as well as microtubule regulation. This points to a cohesive theme of microtubule-based motility in cilia/flagella and related axonemal dynamics, despite a couple of peripheral terms like neurotransmitter vesicle loading. Thus the label captures the dominant function represented by the cluster.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030516","count":1},{"id":"GO:0018094","count":1},{"id":"GO:0003351","count":1},{"id":"GO:0007288","count":1},{"id":"GO:0018095","count":1}]},{"hash":"2294273648090014927","title":"Unknown","description":"The Top Terms are highly varied, spanning cellulose catabolic process, transcription-related terms, placental development, hypoxia response, histone acetylation, and protein oligomerization, with no single enriched function tying most proteins together. The absence of a cohesive biological theme (and zero edges/triangles) suggests there isn\u2019t a clear, interpretable cluster function to label beyond Unknown. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0001892","count":2},{"id":"GO:0070207","count":2},{"id":"GO:0001666","count":2}]},{"hash":"1542849089742761646","title":"Ribosome Biogenesis and RNA Processing","description":"Most of the top GO terms cluster around ribosome assembly, maturation of LSU rRNA, and nuclear mRNA export, plus protein targeting. These point to a core theme of ribosome production and RNA handling, with some outliers that may reflect annotation noise or multi-functional proteins. However, the dominant signal supports a gene-expression machinery focus.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0009432","count":10},{"id":"GO:0042766","count":9},{"id":"GO:0000463","count":9},{"id":"GO:0090394","count":9},{"id":"GO:0048701","count":9}]},{"hash":"282206842306339725","title":"Neural development and brain morphogenesis","description":"This cluster is dominated by GO terms related to brain development and morphogenesis, including cerebral cortex development, hippocampus development, embryonic cranial skeleton morphogenesis, and cortical actin cytoskeleton organization, suggesting a cohesive role in neural development and brain structure formation. While there are a few terms related to general apoptosis regulation and other developmental processes, the strongest signal centers on CNS development and regional brain formation, with some connectivity to neuronal differentiation and morphology.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034351","count":14},{"id":"GO:0060440","count":13},{"id":"GO:2001233","count":13},{"id":"GO:0061368","count":13},{"id":"GO:0030866","count":13}]},{"hash":"1537152710984260246","title":"Cerebral Cortex and Hippocampus Development","description":"Most of the top GO terms center on development of brain structures, notably the cerebral cortex, hippocampus, and orbitofrontal cortex, as well as related cranial morphogenesis and signaling (e.g., FGF receptor signaling) that shapes cortical regions. There is also emphasis on cortical actin cytoskeleton organization and stem cell differentiation, which ties into neural development. Some terms (trachea formation, behavioral pain response) are less directly linked but do not override the dominant neurodevelopmental theme. Overall, the cluster appears to represent neural development and cortical region formation.","confidence":"High","size":15,"edges":15,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":15},{"id":"GO:2001233","count":15},{"id":"GO:0061368","count":15},{"id":"GO:0030866","count":15},{"id":"GO:0048701","count":15}]},{"hash":"1498587966981211869","title":"RNA processing and chromosome condensation during cell division","description":"The cluster\u2019s GO terms connect RNA processing steps (splicing via spliceosome, ncRNA-mediated gene silencing, mRNA polyadenylation regulation, tRNA gene clustering) with chromosome dynamics typical of cell division (spindle assembly, meiotic/mitotic chromosome condensation). Although some terms are labeled obsolete, they point to regulatory RNA processes that interface with chromatin structure during meiosis and mitosis. This combination suggests a theme around RNA-based regulation linked to chromatin organization in cell division, rather than a single, strict function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070058","count":2},{"id":"GO:1903342","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0010032","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1524714978414125356","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoskeleton organization","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0030516","count":3},{"id":"GO:0006046","count":3},{"id":"GO:1904530","count":3},{"id":"GO:0048666","count":3}]},{"hash":"540701082684323577","title":"Metal and Oxidative Stress Response","description":"The cluster is enriched for GO terms describing cellular responses to metal and oxidative stress factors (cadmium ion, diamide, sodium arsenite, singlet oxygen) plus radiation, indicating a coherent theme of stress detection and response. Some terms are obsolete or unrelated, but the strongest signals reflect metal/oxidative stress pathways, supporting this label as representative.","confidence":"High","size":15,"edges":28,"triangles":26,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0071480","count":3},{"id":"GO:1900462","count":3},{"id":"GO:0072738","count":3},{"id":"GO:1903936","count":3}]},{"hash":"1403452103452882197","title":"Bone Development and BMP Signaling","description":"The top GO terms show bone development and positive regulation of BMP signaling, indicating the cluster centers on bone-related signaling pathways. Additional terms related to cell cycle and general cellular regulation may reflect broader growth/differentiation context rather than a separate theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0042981","count":1},{"id":"GO:0016579","count":1},{"id":"GO:0043392","count":1}]},{"hash":"1712233249193739529","title":"Ubiquitin-proteasome regulation and Wnt signaling","description":"This cluster is dominated by ubiquitin-related processes (deubiquitination and SCF-proteasomal degradation) and Wnt/PCP signaling terms, suggesting a module of proteins coordinating protein turnover with Wnt signaling. The presence of endopeptidase regulation and mRNA stability hints at broader post-translational and post-transcriptional control, with stress-response terms like salt stress and zinc ion response possibly reflecting condition-dependent regulation of these pathways.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":11},{"id":"GO:0060071","count":7},{"id":"GO:0090090","count":7},{"id":"GO:0006521","count":7},{"id":"GO:0043488","count":7}]},{"hash":"2225183931144400289","title":"Diverse Transmembrane Transporters","description":"The set centers on multiple transmembrane transport processes across different substrates (sodium, potassium, phosphate, nitrate, vitamin, sialic acid), plus related transporter-related activities like neurotransmitter loading into vesicles, indicating a common theme of membrane transport rather than a single metabolic pathway. This justifies a label focused on diverse transporter functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0098700","count":2}]},{"hash":"696290502201590976","title":"Cerebral cortex development and neural differentiation","description":"The top GO terms strongly point to brain development, especially cerebral cortex development and cortical actin cytoskeleton organization, with DNA-templated transcription and stem cell differentiation signaling, suggesting neural differentiation and cytoskeletal regulation as the core theme. Some terms refer to broader embryonic processes (e.g., trachea formation, cranial skeleton morphogenesis), but the prevailing pattern centers on neural development and transcriptional control of neuronal structure. ","confidence":"Medium","size":15,"edges":29,"triangles":10,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0097011","count":10},{"id":"GO:0060440","count":9},{"id":"GO:2001233","count":9},{"id":"GO:0061368","count":9}]},{"hash":"1427089838919324256","title":"Tissue development and epithelial remodeling","description":"These proteins show enrichment for development- and remodeling-related GO terms: responses to growth factors (VEGF, GM-CSF) signal angiogenic and immune-related cues; hippo signaling and regulation of proliferation point to growth control; keratinocyte differentiation, hyaluronan metabolism, and cell migration reflect epithelial morphogenesis and extracellular matrix remodeling, which are central to placental and skin/epithelial development. Overall, the cluster seems to represent proteins involved in tissue growth, differentiation, and remodeling rather than a single specific pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035924","count":13},{"id":"GO:0097011","count":13},{"id":"GO:0060044","count":13},{"id":"GO:0016477","count":13},{"id":"GO:0010765","count":13}]},{"hash":"235983201974837594","title":"Unknown","description":"The Top Terms span a highly diverse set of processes (cellulose and lignin catabolism, sporulation, metal ion transport and detoxification, antibiotic biosynthesis, nitrate assimilation, bacterial cytokinesis, arsenate transport, and platelet activation) with no clear common function or pathway. The absence of edges and the wide variety of GO terms suggest there is no cohesive biological theme tying these proteins together. Therefore a single interpretable label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0042128","count":1}]},{"hash":"2580700964068229","title":"Cardiac development, growth control, and innate immunity","description":"The cluster is enriched for heart development and Hippo signaling terms, including negative regulation of cardiac muscle cell proliferation, suggesting a cardiac growth-control module. It also includes innate immune terms (innate immune response; defense against Gram-positive bacteria; response to exogenous dsRNA) and transcriptional activity (DNA-templated transcription), indicating a transcriptional program that links development with immune signaling. While these themes could reflect dual roles of certain proteins, the overall signal points to a cardiac development and growth-control module with an innate-immune component.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":12},{"id":"GO:0010800","count":12},{"id":"GO:0060044","count":12},{"id":"GO:0007507","count":12},{"id":"GO:0050830","count":12}]},{"hash":"1298063089401425605","title":"ER stress-induced apoptosis and signaling","description":"This cluster centers on GO terms related to ER-stress\u2013driven intrinsic apoptosis, such as the intrinsic apoptotic pathway in response to ER stress and general apoptotic processes, along with stress-activated signaling like JNK and NF-kappaB pathways, and cell-cycle checkpoints that respond to damage. Together these terms suggest a cohesive theme of cellular stress responses balancing survival and programmed cell death, with connections to mitotic regulation under stress.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000086","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0046330","count":3},{"id":"GO:0051973","count":3}]},{"hash":"890043884258911058","title":"Membrane Transport and Vesicle Trafficking","description":"The GO terms emphasize transport of xenobiotics and folates across membranes (xenobiotic, methotrexate, 5-formyltetrahydrofolate transport) and processes related to plasma membrane localization and regulation of SNARE complex assembly, pointing to a shared role in membrane transport and vesicle trafficking; peripheral terms like muscle regeneration are less central but don\u2019t contradict this theme.","confidence":"Medium","size":15,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0051958","count":1},{"id":"GO:0015885","count":1},{"id":"GO:0072660","count":1},{"id":"GO:0035508","count":1}]},{"hash":"1905031939027422096","title":"Unknown","description":"The top GO terms are heterogeneous (GPCR signaling, polysaccharide catabolism, cell cycle, membrane localization, muscle regeneration, transcription regulation, growth, cold response, SNARE regulation) with no clear common function. Several terms are obsolete and there are no edges linking proteins, so no coherent theme or representative function emerges. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0000272","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0072660","count":2},{"id":"GO:0035508","count":2}]},{"hash":"1329655491300955643","title":"Apoptosis and cellular stress regulation","description":"This cluster is characterized by multiple GO terms related to negative regulation of apoptotic pathways (extrinsic signaling, muscle and epithelial cell contexts) and negative regulation of macroautophagy, alongside related inflammatory/wound healing processes and metabolism terms (spermidine and glutathione). Taken together, the proteins appear to participate in modulating cell survival and stress responses rather than a single specific pathway, so the label captures the overarching theme of apoptosis and stress regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008216","count":1},{"id":"GO:0006749","count":1},{"id":"GO:1902042","count":1},{"id":"GO:0010656","count":1},{"id":"GO:0043433","count":1}]},{"hash":"2001789632493935680","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015938","count":2},{"id":"GO:0006382","count":2},{"id":"GO:0050992","count":2},{"id":"GO:1901911","count":2},{"id":"GO:1901907","count":2}]},{"hash":"57447436925576818","title":"Serine/Threonine Kinase Signaling Regulators","description":"These proteins cluster around regulation of kinase activity, highlighting both negative regulation of protein kinase activity and positive regulation of serine/threonine kinase activity, plus related phosphorylation and growth factor\u2013related signaling terms. The terms suggest a module of signaling regulators that modulate phosphorylation cascades, rather than a single tissue-specific process.","confidence":"Medium","size":14,"edges":49,"triangles":55,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0043950","count":1},{"id":"GO:0071574","count":1},{"id":"GO:0086004","count":1}]},{"hash":"136676231653245329","title":"Energy metabolism and redox homeostasis","description":"The top GO terms are dominated by glycolytic process, mitochondrial electron transport, anaerobic respiration, and cellular redox detoxification and redox homeostasis, which together describe central energy production and maintenance of redox balance. A couple of terms about brain development appear but are not central to the cluster's main function; thus the label reflects the core theme of energy generation and redox regulation.","confidence":"Medium","size":14,"edges":22,"triangles":13,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006096","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0006579","count":2}]},{"hash":"270820266188374851","title":"Ribosome biogenesis and translation","description":"The GO terms are dominated by translation-related processes: translation, initiation, elongation, termination, and ribosomal small subunit biogenesis, as well as positive regulation of cytoplasmic translation and selenocysteine incorporation. A related mRNA decay term suggests coordination between translation and mRNA turnover. Overall, the cluster appears to group proteins involved in the protein synthesis machinery and its regulation.","confidence":"High","size":14,"edges":23,"triangles":10,"max_degree":8,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006413","count":4},{"id":"GO:0042274","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0001514","count":3}]},{"hash":"348666819521648199","title":"Ribosome biogenesis and large subunit assembly","description":"The top GO terms are dominated by ribosome biogenesis and large subunit-related processes (LSU rRNA maturation, preribosome assembly, cytosolic ribosome assembly, and large subunit biogenesis), pointing to a cohesive cluster of proteins involved in ribosome production and maturation. Peripheral terms (antibiotic response, transport, fatty acid catabolism) are less central and do not define the cluster. Confidence reflects a strong link to ribosome assembly functions.","confidence":"High","size":14,"edges":77,"triangles":229,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0000463","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0042273","count":3}]},{"hash":"1386519076723641591","title":"Cellular stress and protein quality control","description":"The top GO terms point to processes dealing with protein handling and quality control under stress (sumoylation, ERAD/unfolded protein response, deglycosylation, mitophagy), detox and toxin responses, and related trafficking/cell cycle terms, suggesting a cohesive theme of maintaining proteostasis and responding to cellular stress. Some immune signaling (MyD88/TLR) and cell division terms add diversity, but the dominant signal fits stress-related protein homeostasis rather than a single specialized pathway.","confidence":"Medium","size":14,"edges":63,"triangles":128,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":8},{"id":"GO:0034126","count":6},{"id":"GO:0000423","count":5},{"id":"GO:1904378","count":5},{"id":"GO:0030474","count":5}]},{"hash":"2096818840599685326","title":"Membrane transporters for ions and nutrients","description":"The top GO terms cluster around transport across membranes\u2014sodium and potassium ion transport, various sugar transports, vitamin transport, nitrate assimilation, and even neurotransmitter loading into vesicles\u2014pointing to a group of diverse membrane transport proteins involved in moving ions and metabolites rather than a single, specific pathway.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0015757","count":1}]},{"hash":"328697445162284950","title":"Nutrient-sensing stress response and growth arrest","description":"The top GO terms cluster around metabolic and oxidative stress responses (glucose and hydrogen peroxide), autophagy/mitophagy, and nutrient signaling (TORC1), coupled with states of growth arrest (diapause, replicative senescence) and DNA damage signaling. This suggests a cohesive theme where nutrient sensing and stress induce autophagic processes and halt cell growth, possibly leading to quiescence or senescence; a few terms (face morphogenesis, actin organization) may reflect peripheral contexts or noise. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000422","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0060325","count":1},{"id":"GO:0038202","count":1}]},{"hash":"1956866548788153199","title":"Purine salvage and nucleotide metabolism","description":"The GO terms are dominated by purine salvage and nucleotide turnover: IMP salvage, GMP salvage, guanine salvage, GMP catabolic process, and PRPP biosynthesis. These point to a shared function in recycling and producing purine nucleotides. The remaining neural- or behavior-related terms (insulin response, amphetamine response, dendrite morphogenesis, grooming) may reflect broader metabolic regulation or multifunctionality in neural contexts, but the core signal centers on purine metabolism.","confidence":"Medium","size":14,"edges":13,"triangles":2,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045892","count":4},{"id":"GO:0032264","count":3},{"id":"GO:0032263","count":3},{"id":"GO:0046038","count":3},{"id":"GO:0032869","count":3}]},{"hash":"1689842608954657737","title":"RNA Methylation and RNA Processing","description":"This cluster is dominated by GO terms related to RNA modification and methylation, including rRNA methylation, rRNA modification, guanine-N7 methylation, and mRNA capping, suggesting a primary theme of RNA maturation and epigenetic-like modifications. Peripheral terms like histone methylation and various biosynthetic processes are present but less central, so the core label reflects RNA methylation/processing.","confidence":"Medium","size":14,"edges":75,"triangles":214,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":3},{"id":"GO:0030961","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0006656","count":2},{"id":"GO:0009877","count":2}]},{"hash":"1405373310061910887","title":"Mitosis and vesicle trafficking regulation","description":"Top GO terms point to mitotic control (cell division, kinetochore localization) plus vesicle trafficking and receptor recycling, suggesting a cluster centered on mitosis coupled with membrane protein sorting; some terms like UV-B response and pheromone are ancillary.","confidence":"Medium","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042068","count":14},{"id":"GO:0051301","count":14},{"id":"GO:0019236","count":14},{"id":"GO:0050709","count":14},{"id":"GO:0006547","count":14}]},{"hash":"1009330000836847880","title":"Mitochondrial Energy Metabolism and Stress Responses","description":"These GO terms cluster around mitochondrial function and cellular energy management: transport across mitochondrial membranes (ATP and CoA), mitochondrial dynamics (membrane fission), and responses to stress and metabolic signals (superoxide, amino acid starvation, insulin, adaptive thermogenesis). The liver regeneration hint suggests metabolic remodeling in tissues. Overall, the cluster represents mitochondrial energy metabolism and stress response.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0032869","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0035349","count":2}]},{"hash":"382514809418005802","title":"Unknown","description":"The GO terms are highly diverse, spanning transcriptional regulation, lipid and antibiotic biosynthesis, photosynthesis, cytokinin signaling, and RNA/protein processing, with no single cohesive function linking all proteins. Therefore, no clear theme can be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0071768","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0000122","count":2}]},{"hash":"2092521711362961945","title":"Chromatin assembly and transcriptional regulation","description":"The cluster centers on chromatin-related processes: replication-dependent chromatin assembly and CENP-A chromatin assembly, plus transcription initiation and chromatin remodeling linked to transcriptional control. Supporting terms include DNA-templated transcription initiation, transcription initiation-coupled remodeling, and beta-catenin-TCF complex assembly, all pointing to regulation of gene expression via chromatin state. A few items like telomere capping and ncRNA-mediated silencing fit this theme as chromatin-associated regulatory layers, while a couple of terms (e.g., megakaryocyte differentiation and NHEJ) are auxiliary but not core. Overall, a chromatin-assembly/transcription-regulation theme best fits this cluster.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006352","count":2},{"id":"GO:0006303","count":2},{"id":"GO:0045815","count":2},{"id":"GO:0006335","count":2},{"id":"GO:0034080","count":2}]},{"hash":"1838667395193623690","title":"Mitochondrial tRNA charging and translation","description":"This cluster is dominated by GO terms related to mitochondrial protein synthesis, including specific mitochondrial tRNA aminoacylation (threonyl, glycyl, prolyl; and selenocysteinyl-tRNA) and general translation, plus regulation of translational fidelity. The combination of tRNA charging and mitochondrial translation points to the core function of mitochondrial protein synthesis machinery, with some older/less specific terms present as ancillary signals.","confidence":"High","size":14,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0070584","count":3},{"id":"GO:0070159","count":2},{"id":"GO:0016260","count":2},{"id":"GO:1903833","count":2}]},{"hash":"1024472018063578194","title":"Chromatin Modification and Transcription Regulation","description":"Proteins in this cluster are enriched for histone methylation/demethylation (H3-K4, H3-K27), negative regulation of transcription by RNA Pol II, and rDNA heterochromatin formation, pointing to a shared role in establishing and maintaining chromatin states and transcriptional repression. Additional signals for rRNA methylation and histone lysine dimethylation reinforce an epigenetic modification theme, despite some obsolete GO terms.","confidence":"High","size":14,"edges":77,"triangles":229,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0034720","count":3},{"id":"GO:0045648","count":3}]},{"hash":"1930809900346484485","title":"Proteostasis and vesicle trafficking","description":"The top GO terms cluster around ubiquitin-dependent ERAD and proteasome assembly, indicating proteostasis via the ubiquitin-proteasome system. Additional terms point to vesicle trafficking and Golgi dynamics (SNARE disassembly, intralumenal vesicle formation, dense core vesicle transport, Golgi retention), suggesting a coherent module where protein quality control intersects with the secretory/vesicular pathway. A CENP-A chromatin assembly term is present but less connected to the main theme. Overall, this cluster centers on protein quality control integrated with vesicle trafficking.","confidence":"Medium","size":14,"edges":21,"triangles":16,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0070682","count":5},{"id":"GO:0045053","count":4},{"id":"GO:0035494","count":4}]},{"hash":"1145947503818312958","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0072089","count":2},{"id":"GO:0010586","count":2},{"id":"GO:1903265","count":2},{"id":"GO:2000637","count":2},{"id":"GO:1902187","count":2}]},{"hash":"1149895662884844732","title":"Skin Development and Pigmentation","description":"The terms cluster around skin development and pigmentation, including explicit GO terms for skin development, pigmentation, and multicellular organism development. Also present are processes tied to cell proliferation and signaling (mitotic cell cycle; serine/threonine kinase activity; autophosphorylation) and protein turnover (ubiquitination), which are commonly involved in epidermal differentiation. While some terms reflect broader cellular processes (cadmium response, mRNA transport), the central theme appears to be epidermal development and pigment formation.","confidence":"Medium","size":14,"edges":9,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0071902","count":5},{"id":"GO:0043588","count":5},{"id":"GO:2001162","count":5},{"id":"GO:0000209","count":5}]},{"hash":"2232250423349455418","title":"Metal Ion Transport and Homeostasis","description":"The cluster\u2019s top GO terms are dominated by metal ion transport and homeostasis (cadmium, cobalt, iron, manganese) and related cellular responses, with occasional xenobiotic or stress-related terms. This suggests a cohesive theme around maintaining metal ion balance and responding to metal- or chemical-stress, despite a few subordinate immune-related terms. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0050790","count":2},{"id":"GO:0071472","count":2},{"id":"GO:0070574","count":1},{"id":"GO:0070627","count":1}]},{"hash":"647415105326557179","title":"Organelle Translation and Biogenesis","description":"The top terms cluster around translation and ribosome biogenesis, plus RNA-templated transcription, pointing to protein synthesis machinery. The presence of photosynthesis and mitochondrial complex IV assembly hints at organelle-associated processes (chloroplasts/mitochondria). Other terms (cell cycle, SOS response, viral replication) may reflect broader regulatory roles, but the dominant signal is organelle protein synthesis/biogenesis.","confidence":"Medium","size":14,"edges":14,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1635885722572881483","title":"Phosphorylation-driven signaling and cell-cycle regulation","description":"The top GO terms show enrichment for regulation of serine/threonine phosphorylation, kinase activity, and related signaling outputs, plus a link to cell-cycle control (G2/M transition) and ubiquitination\u2014together suggesting a module centered on post-translational modification\u2013driven signaling that governs cell division and cytoskeletal organization. Some terms appear noisy or peripheral (e.g., polysaccharide catabolism, terminal web assembly), but the core theme is phosphorylation-mediated signaling and its impact on the cell cycle. ","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":3},{"id":"GO:0043950","count":2},{"id":"GO:0071574","count":2},{"id":"GO:0086004","count":2},{"id":"GO:0071902","count":2}]},{"hash":"204635222855280351","title":"Cerebral Cortex and Cranial Skeleton Morphogenesis","description":"The top terms are dominated by cerebral cortex development, hippocampus development, and orbitofrontal cortex development, along with embryonic cranial skeleton morphogenesis. Additional terms about cortical actin cytoskeleton organization and FGFR signaling support a coordinated neurodevelopmental and craniofacial morphogenesis program. This suggests the cluster represents brain region formation together with skull morphogenesis, rather than a single tissue-type process. ","confidence":"High","size":14,"edges":51,"triangles":81,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":14},{"id":"GO:2001233","count":14},{"id":"GO:0061368","count":14},{"id":"GO:0030866","count":14},{"id":"GO:0048701","count":14}]},{"hash":"701474947305959274","title":"Ubiquitination-Driven Translation Regulation","description":"The top GO terms are dominated by ubiquitination-related processes (autoubiquitination, K63-linked ubiquitination, and ubiquitin-dependent protein catabolic process), with supporting signals for JNK cascade regulation and apoptotic processes. Translation-related terms (translation and positive regulation of cytoplasmic translation) appear alongside, suggesting a link between ubiquitin signaling and control of protein synthesis. Although there is an emphasis on ubiquitin-mediated pathways, the presence of translation and apoptosis terms implies broader roles in protein turnover and cell fate decisions. Overall, these proteins appear to cluster around ubiquitin-driven signaling that influences translation and degradation pathways, with potential developmental and stress-response contexts.","confidence":"Medium","size":14,"edges":6,"triangles":2,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0046328","count":5},{"id":"GO:0070534","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0006412","count":4}]},{"hash":"1397342310764426415","title":"Unknown","description":"The 14 proteins have highly diverse GO terms, including spermatid differentiation, eye/wing cell fate specification, EGF ligand maturation, unfolded protein response, NK cell regulation, megakaryocyte development, ascospore prospore assembly, and ruffle assembly, with no single shared function. There are no edges connecting them, so there isn\u2019t a cohesive functional theme to label. Therefore Unknown, None.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048515","count":1},{"id":"GO:1904211","count":1},{"id":"GO:0042676","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0038005","count":1}]},{"hash":"444375155785986440","title":"Developmental Cell Cycle Regulation and Signaling","description":"The cluster links core cell-cycle processes (DNA replication, centrosome cycle, nuclear export) with developmental signaling pathways (Wnt, Hippo) and differentiation/apoptosis terms (keratinocyte differentiation, cranial skeleton morphogenesis, apoptosis), suggesting coordinated control of proliferation and differentiation during embryogenesis.","confidence":"Medium","size":14,"edges":36,"triangles":32,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0048701","count":8},{"id":"GO:0007098","count":8},{"id":"GO:0010571","count":8},{"id":"GO:0060044","count":7}]},{"hash":"920957995211218738","title":"Membrane Transport and Lipid Metabolism","description":"This cluster is dominated by GO terms involving transmembrane transport of ions (cadmium, zinc, calcium) and membrane-related processes (membrane repolarization, phospholipid translocation, phospholipid dephosphorylation). There is also serine- and lipopolysaccharide-related biosynthesis, which ties into membrane lipid biology and outer-murface components. Taken together, the common theme is membrane-associated transport and lipid dynamics, even though some terms are peripheral. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0006564","count":6},{"id":"GO:0009103","count":5},{"id":"GO:0070574","count":4},{"id":"GO:0086009","count":4},{"id":"GO:0000749","count":4}]},{"hash":"2215697318728316056","title":"Endocytosis and Actin Remodeling","description":"The terms cluster around receptor-mediated endocytosis and actin cytoskeleton dynamics (including actin debranching and guiding protein localization to the leading edge) with supporting signals like EGFR-related responses. While a few terms are unrelated or obsolete, the core theme ties endocytosis to actin remodeling in cellular contexts.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006898","count":2},{"id":"GO:0071364","count":1},{"id":"GO:0070586","count":1},{"id":"GO:1905873","count":1},{"id":"GO:2000249","count":1}]},{"hash":"172737305089281437","title":"Vesicle trafficking and membrane repair","description":"The top GO terms cluster around endocytosis and intracellular transport (ubiquitin-dependent endocytosis, intracellular protein transport) and processes involved in maintaining and repairing the plasma membrane (calcium-regulated lysosome exocytosis, plasma membrane repair). VEGF receptor signaling and Ras pathway regulation point to membrane-associated signaling modulation, which often intersects with trafficking pathways. While there are a couple of terms tied to cell migration and nuclear export, the dominant theme among the terms is vesicle trafficking, membrane dynamics, and membrane-associated signaling, justifying a label centered on trafficking and membrane maintenance.","confidence":"Medium","size":14,"edges":33,"triangles":22,"max_degree":8,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0070086","count":3},{"id":"GO:0006886","count":3},{"id":"GO:1990927","count":2},{"id":"GO:0001778","count":2},{"id":"GO:0021814","count":2}]},{"hash":"959853931250913768","title":"Developmental Signaling and Apoptosis","description":"These proteins cluster around developmental signaling pathways (Wnt canonical signaling, Hippo signaling) and apoptosis regulation, with roles in keratinocyte differentiation and trachea formation, and transcriptional control. While other terms like potassium ion transport and pinocytosis are present, the dominant theme ties to signaling-driven development and programmed cell fate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060044","count":9},{"id":"GO:0090263","count":9},{"id":"GO:0030216","count":9},{"id":"GO:0006915","count":9},{"id":"GO:0035329","count":9}]},{"hash":"707125818112463243","title":"Cerebral Cortex Development and Brain Morphogenesis","description":"This cluster is dominated by brain-development GO terms such as cerebral cortex development, hippocampus development, orbitofrontal cortex development, and FGF receptor signaling involved in cortex development, suggesting a coherent theme of neural development and cortical morphogenesis. Supporting terms point to cytoskeletal remodeling during development, though a few entries (trachea formation, pain response) are less central noise.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":14},{"id":"GO:2001233","count":14},{"id":"GO:0061368","count":14},{"id":"GO:0030866","count":14},{"id":"GO:0048701","count":14}]},{"hash":"514182611686378180","title":"Translation machinery and mRNA turnover","description":"The GO terms cluster around translation at initiation, elongation, termination, and overall translation, plus deadenylation-dependent mRNA decay and selenocysteine incorporation, indicating a cohesive function in protein synthesis and mRNA metabolism. A few outlier terms related to cell cycle and proliferation appear, but the dominant signal is translation and mRNA turnover.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0001514","count":2},{"id":"GO:2000767","count":2},{"id":"GO:0006415","count":2}]},{"hash":"1650412608188907984","title":"Ubiquitin-Dependent Protein Degradation","description":"Most top terms center on ubiquitination (including K48- and K6-linked), autoubiquitination, and ubiquitin-dependent proteolysis, plus histone catabolic processes. This points to a core function in tagging substrates for degradation and regulating protein turnover, with some peripheral links to membrane trafficking and inflammatory signaling. Confidence: High","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0070936","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0042787","count":3}]},{"hash":"2278436537120103114","title":"Muscle Regeneration and Angiogenesis Signaling","description":"Top GO terms point to skeletal muscle tissue regeneration and endothelial cell proliferation in sprouting angiogenesis, with Notch signaling involved in heart field development, suggesting a cohesive theme of muscle repair and vascular development. Ubiquitination and membrane trafficking-related terms imply regulatory control of these processes at the protein level. Thus the cluster likely represents factors coordinating muscle regeneration and angiogenesis, with supporting regulatory mechanisms.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016567","count":9},{"id":"GO:0072660","count":8},{"id":"GO:0035508","count":8},{"id":"GO:0043403","count":8},{"id":"GO:0000083","count":8}]},{"hash":"183988832182637542","title":"Unknown","description":"The terms are highly diverse (polyamine and redox metabolism, various transport and immune signaling processes) and each appears only once, with no edges linking the proteins. There is no clear, shared function unifying the cluster, so a coherent label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008216","count":1},{"id":"GO:0019342","count":1},{"id":"GO:0006749","count":1},{"id":"GO:0014889","count":1},{"id":"GO:0048491","count":1}]},{"hash":"1984766491879092288","title":"Mitochondrial Assembly and Calcium Homeostasis","description":"The top GO terms point to mitochondrial structure and assembly (respiratory chain complex IV assembly, outer membrane translocase assembly, outer membrane organization) as well as calcium import and regulation, plus cytochrome c release control. Together, these indicate a mitochondria-focused cluster involved in assembly and calcium-dependent maintenance, with some related redox/oxygen homeostasis aspects. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0070096","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0007008","count":1},{"id":"GO:0097250","count":1}]},{"hash":"2141801919815736794","title":"Muscle Regeneration and Vascular Development","description":"This cluster shows a developmental theme focused on tissue formation, with skeletal muscle tissue regeneration (GO:0043403) and vascular proliferation during sprouting angiogenesis (GO:1903589), plus a Notch signaling role in cardiac development. Together these suggest coordinated muscle growth/regeneration and vascular remodeling. Other terms like cell growth and cell cycle are general cellular processes that supplement this broader developmental context, while a few localization or housekeeping terms are less informative for clustering function. Overall, the dominant theme is muscle regeneration linked to vascular development.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072660","count":1},{"id":"GO:0035508","count":1},{"id":"GO:0043403","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0016049","count":1}]},{"hash":"1560487756793672927","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms tied to ribosome function: translation (GO:0006412), ribosome biogenesis (GO:0042254), and ribosomal subunit assembly (GO:0000028). These core terms appear repeatedly among proteins, indicating a shared role in protein synthesis and ribosome production. The other annotations (cell cycle regulation, kinetochore localization, Notch signaling, development) may reflect additional, less central roles or annotation pleiotropy, but do not override the central ribosome/translation theme.","confidence":"Medium","size":13,"edges":24,"triangles":35,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":4},{"id":"GO:0045736","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0006407","count":3}]},{"hash":"754276873493171800","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The proteins in this cluster are strongly associated with mRNA splicing and its regulation via the spliceosome, including regulation of alternative splicing, splice site recognition, and related RNA processing steps, as well as regulatory ncRNA-mediated gene silencing. This combination suggests a cohesive function in controlling splicing outcomes rather than core splicing machinery alone.","confidence":"High","size":13,"edges":69,"triangles":198,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:1901407","count":7},{"id":"GO:0006378","count":7},{"id":"GO:0045292","count":7}]},{"hash":"1930364461565208593","title":"Ribosome Biogenesis and Translation","description":"Based on the GO terms, the cluster is dominated by processes related to ribosome production and protein synthesis, including cytoplasmic translation, ribosomal small subunit biogenesis, ribosome biogenesis, and mitochondrial translation. The presence of rRNA processing terms (SSU-rRNA maturation, rRNA export) further supports a focus on ribosome assembly and ribosome function. A few terms like cell cycle or cellular response to nerve growth factor stimulus appear as secondary context but do not override the central ribosome/translation theme. Therefore, \u201cRibosome Biogenesis and Translation\u201d is an intuitive, representative label.","confidence":"High","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0002181","count":5},{"id":"GO:0042274","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0042254","count":3}]},{"hash":"648710478393107884","title":"Chromatin remodeling and DNA damage response","description":"The cluster is dominated by GO terms for chromatin remodeling, nucleosome disassembly, and transcription-coupled remodeling, along with regulation of double-strand break repair and p53-mediated DNA damage signaling, pointing to a shared role in chromatin dynamics and DNA repair; a heart development term likely reflects noise.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0006337","count":2},{"id":"GO:0007089","count":1},{"id":"GO:0048096","count":1},{"id":"GO:0003281","count":1}]},{"hash":"1920363486203166783","title":"Spliceosome-mediated mRNA splicing regulation","description":"GO terms are dominated by regulation of alternative mRNA splicing via the spliceosome, splice-site recognition, and related mRNA processing steps (modification and polyadenylation), indicating a cohesive function in mRNA maturation and splicing control rather than a single enzymatic activity.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0031047","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0006376","count":1}]},{"hash":"410197017483955266","title":"Gene Expression Machinery Under Stress","description":"The GO terms point to core gene-expression processes (DNA-templated transcription, RNA Pol II regulation; translation and translational termination; selenocysteine incorporation) while also highlighting cellular stress responses (ER stress, xenobiotic response). This suggests a cohesive module linking transcription/translation machinery with stress adaptation, possibly supported by mitochondrial function (cytochrome complex assembly) under challenging conditions.","confidence":"Medium","size":13,"edges":13,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0017004","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1496315466675285832","title":"Coagulation and fibrinolysis regulation","description":"This cluster is dominated by GO terms for fibrinolysis, plasminogen activation, bradykinin catabolism, and blood coagulation, indicating a central theme of coagulation control and vascular homeostasis. Some terms like insulin processing and liver regeneration may reflect broader metabolic or tissue-remodeling contexts in this vascular-ready set.","confidence":"High","size":13,"edges":12,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051918","count":1},{"id":"GO:0010815","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0010757","count":1},{"id":"GO:0035610","count":1}]},{"hash":"1851529877814292750","title":"Mitochondrial Translation and Respiration","description":"The terms point to both protein synthesis (translation and translational fidelity) and mitochondrial energy production (mitochondrial electron transport, complex III assembly, aerobic respiration, proton transport), suggesting the proteins cluster around mitochondrial protein synthesis machinery and respiration. ","confidence":"High","size":13,"edges":19,"triangles":15,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045903","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0006412","count":1}]},{"hash":"997263753176190416","title":"Mitochondrial Translation and Respiratory Chain Assembly","description":"This cluster is dominated by GO terms for mitochondrial translation and the assembly of respiratory chain complexes I and IV, suggesting a core role in mitochondrial protein synthesis and assembly of mitochondrial respiratory components; other terms like meiotic cell cycle and spermatogenesis appear peripheral to this central theme.","confidence":"High","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0002184","count":1},{"id":"GO:0032981","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0051321","count":1}]},{"hash":"1004603082088529213","title":"Genome Maintenance and Ribosome Biogenesis","description":"Top GO terms indicate strong signals for DNA damage response and DNA replication (SOS response, nucleotide-excision repair, error-free translesion synthesis, DNA-templated DNA replication) as well as nucleolar functions and protein synthesis (nucleolus organization, translation, rRNA processing). This suggests a coherent theme around genome maintenance and ribosome biogenesis. The ER-to-Golgi vesicle transport and eye-antennal disc development terms appear, but are less central to this cluster's core function and may reflect broader cellular roles.","confidence":"Medium","size":13,"edges":61,"triangles":143,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006261","count":2},{"id":"GO:0070987","count":2}]},{"hash":"715615043660904400","title":"Embryonic Development and Epithelial Morphogenesis","description":"The top terms cluster around embryonic tissue development (ectoderm, lung induction, metanephros morphogenesis, dorsal identity) and epithelial organization (adherens junction assembly, EMT regulation), with supportive gene regulation (chromatin remodeling). This points to a cohesive theme of embryonic morphogenesis and epithelial differentiation, justifying the label.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0048364","count":11},{"id":"GO:0060492","count":10},{"id":"GO:0048096","count":10},{"id":"GO:0045976","count":10},{"id":"GO:0003340","count":10}]},{"hash":"1796458768299200552","title":"Vesicle trafficking and membrane lipid metabolism","description":"This cluster shows a strong emphasis on intracellular transport: protein localization to the nuclear pore, ER-to-Golgi ceramide transport, and post-Golgi vesicle transport, along with maintenance of cell polarity. While a lipid biosynthesis term (sterol biosynthetic process) and a signaling term (insulin receptor pathway regulation) appear, the predominant pattern is vesicle trafficking and related lipid handling, suggesting proteins function in membrane trafficking and lipid homeostasis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090204","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0006892","count":1},{"id":"GO:0046628","count":1},{"id":"GO:0034727","count":1}]},{"hash":"1986889465445008276","title":"Developmental signaling and cell cycle control","description":"The cluster is enriched for organismal development terms (heart development, Schwann cell development, myoblast fusion, multicellular organism development) alongside cell cycle regulation (G2/M transition, phosphorylation). Additional signaling-related terms (abscisic acid signaling, apoptotic regulation) suggest broader regulatory roles. These together point to a theme of signaling that coordinates development and proliferation.","confidence":"Medium","size":13,"edges":70,"triangles":215,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":8},{"id":"GO:0000086","count":8},{"id":"GO:0007507","count":8},{"id":"GO:0009738","count":8},{"id":"GO:0014044","count":8}]},{"hash":"820987942873940392","title":"Ubiquitin-mediated protein regulation and signaling","description":"The cluster centers on ubiquitination processes (autoubiquitination, ubiquitin-dependent proteolysis, ERAD, K48-linked ubiquitination, general ubiquitination) and their role in signaling pathways like JNK and NF-\u03baB. This suggests a cohesive theme of ubiquitin-driven protein modification and degradation modulating cellular signaling, with immune-related terms as downstream connections. ","confidence":"High","size":13,"edges":5,"triangles":0,"max_degree":5,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0016567","count":7},{"id":"GO:0070936","count":7}]},{"hash":"1505608970328040971","title":"Muscle Development and Regeneration Signaling","description":"Top terms point to skeletal muscle regeneration and Notch signaling in heart-field cardioblast proliferation, implying a focus on muscle development and cardiac-associated signaling. Additional terms on cell growth, cell cycle, and ubiquitin-mediated regulation suggest muscle remodeling involves protein turnover and membrane trafficking, aligning with cytoskeletal and membrane dynamics in developing and regenerating muscle tissue. Overall, the cluster centers on muscle development and regeneration with related signaling and protein homeostasis processes.","confidence":"Medium","size":13,"edges":19,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0072660","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0043403","count":2},{"id":"GO:0000083","count":2}]},{"hash":"246539710610136965","title":"Zinc Homeostasis and Cadmium Transport","description":"This cluster features multiple GO terms tied to zinc handling and metal detox: zinc ion import across the plasma membrane, zinc ion starvation response, detoxification of zinc ion, and cadmium ion transmembrane transport. These terms point to a cohesive theme of zinc homeostasis and coping with toxic metal exposure, with a few general metabolism terms (e.g., nitrate assimilation) that are less central to the main signal. Overall, the proteins appear to function in metal ion homeostasis, particularly zinc, with a component related to cadmium transport.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006796","count":1},{"id":"GO:0010312","count":1}]},{"hash":"108888917416769767","title":"Hormone Biosynthesis and Gland Development","description":"The cluster is dominated by GO terms for signaling molecule biosynthesis (prostaglandins, ecdysone) and development of hormone-responsive tissues (mammary gland, prostate) as well as retina vasculature development, suggesting a core theme around hormone-related biosynthesis and tissue development. Oxidative stress-related terms appear but are secondary to the hormonal/gland-development signals. Confidence: Medium","confidence":"","size":13,"edges":25,"triangles":17,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":5},{"id":"GO:0001516","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0098869","count":4}]},{"hash":"361672901635819310","title":"Lipid Biosynthesis and Signaling","description":"The terms are dominated by lipid-related processes (triglyceride biosynthesis, CDP-diacylglycerol biosynthesis, cardiolipin remodeling, platelet activating factor biosynthesis, cutin biosynthesis), suggesting a cohesive theme around lipid metabolism and lipid-derived signaling. A few immune or DNA repair terms appear as outliers, but do not strongly redefine the cluster\u2019s primary signal.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:2001246","count":1},{"id":"GO:0070236","count":1},{"id":"GO:0006663","count":1},{"id":"GO:0070970","count":1}]},{"hash":"695783300800318381","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0006370","count":1},{"id":"GO:0098507","count":1},{"id":"GO:0036265","count":1}]},{"hash":"184721296156319616","title":"Ciliary assembly and intraflagellar transport","description":"The terms show a clear emphasis on ciliogenesis and intraciliary transport (cilium assembly; intraciliary retrograde transport) and retina development linked to photoreceptor cilia, suggesting the proteins function in ciliary structure and signaling. While a few rRNA maturation and kinase-signaling terms appear, they are likely ancillary; the dominant theme centers on cilium formation and transport, consistent with a cohesive ciliary protein cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":3},{"id":"GO:0060041","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0038202","count":2}]},{"hash":"1726822633978029501","title":"ER Protein Folding and Ca2+ Homeostasis","description":"This cluster's strongest shared annotation is ER-related processes: protein folding in the endoplasmic reticulum and ER calcium ion homeostasis, which suggests a role in ER protein quality control and calcium regulation. The other GO terms are either obsolete or not clearly connected, and the network shows no edges, indicating a loose or fragmented functional linkage. Thus the name captures the primary ER-centered theme, with limited confidence due to annotation noise and lack of corroborating interactions.","confidence":"Low","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:0032469","count":1},{"id":"GO:2000584","count":1},{"id":"GO:1901536","count":1},{"id":"GO:0090308","count":1}]},{"hash":"1760101509938325164","title":"Regulators of catalytic activity and tissue remodeling","description":"Most represented terms center on regulation of catalytic activity, with several proteolysis and remodeling processes (bradykinin catabolic process, collagen catabolic process, extracellular region localization) and development-related signals (lung branching, decidualization, thyroid hormone response). Although immune and reproductive terms appear, the common thread is proteins that modulate enzyme activity and signaling during remodeling and development. This suggests a cohesive theme of catalytic regulation and tissue remodeling across contexts.","confidence":"Medium","size":13,"edges":51,"triangles":96,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":7},{"id":"GO:0001913","count":7},{"id":"GO:0097067","count":7},{"id":"GO:0010815","count":7},{"id":"GO:0046697","count":7}]},{"hash":"1412260397613034143","title":"Transmembrane nutrient and xenobiotic transporters","description":"The top GO terms are dominated by transmembrane transport activities for vitamins, xenobiotics, and sodium ions, pointing to membrane transporter functions. Additional terms for fucose metabolism, nitrate assimilation, and glucose starvation response suggest linked nutrient uptake and metabolic regulation. Together, these terms indicate a cluster of proteins mainly involved in transporting various nutrients and xenobiotics across membranes, with related metabolic context. ","confidence":"High","size":13,"edges":31,"triangles":23,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":13},{"id":"GO:0042891","count":13},{"id":"GO:0006855","count":13},{"id":"GO:1904728","count":11},{"id":"GO:0035725","count":11}]},{"hash":"1455307022018024373","title":"Neural and craniofacial development","description":"This cluster\u2019s GO terms are dominated by neural development (cerebral cortex development, hippocampus development, orbitofrontal cortex development) and craniofacial morphogenesis (trachea formation, embryonic cranial skeleton morphogenesis). Additional signals such as FGFR signaling and cortical actin cytoskeleton organization align with developmental processes in brain and facial structures. Together, they point to a shared theme of developmental programs shaping neural tissues and craniofacial structures.","confidence":"High","size":13,"edges":47,"triangles":74,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":13},{"id":"GO:2001233","count":13},{"id":"GO:0061368","count":13},{"id":"GO:0030866","count":13},{"id":"GO:0048701","count":13}]},{"hash":"714336663503539226","title":"Cerebral Cortex Development","description":"This cluster is strongly enriched for terms related to brain development, especially cerebral cortex development, hippocampus development, and orbitofrontal cortex formation, as well as FGFR signaling involved in cortex development and neural differentiation. While a few terms touch on broader craniofacial morphogenesis and other organs, the dominant signal points to cortical and neural tissue development and differentiation. ","confidence":"High","size":13,"edges":52,"triangles":86,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":13},{"id":"GO:2001233","count":13},{"id":"GO:0061368","count":13},{"id":"GO:0030866","count":13},{"id":"GO:0048701","count":13}]},{"hash":"302750380195903637","title":"DNA replication and cell-cycle with organelle trafficking","description":"The terms cluster around DNA replication and cell-cycle control (DNA replication, mitotic checkpoint, centriole elongation) alongside protein trafficking and organelle maintenance (peroxisome import, Golgi retention, SNARE disassembly) and energy-related regulation (ATP biosynthesis). This suggests a cohesive theme where DNA replication/cell-cycle events are coordinated with vesicle trafficking and organelle dynamics.","confidence":"Medium","size":13,"edges":47,"triangles":109,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0016558","count":4},{"id":"GO:0045053","count":4},{"id":"GO:0033314","count":4}]},{"hash":"619084000223590681","title":"Secretory Pathway Protein Processing and Redox Regulation","description":"The GO terms point to processes in the secretory pathway, especially ER to Golgi transport, glycosylation, and post-translational modifications like proline hydroxylation, alongside protein repair and redox-regulation (deglutathionylation). While a couple of terms reference nuclear regulation, the dominant themes are secretory protein maturation and redox maintenance, suggesting these proteins function together in quality control and processing of secreted/membrane proteins in the ER-Golgi system.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":1},{"id":"GO:0046354","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0046826","count":1},{"id":"GO:1903026","count":1}]},{"hash":"1369333824608437324","title":"Cortical signaling and cytoskeletal regulation","description":"The top terms emphasize phosphorylation-dependent signaling (serine/threonine kinase activity, peptidyl-threonine phosphorylation, ubiquitination) and cortical/cytoskeletal context (localization to medial cortex, terminal web assembly). Although a few terms are broader, the common thread is signaling control at the cell cortex linked to cytoskeletal dynamics, justifying a cortical signaling and cytoskeletal regulation label.","confidence":"Medium","size":13,"edges":12,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097274","count":4},{"id":"GO:0043950","count":3},{"id":"GO:0071574","count":3},{"id":"GO:0086004","count":3},{"id":"GO:0071902","count":3}]},{"hash":"67214319648996954","title":"Peptide Hormone Processing and Receptor Regulation","description":"The top GO terms cluster around processing and maturation of secreted peptides (insulin processing, enkephalin processing, peptide pheromone maturation) and hormone secretion (renin secretion), with additional terms pointing to receptor trafficking and recycling (LDL receptor activity/clearance, receptor recycling). This suggests a shared theme of secretory peptide maturation and receptor handling, though the presence of unrelated terms like sporulation and developmental axis determination indicates heterogeneity. Therefore, the cluster is best described as peptide hormone processing and receptor regulation, albeit with cautious interpretation.","confidence":"Low","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002001","count":1},{"id":"GO:0032802","count":1},{"id":"GO:0030435","count":1},{"id":"GO:1905598","count":1},{"id":"GO:0007354","count":1}]},{"hash":"2286943732868592899","title":"Light- and Hypoxia-Responsive Transcription Regulation","description":"The cluster is dominated by GO terms for DNA-templated transcription and transcriptional regulation, with additional signals related to sensing environmental cues such as hypoxia and visible/red light. This suggests a group of proteins involved in regulating gene expression in response to light and oxygen status, possibly including sensors or transcription factors that respond to these cues. Some other terms point to metabolic and cofactor-related processes (e.g., tetrapyrrole linkage and PTS system), which may reflect integration of metabolic state with transcriptional control.","confidence":"Medium","size":13,"edges":56,"triangles":112,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0017006","count":6},{"id":"GO:0009401","count":6},{"id":"GO:0030823","count":6},{"id":"GO:0070483","count":6}]},{"hash":"1885378748291653320","title":"RNA processing and ribosome biogenesis","description":"Most of the top GO terms point to RNA metabolism and ribosome-related processes (ribosomal subunit export, 5S rRNA maturation, spliceosomal assembly, and mRNA splicing). This suggests the proteins in this cluster are involved in RNA processing and ribosome biogenesis, despite some remaining terms that appear less related, likely due to annotation noise or cross-species differences.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0000481","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0045585","count":2}]},{"hash":"1955323720202013524","title":"Neural development and chromatin remodeling","description":"This cluster is dominated by terms related to brain development, oligodendrocyte differentiation, and transcriptional control (DNA-templated transcription and chromatin remodeling), alongside signals like TGF-beta response and proliferation regulation. The convergence on neural lineage specification and epigenetic regulation suggests a coherent neural development program governed by transcriptional and chromatin-level control, with metabolism playing a smaller supporting role.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0048709","count":2}]},{"hash":"846889302792077812","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":11,"triangles":0,"max_degree":4,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045116","count":5},{"id":"GO:0032258","count":4},{"id":"GO:0006296","count":4},{"id":"GO:0042769","count":4},{"id":"GO:0033280","count":4}]},{"hash":"755135086387393753","title":"Neuronal Synaptic Signaling and Spine Morphogenesis","description":"This cluster's terms cluster around neuronal signaling and synapse structure: retrograde nitric oxide signaling, positive regulation of excitatory postsynaptic potentials, dendritic spine morphogenesis, and receptor guanylyl cyclase signaling, with Wnt regulation linked to neural development. A couple of nucleotide transport terms are less central but do not overturn the dominant synaptic theme.","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035364","count":2},{"id":"GO:0015862","count":2},{"id":"GO:0030111","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0007168","count":1}]},{"hash":"1719546959194451976","title":"Unknown","description":"The terms are highly heterogeneous (metal ion response, neuronal signaling, imaginal disc polarity, lysosomal pH, actin severing, chromatin localization, organ size regulation), with no clear unifying function to define a specific cluster label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":3},{"id":"GO:0090394","count":3},{"id":"GO:0016336","count":2},{"id":"GO:0035751","count":2},{"id":"GO:0051014","count":2}]},{"hash":"524597108797942247","title":"Protein turnover and endosomal trafficking regulation","description":"The top GO terms point to regulation of proteolysis and autophagy, along with endosomal processes (receptor recycling, endosome size) and trafficking-related signaling (Rho pathway). Although some terms are broad or plant-specific, the recurring theme is regulation of protein turnover and vesicular trafficking rather than a single enzymatic function.","confidence":"Low","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904715","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0043085","count":2},{"id":"GO:0046938","count":2},{"id":"GO:0060316","count":2}]},{"hash":"1402291019169907785","title":"Embryonic cytoskeleton and adhesion remodeling","description":"The cluster top terms center on microtubule dynamics (polymerization/depolymerization, spindle elongation, oocyte cytoskeleton) and processes tied to cell movement and tissue remodeling (hemocyte migration, regulation of gastrulation, focal adhesion assembly, ECM disassembly). This suggests a developmental program coordinating cytoskeletal changes with cell-ECM interactions to drive embryogenesis and morphogenesis. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031112","count":1},{"id":"GO:0090091","count":1},{"id":"GO:0035099","count":1},{"id":"GO:0016325","count":1},{"id":"GO:1904261","count":1}]},{"hash":"30691493693314975","title":"Proteostasis and Translation Regulation","description":"The cluster\u2019s top GO terms cluster around translation and its negative regulation, along with post-translational protein targeting, tRNA transport, protein oligomerization, and cellular stress responses such as heat and redox homeostasis. Together these point to a coherent theme of maintaining protein homeostasis: controlling protein synthesis, folding/quality control, and trafficking. An outlier developmental signaling term likely reflects incidental context rather than a defining cluster feature. Overall, the label captures the central function suggested by the prevalent terms.","confidence":"High","size":12,"edges":64,"triangles":200,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0017148","count":2},{"id":"GO:0051259","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0045454","count":2}]},{"hash":"119162581735227386","title":"Spliceosome-regulated mRNA splicing","description":"This cluster is dominated by GO terms related to spliceosome-mediated mRNA splicing, including regulation (positive and negative) and alternative splicing, as well as splice site recognition and general mRNA processing. The inclusion of regulatory ncRNA-mediated gene silencing and mRNA modification supports a broader RNA-processing/regulation theme centered on splicing control. Confidence in this label is High.","confidence":"","size":12,"edges":25,"triangles":27,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0016556","count":4},{"id":"GO:1902625","count":4},{"id":"GO:0006376","count":4}]},{"hash":"2187211543100156755","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The GO terms are dominated by regulation of mRNA splicing via the spliceosome, including positive/negative regulation, alternative splicing, and splice-site recognition, with related mRNA processing terms such as mRNA modification and translation reinitiation, pointing to proteins involved in controlling splicing decisions and spliceosome activity.","confidence":"Medium","size":12,"edges":12,"triangles":2,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0016556","count":3},{"id":"GO:1902625","count":3},{"id":"GO:0006376","count":3}]},{"hash":"1315378118259487184","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006370","count":2}]},{"hash":"1611781236388121280","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA maturation and ribosome assembly: pseudouridine synthesis in snRNA and rRNA, rRNA processing, and ribosome biogenesis, plus telomerase RNA localization to Cajal bodies. These indicate a shared theme of RNA modification and ribosome construction in the nucleus, though a few terms (mitochondrial complex I assembly, endosome sorting, abscission) are more peripheral.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031120","count":1},{"id":"GO:0007004","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0031118","count":1}]},{"hash":"1223477531186129523","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0019068","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0075713","count":1}]},{"hash":"411091907468840374","title":"Heterochromatin formation and histone modification","description":"This cluster is driven by GO terms tied to heterochromatin formation/maintenance (rDNA heterochromatin formation; silent mating-type cassette heterochromatin formation), nucleosome density regulation, and histone modifications (H3K9, H4K16). It also includes deacetylation and transcription-related terms, supporting a theme of chromatin state controlling transcription; a few metabolic or stress-related terms are present but less central. ","confidence":"High","size":12,"edges":44,"triangles":69,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0034983","count":3},{"id":"GO:0006344","count":3},{"id":"GO:0045820","count":3}]},{"hash":"1989778208919563172","title":"Cell Division and RNA Processing Control","description":"The top terms cluster around cell cycle and cytokinesis (cell division, cell cycle, mitotic spindle pole body duplication, FtsZ-dependent cytokinesis) along with RNA processing and translation regulation (splicing regulation, translation initiation, translation reinitiation). This suggests proteins involved in coordinating cell division with gene expression control, with a few neuron-related terms as incidental. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0001764","count":1}]},{"hash":"1563512778519807919","title":"Hormone biosynthesis and organ development","description":"The cluster is enriched for multiple hormone biosynthetic processes (prostaglandin, ecdysone, aldosterone, brassinosteroid), pointing to a core theme of hormone production across systems. This is complemented by developmental terms for tissues such as retina vasculature, mammary gland, and prostate, suggesting a link to hormone-driven organ development and patterning. A few outliers (e.g., immune and unusual catabolic terms) exist but do not override the main theme. Confidence: Medium","confidence":"","size":12,"edges":25,"triangles":18,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":8},{"id":"GO:0006697","count":5},{"id":"GO:0061298","count":5},{"id":"GO:0030879","count":5},{"id":"GO:0019383","count":5}]},{"hash":"1957377974946448588","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032781","count":1},{"id":"GO:0016973","count":1},{"id":"GO:0051096","count":1},{"id":"GO:0033260","count":1},{"id":"GO:0006398","count":1}]},{"hash":"1055871448162795839","title":"Gene Expression & Proteostasis Under Stress","description":"Top terms indicate a focus on transcriptional and translational regulation, ribosome biogenesis, ER protein folding, and redox-related processes, suggesting a cohesive cluster of gene expression control coupled with proteostasis under stress. Some outliers (heart development, viral process) appear peripheral.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0006413","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0006351","count":1}]},{"hash":"608277932357384960","title":"Ubiquitin-Mediated Regulation and Stress Signaling","description":"The cluster shows enrichment for ubiquitin-related processes (polyubiquitination, ERAD, sumoylation) alongside regulators of cell fate and stress responses (apoptosis, necroptosis, TLR signaling, heat response, cell growth). This points to a theme where post-translational modification governs signaling and growth under stress.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0071157","count":2}]},{"hash":"542439659139177052","title":"Translation and nucleotide metabolism proteins","description":"This cluster contains GO terms tied to protein synthesis (translational elongation and translational fidelity) alongside nucleotide metabolism (adenosine/guanosine metabolism and ribonucleoside monophosphate catabolism) and even mitochondrial complex I assembly, plus a methylation term. The connectivity is weak (one edge, no triangles), so the shared theme is a loose mix of translation-related and nucleotide metabolism processes with some energy/metabolic context.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0006414","count":1},{"id":"GO:0032232","count":1},{"id":"GO:1990145","count":1},{"id":"GO:0019918","count":1}]},{"hash":"1408366367737257657","title":"Ubiquitin-Dependent Proteolysis and NF-kappaB Signaling","description":"The cluster is dominated by ubiquitination processes (K48-linked ubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process) and NF-kappaB pathway activation (IKK activity and I-kappaB phosphorylation). A few terms relate to X-chromosome inactivation and V(D)J recombination, but the strongest signal ties ubiquitin-mediated proteolysis to NF-kB signaling.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0038018","count":4},{"id":"GO:0070936","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0060816","count":4},{"id":"GO:0042787","count":4}]},{"hash":"1460100241858076080","title":"Intracellular protein trafficking and maturation","description":"This cluster centers on GO terms related to moving and processing proteins within the cell\u2014ER-to-Golgi transport, Golgi retention, peroxisomal import, SNARE disassembly, protein unfolding, and protein oligomerization\u2014pointing to intracellular trafficking, sorting, and quality control in the secretory pathway. Although a few terms touch on cell-cycle or metabolic processes, the dominant theme is protein trafficking and maturation.","confidence":"Medium","size":12,"edges":18,"triangles":16,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016558","count":3},{"id":"GO:0045053","count":3},{"id":"GO:0035494","count":3},{"id":"GO:0033314","count":3},{"id":"GO:2001171","count":3}]},{"hash":"1761623681020440049","title":"Cerebellar neuron development and organization","description":"This cluster is best described by neural development with a focus on cerebellar neurons: multiple terms reference neuron differentiation and Purkinje cell layer structural organization, implying roles in cerebellar neuron development and organization. Additional signals for vesicle transport and nucleotide biosynthesis support neuronal function, while inflammatory terms are present but less central.","confidence":"Medium","size":12,"edges":8,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":3},{"id":"GO:0030182","count":3},{"id":"GO:0046086","count":3},{"id":"GO:0006196","count":3},{"id":"GO:0050728","count":3}]},{"hash":"1791942014505678161","title":"Diverse substrate membrane transporters","description":"The top GO terms show a strong enrichment for transmembrane transport across a wide range of substrates (sodium and potassium ions, several sugars like galactose and arabinose, fucose, vitamins, and even a vesicular neurotransmitter loading term). This points to a cluster of membrane transporter proteins with diverse specificities rather than a single, narrowly defined pathway. The presence of a vesicle-related transport term alongside general transport terms suggests both vesicular and plasma-m membrane transporter activities.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0006004","count":3},{"id":"GO:0015757","count":3}]},{"hash":"291334171118360216","title":"Vascular Coagulation and Calcium Signaling","description":"This cluster centers on vascular/hemostatic functions, with GO terms for blood coagulation and clotting cascade activation, purinergic signaling, and endothelial regulation. Calcium-related processes (calcium-activated scrambling, endothelial/apoptotic regulation, and ion homeostasis) appear as common motifs, suggesting a role in calcium-driven coagulation signaling and endothelial function. A few terms about bone mineralization seem incidental noise rather than core to the cluster\u2019s theme. Overall, the cluster likely reflects proteins involved in vascular coagulation regulation and related calcium signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":1},{"id":"GO:0007596","count":1},{"id":"GO:0035630","count":1},{"id":"GO:1902939","count":1},{"id":"GO:0035590","count":1}]},{"hash":"486188858271347367","title":"Plant Hormone Signaling and Development","description":"The terms point to plant hormone responses (abscisic acid, salicylic acid, cytokinin signaling) and development-related processes (leaf senescence, trichome patterning), suggesting a theme of hormonal control over growth and stress responses in plants. Some outliers (telomere/shelterin-related terms) may reflect broader cellular regulation, but the core pattern is plant hormone signaling tied to development.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010520","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1904792","count":1},{"id":"GO:1903086","count":1}]},{"hash":"670788254258687742","title":"RNA Processing and Ribosome Biogenesis","description":"The cluster is dominated by RNA- and ribosome-related GO terms: nonsense-mediated decay, maturation of LSU-rRNA, and ribosomal large subunit biogenesis, pointing to RNA metabolism and ribosome assembly. Other terms (DNA replication, SOS response, development, behavior) are more peripheral or likely ancillary annotations, so the core theme is RNA processing and ribosome biogenesis.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000184","count":4},{"id":"GO:0048568","count":4},{"id":"GO:0006265","count":4},{"id":"GO:0006306","count":4},{"id":"GO:0006269","count":4}]},{"hash":"1926066629081454489","title":"Amino acid transport and potassium homeostasis","description":"This cluster is enriched with GO terms for importing various amino acids (D-aspartate, threonine, serine, glutamate) and GABA biosynthesis, plus several transmembrane transport and potassium-related terms and membrane potential stabilization. The common thread appears to be membrane transport proteins that mediate amino acid uptake and regulate K+ balance and membrane potential, supporting a cohesive function around nutrient transport and ionic homeostasis.","confidence":"High","size":12,"edges":40,"triangles":60,"max_degree":11,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0070779","count":5},{"id":"GO:0009449","count":5},{"id":"GO:0055085","count":5},{"id":"GO:0015826","count":5},{"id":"GO:0032329","count":5}]},{"hash":"1677584934831350484","title":"Brain synaptic vesicle exocytosis regulation","description":"The top terms cluster around brain and hippocampus development and regulation of synaptic vesicle exocytosis, including calcium-dependent exocytosis and JNK cascade regulation, indicating a neuronal development and synaptic transmission theme. Some outlier terms (yeast mating, beta selection) appear, but the dominant signal supports a neuronal exocytosis/regulatory function.","confidence":"High","size":12,"edges":27,"triangles":14,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:0010796","count":6},{"id":"GO:2000300","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0021766","count":5}]},{"hash":"624343998564827209","title":"Ciliary assembly and vesicle trafficking in development","description":"This cluster centers on ciliogenesis and flagellar development (intraciliary transport, spermatid development) and intracellular vesicle trafficking (ER-Golgi and endosome transport). Developmental processes in the nervous system and neuromuscular balance support a cohesive theme of ciliary/flagellar assembly coupled with vesicular transport during development and cell division. A few terms touch on cell cycle regulation and drug response, but the dominant signal is ciliary/flagellar assembly with associated transport pathways.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097327","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0035735","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007399","count":2}]},{"hash":"130850047520010957","title":"Cerebral Cortex and Brain Development","description":"The cluster is dominated by terms related to brain development, especially cerebral cortex and hippocampus formation, orbitofrontal cortex development, and cranial skeleton morphogenesis, suggesting a shared role in neural development and regional brain specification. Supporting signals include cortex-related signaling (FGF receptor pathways), cortical actin cytoskeleton organization, and regulation of stem cell differentiation, all of which are key in neural differentiation and cortical formation. While a couple of terms (like trachea formation) are less directly brain-specific, they can reflect broader craniofacial developmental processes linked to neural development.","confidence":"High","size":12,"edges":36,"triangles":39,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":12},{"id":"GO:2001233","count":12},{"id":"GO:0061368","count":12},{"id":"GO:0030866","count":12},{"id":"GO:0048701","count":12}]},{"hash":"973811343047715560","title":"Cerebral cortex and craniofacial development","description":"The cluster is strongly enriched for terms tied to nervous system development and craniofacial morphogenesis, notably cerebral cortex development, embryonic cranial skeleton morphogenesis, and visual perception. Additional terms related to cytoskeletal organization and signaling support a developmental/morphogenetic theme, with some nociception-related and general mitotic processes that commonly accompany development. This makes a neurodevelopmental + craniofacial morphogenesis label appropriate and specific.","confidence":"High","size":12,"edges":26,"triangles":13,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":12},{"id":"GO:0007601","count":12},{"id":"GO:0060440","count":11},{"id":"GO:2001233","count":11},{"id":"GO:0061368","count":11}]},{"hash":"2284954058587191177","title":"Amino acid import across the plasma membrane","description":"The top GO terms are dominated by transmembrane import of various amino acids (L-lysine, L-arginine, L-ornithine, methionine, D-alanine, D-serine) plus related processes like arginine catabolism and NO production, pointing to a shared function of amino acid transport/metabolism. A few terms (hair follicle maturation, GPCR signaling) seem less connected, but do not outweigh the core theme.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048820","count":1},{"id":"GO:0002537","count":1},{"id":"GO:0042941","count":1},{"id":"GO:0097639","count":1},{"id":"GO:0044690","count":1}]},{"hash":"1031503046654702072","title":"Epithelial development and growth signaling","description":"Most terms center on transcriptional regulation and signaling pathways that drive epithelial development: DNA-templated transcription, Hippo and Wnt signaling, keratinocyte differentiation, and tracheal development, with accompanying regulation of apoptosis. Together they describe a module coordinating gene expression with growth and differentiation in epithelial tissues, including airway formation.","confidence":"Medium","size":12,"edges":13,"triangles":4,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0097011","count":7},{"id":"GO:0060044","count":6},{"id":"GO:0046827","count":6},{"id":"GO:0035329","count":6}]},{"hash":"1948958281598402575","title":"Diverse membrane transporters for ions and nutrients","description":"GO terms indicate transmembrane transport across a range of substrates (sodium, potassium, phosphate, nitrate, sialic acid, fucose, vitamins) and related processes like neurotransmitter loading, suggesting a cohesive role for membrane transport proteins handling diverse ions and metabolites. The common theme is transport across membranes rather than enzymatic activity, so this label captures the cluster\u2019s overarching function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0098700","count":2}]},{"hash":"80905763633995094","title":"Peptide processing and hormone maturation","description":"The top GO terms point to processing and maturation of peptide hormones and neuropeptides (insulin processing, enkephalin processing, peptide pheromone maturation, renin secretion). There are also terms related to receptor regulation, which can tie into peptide signaling pathways. While some terms (sporulation, axis determination, LDL receptor turnover) are less aligned, the strongest shared feature across the cluster appears to be peptide maturation and hormone-related processing. Confidence in this theme is moderate due to some outliers and sparse connectivity.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002001","count":2},{"id":"GO:0032802","count":2},{"id":"GO:0030435","count":2},{"id":"GO:1905598","count":2},{"id":"GO:0007354","count":2}]},{"hash":"1249748439629933331","title":"Brain Development and Cortex Formation","description":"The top GO terms are dominated by brain development and cortex-related processes: cerebral cortex development, hippocampus development, orbitofrontal cortex development, and embryonic cranial morphogenesis, plus FGFR signaling involved in cortex development. A few terms reflect general cellular processes like actin cytoskeleton organization and apoptotic signaling that commonly accompany development. Overall, the cluster appears to reflect brain morphogenesis and cortical formation.","confidence":"High","size":12,"edges":24,"triangles":14,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":12},{"id":"GO:2001233","count":12},{"id":"GO:0061368","count":12},{"id":"GO:0030866","count":12},{"id":"GO:0048701","count":12}]},{"hash":"2105026489425341285","title":"Chemical and Hormonal Stimulus Responses","description":"Top terms indicate diverse cellular responses to chemical and hormonal stimuli (methylmercury, herbicide, zinc ion, IL-4, dexamethasone, vitamin E, TGF-beta), with additional mentions of collagen biosynthesis and liver development suggesting a tissue remodeling context. This points to a broader theme of how cells respond to external cues impacting tissue state, rather than a single cohesive pathway. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051597","count":1},{"id":"GO:0032964","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0033388","count":1},{"id":"GO:0009635","count":1}]},{"hash":"1215110927354485576","title":"Plant Hormone Signaling and Development Regulation","description":"The top GO terms point to plant hormone signaling and developmental processes, including responses to ABA, cytokinins, and salicylic acid, as well as regulation of leaf senescence and trichome patterning. This suggests a cohesive theme of how hormonal signaling pathways regulate growth and development in plants, with many entries framed as negative regulation of various processes, aligning with a regulatory protein cluster. Some outliers (e.g., telomere- and metabolism-related terms) may reflect broader cellular regulation but do not outweigh the hormone-development signal.","confidence":"Medium","size":12,"edges":35,"triangles":46,"max_degree":9,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010520","count":12},{"id":"GO:0009737","count":12},{"id":"GO:0009736","count":12},{"id":"GO:1904792","count":12},{"id":"GO:1903086","count":12}]},{"hash":"894503721718828472","title":"RNA processing and chromatin remodeling","description":"These proteins show a consistent signal for RNA biogenesis and chromatin-related activities: tRNA dihydrouridine synthesis, snoRNA localization and snoRNP assembly, along with chromatin remodeling and regulation of histone deacetylation. Despite some obsolete GO terms, the repeated emphasis on RNA processing and chromatin dynamics suggests a shared role in nucleic acid metabolism and chromatin control rather than other processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0002943","count":1},{"id":"GO:0006338","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0000492","count":1}]},{"hash":"1354341590785409496","title":"Muscle regeneration and cardiovascular development","description":"Top terms converge on skeletal muscle tissue regeneration, heart-field cardioblast proliferation, and sprouting angiogenesis, with supporting roles for cell growth and migration. While a few terms are peripheral (vitamin D response, temperature sensing, kinase activity regulation), the dominant theme is muscle and vascular/cardiovascular formation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035508","count":3},{"id":"GO:0043403","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0003270","count":3},{"id":"GO:1903589","count":3}]},{"hash":"1179585227318685042","title":"Mitochondrial Bioenergetics and Stress Response","description":"Top GO terms cluster around mitochondrial energy production and regulation, with ATP transmembrane transport and membrane fission pointing to bioenergetics and organelle dynamics, and CoA/manganese transport tying to metabolic and redox homeostasis. Nutrient-sensing and adaptive signaling terms (insulin response, amino acid starvation, adaptive thermogenesis) suggest coordinated metabolic regulation, while oxidative stress and liver regeneration indicate stress adaptation and tissue remodeling. Altogether, this cluster appears to reflect mitochondrial energy metabolism coupled with stress and adaptive pathways.","confidence":"High","size":12,"edges":12,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":10},{"id":"GO:0034198","count":10},{"id":"GO:0032869","count":10},{"id":"GO:1990845","count":10},{"id":"GO:0035349","count":10}]},{"hash":"1527432430283145138","title":"Chromatin organization and DNA repair","description":"The proteins cluster around nuclear processes, especially nucleosome assembly, DNA-templated transcription, RNA polymerase II\u2013mediated transcription, and DNA repair, pointing to chromatin organization and genome maintenance as the central theme. Additional terms touch meiosis, telomere-associated assembly, and plant hormone signaling, which may reflect contextual or multifunctional roles, but the core shared function seems to be chromatin dynamics and genome integrity in the nucleus.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006281","count":2}]},{"hash":"1182492291486402044","title":"Unknown","description":"The Top Terms span immune (T cell cytotoxicity), hormone response (thyroid hormone), peptide processing (bradykinin catabolic), development/differentiation (decidualization), extracellular remodeling (collagen catabolic), signaling (Wnt-related), neural proliferation, and lung development. This broad, non-overlapping mix lacks a single cohesive biological theme, suggesting either heterogeneous functional annotations or a mixed protein set. ","confidence":"","size":12,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":1},{"id":"GO:0001913","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0010815","count":1},{"id":"GO:0046697","count":1}]},{"hash":"1808068137295894355","title":"Amino Acid Metabolism and Redox Detox","description":"The terms cluster around amino acid metabolism (L-serine biosynthesis; L-tyrosine and L-phenylalanine catabolism) and redox-related processes (glutathione metabolism; oxidation-reduction; methylglyoxal detoxification via lactoyl-glutathione). While a couple of terms (brain development; transcription regulation) are broader or less directly tied, the dominant themes are metabolic processing and redox balance, justifying a metabolism/redox-focused label.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0032024","count":2},{"id":"GO:0006572","count":2}]},{"hash":"1084192544171316301","title":"Actin Cytoskeleton Remodeling in Neuronal Morphogenesis","description":"The GO terms repeatedly highlight actin cytoskeleton organization, Rho GTPase activation, and regulation of Rho signaling, along with dendritic spine morphogenesis and adherens junction assembly, pointing to coordinated actin remodeling underlying neuronal development and synapse-related structures; sensory perception of sound aligns with actin-rich hair cell structures, while a few terms (viral process, opioid signaling) may reflect broader regulatory networks.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0016032","count":2}]},{"hash":"17403844983830997","title":"TOR-PI3K Signaling","description":"The dominant GO terms point to TORC1 and TORC2 signaling and PI3K/AKT signal transduction, indicating a growth and nutrient-sensing module. Some terms pertain to plant development or other processes, which may reflect context-specific annotations or pleiotropy, but the core theme is TOR- and PI3K-driven signaling. Overall, this cluster appears to capture TOR-PI3K signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":2},{"id":"GO:0043491","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0038203","count":2},{"id":"GO:0031623","count":1}]},{"hash":"455338491510027922","title":"Unknown","description":"The top terms are a scattered mix of regulatory processes (Ras signaling, SNARE regulation, Notch signaling, neutrophil degranulation), muscle-related functions, and general cell growth, with several obsolete terms, offering no single cohesive theme to name the cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072660","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0043403","count":2}]},{"hash":"1394692379345419088","title":"Neurovascular development and axon morphogenesis","description":"The cluster is dominated by neural development terms such as optic nerve morphogenesis, CNS projection neuron axonogenesis, axon fasciculation, and dendritic spine morphogenesis, plus endothelial sprouting and pericyte differentiation that point to vascular support of developing tissues. Together these suggest a coordinated neurovascular development role, with some outlier terms (T cell costimulation, cone cell differentiation) likely incidental.","confidence":"Medium","size":11,"edges":19,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007050","count":2},{"id":"GO:2000525","count":1},{"id":"GO:0060997","count":1},{"id":"GO:1904238","count":1},{"id":"GO:0042675","count":1}]},{"hash":"121078713325288446","title":"Vacuolar amino acid transport (import/export)","description":"The top GO terms point to transport of multiple amino acids (tyrosine, arginine, histidine, alanine, proline, glutamine) across the vacuolar membrane, suggesting a function in vacuolar amino acid flux and homeostasis; the transport/export/import terms dominate, while non-transport terms (e.g., root cap development) appear incidental.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051365","count":2},{"id":"GO:0090514","count":2},{"id":"GO:0015824","count":2},{"id":"GO:1990818","count":2},{"id":"GO:0089708","count":2}]},{"hash":"124914935293973532","title":"Sugar transport and carbohydrate metabolism","description":"Reason: Several terms point to transport and metabolism of carbohydrates\u2014D-glucose transmembrane transport, lactose biosynthetic process, fucose metabolic process\u2014alongside vitamin and sodium transmembrane transport. While a few terms are incidental (nitrate assimilation, intestinal epithelial maintenance), the shared theme centers on membrane-associated sugar transport and carbohydrate metabolism.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904728","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0042149","count":2}]},{"hash":"1378485172114958034","title":"Cell wall biosynthesis and cytoskeletal dynamics","description":"The GO terms converge on building and remodeling the cell surface and wall structures (chitin biosynthesis, capsule polysaccharide biosynthesis, mycolate cell wall layer assembly) along with associated sugar metabolism (UDP-D-galactose). In parallel, terms for actin/cytoskeletal organization and division (actin cortical patch localization, actomyosin contractile ring contraction, division septum site selection) suggest coordinated structural assembly and cell division processes. Some developmental adhesion/organization terms appear tangentially related, but the dominant theme is cell wall/surface biosynthesis with cytoskeletal coordination.","confidence":"Medium","size":11,"edges":26,"triangles":26,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051666","count":1},{"id":"GO:1900027","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0006031","count":1},{"id":"GO:0052573","count":1}]},{"hash":"1227565398045509798","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007064","count":4},{"id":"GO:1904263","count":4},{"id":"GO:0030042","count":4},{"id":"GO:0061641","count":4},{"id":"GO:0040020","count":4}]},{"hash":"1185597550980614511","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":2},{"id":"GO:0032147","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0034475","count":1},{"id":"GO:0071036","count":1}]},{"hash":"2088376614070210738","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":45,"triangles":96,"max_degree":10,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0008033","count":3}]},{"hash":"1754574404326628524","title":"Wnt and T cell signaling with cell-cycle regulation","description":"The terms show strong enrichment for Wnt signaling (canonical and planar cell polarity) and T cell receptor signaling, plus mitotic spindle assembly, pointing to signaling networks that coordinate immune/developmental pathways with cell-cycle control. Additional regulatory processes (ubiquitin-proteasome degradation, mRNA stability, endopeptidase activity) support a broader theme of signaling intertwined with protein turnover and regulation. Overall, this label captures the dominant themes without overreaching into unrelated functions.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0090307","count":2},{"id":"GO:0060071","count":2},{"id":"GO:0090090","count":2}]},{"hash":"338336937293497893","title":"Mitochondrial lipid metabolism and dopaminergic signaling","description":"This cluster centers on mitochondrial-specific lipid and DNA-related processes (positive regulation of mitochondrial DNA replication; positive regulation of cardiolipin metabolism; lipid localization) and neuronal signaling pathways (protein kinase C signaling; dopaminergic synaptic transmission). While there are some extracellular matrix/adhesion terms present, the strongest and most coherent themes tie mitochondria to lipid metabolism and neuronal signaling, suggesting a role in mitochondrial-lipid regulation of dopaminergic function.","confidence":"Medium","size":11,"edges":37,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":3},{"id":"GO:0090297","count":2},{"id":"GO:2000049","count":2},{"id":"GO:0010876","count":2}]},{"hash":"1868744370675628379","title":"Negative regulation of LPS-TLR signaling","description":"The GO terms show a clear emphasis on cellular response to lipopolysaccharide and multiple layers of negative regulation of inflammatory signaling (TLR pathway, NF-kappaB activity, TNF and IL-8 production, IFN-beta), suggesting these proteins function to dampen LPS-triggered immune responses. The presence of a spliceosome-related term is likely ancillary. Overall, the cluster appears to group regulators that restrain LPS/TLR-driven inflammation.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0032717","count":1},{"id":"GO:0032720","count":1}]},{"hash":"1381733798448592798","title":"Transcriptional Regulation and Chromatin Modification","description":"The terms point to nuclear gene expression control: DNA-templated transcription, SAGA complex localization to transcription regulatory region, and histone deubiquitination, along with mRNA export. Additional items like proteasome assembly and DNA repair also relate to chromatin state and genome maintenance, supporting a cohesive theme of transcription regulation and chromatin modification, despite limited edge connections among proteins.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0072742","count":1},{"id":"GO:0035753","count":1},{"id":"GO:0043248","count":1},{"id":"GO:0030447","count":1}]},{"hash":"2048163878782146191","title":"RNA Splicing and Deubiquitination","description":"Based on the top terms, there is a clear emphasis on RNA processing, with multiple GO terms for RNA splicing, along with ubiquitin-related regulation via deubiquitination. This suggests a cluster centered on post-transcriptional RNA processing and ubiquitin-mediated protein regulation. Other terms (chloroplast mRNA modification, otic vesicle morphogenesis, circadian clock temperature compensation, stress responses) appear peripheral and may reflect broader or multifunctional roles of the proteins. Overall, the core theme appears to be RNA splicing together with protein deubiquitination.","confidence":"Medium","size":11,"edges":26,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0071600","count":1},{"id":"GO:0070536","count":1},{"id":"GO:1900871","count":1},{"id":"GO:0008380","count":1}]},{"hash":"626710144570989502","title":"Embryonic neural development and gene regulation","description":"The cluster\u2019s top GO terms cluster around neural and embryonic development (neural tube closure, forebrain development, multicellular organism development) and general transcriptional control (DNA-templated transcription), with supporting signals for cell proliferation and stress-related pathways often active during development. This points to an embryonic developmental program with neural specification and transcriptional regulation as the main theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001501","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0071276","count":4}]},{"hash":"1127583028202116162","title":"Unknown","description":"This cluster contains a mix of disparate processes\u2014aromatic amino acid and related biosynthesis, lipid biosynthesis, RNA metabolism, DNA repair, and protein autoprocessing\u2014without a single dominant function, making a cohesive, intuitive label inappropriate.","confidence":"","size":11,"edges":51,"triangles":131,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009423","count":1},{"id":"GO:0019630","count":1},{"id":"GO:0009073","count":1},{"id":"GO:0040007","count":1},{"id":"GO:0046279","count":1}]},{"hash":"1767028056598040840","title":"General Cellular Stress and Gene Expression","description":"The top GO terms span heat response, protein quality control (ERAD), RNA processing (splicing), DNA replication, cell growth, and protein localization, with a few transport-related terms. This mix suggests a cluster of broad housekeeping and stress-related cellular processes rather than a single specific function, so a label emphasizing general maintenance and gene expression is appropriate.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000398","count":2}]},{"hash":"647984477868941381","title":"Epithelial morphogenesis and cytoskeletal signaling","description":"Top GO terms point to epithelial biology: keratinocyte differentiation, tracheal epithelium formation, and processes of cell\u2013ECM interaction (focal adhesion) with cortical actin remodeling. The inclusion of Hippo and Wnt signaling suggests regulation of tissue size and differentiation in developing epithelia, while apoptotic signaling reflects tissue remodeling during morphogenesis. A few terms (e.g., pain-related responses) may reflect cross-talk or pleiotropy across tissues, but the dominant theme is epithelial differentiation and cytoskeletal dynamics.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060044","count":8},{"id":"GO:0035329","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0030216","count":8},{"id":"GO:0006915","count":8}]},{"hash":"1895598795242869600","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by terms tied to translation and ribosome assembly (translation, ribosome biogenesis, small subunit biogenesis) and includes related translation-related processes such as regulation of translational fidelity and selenocysteine incorporation, indicating proteins involved in ribosome function and protein synthesis.","confidence":"High","size":11,"edges":50,"triangles":126,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071549","count":1}]},{"hash":"859039549595415667","title":"Unknown","description":"The GO terms are highly heterogeneous, ranging from calcium release from the sarcoplasmic reticulum to nervous system/heart development, protein sumoylation, amyloid fibril formation, chaperone-related folding, histone isomerization (obsolete), and cell division. There isn\u2019t a single cohesive function or pathway that ties all 11 proteins together, and several terms are obsolete, so there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":11,"edges":14,"triangles":10,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0014808","count":3},{"id":"GO:0021750","count":2},{"id":"GO:0007183","count":2},{"id":"GO:0060347","count":2},{"id":"GO:0016925","count":2}]},{"hash":"855309684543151789","title":"Organ development and tissue homeostasis","description":"The top GO terms show a clear emphasis on organ- and tissue-level development (heart development, post-embryonic development, hepatocyte homeostasis, uterine gland development), with a secondary thread of genome maintenance (DNA repair, histone modification) and cell-cycle regulation. This combination suggests the cluster broadly centers on development and maintenance of tissues, supported by genome stability mechanisms. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0009791","count":2},{"id":"GO:0055114","count":2},{"id":"GO:2000134","count":1}]},{"hash":"1129559469998295189","title":"Unknown","description":"The GO terms show a mix of development (nigra, muscle, lung, EMT) and signaling (calcium detection, calcineurin\u2013NFAT) alongside transcription and meiosis-associated DNA repair terms. There isn\u2019t a clear, single functional theme connecting these terms, suggesting the cluster spans multiple diverse processes rather than a cohesive pathway.","confidence":"","size":11,"edges":52,"triangles":141,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0021762","count":11},{"id":"GO:0048741","count":11},{"id":"GO:0010780","count":8},{"id":"GO:0051037","count":8},{"id":"GO:0010791","count":8}]},{"hash":"261358295385392595","title":"Cilium-Driven Developmental Signaling","description":"The term set centers on non-motile cilium assembly and left/right asymmetry determination, classic ciliary functions in development, suggesting the cluster reflects cilium-associated signaling and developmental coordination. Additional terms like response to cAMP and protein secretion/trimerization may reflect related signaling and assembly processes, while a couple terms (chlorophyll biosynthesis) could be species-specific or less connected. Overall, the strongest theme is cilium-related development and signaling.","confidence":"Medium","size":11,"edges":42,"triangles":75,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042136","count":2},{"id":"GO:0051591","count":2},{"id":"GO:1905515","count":2},{"id":"GO:0050714","count":2},{"id":"GO:0070206","count":2}]},{"hash":"1001277124638343200","title":"Seed lipid metabolism","description":"The cluster is dominated by fatty-acyl-CoA and fatty acid metabolic terms (medium- and very long-chain), plus fatty acid transport, pointing to lipid utilization and processing. The presence of plant-specific terms like positive regulation of seed germination and phenylpropanoid metabolism suggests a seed-related plant metabolic context, reinforcing a theme around seed lipid metabolism and related carbon flux.","confidence":"Medium","size":11,"edges":29,"triangles":30,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0036112","count":5},{"id":"GO:0010030","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0019427","count":4},{"id":"GO:0044539","count":4}]},{"hash":"303495575634293712","title":"ER protein folding and redox stress response","description":"Top terms indicate ER-associated protein folding and retention, redox homeostasis, and stress signaling (MAPK), pointing to an ER quality-control and oxidative-stress response module. A secondary feature is ER-related post-translational modification, with viral process appearing as a peripheral annotation. ","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0016032","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0030416","count":3},{"id":"GO:0006621","count":3}]},{"hash":"1449324196209963961","title":"Unknown","description":"The top GO terms span immune (T cell-mediated cytotoxicity), hormonal signaling (cellular response to thyroid hormone stimulus), tissue remodeling (collagen catabolic process, bradykinin catabolic process, decidualization), and developmental processes (lung branching, neural precursor proliferation). The lack of a unifying biological theme across these diverse processes suggests no cohesive cluster function, so an Unknown label is most appropriate.","confidence":"","size":11,"edges":31,"triangles":40,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":3},{"id":"GO:0001913","count":3},{"id":"GO:0097067","count":3},{"id":"GO:0010815","count":3},{"id":"GO:0046697","count":3}]},{"hash":"633221133593637059","title":"DNA Damage Response and Stress Regulation","description":"Top GO terms point to xenobiotic response, redox homeostasis, apoptosis, base-excision repair, and post-transcriptional control, all hallmarks of a cellular stress response and genome maintenance program. The presence of repair and apoptotic processes supports DNA damage response involvement, while redox balance and mRNA stability regulation reflect broader stress signaling; a couple terms hint tissue-specific roles, but the cluster overall aligns with damage response and stress signaling pathways.","confidence":"Medium","size":11,"edges":20,"triangles":11,"max_degree":8,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042493","count":5},{"id":"GO:0043488","count":4},{"id":"GO:0080111","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0071375","count":4}]},{"hash":"392169882432366169","title":"Ubiquitin-proteasome turnover and TORC1 signaling","description":"The strongest signals are ubiquitin-dependent proteasomal protein catabolic processes and protein polyubiquitination, along with TORC1 signaling, suggesting a core theme of proteostasis and nutrient-signaling; additional terms like mRNA transport and GTPase activity regulation appear as secondary associations, and immune-related terms may reflect incidental connections.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0038202","count":3}]},{"hash":"1870481214402020208","title":"Neuronal vesicle trafficking and development","description":"The top GO terms show brain and dendrite development alongside multiple vesicle transport processes (ER-Golgi transport, retrograde transport, and synaptic vesicle exocytosis), suggesting a cohesive cluster of proteins involved in vesicle trafficking with roles in neural development. Some mitotic terms appear but are likely background; the dominant theme is vesicle transport in neuronal contexts.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0006888","count":5},{"id":"GO:2000300","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0031384","count":4}]},{"hash":"1173809699485760702","title":"Neurodevelopmental Signaling","description":"The cluster is dominated by neural development and signaling terms (Roundabout/ROBO pathway, Smoothened/Hedgehog signaling, neurogenesis, nervous system development, dendritic spine morphogenesis, behavior), suggesting roles in neural patterning and connectivity, with a few immune signaling terms appearing as incidental cross-talk.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035385","count":7},{"id":"GO:0001822","count":7},{"id":"GO:0007224","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0022008","count":7}]},{"hash":"332667040559692989","title":"Redox-linked prostaglandin biosynthesis and platelet function","description":"This cluster combines prostaglandin biosynthesis and platelet aggregation with multiple redox-related processes (cell redox homeostasis, protein glutathionylation, glutathione metabolism, cellular oxidant detoxification) and mitochondrial membrane potential regulation. The convergence of eicosanoid production, platelet activity, and redox/homeostatic pathways suggests a cohesive module where redox state influences prostaglandin signaling and platelet function, with supporting metabolic context from aromatic amino acid metabolism and homogentisate catabolism.","confidence":"High","size":11,"edges":43,"triangles":85,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":4},{"id":"GO:0070527","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0010731","count":3},{"id":"GO:0009072","count":3}]},{"hash":"1662173880509996910","title":"Cerebral cortex development and neuronal morphogenesis","description":"The prominent terms center on brain development (neuron development, cerebral cortex development, cortical actin organization, cranial skeleton morphogenesis), with supportive mentions of stem cell differentiation and apoptotic signaling. This pattern suggests proteins implicated in neural differentiation and cortical neuron morphogenesis rather than unrelated processes.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0048666","count":3},{"id":"GO:0060440","count":2},{"id":"GO:2001233","count":2},{"id":"GO:0061368","count":2}]},{"hash":"1626155025002749482","title":"Plant fatty acid biosynthesis and transport","description":"This cluster is dominated by GO terms for fatty acid biosynthesis across chain lengths (short, medium, long, very-long) and for fatty acid transport/import, with additional related lipid and phenylpropanoid metabolism terms and a plant-specific seed germination regulator term. The cohesive theme centers on lipid production and trafficking in plants, with seed-related regulatory signals possibly linking metabolism to development.","confidence":"High","size":11,"edges":28,"triangles":24,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":6},{"id":"GO:1902987","count":5},{"id":"GO:0010030","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0019427","count":4}]},{"hash":"1564249928267206396","title":"Methyltransferases for histone, RNA, and protein methylation","description":"This cluster is dominated by GO terms describing various methylation processes, including lysine methylation on proteins, rRNA methylation, and mRNA cap methylation, along with a connection to chromatin structure (rDNA heterochromatin formation). While a few terms are peripheral (e.g., antibiotic biosynthesis, nodulation), the strongest signal is methyltransferase activity across substrates, suggesting a cohesive group of methylation-related enzymes and regulators.","confidence":"High","size":11,"edges":34,"triangles":52,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":6},{"id":"GO:0031167","count":6},{"id":"GO:0018013","count":5},{"id":"GO:0018023","count":5},{"id":"GO:0000183","count":5}]},{"hash":"1816553669507233822","title":"Peptide hormone maturation and receptor regulation","description":"This cluster is dominated by GO terms for processing and maturation of peptide hormones (insulin, enkephalin, peptide pheromones) and for regulation of receptor activity and trafficking (LDL receptor pathways and receptor recycling). Some terms like sporulation or axis development appear as noise, but the common theme centers on peptide hormone processing and membrane receptor regulation.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002001","count":3},{"id":"GO:0032802","count":3},{"id":"GO:0030435","count":3},{"id":"GO:1905598","count":3},{"id":"GO:0007354","count":3}]},{"hash":"1750783445231277596","title":"Unknown","description":"The listed GO terms cover immune processes (T cell mediated cytotoxicity), hormone signaling (cellular response to thyroid hormone stimulus), and multiple remodeling/proteolysis processes (bradykinin catabolic process, collagen catabolic process, decidualization, lung branching morphogenesis), plus broad regulatory activity. There is no clear single biological function that ties these terms together, suggesting this cluster does not cohere around a specific pathway or process. Therefore, the appropriate label is Unknown.","confidence":"","size":11,"edges":44,"triangles":90,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":7},{"id":"GO:0001913","count":7},{"id":"GO:0097067","count":7},{"id":"GO:0010815","count":7},{"id":"GO:0046697","count":7}]},{"hash":"1695547747771184949","title":"Amino acid transport across membranes","description":"The top GO terms are dominated by transmembrane transport and import of specific amino acids (D-aspartate, threonine, serine, L-glutamate) along with GABA biosynthesis, indicating the proteins mainly function in amino acid uptake across the membrane. Some unrelated terms (lipid biosynthesis, photomorphogenesis, signaling) are present but do not override the amino acid transport theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0070779","count":3},{"id":"GO:0009449","count":3},{"id":"GO:0055085","count":3},{"id":"GO:0015826","count":3},{"id":"GO:0032329","count":3}]},{"hash":"1951454836811613043","title":"Unknown","description":"The GO terms in this cluster are highly diverse (hemopoiesis, cholesterol biosynthesis, regulation of senescence, responses to glucose starvation, various transport and biosynthesis processes) with little overlap or a single dominant function, so a cohesive, specific label is not supported.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030097","count":1},{"id":"GO:0006695","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0052106","count":1}]},{"hash":"839960782851667167","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042311","count":1},{"id":"GO:0014916","count":1},{"id":"GO:0051000","count":1},{"id":"GO:0032496","count":1},{"id":"GO:0035998","count":1}]},{"hash":"521290615901616785","title":"Cardiac electrophysiology and stress responses","description":"The top GO terms cluster around cardiac electrical activity, including regulation of atrial and His bundle cell membrane repolarization and overall membrane potential changes during cardiac action potentials, suggesting a focus on cardiac electrophysiology. Additional terms touch on stress-related and autonomic processes (temperature/cold responses, startle, cortisol biosynthesis, gastric acid secretion, GABA secretion, CO2 detection), implying broader neuroendocrine and autonomic regulation that can influence heart function. Overall, this cluster appears to connect cardiac excitability with stress-response pathways.","confidence":"Medium","size":11,"edges":11,"triangles":3,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060372","count":9},{"id":"GO:0003031","count":9},{"id":"GO:0071502","count":9},{"id":"GO:0086048","count":9},{"id":"GO:0009409","count":9}]},{"hash":"1875892331547416658","title":"Ribosome Biogenesis and Translation","description":"The top terms are centered on translation and ribosome assembly (translation; ribosome biogenesis; ribosomal subunit export from nucleus; ribosomal subunit biogenesis), indicating the proteins predominantly participate in ribosome production and protein synthesis. A few other terms (cell septum assembly, iron ion transport) appear but do not define the main function of the cluster, which remains ribosome-related.","confidence":"High","size":10,"edges":15,"triangles":7,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0090529","count":2}]},{"hash":"599953173123837246","title":"Ribosome biogenesis and ER protein trafficking","description":"This cluster is dominated by terms for ribosome biogenesis, LSU rRNA maturation, and RNA modification, with strong signals for cotranslational targeting to the ER (SRP) and Sec-dependent protein transport, plus ER quality control (retrograde transport and ERAD). These together point to a cohesive theme of ribosome assembly linked to ER protein handling and trafficking. Some developmental terms appear but are secondary to the ribosome/ER axis.","confidence":"High","size":10,"edges":35,"triangles":61,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0007338","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0036265","count":2}]},{"hash":"118709564243316800","title":"Pseudouridine Synthesis Enzymes","description":"Most frequent GO terms are for pseudouridine synthesis across mRNA, snRNA, and tRNA, suggesting RNA modification enzymes as the cluster's core function; other terms (calcium signaling, EMT, ascospore formation) are sporadic and less cohesive with this theme, indicating pleiotropy rather than a unifying function beyond RNA modification.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990481","count":2},{"id":"GO:0031120","count":2},{"id":"GO:0031119","count":2},{"id":"GO:0033173","count":2},{"id":"GO:0005513","count":2}]},{"hash":"221254578568441795","title":"Mitochondrial energy metabolism and stress response","description":"The Top Terms cluster centers on mitochondrial function\u2014ATP and CoA transmembrane transport, and mitochondrial membrane fission\u2014pointing to energy production and metabolite handling. It also includes stress- and signaling-related terms (response to superoxide, amino acid starvation, insulin stimulus, adaptive thermogenesis), suggesting coordinated mitochondrial metabolic regulation in response to cellular conditions. Some terms like liver regeneration and obsolete genome maintenance hint broader tissue-level metabolism, but the core theme remains mitochondrial energy metabolism and stress signaling.","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0032869","count":3},{"id":"GO:1990845","count":3},{"id":"GO:0035349","count":3}]},{"hash":"577317594842806962","title":"Folate Transport and Antifolate Drug Transport","description":"The top GO terms point to transport of folate-related compounds: 5-formyltetrahydrofolate and methotrexate (an antifolate drug). This suggests the cluster's function centers on folate/antifolate transport rather than stem cell maintenance, which is only weakly represented. Therefore, Folate transport is the best characteristic label, with antifolate transport included to reflect methotrexate-related transport.","confidence":"Medium","size":10,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1902455","count":1},{"id":"GO:0051958","count":1},{"id":"GO:0015885","count":1}]},{"hash":"276945016364575500","title":"Developmental Transcription Regulation","description":"This cluster is dominated by terms related to transcription (e.g., DNA-templated transcription) and transcriptional regulation across various developmental contexts, including eyelid development, outflow tract morphogenesis, and differentiation. The mix of development-related GO terms plus transcription-centric terms suggests a group of proteins involved in controlling gene expression during development, rather than a single, specific pathway. Confidence: Medium","confidence":"","size":10,"edges":15,"triangles":8,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035994","count":4},{"id":"GO:0000117","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007296","count":3},{"id":"GO:0034198","count":3}]},{"hash":"863107755755829160","title":"Sister Chromatid Cohesion & Spindle Checkpoint","description":"Top GO terms cluster around sister chromatid cohesion during mitosis and meiosis, centromeric cohesion, and the mitotic spindle assembly checkpoint signaling, including metaphase/anaphase transition. This suggests proteins in this cluster mainly function in chromosome segregation control and checkpoint signaling during cell division. A lone term on Cajal body organization is less representative of the core theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030576","count":1},{"id":"GO:0007091","count":1},{"id":"GO:0032837","count":1},{"id":"GO:0051754","count":1},{"id":"GO:0072480","count":1}]},{"hash":"478699347029465699","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":22,"triangles":27,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0006006","count":2}]},{"hash":"1809937478859670328","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by translation and ribosome biogenesis/export: translation, ribosomal large and small subunit biogenesis, and ribosomal subunit export from the nucleus, indicating a cohesive role in ribosome assembly and protein synthesis. Some related terms (cell division, septum assembly) appear as secondary processes but do not outweigh the central ribosome/translation theme. Confidence is high that this label captures the core function of the cluster.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000055","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0042274","count":2}]},{"hash":"288318310907370714","title":"Plant fatty acid transport and metabolism","description":"The cluster is dominated by GO terms for fatty acid transport and metabolism (long-, medium-, very long-chain fatty acids) and related energy-related processes, plus a term linking to seed germination, which in plants involves mobilization of seed lipids. The presence of phenylpropanoid metabolism also fits within plant metabolic networks that connect lipid-derived signals to growth processes. While some terms are obsolete or less plant-specific, the central theme of lipid transport/metabolism in a plant context is clear.","confidence":"High","size":10,"edges":19,"triangles":16,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1902987","count":6},{"id":"GO:0010030","count":5},{"id":"GO:0009234","count":5},{"id":"GO:0019427","count":5},{"id":"GO:0044539","count":5}]},{"hash":"2032080695789692948","title":"DNA replication and cell cycle maintenance","description":"This cluster is dominated by GO terms linked to DNA replication, mitotic cell cycle, and DNA repair, with supporting signals for oxidative stress response and apoptosis regulation, suggesting a core theme of genome maintenance and cell division. Some terms (peroxisome import, cytoskeleton organization, development) are more peripheral noise but do not override the primary signal. ","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0000278","count":7},{"id":"GO:0006281","count":7},{"id":"GO:0016558","count":5},{"id":"GO:0034599","count":5}]},{"hash":"1159880441615121655","title":"RNA Splicing Machinery","description":"Most of the top GO terms point to RNA processing and splicing: mRNA processing, RNA splicing, and spliceosomal tri-snRNP complex assembly. The presence of ubiquitination may reflect regulation of splicing factors or protein turnover within the spliceosome pathway. A few outliers exist, but the spliceosome/RNA-processing theme dominates, so the cluster likely represents spliceosome components and RNA-processing proteins.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0000244","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0072660","count":1}]},{"hash":"720115808067139592","title":"Phosphatidylserine biosynthesis","description":"This cluster shows a single GO term related to lipid biosynthesis (phosphatidylserine biosynthetic process), suggesting a potential but weak connection to phospholipid synthesis across the proteins. With only one annotation and limited enrichment signals (no triangles, modest connectivity), the label is tentative.","confidence":"Low","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006659","count":1}]},{"hash":"483217702666982915","title":"Diverse Metabolic Biosynthesis","description":"The terms point to a mix of metabolic and biosynthetic processes (inositol phosphate and purine metabolism, proteoglycan biosynthesis, lipid metabolism) plus some regulatory and stress-related aspects (dephosphorylation, anoxia, phosphate starvation). With no edges or clear single pathway linking them, it reads as a broad metabolic/biosynthetic cluster rather than a specific module.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071454","count":1},{"id":"GO:0016036","count":1},{"id":"GO:0060168","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0032958","count":1}]},{"hash":"1853080287890864320","title":"DNA replication and repair proteins","description":"This cluster centers on core replication activities (DNA replication initiation and pre-replicative complex assembly) and multiple DNA repair pathways (base-excision and nucleotide-excision repair), with supporting terms for protein repair/modification and oxidative stress response, suggesting a cohesive group of replication- and repair-related proteins, possibly dealing with maintenance under redox stress.","confidence":"High","size":10,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0030091","count":2}]},{"hash":"2113196300196680828","title":"Cell Cycle and Organelle Trafficking","description":"The top GO terms cluster around cell division and centriole-related processes, alongside vesicle trafficking and organelle maintenance (peroxisome import, SNARE disassembly, Golgi retention). Energy metabolism and protein turnover (ATP biosynthesis, FAD catabolism, proteolysis) likely support these proliferative and organelle-dynamics functions, giving a coherent theme of cell-cycle progression coupled with organelle dynamics.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0016558","count":2},{"id":"GO:0045053","count":2}]},{"hash":"51149605463843994","title":"Unknown","description":"The top GO terms span a broad, unrelated mix of processes (NF-kappaB signaling regulation, mRNA capping, nodulation, antibiotic biosynthesis, histone methylation, cobalamin and chlorophyll biosynthesis, rRNA modification, polyamine biosynthesis, cell growth). There isn't a clear, shared functional theme linking these proteins, so a cohesive label cannot be assigned.","confidence":"","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0009877","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0043985","count":2}]},{"hash":"1781208241132552988","title":"Cell cycle and DNA replication proteins","description":"This cluster is dominated by GO terms for meiotic/mitotic cell cycle, G1/S transition, DNA replication, and kinetochore localization, pointing to a core cell-cycle function. Other terms about synapse localization and developmental processes appear as broader or pleiotropic roles, but the strongest signal centers on cell-cycle machinery. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0051321","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0060079","count":3}]},{"hash":"298386546571204218","title":"Central carbon metabolism and lipid biosynthesis","description":"Top GO terms point to core metabolic pathways (glycolysis, gluconeogenesis, pyruvate to acetyl-CoA, 2-oxoglutarate, alanine and kynurenine catabolism) and long-chain fatty acid biosynthesis, suggesting a central metabolism and lipid biosynthesis theme. The presence of Notch signaling and protein homooligomerization hints at regulatory or structural protein interactions associated with these metabolic processes. Overall, the cluster seems to represent a central-carbon\u2013lipid synthesis module with some signaling/regulatory associations.","confidence":"Medium","size":10,"edges":22,"triangles":19,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042759","count":4},{"id":"GO:0033512","count":3},{"id":"GO:0007219","count":3},{"id":"GO:0097053","count":3},{"id":"GO:0042853","count":3}]},{"hash":"1672522749104162673","title":"Redox Homeostasis and Detoxification","description":"This cluster is driven by redox-related processes: cellular redox homeostasis, oxidant detoxification, removal of superoxide radicals, and peptidyl-cysteine oxidation. The presence of cytochrome complex assembly and regulation of stress-activated MAPK cascades, along with I-kappaB phosphorylation, suggests a link between redox balance and signaling. Additional terms like methylamine metabolism and regulation of germ cell proliferation may reflect broader metabolic or developmental connections, but the core theme centers on managing oxidative stress.","confidence":"High","size":10,"edges":42,"triangles":98,"max_degree":9,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0045454","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0030416","count":5},{"id":"GO:0055114","count":5},{"id":"GO:2000255","count":5}]},{"hash":"823861846307825838","title":"Unknown","description":"The GO terms span cell-cycle processes (DNA replication, mitotic sister chromatid cohesion) and a variety of transport/metabolism functions (drug transport, vitamin and taurine transport, fatty acid catabolism, cholesterol regulation) plus an immunology term (antigen processing via MHC I). With no edges or clear functional coherence linking these terms, there isn\u2019t a single unifying theme for this cluster. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0019885","count":2},{"id":"GO:1900753","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0071232","count":2}]},{"hash":"2205572333803701537","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":35,"triangles":60,"max_degree":9,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006284","count":5},{"id":"GO:0042493","count":5},{"id":"GO:0007568","count":5},{"id":"GO:0006296","count":4},{"id":"GO:0006310","count":4}]},{"hash":"1553165119129955969","title":"Calcineurin\u2013NFAT Calcium Signaling Proteins","description":"Top terms are dominated by calcium detection, dephosphorylation, and calcineurin-NFAT signaling, with regulatory links to xenobiotic response. This suggests a cluster of calcium-dependent phosphatases and NFAT pathway regulators; a few outliers (meiotic repair, EMT) exist, but the core theme is calcium-driven NFAT signaling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":5},{"id":"GO:0035690","count":3},{"id":"GO:0051531","count":3},{"id":"GO:0010780","count":2},{"id":"GO:0051037","count":2}]},{"hash":"1101358162774574986","title":"Immune and ECM remodeling processes","description":"This cluster features immune-related terms (T cell mediated cytotoxicity; bradykinin catabolic process) alongside tissue remodeling activities (collagen catabolic process; decidualization; lung branching morphogenesis) and hormonal signaling (cellular response to thyroid hormone stimulus), plus regulatory notes on catalytic activity. Together, these suggest proteins involved in dynamic tissue remodeling governed by immune and hormonal signals, rather than a single cohesive pathway. Some terms are obsolete, which lowers coherence, but the overarching theme of remodeling with signaling remains detectable.","confidence":"Medium","size":10,"edges":38,"triangles":75,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":5},{"id":"GO:0001913","count":5},{"id":"GO:0097067","count":5},{"id":"GO:0010815","count":5},{"id":"GO:0046697","count":5}]},{"hash":"2090426519142844397","title":"Cardiovascular development and muscle regeneration","description":"The cluster shows enrichment for heart development and vascularization terms (Notch signaling in secondary heart field cardioblast proliferation; sprouting angiogenesis) along with skeletal muscle regeneration and growth/cell cycle terms. This indicates a coherent theme of cardiovascular development with muscle regeneration and growth, with some membrane-trafficking terms present as ancillary functions. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072660","count":4},{"id":"GO:0035508","count":4},{"id":"GO:0043403","count":4},{"id":"GO:0000083","count":4},{"id":"GO:0016049","count":4}]},{"hash":"1731546982600323137","title":"Ion Transport and Cellular Homeostasis","description":"This cluster centers on membrane-associated ion transport and homeostasis, highlighted by proton transmembrane transport, sodium and potassium ion import/export, vacuolar acidification, and cell volume regulation, as well as salt-stress responses. The GO terms point to a cohesive theme of maintaining ionic balance and pH across membranes.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051595","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0006884","count":1},{"id":"GO:0086092","count":1}]},{"hash":"1851157213074270395","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning lipid transport and biosynthesis, defense and pathogenesis, endomembrane organization, sporulation-related processes, and unrelated developmental terms, with no clear single function tying the proteins together. This suggests no coherent shared role for the cluster beyond general membrane/organellar activity, so Unknown with no confidence.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006869","count":1},{"id":"GO:0034053","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0009246","count":1}]},{"hash":"2263895358358875662","title":"Muscle regeneration and heart/vascular development","description":"The set includes skeletal muscle tissue regeneration, Notch signaling in regulation of secondary heart field cardioblast proliferation, and sprouting angiogenesis in endothelial cells, all pointing to coordinated muscle repair with heart and vascular development. Other terms like cell growth and SNARE regulation are supportive cellular processes, but the dominant theme is regeneration and cardiovascular development.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072660","count":1},{"id":"GO:0035508","count":1},{"id":"GO:0043403","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0016049","count":1}]},{"hash":"2036156691961277117","title":"Muscle and cardiovascular development signals","description":"The terms point to developmental and regenerative processes in muscle and heart/vasculature (Notch signaling in heart field proliferation, angiogenesis, and skeletal muscle regeneration). General processes like cell growth and cell cycle support these tissues, while some terms are broader or more technical; overall, a cohesive theme of muscle/heart vascular development and regeneration emerges.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072660","count":1},{"id":"GO:0035508","count":1},{"id":"GO:0043403","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0016049","count":1}]},{"hash":"371875926691934830","title":"Membrane Transport and Sugar Metabolism","description":"The top GO terms cluster around transmembrane transport of small molecules (sodium, D-glucose, vitamin transport), sugar metabolism (fucose, lactose biosynthesis, glucose starvation response), and related nutrient processing (nitrate assimilation). These suggest a functional grouping of proteins involved in moving and processing sugars and related ions across membranes, rather than a single fixed pathway; hence the label emphasizes membrane transport plus carbohydrate metabolism. Some terms relate to growth or host interactions, but the strongest signal is transport/metabolism.","confidence":"Medium","size":9,"edges":24,"triangles":27,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1904728","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0006004","count":3},{"id":"GO:0042149","count":3}]},{"hash":"2002902519704707300","title":"Hematopoiesis and T cell differentiation","description":"The top GO terms converge on immune cell lineage development, including granulocyte differentiation, T cell differentiation in thymus, and hematopoietic stem cell proliferation, indicating a focus on blood cell formation and immune system development. A few terms are obsolete or relate to broad cell-cycle processes, but the dominant signal is hematopoietic/immune differentiation.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030851","count":1},{"id":"GO:0046638","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0033077","count":1},{"id":"GO:0071425","count":1}]},{"hash":"2172201923276213697","title":"RNA processing and gene expression regulation","description":"This cluster centers on multiple layers of RNA-based gene expression control: miRNA- and ncRNA-mediated silencing, transcription regulation, mRNA splicing and spliceosome regulation, mRNA modification, and translation reinitiation control. The shared theme is post-transcriptional and translational regulation that modulates gene expression rather than a single enzymatic pathway.","confidence":"Medium","size":9,"edges":9,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0031047","count":1}]},{"hash":"1608656605590515018","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006369","count":6},{"id":"GO:0000464","count":4},{"id":"GO:0034475","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0034476","count":4}]},{"hash":"2149169797588656417","title":"Ribosome Biogenesis","description":"The strongest signals are maturation of 5.8S and LSU rRNA, pointing to ribosomal RNA processing and ribosome assembly; thus the cluster most likely reflects factors involved in ribosome biogenesis, with other annotations (mitochondrial regulation, DNA processes) as secondary or collateral associations.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:1903955","count":2},{"id":"GO:1903146","count":2},{"id":"GO:0000470","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1259366503068206726","title":"Embryonic development and adherens junctions","description":"These proteins cluster around developmental processes such as ectoderm development, dorsal identity, lung induction, and root development, along with adherens junction assembly and regulation of EMT/embryonic cell cycles. The shared theme appears to be developmental patterning and epithelial organization, with chromatin remodeling linked to transcription initiation reinforcing gene regulation during development. While some terms span different organisms, the overarching connection is development-focused regulation of cell adhesion and tissue patterning.","confidence":"Medium","size":9,"edges":25,"triangles":34,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060492","count":3},{"id":"GO:0048096","count":3},{"id":"GO:0045976","count":3},{"id":"GO:0003340","count":3},{"id":"GO:0034333","count":3}]},{"hash":"987552154055227545","title":"RNA processing and ncRNA-mediated gene silencing","description":"The cluster is enriched for RNA-centric terms: regulatory ncRNA-mediated gene silencing, positive regulation of mRNA splicing via the spliceosome, and mRNA export, along with rRNA maturation. These collectively point to proteins involved in RNA processing and post-transcriptional regulation of gene expression, rather than signaling or structural roles.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:1901407","count":5},{"id":"GO:0042766","count":4},{"id":"GO:0000463","count":4}]},{"hash":"1736247687705370773","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007032","count":2},{"id":"GO:0072752","count":1},{"id":"GO:0034414","count":1},{"id":"GO:0038202","count":1},{"id":"GO:1903608","count":1}]},{"hash":"1453278137655587607","title":"mRNA Splicing Regulation and Processing","description":"This cluster is characterized by spliceosome-dependent mRNA processing terms: splice-site recognition, regulation of alternative splicing via the spliceosome, and negative regulation of splicing, plus broader mRNA modification and poly(A) tail regulation. The inclusion of translation reinitiation and regulatory ncRNA-mediated gene silencing suggests a broader post-transcriptional control layer affecting mRNA maturation and translation. Overall, the proteins likely function in splicing and processing regulation rather than transcriptional control.","confidence":"High","size":9,"edges":18,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0000381","count":2}]},{"hash":"1561535434810288481","title":"Ribosome Biogenesis and RNA Processing","description":"These proteins collectively map to processes of ribosome biogenesis, rRNA maturation, and general RNA metabolism, with strong emphasis on 90S preribosome assembly and cytoplasmic translation. Some entries also touch on mRNA processing and miRNA regulation, reflecting broader RNA-processing roles within the same cellular machinery.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1666759084463385466","title":"Hematopoiesis and Immune Signaling","description":"This cluster centers on hematopoietic development and immune-related signaling, with terms for hemopoiesis, DNA replication (proliferation), cytokine responses (VEGF, GM-CSF), T cell activation/death, and cell migration, all connected through PI3K-AKT signaling and tissue remodeling processes like hyaluronan metabolism and placental development. The mix suggests a module of blood/immune cell development and dynamics rather than a single narrow function.","confidence":"Medium","size":9,"edges":15,"triangles":9,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0035924","count":2},{"id":"GO:0006924","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1457803648355517469","title":"Meiotic DNA replication and repair","description":"The dominant GO terms point to DNA replication and meiotic double-strand break formation and repair (including SDSA and mitochondrial HR), suggesting a core role in DNA maintenance during meiosis. Some other terms (calcium signaling, EMT, lung development) appear less tightly connected and may reflect multifunctional annotations or artifacts. Overall, the strongest signal supports a meiotic DNA replication/repair theme. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0010780","count":2},{"id":"GO:0051037","count":2},{"id":"GO:0010791","count":2},{"id":"GO:0033173","count":2}]},{"hash":"263282731793071504","title":"Nuclear RNA processing and ribosome biogenesis","description":"This cluster centers on RNA maturation, processing, and export, plus ribosome biogenesis within the nucleus. GO terms point to splicing (mRNA via spliceosome), tRNA processing, mRNA export, ribosomal subunit export, ribosome biogenesis, and transcriptional regulation, all core to gene expression and nuclear RNA handling, with a minor outlier term on lipid droplets. Overall, the group reflects coordinated RNA processing and ribosome assembly activities.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0000055","count":2}]},{"hash":"1487978611346939960","title":"Fungal metabolism and biofilm formation","description":"The cluster centers on fungal metabolism and biofilm behavior: carbohydrate catabolism (cellulose, mannan, xylan), fungal-type cell wall beta-glucan remodeling, ergosteryl glucoside turnover, and pyridoxine biosynthesis, plus biofilm formation on inanimate substrates and in host. A mitochondrial complex IV assembly term suggests general energy metabolism in fungi as well. This cohesive theme supports a fungal metabolic/biofilm focus. ","confidence":"Medium","size":9,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":1},{"id":"GO:0030245","count":1},{"id":"GO:0046355","count":1},{"id":"GO:0070879","count":1},{"id":"GO:0044011","count":1}]},{"hash":"634826816382304222","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":26,"triangles":37,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0071548","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0060416","count":2}]},{"hash":"26262927176545814","title":"Mitochondrial Energy Metabolism and Stress Response","description":"The top terms are dominated by mitochondrial processes (ATP and CoA transport, membrane fission, genome maintenance) and energy/ stress responses (amino acid starvation, insulin signaling, adaptive thermogenesis, superoxide response), suggesting a cluster centered on mitochondrial energy metabolism and adaptive stress responses.","confidence":"High","size":9,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":7},{"id":"GO:0034198","count":7},{"id":"GO:0032869","count":7},{"id":"GO:1990845","count":7},{"id":"GO:0035349","count":7}]},{"hash":"357609242896411795","title":"Mitotic Phosphorylation Regulation","description":"This cluster is best captured by a phosphorylation-centric theme: there are GO terms for G2/M transition (mitotic cell cycle) and for positive regulation of serine/threonine kinase activity and peptidyl-threonine phosphorylation, suggesting regulation of kinase activity during mitosis. While some terms (phototransduction, terminal web assembly) appear, the strongest shared signal is phosphorylation-driven control of the cell cycle. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0043950","count":1},{"id":"GO:0071574","count":1},{"id":"GO:0086004","count":1},{"id":"GO:0071902","count":1}]},{"hash":"2237757939177113511","title":"Unknown","description":"The top GO terms span diverse metabolic routes (pyruvate biosynthesis, glyoxylate and various amino acid catabolic processes, menaquinone biosynthesis) and include an outlier Notch signaling term, with several obsolete annotations. There isn\u2019t a single cohesive function that clearly ties all proteins together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":3},{"id":"GO:0032869","count":2},{"id":"GO:0033512","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0007219","count":2}]},{"hash":"182633519459087005","title":"Neural development and pain response","description":"The cluster shows strong representation of nervous system and brain development terms (cerebral cortex development, embryonic cranial skeleton morphogenesis, cortical actin cytoskeleton organization) along with nociception-related terms (sensory perception of pain, behavioral response to formalin-induced pain). This suggests the proteins are involved in neural development with links to pain signaling, rather than a single metabolic or cellular process. Some related terms are broader development categories, but the core theme appears to be neural ontogeny and pain response.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0019233","count":5},{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0060440","count":3}]},{"hash":"511748050502813771","title":"Mitotic spindle assembly and cytokinesis","description":"The top GO terms are dominated by cell cycle, mitosis, and cytokinesis-related processes (mitotic spindle pole body duplication, mitotic cytokinesis, spindle midzone assembly, microtubule nucleation, division site positioning), indicating proteins involved in organizing the mitotic spindle and completing cell division. A few terms like neuron migration or chloroplast fission hint at broader cytoskeletal roles or organelle division, but the prevailing signal is mitosis/cytokinesis machinery.","confidence":"Medium","size":9,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001764","count":2},{"id":"GO:1903087","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0010020","count":2}]},{"hash":"1742053137130182980","title":"Brain development and GABA metabolism","description":"The cluster is enriched for neural-related terms: nucleus accumbens development, neuromuscular balance, and especially GABA catabolic process, suggesting a focus on brain development and GABA neurotransmitter regulation. Some other terms are broader development terms or obsolete, but the neural signaling theme appears strongest.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0050885","count":9},{"id":"GO:0019544","count":9},{"id":"GO:0001568","count":9},{"id":"GO:0055129","count":9},{"id":"GO:0009450","count":9}]},{"hash":"1205642763533713652","title":"Peroxisomal Fatty Acid Oxidation and Glyoxysome Pathways","description":"The cluster is dominated by terms tied to peroxisomal metabolism: fatty acid beta-oxidation, glyoxysome organization, and ketone body catabolism, all hallmarks of peroxisomal/glyoxylate cycle activity. Additional terms related to starvation and hormone responses reflect regulation of this energy metabolism under stress, while other terms like sporulation or PHB biosynthesis suggest broader, context-dependent metabolic capabilities but do not outweigh the core peroxisomal theme.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042594","count":5},{"id":"GO:0001889","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0019619","count":4},{"id":"GO:0030435","count":3}]},{"hash":"1568401817800863693","title":"Unknown","description":"The GO terms are pulled from a broad mix of processes (metabolic, cilium-related, plant-specific biosynthesis/hormone signaling, retinal development, adipose tissue development, and cell division) with several obsolete terms. There isn\u2019t a single coherent biological theme tying these proteins together, so a concise, representative label isn\u2019t justified beyond Unknown.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006108","count":3},{"id":"GO:1905515","count":2},{"id":"GO:2000531","count":2},{"id":"GO:1903646","count":2},{"id":"GO:1902325","count":2}]},{"hash":"1223949739942488052","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051259","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0035719","count":2},{"id":"GO:0031204","count":2}]},{"hash":"1839355441706703856","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0044656","count":1},{"id":"GO:0032796","count":1}]},{"hash":"1880949398295809457","title":"Triglyceride catabolism and lipid remodeling","description":"The cluster is dominated by GO terms for triglyceride catabolic processes, triglyceride mobilization, and lipid remodeling (phosphatidylcholine and phosphatidylethanolamine catabolism), indicating a core theme of triglyceride breakdown and lipid turnover, with other terms (transcription-related) being much less represented. This supports a specific label around triglyceride metabolism and lipid remodeling.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":3},{"id":"GO:0046827","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0036153","count":2}]},{"hash":"296006091206468451","title":"Unknown","description":"The terms are highly diverse, spanning cell cycle regulation, metabolic/insulin signaling, immune signaling, neural development, and organ formation, with no single shared function to cohesively label the cluster.","confidence":"","size":9,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034501","count":9},{"id":"GO:0045736","count":9},{"id":"GO:2001275","count":8},{"id":"GO:0050852","count":8},{"id":"GO:0008286","count":8}]},{"hash":"1112485937283062862","title":"Secondary Metabolite Biosynthesis","description":"The top GO terms point to biosynthetic and catabolic processes for a variety of metabolites (antibiotics, tropane alkaloids, phylloquinone, mycolic acids, tetrahydrobiopterin) and related transcription regulation. While one term (lung development) is an outlier, the dominant signal is metabolic pathway activity across diverse secondary metabolites, suggesting a cluster of biosynthetic enzymes and regulatory proteins. ","confidence":"Medium","size":9,"edges":9,"triangles":5,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030324","count":5},{"id":"GO:0008207","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0009710","count":4}]},{"hash":"2059906178487226196","title":"Carbohydrate Transport and Metabolism","description":"The GO terms cluster around transmembrane transport and metabolism of carbohydrates and related nutrients (D-glucose and lactose transport, fucose metabolism, vitamin transport), suggesting a function focused on sugar handling and carbohydrate utilization. Some terms reference broader nutrient transport (sodium ion, nitrate assimilation) or peripheral regulatory processes, but the sugar-related terms bias toward carbohydrate transport/metabolism.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904728","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0042149","count":1}]},{"hash":"196236760360666065","title":"Transcriptional Regulation and Cell Cycle Control","description":"Dominant GO terms point to nuclear gene expression control: DNA-templated transcription, its regulation, and mRNA processing, plus mitotic cell cycle and CDK activity regulation. This suggests proteins in this cluster function primarily in transcriptional control and cell-cycle progression, with additional hints toward differentiation signaling (fat cell differentiation) and telomere maintenance; some bacterial-like terms may reflect annotation noise or multifunctionality.","confidence":"High","size":9,"edges":21,"triangles":20,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0097011","count":6},{"id":"GO:0009401","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0000160","count":5}]},{"hash":"872202732249853679","title":"Mitosis and Cytoskeleton Regulation","description":"The cluster shows strong signals for mitotic cell cycle and G2/M transition, plus microtubule nucleation, with supporting terms for Rho signaling, phosphatidylinositol signaling, and Golgi organization. This points to a cohesive role in coordinating cell division with cytoskeletal dynamics and membrane/organelle remodeling.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0010800","count":2},{"id":"GO:0000086","count":2},{"id":"GO:1903358","count":2},{"id":"GO:0035023","count":2}]},{"hash":"673432744779279029","title":"Ion and amino acid membrane transport","description":"Top GO terms show ion transport (manganese, calcium, potassium) and import of several amino acids (D-aspartate, threonine, serine, glutamate), plus a general transmembrane transport term and membrane hyperpolarization. This combination indicates a cluster of membrane transport proteins that move ions and amino acids across membranes, with potential relevance to membrane potential and neurotransmitter-related metabolism (GABA biosynthesis).","confidence":"High","size":9,"edges":16,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":4},{"id":"GO:0098703","count":4},{"id":"GO:0071805","count":3},{"id":"GO:0060081","count":3},{"id":"GO:0070779","count":2}]},{"hash":"1230566243123413896","title":"Unknown","description":"The GO terms are a highly diverse mix, spanning Notch signaling, amino acid catabolism, gas vesicle organization, peroxisome import, Golgi retention, SNARE disassembly, DNA replication checkpoints, ATP biosynthesis, and centriole elongation, with no single cohesive function tying them together. This suggests there isn't a clear, common biological role for the cluster.","confidence":"","size":9,"edges":22,"triangles":25,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007219","count":3},{"id":"GO:0097053","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0031412","count":2},{"id":"GO:0016558","count":2}]},{"hash":"104386358843471286","title":"Craniofacial cartilage and neural crest morphogenesis","description":"The top GO terms point to cartilage development and morphogenesis, neural crest cell migration, and craniofacial/brain morphogenesis (roof of mouth, cochlea, corpus callosum), indicating roles in craniofacial cartilage formation and neural crest\u2013derived tissue patterning. A few terms like interferon regulation and placental development appear minor, likely incidental to the main craniofacial/neural crest theme.","confidence":"High","size":9,"edges":27,"triangles":38,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051216","count":2},{"id":"GO:0021846","count":2},{"id":"GO:0001755","count":2},{"id":"GO:0060021","count":2},{"id":"GO:0090103","count":2}]},{"hash":"1689649691371993787","title":"Cerebral cortex development and actin dynamics","description":"The proteins show a clear link to brain development and cortical structure (cerebral cortex development, embryonic cranial skeleton morphogenesis, cortical actin cytoskeleton organization), indicating a coordinated role in neural development with actin remodeling, even though a few terms relate to unrelated processes like lipid biosynthesis or sperm capacitation that may reflect broader cellular functions. ","confidence":"Medium","size":9,"edges":14,"triangles":6,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0006655","count":2},{"id":"GO:0060440","count":1},{"id":"GO:2001233","count":1}]},{"hash":"2040359126395620892","title":"Nuclear chromatin modification and RNA processing","description":"The cluster shows histone modification terms (acetylation/phosphorylation) indicating chromatin regulation, plus RNA processing and ribosome export terms, all pointing to nucleus-centric gene expression processes. Some terms are obsolete, but the recurring theme centers on chromatin modification and RNA processing within the nucleus.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043987","count":1},{"id":"GO:0044154","count":1},{"id":"GO:0043967","count":1},{"id":"GO:0043970","count":1},{"id":"GO:0090043","count":1}]},{"hash":"761614269535391363","title":"Oxidative and metal stress response","description":"The proteins are enriched for GO terms describing cellular responses to oxidative and chemical/metal stressors, including gamma radiation, diamide, arsenite, cadmium, and singlet oxygen, suggesting a shared role in environmental stress response. Some terms appear obsolete and one unrelated term (embryonic placenta development) may reflect annotation noise, but the dominant signal supports a cohesive oxidative/chemical stress response theme.","confidence":"Medium","size":9,"edges":7,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":2},{"id":"GO:1900462","count":2},{"id":"GO:0072738","count":2},{"id":"GO:1903936","count":2},{"id":"GO:0043497","count":2}]},{"hash":"1165130942337968594","title":"Cardiac Electrophysiology and Stress Reflexes","description":"The cluster centers on cardiac electrical activity, with terms for atrial and His bundle action potential depolarization/repolarization, complemented by reflexive and temperature/stress responses (startle, response to cold, cellular response to temperature). The presence of GABA secretion suggests neural regulation of heart function, tying the electrical and autonomic/neuronal signals together into a coherent theme.","confidence":"Medium","size":9,"edges":18,"triangles":14,"max_degree":8,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:1903759","count":5},{"id":"GO:0060372","count":4},{"id":"GO:0003031","count":4},{"id":"GO:0071502","count":4},{"id":"GO:0086048","count":4}]},{"hash":"906059103964040479","title":"Chromatin remodeling and epigenetic regulation","description":"The terms strongly point to chromatin organization, including nucleosome assembly and chromatin remodeling, with several histone modification/epigenetic regulation references. Although a few metabolic terms appear, the core signal remains chromatin dynamics and epigenetic control, suggesting this cluster centers on chromatin-related functions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":2},{"id":"GO:0098532","count":2},{"id":"GO:0045857","count":2},{"id":"GO:0006334","count":2},{"id":"GO:2000616","count":2}]},{"hash":"765776617289582967","title":"Ubiquitin-Dependent Proteolysis and Cell Cycle Regulation","description":"The terms cluster around ubiquitin-dependent protein catabolic processes (e.g., SCF-dependent degradation) and cell-cycle control events such as meiotic chromatid segregation and metaphase/anaphase transitions. Additional terms involve turnover of chromatin and receptors (histones, Wnt receptor) and regulation of apoptosis and signaling (I-kappaB). The common thread is targeted proteolysis governing cell cycle progression and signaling pathways, making this a coherent proteolysis-driven cell cycle/signaling cluster.","confidence":"High","size":9,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0031146","count":4},{"id":"GO:0051759","count":3},{"id":"GO:1902104","count":3},{"id":"GO:0038018","count":3}]},{"hash":"1303407704610840567","title":"Neuronal amino acid transport and synaptic signaling","description":"The top GO terms point to membrane hyperpolarization, transmembrane transport, and chemical synaptic transmission, combined with transport of several amino acids (D-aspartate, threonine, serine, L-glutamate) and GABA biosynthesis. This pattern suggests proteins involved in neuronal signaling and amino acid transport/metabolism, with thermosensory behavior also aligning with sensory neuron function. A few outliers (like bile acid secretion) may reflect annotation noise, but the dominant theme is neuronal transport and synaptic activity.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0060081","count":3},{"id":"GO:0055085","count":3},{"id":"GO:0040040","count":3},{"id":"GO:0032782","count":2},{"id":"GO:0007268","count":2}]},{"hash":"1640068328973764733","title":"Unknown","description":"The GO terms are diverse, covering transport (calcium and amino acid export), multiple catabolic pathways, protein demethylation, matrix remodeling, apoptosis, and proliferation regulation, with no single shared function uniting the proteins.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":1},{"id":"GO:0032973","count":1},{"id":"GO:0010710","count":1},{"id":"GO:1990577","count":1},{"id":"GO:0030245","count":1}]},{"hash":"1069873581569457474","title":"Insect development and morphogenesis","description":"The top GO terms point to diverse insect developmental processes, including organ/tissue morphogenesis (Malpighian tubule, eye, mushroom body), larval development and molting (instar development, cuticle biosynthesis), and germ-band dynamics. A common theme is transcriptional regulation of developmental programs guiding morphogenesis in insects, making this cluster representative of insect development and morphogenesis rather than a single metabolic function.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007443","count":1},{"id":"GO:0007458","count":1},{"id":"GO:0016319","count":1},{"id":"GO:0007591","count":1}]},{"hash":"1500808902737049335","title":"Actin Cytoskeleton Regulation","description":"The top GO terms show a clear emphasis on Rho signaling regulation, actin cytoskeleton organization, and GTPase activation, plus microvillus assembly. Collectively they suggest proteins involved in cytoskeletal dynamics and signal transduction that governs cell shape and movement. Other terms like apoptosis, barrier establishment, sensory perception, and mitochondrial fission appear less central to the core function, likely reflecting multifunctionality or context-specific roles. Overall the cluster best fits actin cytoskeleton regulation and related GTPase signaling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0007605","count":2},{"id":"GO:0019933","count":2},{"id":"GO:2000670","count":2},{"id":"GO:0090557","count":2}]},{"hash":"162658456560907631","title":"Immune and vascular inflammatory signaling","description":"The Top Terms show immune-related processes (adaptive immune response, MHC I antigen processing) alongside inflammation and vascular regulation (leukotriene biosynthesis, angiogenesis, angiotensin maturation, renin-angiotensin\u2013dependent blood pressure regulation). There is also cell signaling and differentiation, which can tie immune responses to tissue remodeling. The combination suggests a coherent theme where immune activity intersects with vascular/inflammatory pathways, rather than unrelated processes, justifying a label that captures immune\u2013vascular inflammation signaling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0019885","count":1},{"id":"GO:0007267","count":1},{"id":"GO:0003081","count":1},{"id":"GO:0030154","count":1}]},{"hash":"1953215559059398411","title":"Ribosome biogenesis and RNA modification","description":"This cluster centers on ribosome assembly and rRNA maturation, including LSU preribosome formation, LSU rRNA maturation, and cytosolic ribosome assembly, with RNA base methylation and wobble cytosine methylation as supporting signals of RNA processing; a few terms like transcription regulation or iron response may be peripheral rather than core drivers. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902626","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0070475","count":1},{"id":"GO:0002127","count":1},{"id":"GO:0042256","count":1}]},{"hash":"1217757085346588912","title":"Neuronal synaptic vesicle cycling and signaling","description":"The cluster is dominated by GO terms for regulation of synaptic vesicle exocytosis and endocytosis, endosomal vesicle fusion, and excitatory postsynaptic potential, indicating a neuronal synaptic transmission role. Substantia nigra development and filopodium assembly reinforce a brain/neuronal context, though a few terms (mitotic cell cycle, ossification) are less directly connected. ","confidence":"Medium","size":8,"edges":9,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1900242","count":2},{"id":"GO:0021762","count":2}]},{"hash":"754844684053499189","title":"Cardiovascular development and angiogenesis","description":"This cluster shows a primary signal for heart development (GO:0007507) and VEGF-related signaling (GO:0035924), pointing to cardiovascular development and angiogenesis. Supporting terms on morphogenesis and signaling (filopodium assembly, basement membrane morphogenesis, GPCR signaling, Ras regulation) reinforce a developmental/vascular theme, though some immune and metabolic terms are present but less connected. Confidence: Medium","confidence":"","size":8,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0035924","count":1},{"id":"GO:0007213","count":1},{"id":"GO:0006924","count":1},{"id":"GO:0030259","count":1}]},{"hash":"1027975084196084907","title":"Diverse bacterial metabolism and metal ion transport","description":"The terms cluster around core metabolic biosynthesis (amino acids like isoleucine, proline, pantothenate), the pentose phosphate shunt, and basic translation, along with iron and copper ion import and a sporulation-related process. This suggests a broad theme of bacterial metabolism with nutrient acquisition, rather than a single, tightly defined pathway. Some terms are obsolete or very general, which lowers the specificity, hence a Medium confidence level.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0009051","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0098706","count":1}]},{"hash":"1477091295886056111","title":"Neural Development and Synaptic Signaling","description":"Top terms center on brain development and synaptic activity, notably substantia nigra development, neuroblast proliferation, and excitatory postsynaptic potentials, with smoothened signaling linking to neural patterning. While vesicle transport and xenobiotic response features appear, the neural development/synaptic theme is dominant, justifying this label as representative of the cluster.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0035690","count":2}]},{"hash":"2167310127574146624","title":"Unknown","description":"The GO terms are highly diverse (neural development, Hedgehog signaling, autophagy, learning, vesicle transport, iron transport, epithelial polarity, and liver development) with only single-term representation and a single-edge cluster, offering no clear cohesive function. Therefore, Unknown with no confidence is most appropriate.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021943","count":1},{"id":"GO:0007224","count":1},{"id":"GO:0034497","count":1},{"id":"GO:0007612","count":1},{"id":"GO:1902953","count":1}]},{"hash":"2051935540322059445","title":"Synaptic Transmission and Plasticity","description":"GO terms mainly point to neuronal signaling and memory-related plasticity, including neurotransmitter secretion, synaptic vesicle exocytosis, calcium signaling, and long-term potentiation. While VEGF signaling terms appear, the dominant theme centers on synaptic function and memory formation, rather than vascular growth. Therefore, the cluster is best described as Synaptic Transmission and Plasticity.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007613","count":2},{"id":"GO:0001302","count":2},{"id":"GO:0036324","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0030948","count":2}]},{"hash":"297474145570440118","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":23,"triangles":32,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0034475","count":3},{"id":"GO:0042273","count":3}]},{"hash":"525082538427697052","title":"RNA processing and chromatin remodeling","description":"This cluster shows enrichment for RNA-based regulation (regulatory ncRNA silencing, mRNA splicing regulation, rRNA maturation) and chromatin dynamics (nucleosome mobilization/positioning), with a few terms related to DNA/viral replication, suggesting a general theme of nucleic acid processing and chromatin regulation. ","confidence":"Medium","size":8,"edges":23,"triangles":32,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0019079","count":4},{"id":"GO:0042766","count":3}]},{"hash":"1778869862198641558","title":"Unknown","description":"The top GO terms span lipid metabolism (ergosterol and unsaturated fatty acid biosynthesis) and various nitrogen and signaling processes, plus disparate developmental/tissue-specific functions, with no clear single function linking all proteins. There isn't a coherent shared function here, so I label the cluster Unknown.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":3},{"id":"GO:0050679","count":2},{"id":"GO:0032024","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0032286","count":2}]},{"hash":"363779550674604040","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0019079","count":4},{"id":"GO:0034475","count":3}]},{"hash":"1945865979745754262","title":"Unknown","description":"The GO terms are heterogeneous, spanning kinase activity and phosphorylation regulation, monoubiquitination, phototransduction, cellular localization, cytoskeletal/terminal web assembly, cardiac muscle contraction, and cell cycle progression. There isn\u2019t a single cohesive function uniting these proteins, so no intuitive, specific label can be assigned.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043950","count":1},{"id":"GO:0071574","count":1},{"id":"GO:0086004","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0007602","count":1}]},{"hash":"357446278192569218","title":"Mitochondrial transcription and Complex IV assembly","description":"The GO terms show a clear focus on mitochondrial gene expression (mitochondrial transcription, transcription initiation at mitochondrial promoter) and the assembly/ regulation of the respiratory chain (Complex IV/cytochrome c oxidase activity), pointing to a theme of mitochondrial transcription and oxidative phosphorylation assembly.","confidence":"High","size":8,"edges":23,"triangles":33,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0008535","count":1},{"id":"GO:1904960","count":1},{"id":"GO:0033132","count":1},{"id":"GO:0039695","count":1},{"id":"GO:0006390","count":1}]},{"hash":"1841133563751152881","title":"Metal Ion Transport and Homeostasis","description":"The top GO terms are dominated by metal ion transmembrane transport and homeostasis (cadmium, iron, cobalt, manganese, aluminum), suggesting a cohesive function in metal ion handling. A small subset references cytokine production and Th1 regulation, which may indicate secondary roles or annotation noise, but the core signal is metal ion transport/homeostasis.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":1},{"id":"GO:0070627","count":1},{"id":"GO:0006876","count":1},{"id":"GO:0002827","count":1},{"id":"GO:0006877","count":1}]},{"hash":"1391363575074440754","title":"Glutathione metabolism and redox detoxification","description":"The cluster shows enrichment for glutathione metabolic process and cellular oxidant detoxification, which point to antioxidant and redox-related roles as the dominant theme. Other terms present (some marked obsolete) are scattered and less representative of the core function, suggesting a primary redox/detox signature despite heterogeneity. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006749","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006212","count":2},{"id":"GO:1903779","count":1}]},{"hash":"1825691632398643808","title":"Meiosis-linked DSB repair and calcium signaling","description":"The cluster is enriched for meiotic double-strand break formation and repair pathways (DSB formation, SDSA processing) and even mitochondrial DSB repair, suggesting a core focus on meiotic DNA damage response. Calcium signaling terms (calcium detection, calcineurin-NFAT) accompany these processes, supporting a link between DNA repair and calcium-mediated signaling; additional terms related to transcription termination and development may reflect broader pleiotropy but do not override the main meiotic repair signal.","confidence":"Medium","size":8,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010780","count":2},{"id":"GO:0051037","count":2},{"id":"GO:0010791","count":2},{"id":"GO:0033173","count":2},{"id":"GO:0005513","count":2}]},{"hash":"1359338346252605316","title":"Unknown","description":"The terms are highly diverse, spanning DNA replication, neural development, fungal cell wall biosynthesis, cell morphogenesis, stress and apoptosis regulation, metal ion handling, and membrane protein targeting. There is no clear, cohesive theme tying these functions together, so a single descriptive label cannot be confidently assigned.","confidence":"","size":8,"edges":15,"triangles":8,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0021510","count":2},{"id":"GO:0070880","count":1},{"id":"GO:0000902","count":1},{"id":"GO:1903382","count":1}]},{"hash":"1296800511434342751","title":"Neural development and transcription regulation","description":"The cluster shows enrichment for mRNA processing and DNA-templated transcription, along with terms tied to cerebral cortex development, embryonic cranial morphogenesis, and cortical actin cytoskeleton organization. This pattern suggests proteins involved in gene expression regulation during brain development and neural differentiation, with supporting roles in cytoskeletal dynamics and signaling (phosphorylation) that shape neural morphogenesis and lineage decisions.","confidence":"Medium","size":8,"edges":8,"triangles":5,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0060440","count":2},{"id":"GO:2001233","count":2},{"id":"GO:0061368","count":2}]},{"hash":"59772165205724189","title":"Plasma membrane amino acid transport","description":"This cluster is dominated by GO terms for importing various amino acids across the plasma membrane (L-lysine, L-arginine, L-ornithine, methionine, D-alanine, D-serine), indicating a membrane transport/uptake theme. Additional terms touch on arginine metabolism and nitric oxide production, which can connect metabolically to arginine transport, and a couple trafficking-related terms are present but secondary. Overall, the common thread is amino acid import at the plasma membrane.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002537","count":1},{"id":"GO:0042941","count":1},{"id":"GO:0097639","count":1},{"id":"GO:0044690","count":1},{"id":"GO:0006527","count":1}]},{"hash":"267457409982967288","title":"Protein quality control and stress response","description":"The GO terms cluster around proteostasis and cellular stress handling: ER-associated degradation (ERAD) maintenance, protein deglycosylation, autoubiquitination, sumoylation, mitophagy, and regulation of endocytosis, with additional hints from transcription regulation and cell-cycle related processes. Together these suggest a group of proteins involved in protein homeostasis, turnover, and trafficking under stress conditions. While some terms are peripheral (spindle pole body duplication, insecticide response), the central theme aligns with quality control and stress-responsive pathways.","confidence":"Medium","size":8,"edges":11,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006357","count":3},{"id":"GO:1904378","count":2},{"id":"GO:0030474","count":2},{"id":"GO:0006517","count":2},{"id":"GO:0000423","count":2}]},{"hash":"417688439233176476","title":"NF-kappaB Signaling and Transcription Regulators","description":"The top GO terms point to regulators of transcription and signaling, notably positive regulation of DNA binding, DNA-templated transcription, and canonical NF-kappaB signaling, with kinase activity modulation as a related axis. Peripheral terms like phototransduction and cardiac contraction are present but do not redefine the core theme, which centers on transcriptional regulation and signaling control.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043388","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043950","count":2},{"id":"GO:0071574","count":2}]},{"hash":"566196468774453066","title":"Developmental transcription and ER stress signaling","description":"The cluster shows a strong representation of developmental processes (multicellular organism development, neural tube closure, skeletal system development) and DNA-templated transcription, along with an ER stress\u2013related apoptotic signaling term. This combination suggests a core theme of developmental regulation linked to transcription, with a component of ER stress response.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070059","count":3}]},{"hash":"1539562311967899533","title":"Chitin-based Cuticle Development and Ecdysis","description":"Most GO terms in this cluster point to chitin-containing cuticle biology and molting (ecdysis): ecdysis, chitin-based cuticle, chitin catabolic process, and chitin-based cuticle development. The remaining terms relate to immune signaling and general development, which may reflect annotation noise, but the core signal supports cuticle formation and molting.","confidence":"Medium","size":8,"edges":15,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0018990","count":1},{"id":"GO:0070741","count":1},{"id":"GO:0051216","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0006032","count":1}]},{"hash":"1057329036982951142","title":"Neural signaling and membrane excitability","description":"The cluster\u2019s top GO terms center on nervous system functions and cellular excitability: sensory perception (pain), responses to temperature and cold, CO2 detection, startle response, and GABA secretion, along with membrane potential dynamics (hyperpolarization, depolarization, and atrial/His bundle repolarization). This combination points to proteins involved in neural signaling and electrical activity, with a secondary link to cardiac membrane regulation. The broad developmental term is less informative for the core theme, so the main interpretation is neural signaling and membrane excitability.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0019233","count":7},{"id":"GO:0060081","count":6},{"id":"GO:0060372","count":5},{"id":"GO:0003031","count":5}]},{"hash":"1937368677467957199","title":"Brain development and cortical morphogenesis","description":"The top GO terms cluster around brain and cranial development, including cerebral cortex development, hippocampus development, orbitofrontal cortex development (FGFR signaling), and cortical actin cytoskeleton organization, with accompanying cranial skeleton morphogenesis and embryonic development terms. Although a few non-brain terms appear (e.g., trachea formation), the dominant theme is neural development and cortex formation, suggesting these proteins function together in brain development and cortical structuring.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":7},{"id":"GO:2001233","count":7},{"id":"GO:0061368","count":7},{"id":"GO:0030866","count":7},{"id":"GO:0048701","count":7}]},{"hash":"1245383120855080604","title":"Neural development and brain morphogenesis","description":"Top terms emphasize cerebral cortex development, hippocampus development, cortical actin cytoskeleton organization, embryonic cranial skeleton morphogenesis, and related developmental processes, with additional signals related to stem cell differentiation and cytoskeletal regulation. This points to a cluster focused on neural development and brain structure formation, spanning cortical and hippocampal formation and craniofacial morphogenesis, rather than unrelated pathways.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007100","count":7},{"id":"GO:0060440","count":6},{"id":"GO:2001233","count":6},{"id":"GO:0061368","count":6},{"id":"GO:0030866","count":6}]},{"hash":"1516667589227207135","title":"GPCR-Driven Angiogenic Signaling and Filopodium Dynamics","description":"The top GO terms cluster around GPCR signaling (thrombin-activated receptor signaling; acetylcholine receptor signaling) and cellular responses to VEGF, together with regulation and assembly of filopodia. This points to a core theme of GPCR-mediated signaling coordinating cytoskeletal remodeling and angiogenic responses, with filopodium dynamics as a key readout. Some immune-related and obsolete terms are present but do not outweigh the central GPCR-angiogenesis\u2013cytoskeletal motif.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0070493","count":4},{"id":"GO:0051489","count":4},{"id":"GO:0035924","count":3},{"id":"GO:0007213","count":3},{"id":"GO:0006924","count":3}]},{"hash":"1145683087098547104","title":"GPI Anchor Biosynthesis","description":"The only top GO term is GPI anchor biosynthetic process, pointing to a possible shared role in GPI-anchor assembly among these proteins; the small, sparsely connected cluster supports a focused function, but with only one annotated member the confidence is moderate.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1}]},{"hash":"835641044838605297","title":"DNA Repair and Neural Development with Apoptosis","description":"This cluster shows strong representation of genome maintenance processes (DNA replication, DNA repair, DNA-templated transcription) alongside protein turnover (proteasome regulatory particle assembly) and cell fate decisions (ER stress\u2013induced apoptotic signaling, apoptosis) as well as neural development features (dendrite morphogenesis, nervous system development, multicellular development). The combination suggests a group of proteins coordinating DNA maintenance and stress-induced apoptosis within neural development contexts.","confidence":"High","size":8,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006281","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0070682","count":5},{"id":"GO:0070059","count":5}]},{"hash":"455059508447799439","title":"Polyamine biosynthesis and transport","description":"The cluster shows strong representation of polyamine metabolism: putrescine biosynthetic process from arginine via ornithine, spermidine biosynthesis, and positive regulation of polyamine transmembrane transport. These terms point to synthesis and transport of polyamines (putrescine, spermidine) as a unifying theme, with other terms (menaquinone biosynthesis, endocannabinoid signaling, etc.) being less cohesive but not dominant. Confidence: Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0019373","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0001822","count":1}]},{"hash":"847019610059383927","title":"Diverse metabolite biosynthesis","description":"Top GO terms point to biosynthesis of a wide range of compounds (antibiotics, PHB, alkaloids, phylloquinone, mycolic acids, tetrahydrobiopterin, steroids) and related processes, with no interconnecting edges. This suggests the cluster groups enzymes involved in multiple distinct biosynthetic pathways rather than a single pathway, justifying a broad label for diverse metabolite biosynthesis.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0008207","count":2},{"id":"GO:0046677","count":2}]},{"hash":"2144608035697034812","title":"Unknown","description":"The GO terms here cover a wide range of metabolism and cellular logistics (cobalamin and carnitine biosynthesis, methylation, redox, and xenobiotic responses) plus some ER-related protein processing and trafficking terms. There isn\u2019t a single cohesive function or pathway connecting all these annotations, suggesting a mixed or heterogeneous cluster rather than a single biological theme.","confidence":"","size":8,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0046685","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0046232","count":2}]},{"hash":"1135342083208606964","title":"Neuronal development and synapse assembly","description":"The top GO terms are dominated by neural development and synaptic processes (nerve branching morphogenesis, dendritic spine morphogenesis, myelination regulation, synapse assembly, axon guidance, eye morphogenesis, SHH signaling). A couple of immune-related terms appear but are limited, so the cluster most plausibly reflects neuronal development and connectivity.","confidence":"High","size":8,"edges":13,"triangles":8,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048755","count":1},{"id":"GO:2000525","count":1},{"id":"GO:0001655","count":1},{"id":"GO:0031641","count":1},{"id":"GO:0060997","count":1}]},{"hash":"892496799203175620","title":"Rho-Driven Filopodium Formation and Endosomal Transport","description":"The cluster shows strong enrichment for filopodium assembly and regulation of Rho signaling, together with endosomal transport, pointing to a module that coordinates actin-driven membrane protrusions with receptor trafficking. Thrombin-activated receptor signaling further suggests GPCR-driven cytoskeletal remodeling, reinforcing a cytoskeleton and trafficking-associated function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070493","count":2},{"id":"GO:0051489","count":2},{"id":"GO:1904261","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0035023","count":2}]},{"hash":"933489434098268529","title":"Cell cycle and development processes","description":"The top GO terms are dominated by cell cycle and DNA replication (G1/S transition, DNA replication, meiotic cell cycle, kinetochore localization), indicating a core function in cell division. Other terms touch on development (Schwann cell development, trachea formation) and neural/pain-related processes, suggesting some secondary associations but not a single cohesive pathway beyond cell cycle regulation. Overall, the cluster seems best described by cell cycle and development-related processes, with some peripheral signals. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":4},{"id":"GO:0000082","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0014044","count":4}]},{"hash":"608187959790724895","title":"Unknown","description":"The GO terms span a very broad and disparate set of processes (drug response, yeast bud neck localization, Ras signaling, cardiac muscle proliferation, guanylyl cyclase signaling, sarcomere organization, aerotaxis, meiotic cell cycle regulation, nuclear protein export, and DNA-templated transcription), with no clear unifying function or pathway across the cluster. This lack of a cohesive theme means there is no reliable single label to aptly describe the group.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097332","count":1},{"id":"GO:0097271","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0060038","count":1},{"id":"GO:0010754","count":1}]},{"hash":"707466167297959311","title":"Ribosome Biogenesis and tRNA Processing","description":"The top terms are heavily centered on ribosome biogenesis and tRNA-related processes (ribosomal subunit biogenesis, ribosome biogenesis, tRNA modification, threonyl-tRNA aminoacylation), indicating a cluster focused on translation machinery assembly and tRNA maturation. A few other terms (cell septum assembly, iron transport, ppGpp biosynthesis, amino acid starvation response) are present but less representative of the core function.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0015684","count":1}]},{"hash":"1014482112935898279","title":"Unknown","description":"The top GO terms span diverse processes (gland development, thrombocyte differentiation, hormone signaling, histone modification, cytokine production, and tubulin deacetylation) with no clear shared function or pathway across the eight proteins, and no edges connecting them. There isn\u2019t a coherent theme to group these proteins meaningfully, so the cluster is labeled Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903709","count":1},{"id":"GO:0002574","count":1},{"id":"GO:0060765","count":1},{"id":"GO:0097676","count":1},{"id":"GO:1903699","count":1}]},{"hash":"1081807897718519854","title":"Unknown","description":"The GO terms span carbohydrate catabolism (polysaccharide, glucuronoside, lactose catabolic processes), coagulation (blood coagulation, regulation of circulating fibrinogen levels), development (midbrain development, multicellular organism growth), and immune responses (defense against fungus, Toll signaling). There are no edges or cohesive shared functions linking these terms, so there is no clear single theme; thus a specific, meaningful cluster label cannot be assigned beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":1},{"id":"GO:0019391","count":1},{"id":"GO:0005990","count":1},{"id":"GO:0044537","count":1},{"id":"GO:0035264","count":1}]},{"hash":"113512875357844431","title":"Membrane Transport of Ions and Metabolites","description":"Based on the GO terms, the cluster is enriched for transmembrane transport of various ions (sodium, potassium, phosphate, nitrate) and small molecules (vitamins, fucose, sialic acid), plus vesicular processes such as neurotransmitter loading into synaptic vesicles. The recurring theme is membrane transport activity, with transporter roles and vesicle-related transport being the dominant function across the proteins in this cluster.","confidence":"High","size":7,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":5},{"id":"GO:0035725","count":5},{"id":"GO:0006004","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0098700","count":5}]},{"hash":"1662510511692722775","title":"Carbohydrate Transport and Metabolism","description":"The cluster\u2019s top terms center on sugar-related transmembrane transport (glucose, vitamin, sodium) and carbohydrate metabolism (fucose, lactose), suggesting a cohesive theme of sugar transport and metabolism with some broader transport roles.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904728","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0042149","count":2}]},{"hash":"863350379177161208","title":"Unknown","description":"The top GO terms are scattered across RNA metabolism (transcription elongation, deadenylation and decay, mRNA tail regulation), intracellular transport (vesicle fusion with Golgi, protein transport), and various signaling/differentiation processes, with no clear, cohesive function connecting them. There are no edges among the proteins, suggesting a lack of a shared pathway or functional cluster. Therefore, there isn\u2019t a well-supported label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0000289","count":1}]},{"hash":"2116865146934536361","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0000398","count":2}]},{"hash":"556584239517899941","title":"Translation and cell division machinery","description":"This cluster combines translation-related processes (ribosomal biogenesis, cytoplasmic translation, selenocysteine incorporation) with cell division-related activities (cell cycle, cell septum assembly). The overlap suggests proteins involved in coordinating protein synthesis with division, common in bacterial/archaeal systems; other terms appear more peripheral (antibiotic response, amino acid starvation). Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0001514","count":1},{"id":"GO:0000747","count":1},{"id":"GO:0051301","count":1}]},{"hash":"444703456345894123","title":"RNA pseudouridylation and ribosome biogenesis","description":"The proteins show strong enrichment for translation-related processes and RNA modification, with multiple terms for ribosome biogenesis and pseudouridine synthesis across rRNA, tRNA, and mRNA, plus SSU-rRNA maturation and related RNA-processing activities, suggesting a coordinated RNA-processing machinery feeding into cytoplasmic translation.","confidence":"High","size":7,"edges":14,"triangles":11,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0031120","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000462","count":2},{"id":"GO:1990481","count":2}]},{"hash":"2259528727421130119","title":"Cell Division and Vesicle Trafficking Proteins","description":"This cluster contains mitosis-related terms (cell division, centriole elongation, mitotic DNA replication checkpoint signaling) alongside vesicle trafficking and protein handling terms (peroxisome import, Golgi retention, SNARE disassembly, protein unfolding), suggesting a mix of cell-cycle machinery and membrane/organelle dynamics components.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0016558","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0035494","count":2},{"id":"GO:0033314","count":2}]},{"hash":"1472912361388842923","title":"Ribosome biogenesis and cell growth","description":"The cluster is characterized by ribosome biogenesis and translation-related terms (ribosome biogenesis, translation initiation and reinitiation, snoRNP assembly) combined with growth and proliferation signals (TORC1 signaling, cell cycle and cell division). This suggests a cohesive theme of protein synthesis machinery supporting cell growth, with a few outlier terms that may reflect incidental associations.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0051301","count":2}]},{"hash":"933308133767075779","title":"Unknown","description":"The GO terms in this cluster span several distinct biological areas\u2014vesicle transport and membrane trafficking, nuclear membrane disassembly, immune cell differentiation, and post-translational modification\u2014without a clear, common function linking them. Because there is no coherent, dominant theme, this cluster is best labeled Unknown. ","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0014889","count":1},{"id":"GO:0048491","count":1},{"id":"GO:0051081","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0010803","count":1}]},{"hash":"1528795737450033312","title":"Ubiquitin-mediated proteolysis","description":"This cluster is dominated by GO terms related to ubiquitin-dependent protein degradation, including SCF-dependent proteasomal proteolysis and ubiquitin-based ERAD, indicating a shared role in protein turnover. Other terms reference brain development and stress responses, which may reflect broader signaling roles of ubiquitination rather than a distinct separate function for this cluster. Overall, the core theme is proteasome-mediated degradation of proteins.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0050830","count":2},{"id":"GO:1990637","count":1}]},{"hash":"1982734706818314966","title":"Mitotic spindle organization and contractile ring assembly","description":"The top GO terms point to mitosis and cytoskeletal dynamics: spindle organization, mitotic contractile ring actin filament bundle assembly, and establishment of mitotic spindle orientation. Together these indicate a cohesive function in mitotic progression and actin-driven contractile ring formation, with a few peripheral terms that are less central to this cluster.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903478","count":2},{"id":"GO:0001778","count":2},{"id":"GO:0007051","count":2},{"id":"GO:1903477","count":2},{"id":"GO:0000132","count":2}]},{"hash":"2072428050878983532","title":"Mitochondrial Energy Metabolism and Stress Response","description":"This cluster centers on mitochondrial functions and metabolic stress signaling: mitochondrial ATP transmembrane transport, membrane fission, and genome maintenance; coenzyme A and manganese ion transport; plus responses tied to amino acid starvation, insulin signaling, thermogenesis, and oxidative stress. These converging terms point to a core theme of mitochondrial energy production and adaptive stress responses, justifying the label.","confidence":"High","size":7,"edges":12,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":6},{"id":"GO:0034198","count":6},{"id":"GO:0032869","count":6},{"id":"GO:1990845","count":6},{"id":"GO:0035349","count":6}]},{"hash":"370687981830636131","title":"Ribosome biogenesis and translation","description":"This cluster's top GO terms are dominated by ribosome-related processes\u2014maturation of SSU-rRNA, ribosome biogenesis, translation, and small subunit assembly\u2014indicating a core function in ribosome construction and protein synthesis. While a few signaling-related terms appear, they are sparsely represented and do not define the cluster; the ribosome/translation theme best explains the majority of terms and likely reflects the proteins' shared role in ribosome biogenesis and function.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0030111","count":1}]},{"hash":"866074031363151851","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051259","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0035719","count":2},{"id":"GO:0031204","count":2}]},{"hash":"907052034668383143","title":"Cerebral cortex and hippocampus development","description":"This cluster is dominated by GO terms tied to brain development and cortical morphogenesis, including cerebral cortex development, hippocampus development, orbitofrontal cortex signaling, embryonic cranial morphogenesis, and cortical actin cytoskeleton organization. It also includes cues about neural differentiation and regulation of signaling pathways (FGFR signaling, peptidyl-threonine phosphorylation). An outlier term about trachea formation exists, but the strongest, recurring themes point to neural development and cortical/hippocampal maturation.","confidence":"Medium","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":6},{"id":"GO:2001233","count":6},{"id":"GO:0061368","count":6},{"id":"GO:0030866","count":6},{"id":"GO:0048701","count":6}]},{"hash":"816521457756222767","title":"Mitotic spindle assembly and microtubule dynamics","description":"Based on GO terms, the cluster centers on mitotic spindle assembly, spindle pole separation, regulation of microtubule-based processes, and actomyosin ring formation, all key steps in cell division and cytokinesis. While a couple terms touch on transcription or neuronal maintenance, the prevailing signals point to mitosis- and microtubule\u2013related functions, suggesting these proteins work together in organizing the spindle and driving cytokinesis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0045218","count":2},{"id":"GO:0032886","count":2}]},{"hash":"507950672946900098","title":"Unknown","description":"The top terms span mitochondrial assembly and regulation, synaptic receptor activity, and developmental mRNA localization, showing no single coherent function for the cluster. This heterogeneity makes it inappropriate to assign a specific biological theme.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097250","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0090201","count":1},{"id":"GO:1902684","count":1},{"id":"GO:0030722","count":1}]},{"hash":"663835032370617463","title":"Synaptic Signaling and Receptor Trafficking","description":"The top GO terms cluster around glutamatergic synaptic transmission, receptor recycling, and endosome size regulation, with supporting hints of Ca2+ signaling and mitochondrial involvement. This suggests a theme of neuronal communication at synapses and vesicle trafficking, rather than a single, tightly shared molecular function.","confidence":"Medium","size":7,"edges":10,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0034968","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0051036","count":2}]},{"hash":"644832655466469021","title":"Unknown","description":"There are no GO terms provided to define a common function for these seven proteins, and the limited interaction data (6 edges, no triangles) does not reveal a clear shared biological process or molecular function. Without functional annotations, a coherent label cannot be assigned.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[]},{"hash":"1309621110624731533","title":"Hippo signaling and cardiac development","description":"The top terms cluster around heart development (GO:0007507), regulation of cardiac muscle cell proliferation, and Hippo signaling (GO:0035329), suggesting proteins involved in cardiac growth control and developmental signaling. While other terms touch on transcription, mitotic/meiotic cycles, and axonogenesis, the dominant theme is cardiac development linked to the Hippo pathway.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010800","count":4},{"id":"GO:0060044","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0034501","count":4},{"id":"GO:0006351","count":4}]},{"hash":"1308602315995306407","title":"Multistimulus Response and Signaling Regulation","description":"The GO terms show responses to multiple different stimuli (ethanol, EGF, insulin, ascorbic acid, aluminum ions) alongside regulatory processes such as negative regulation of ERK1/ERK2 signaling and MCP-1 production, plus xenobiotic metabolism and cytoplasmic translational elongation. This points to a theme of cells coordinating diverse environmental and metabolic cues while modulating signaling pathways and basic translation/metabolism, rather than a single specific function. Therefore, this label reflects the cluster\u2019s broad, stimulus-responsive regulatory role.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":7},{"id":"GO:0071364","count":7},{"id":"GO:0032869","count":7},{"id":"GO:0033591","count":7},{"id":"GO:0010044","count":7}]},{"hash":"1469966563286393717","title":"Mitochondrial energy metabolism and stress responses","description":"This cluster centers on mitochondrial functions: transport of ATP and CoA, mitochondrial membrane fission, and genome maintenance signals, plus related metabolic and stress-response processes (amino acid starvation, insulin signaling, adaptive thermogenesis, oxidative stress). The GO terms collectively point to mitochondrial energy production and regulation under stress, rather than a single isolated pathway.","confidence":"High","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0032869","count":3},{"id":"GO:1990845","count":3},{"id":"GO:0035349","count":3}]},{"hash":"1734559680323932048","title":"Unknown","description":"The GO terms are scattered across signaling (GTPase activity, TORC1 signaling, kinase activity) and diverse biological processes (immune cytokine production, mitosis, rRNA maturation, histone deacetylation, glial apoptosis, reproductive development), with no clear cohesive function linking the proteins, so this cluster does not map to a single interpretable module.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0038202","count":3},{"id":"GO:0002534","count":3},{"id":"GO:0007064","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1871663413561089922","title":"RNA modification and ribosome biogenesis","description":"The cluster is dominated by GO terms for RNA methylation (peptidyl-glutamine methylation, tRNA methylation) and rRNA maturation (SSU/rRNA and LSU/rRNA), pointing to RNA processing and ribosome assembly as a core function. Other terms like prostaglandin/ecdysone biosynthesis and retina development appear ancillary and do not align with the primary theme, so the label captures the central function with moderate confidence.","confidence":"Medium","size":7,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":3},{"id":"GO:0018364","count":2},{"id":"GO:0070476","count":2},{"id":"GO:0030490","count":2},{"id":"GO:0030488","count":2}]},{"hash":"1577293323535292890","title":"Plant cell cycle and mitosis proteins","description":"The GO terms are dominated by cell cycle, spindle assembly, and mitotic sister chromatid cohesion, with additional hints of proteasome assembly and membrane trafficking. Together these indicate a cluster of plant proteins involved in cell division and its regulation, including protein turnover and vesicle trafficking that support mitosis and cytokinesis. The chloroplast thylakoid import term reflects plant-specific context but does not refute the core cell-division theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0045038","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0018142","count":1}]},{"hash":"528031570185884342","title":"Mitochondrial inner membrane protein insertion","description":"The dominant non-obsolete signal is GO:0045039, which directly references protein insertion into the mitochondrial inner membrane, implying the cluster gathers proteins involved in mitochondrial import/assembly. Other terms point to related mitochondrial targeting/transport concepts but are marked obsolete, so the link is inferred from the mitochondrial insertion theme. Confidence reflects that the connection is plausible but not strongly reinforced by current non-obsolete terms.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0044179","count":1}]},{"hash":"711203414465501575","title":"Lipid metabolism and lipoprotein regulation","description":"The proteins in this cluster show a cohesive focus on lipid handling, including ceramide and diacylglycerol metabolism, acylglycerol remodeling, fatty-acyl-CoA pathways, lipid storage, intestinal lipid absorption, and regulation of plasma lipoprotein particle levels such as LDL clearance. Although one term (phytol metabolism) is less central, the overall theme centers on lipid synthesis, remodeling, transport, and storage, supporting a lipid metabolism/lipoprotein regulation label.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006672","count":1},{"id":"GO:0036155","count":1},{"id":"GO:0034383","count":1},{"id":"GO:0050892","count":1},{"id":"GO:0097006","count":1}]},{"hash":"298279358170065563","title":"Amino acid and ammonium transport","description":"This cluster is dominated by GO terms about transport of amino acids and related metabolites across membranes (L-lysine, methionine, L-ornithine, L-arginine, D- and gamma-aminobutyric acid, polyamines) and transepithelial transport, suggesting a group of membrane transport proteins specialized for amino acids and related compounds, with a possible role in osmotic balance. The nitric oxide production term is a minor outlier and does not drive the overall theme.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002537","count":1},{"id":"GO:0070634","count":1},{"id":"GO:0042941","count":1},{"id":"GO:0097639","count":1},{"id":"GO:0015812","count":1}]},{"hash":"548535613456502949","title":"Chromatin Organization and Nucleosome Assembly","description":"Top GO terms are dominated by chromatin-related processes (heterochromatin organization, nucleosome assembly, establishment of protein localization to chromatin, histone modification), with a few potentially incidental terms (translation, ribosomal export). Overall, the cluster appears to group proteins involved in chromatin structure and regulation, despite some noise.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0017085","count":1},{"id":"GO:0098532","count":1},{"id":"GO:0071169","count":1}]},{"hash":"1644795460871657623","title":"Immune Activation and Migration Signaling","description":"Members of this cluster are associated with immune system processes and cellular movement. Frequent GO terms include positive regulation of T cell differentiation and chemotaxis, monocyte activation, and integrin-mediated cell adhesion, alongside PKC and MAPK signaling and TNF-family production. Together these suggest a cluster of proteins that drive immune cell activation and guided migration via signaling pathways.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051549","count":2},{"id":"GO:0000186","count":1},{"id":"GO:0051088","count":1},{"id":"GO:0033089","count":1},{"id":"GO:0010820","count":1}]},{"hash":"693194241811898601","title":"Innate Immune Activation and Non-canonical NF-kappaB Signaling","description":"This cluster is driven by immune-related processes: innate immune response and positive regulation of non-canonical NF-kappaB signaling are the strongest shared themes among the proteins, with additional supports from phagocytosis, dendritic cell chemotaxis, and vitamin D\u2013related responses. Some cell-cycle and mRNA processing terms appear, but the dominant theme is innate immune activation.","confidence":"High","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901224","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0051225","count":2}]},{"hash":"1314592392940971771","title":"Organogenesis and tissue morphogenesis","description":"These proteins appear involved in multiple developmental processes across different tissues (cartilage condensation, trachea formation, thymus development) and in cell adhesion and related signaling; the shared theme points to organogenesis and tissue morphogenesis rather than a single pathway. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035924","count":5},{"id":"GO:0060440","count":5},{"id":"GO:2001233","count":5},{"id":"GO:0001502","count":5},{"id":"GO:0007160","count":5}]},{"hash":"1654351970403398412","title":"Sodium/Potassium Ion Transport and Membrane Potential","description":"The cluster is dominated by GO terms for ion transport across the plasma membrane (sodium import, potassium homeostasis/export) and membrane potential dynamics (repolarization), pointing to a group of ion transporters/channels that regulate ionic balance and electrical activity. The other terms (development, sensory perception) may reflect pleiotropy or annotation noise but do not override the core ion-transport theme.","confidence":"High","size":6,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0019233","count":2}]},{"hash":"559799995414120477","title":"Nuclear transport and mitotic spindle regulation","description":"Most enriched GO terms point to nuclear import/localization (protein import into nucleus, NLS-bearing protein import into nucleus) and mitotic/spindle processes (spindle organization, regulation of centrosome separation). This suggests a cluster of proteins involved in nuclear transport and chromosome segregation during cell division, with some chromatin regulation and metabolic signaling terms that may reflect broader regulatory roles or annotation noise.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0036228","count":2},{"id":"GO:0033132","count":2},{"id":"GO:0046604","count":2},{"id":"GO:0000061","count":2},{"id":"GO:0007051","count":2}]},{"hash":"155380618654203068","title":"Phosphate Transport Regulation","description":"This cluster's GO terms cluster around phosphate handling: phosphate ion transport and regulation of phosphate transmembrane transport, implying a shared function in moving phosphate across membranes. The inclusion of a maturation term is less directly linked, so the label prioritizes transport regulation as the core theme given the transport-related terms.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000185","count":1},{"id":"GO:0051604","count":1},{"id":"GO:0006817","count":1}]},{"hash":"830678021566360678","title":"Plant hormone signaling regulators","description":"This cluster\u2019s GO terms center on responses to abscisic acid, salicylic acid, and cytokinin-activated signaling, along with negative regulation of leaf senescence and related development processes, which together point to proteins that regulate plant hormone signaling and stress responses. While a couple of terms touch on chromatin/telomere regulation, the prevailing pattern is regulatory roles in hormonal signaling networks in plants.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010520","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1904792","count":1},{"id":"GO:1903086","count":1}]},{"hash":"2215759145545510229","title":"Neural Development and Synaptic Organization","description":"The cluster includes terms tied to neural development (hippocampus development, cerebral cortex migration) and synaptic structure/maintenance (presynaptic active zone), plus vesicle trafficking (endosome transport, Golgi transport) and cell polarity. Together these suggest proteins involved in establishing neuronal circuits and synaptic organization, with vesicular trafficking as a key shared mechanism. However, the terms span related processes, so the label is indicative rather than definitive.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050885","count":1},{"id":"GO:0045022","count":1},{"id":"GO:0050919","count":1},{"id":"GO:0021799","count":1},{"id":"GO:0038027","count":1}]},{"hash":"540764203095533117","title":"RNA splicing regulation and deubiquitination","description":"The cluster's GO terms strongly point to RNA processing (RNA splicing and regulation of alternative splicing via spliceosome) and ubiquitin-related protein regulation (K63-linked deubiquitination, ubiquitin-dependent protein catabolic process). This suggests a cohesive theme of post-transcriptional RNA processing coupled with protein turnover. Some terms are less related (e.g., otic vesicle morphogenesis, chloroplast mRNA modification, temperature compensation), but the dominant signal supports the label.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071600","count":1},{"id":"GO:0070536","count":1},{"id":"GO:1900871","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0043066","count":1}]},{"hash":"1534422011529310997","title":"Metal- and oxidative-stress response","description":"This cluster is dominated by GO terms for cellular responses to gamma radiation, diamide, arsenite, singlet oxygen, and cadmium ion, plus general oxidative stress, pointing to a shared role in sensing or responding to oxidative and metal-induced damage. A placenta development term appears as potential noise, but the core signal is oxidative/metal stress response.","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":2},{"id":"GO:1900462","count":2},{"id":"GO:0072738","count":2},{"id":"GO:1903936","count":2},{"id":"GO:0043497","count":2}]},{"hash":"1694080483703941386","title":"Unknown","description":"The terms span distinct areas (cell migration, muscle stretch response, adipocyte differentiation, telomere maintenance, mRNA processing, protein localization, and kinase regulation) with no clear unifying function or pathway, so a concise, representative name cannot be confidently assigned.","confidence":"","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0035994","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0045736","count":4}]},{"hash":"1362837531373314258","title":"Mitochondrial Respiration and Complex Assembly","description":"The top GO terms point to aerobic respiration and proton transport across membranes, core functions of mitochondrial energy metabolism. Several terms also note protein oligomerization (homotetramerization/heterooligomerization), which underpins the assembly of mitochondrial respiratory complexes. Some unrelated terms (viral process, PQQ biosynthesis) appear, but the dominant signal aligns with mitochondria-driven energy production and protein complex assembly, justifying this label.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0009060","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0006627","count":3},{"id":"GO:0071432","count":3},{"id":"GO:0051289","count":3}]},{"hash":"1871122544264514865","title":"Bacterial energy metabolism and quinone biosynthesis","description":"The top GO terms reveal a cluster of central carbon metabolism activities (phenylacetate and valine catabolism, glycolysis/gluconeogenesis, pyruvate to acetyl-CoA, fatty acid oxidation) alongside biosynthesis of quinones (menaquinone and phylloquinone) and fatty acids. This indicates a cohesive theme around energy production and lipid/quinone metabolism rather than a single narrow pathway, supporting a label that emphasizes energy metabolism with quinone biosynthesis.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":4},{"id":"GO:0006574","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0006635","count":4}]},{"hash":"2040195001983454446","title":"Unknown","description":"The GO terms span metabolism (TCA cycle, heme A biosynthesis), calcium signaling (calcium detection, calcineurin-NFAT cascade), transcription-related processes (RNA polymerase II termination), and meiotic DNA repair, with several obsolete terms, showing no clear, shared function for the protein set. This makes it hard to assign a cohesive label beyond Unknown; the cluster may reflect noise or diverse roles rather than a single pathway.","confidence":"","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0006784","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0010780","count":1}]},{"hash":"1255977375280931154","title":"Lipid metabolism and secondary metabolite biosynthesis","description":"Top GO terms point to lipid turnover (triglyceride catabolic process, phospholipid dephosphorylation) and production of secondary metabolites (strigolactone, alkaloids, antibiotics), with aromatic compound processing (beta-ketoadipate pathway) and detoxification. This suggests a cohesive theme of lipid metabolism linked to secondary metabolite biosynthesis, with one outlier term that could be noise. Therefore: Lipid metabolism and secondary metabolite biosynthesis.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:0042952","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0009820","count":1},{"id":"GO:2000124","count":1}]},{"hash":"16932990965188986","title":"Unknown","description":"The GO terms span vesicle trafficking and a mosaic of biosynthetic processes (antibiotics, fatty acids, steroids, alkaloids, phylloquinone), with no clear shared function among the proteins, so a single representative label cannot be determined.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":1},{"id":"GO:0048279","count":1},{"id":"GO:0016320","count":1},{"id":"GO:0008207","count":1},{"id":"GO:0017000","count":1}]},{"hash":"961418950639690787","title":"Muscle regeneration and cardiovascular development signaling","description":"The cluster is enriched for skeletal muscle tissue regeneration, Notch signaling involved in secondary heart field cardioblast proliferation, and sprouting angiogenesis (endothelial proliferation), with supporting terms like cell growth and cell cycle. Together these point to coordinated muscle regeneration and heart/vasculature development processes, making a label focused on muscle and cardiovascular development appropriate.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072660","count":3},{"id":"GO:0035508","count":3},{"id":"GO:0043403","count":3},{"id":"GO:0000083","count":3},{"id":"GO:0016049","count":3}]},{"hash":"1159959655558755766","title":"DNA replication and chromatin remodeling","description":"The top GO terms cluster around DNA replication and chromatin dynamics, including DNA replication and nucleosome mobilization/histone exchange, suggesting proteins involved in genome duplication and chromatin remodeling. Some unrelated or obsolete terms appear, likely due to annotation noise or multi-functional proteins, but the dominant signal points to replication-associated chromatin regulation.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0043486","count":3},{"id":"GO:0032079","count":3},{"id":"GO:0070880","count":2}]},{"hash":"1044101903859364298","title":"TORC1 signaling and ribosome biogenesis","description":"This cluster\u2019s strongest signals are TORC1 signaling terms (GO:0038202 and GO:1904263) and the ribosome-related maturation term (GO:0000463), pointing to TORC1-controlled growth via enhanced ribosome biogenesis and protein synthesis. A related term about protein serine/threonine kinase activity supports a kinase-regulated growth program. Some other terms (inflammatory, neural development, ciliary transport) may reflect broader cellular contexts or annotations rather than core Function of the cluster, but the TORC1-ribosome biogenesis axis appears to be the unifying theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0007064","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0071902","count":1}]},{"hash":"1135332918746493714","title":"ER-Golgi Vesicle Trafficking and Proliferation","description":"This cluster is driven by vesicle transport terms between the ER and Golgi (COPII budding, ER-Golgi and retrograde transport), indicating a shared role in the secretory pathway. The presence of cell cycle, ribosome biogenesis, and growth terms suggests a connection to cellular proliferation or development, but the strongest signal centers on COPII/ER-Golgi trafficking as the core function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000747","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0000278","count":3}]},{"hash":"82165387690368313","title":"Vertebrate Development and Morphogenesis","description":"Reasoning: Several top GO terms denote developmental and morphogenetic processes (heart development, embryonic cranial skeleton morphogenesis, cerebral cortex development, trachea formation) as well as cytoskeletal organization (cortical actin cytoskeleton organization) and apoptotic regulation, suggesting a cluster of proteins involved in vertebrate embryonic tissue formation and tissue architecture. Some terms like innate immune response and response to toxic substance may reflect broader stress signaling and are less central to the theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0060440","count":1},{"id":"GO:2001233","count":1}]},{"hash":"1164414956080912196","title":"Membrane signaling and trafficking","description":"Top GO terms point to cell-surface signaling (GPCR acetylcholine receptor signaling; cellular response to VEGF) and membrane-associated transport/trafficking (D-glucose transmembrane transport; ER to Golgi ceramide transport; filopodium assembly), with additional links to Ras signaling and cytoskeletal remodeling. Despite a mix of diverse processes and a couple of obsolete terms, the overarching theme is membrane- and trafficking-related functions, making this label a reasonable summary of the cluster.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035924","count":4},{"id":"GO:0007213","count":4},{"id":"GO:0006924","count":4},{"id":"GO:0030259","count":4},{"id":"GO:0046847","count":4}]},{"hash":"1628517966672361172","title":"Unknown","description":"The GO terms span cell cycle (DNA replication, G1/S transition, meiotic cycle), kinetochore localization, various developmental processes (neural tube, Schwann cell, trachea formation), signaling (insulin pathway), and neuronal activities (excitatory postsynaptic potential), plus behavioral response to cocaine. This broad, heterogeneous mix shows no single cohesive function tying all proteins together, so a single representative label is not evident.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0006260","count":2}]},{"hash":"317658802860920405","title":"Cranial and cortical neurodevelopment with actin cytoskeleton","description":"This cluster is dominated by terms related to brain and skull development, such as cerebral cortex development and embryonic cranial skeleton morphogenesis, and includes cortical actin cytoskeleton organization, suggesting a neurodevelopmental and cytoskeletal remodeling theme. Other terms about cellular stress responses (amino acid starvation, ethanol) and pain/behavior are more peripheral signals that do not define the core function of the cluster.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0071361","count":2},{"id":"GO:0060440","count":1},{"id":"GO:2001233","count":1}]},{"hash":"1435256229289786436","title":"Unknown","description":"The GO terms are scattered across chromatin-related processes, various biosynthetic and acetylation pathways, and plant development, with no single, cohesive function linking the proteins. The absence of edges and a unified theme suggests no clear common biology for this cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":5},{"id":"GO:0032918","count":4},{"id":"GO:0010125","count":4},{"id":"GO:2000025","count":4},{"id":"GO:0046208","count":4}]},{"hash":"403328808085369951","title":"Carbohydrate Transporters","description":"Top GO terms cluster around sodium ion transport, transmembrane transport, and carbohydrate transport, with several sugar-specific catabolic and biosynthetic processes also represented. This pattern suggests a module of membrane proteins primarily involved in importing or exporting carbohydrates, i.e., carbohydrate transporters, sometimes coupled to sugar metabolism. ","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":2},{"id":"GO:0055085","count":2},{"id":"GO:0008643","count":2},{"id":"GO:0090502","count":2},{"id":"GO:1902777","count":1}]},{"hash":"1371074140619665090","title":"Diverse Metabolic Enzymes","description":"The GO terms point to enzymes involved in multiple, distinct metabolic pathways\u2014glycolysis, tagatose-6-phosphate catabolism, aromatic compound degradation, and various biosynthetic and lipid-related processes\u2014suggesting a cluster of proteins with broad metabolic roles rather than a single, specific function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006096","count":2},{"id":"GO:2001059","count":2},{"id":"GO:1990577","count":1},{"id":"GO:0042952","count":1}]},{"hash":"1074082633829455469","title":"Developmental signaling and tissue remodeling","description":"The GO terms cluster around regulation of catalytic activity and several remodeling/developmental processes (collagen catabolic process, decidualization, lung branching morphogenesis), with a through-line of signaling involvement (Wnt localization). Some terms are outliers (T cell cytotoxicity, thyroid hormone response), suggesting functional diversity or annotation noise; overall, the set most strongly points to signaling regulation and tissue remodeling during development.","confidence":"Medium","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":3},{"id":"GO:0001913","count":3},{"id":"GO:0097067","count":3},{"id":"GO:0010815","count":3},{"id":"GO:0046697","count":3}]},{"hash":"1296871190885677986","title":"Unknown","description":"The top GO terms span ubiquitin-dependent proteolysis, mRNA capping, transcription, immune activation, coagulation, and various developmental processes, with no single cohesive theme linking the proteins. The absence of any edges and the diversity of functions suggest there isn\u2019t a shared pathway or biological process defining this cluster, so a non-specific Unknown label is most appropriate.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":2},{"id":"GO:0006370","count":1},{"id":"GO:0048455","count":1},{"id":"GO:0006294","count":1},{"id":"GO:0002291","count":1}]},{"hash":"832684497483366828","title":"DNA Damage Response and Cell Cycle Regulation","description":"This cluster centers on DNA maintenance activities (DNA recombination, base-excision repair) and control of the cell cycle (positive regulation of G1/S), with apoptotic processes and redox-related stress responses supporting a broader DNA damage/stress signaling theme. Some terms (corneocyte development, renal water transport) appear peripheral and do not change the core interpretation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0043488","count":2},{"id":"GO:0080111","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0071375","count":2}]},{"hash":"2207287158812167668","title":"Ubiquitin-Dependent Bud Neck Organization","description":"This cluster centers on ubiquitin-mediated protein turnover (K48-linked ubiquitination, autoubiquitination, ubiquitin-dependent catabolic process) and proteins localizing to the yeast bud neck, including septin ring organization and regulation of actin cable assembly. Together, these terms point to a module coordinating protein degradation with bud neck cytoskeleton dynamics during budding. Some terms seem peripheral, but the core signal is ubiquitin-dependent regulation of bud neck structure.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038018","count":1},{"id":"GO:0070936","count":1},{"id":"GO:0097271","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0060816","count":1}]},{"hash":"1681077660546616132","title":"Xylan and Cellulose Degradation","description":"Two GO terms dominate: xylan catabolic process and cellulose catabolic process, each appearing twice, indicating a cohesive function in degrading plant cell wall polysaccharides (hemicellulose and cellulose). The other terms are sparse and less representative, which supports naming the cluster by its core polysaccharide degradation activity.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0072660","count":1},{"id":"GO:0035508","count":1},{"id":"GO:0043403","count":1}]},{"hash":"212265468191266096","title":"Amino acid transport and GABA biosynthesis","description":"The cluster is dominated by transmembrane transport of amino acids (D-aspartate, threonine, serine, glutamate) and includes GABA biosynthesis, suggesting a functional group of amino acid transporters feeding neurotransmitter metabolism, with a few ancillary ion transport terms. ","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0070779","count":3},{"id":"GO:0009449","count":3},{"id":"GO:0055085","count":3},{"id":"GO:0015826","count":3},{"id":"GO:0032329","count":3}]},{"hash":"1103812377108382441","title":"Redox Homeostasis and Protein Repair","description":"The Top Terms cluster around redox balance and handling oxidative damage (cellular redox homeostasis, cellular oxidant detoxification, deglutathionylation) and protein maintenance (protein repair), with supporting hints from cytochrome complex assembly and a post-translational modification (proline hydroxylation). While a couple terms may reflect regulatory roles, the dominant signal is oxidative stress management and protein integrity maintenance.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":1},{"id":"GO:0046826","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0017004","count":1}]},{"hash":"446948745605809093","title":"Fungal cell wall biosynthesis and sporulation","description":"The cluster is dominated by GO terms related to fungal cell wall formation, including (1\u21923)-beta-D-glucan biosynthesis, ascospore wall assembly, and division septum assembly, plus filamentous growth. These indicate a cohesive function around fungal cell wall biosynthesis and morphogenesis, with glycerol metabolism and guard cell morphogenesis terms likely incidental. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006071","count":1},{"id":"GO:0010442","count":1},{"id":"GO:0030643","count":1},{"id":"GO:0034478","count":1},{"id":"GO:0071970","count":1}]},{"hash":"703572413444946569","title":"Unknown","description":"This cluster has no edges, no triangles, and no GO terms listed, so there is no detectable shared function or theme among the six proteins. Without functional signals, the safe label is Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"791022368795461825","title":"Oxidative and Radiation Stress Response","description":"These proteins collectively point to cellular defenses against oxidative and environmental stresses: responses to gamma radiation, diamide, singlet oxygen, arsenite, and cadmium. The dominant theme is stress response and oxidative damage mitigation, even though a few terms are unrelated or obsolete; the overall signal supports a stress-response cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":1},{"id":"GO:1900462","count":1},{"id":"GO:0072738","count":1},{"id":"GO:1903936","count":1},{"id":"GO:0043497","count":1}]},{"hash":"1917663096297604298","title":"Broad-substrate membrane transporters","description":"This cluster's top GO terms predominantly indicate transmembrane transport for a variety of substrates (sodium, potassium, galactose, arabinose, fucose, vitamins, etc.), and also include a vesicle-related term for neurotransmitter loading. The diversity of substrates points to a group of broad-specificity membrane transporters that move solutes across membranes, rather than a single small-molecule target, suggesting a transporter family with wide substrate scope.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0015757","count":2}]},{"hash":"483708092041344572","title":"Ubiquitin-Dependent MVB Sorting and Trafficking","description":"The top GO terms cluster around ubiquitin-dependent protein catabolic processes via the multivesicular body (MVB) sorting pathway, including transport to the vacuole/lysosome and membrane-targeting steps. This points to a coherent role in ubiquitin-mediated degradation and trafficking of membrane/vesicular cargo, with a minor note of development-related annotations that may reflect context-specific functions.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044130","count":1},{"id":"GO:0031397","count":1},{"id":"GO:0010796","count":1},{"id":"GO:0043328","count":1},{"id":"GO:0006612","count":1}]},{"hash":"1699275061402257072","title":"mRNA Splicing and Processing Regulation","description":"The top GO terms cluster around spliceosome-mediated mRNA processing, including splicing, splice site recognition, alternative splicing regulation, polyadenylation, and mRNA modification. This points to a group of proteins involved in RNA maturation and regulation of transcripts, with translation reinitiation being a related downstream process. Overall, the functions align with mRNA processing and splicing control.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1902625","count":2}]},{"hash":"2182496013088673951","title":"Unknown","description":"The terms span unrelated areas: bacterial secretion (type III system), proteasome storage granules, lipid metabolism, cell migration regulation, proton-driven energy processes, vascular development, vacuolar acidification, histidine homeostasis, and osteoblast differentiation. They do not converge on a single biological function or pathway for these five proteins, making a coherent label unreliable.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030254","count":1},{"id":"GO:1902906","count":1},{"id":"GO:0006629","count":1},{"id":"GO:0006933","count":1},{"id":"GO:0042777","count":1}]},{"hash":"346835092745125844","title":"Muscle signaling and contraction regulation","description":"This cluster centers on muscle-related processes, including responses to muscle stretch, skeletal muscle regeneration, and modulation of cardiac muscle membrane depolarization, suggesting a cohesive theme of muscle signaling and contraction. Some GO terms (e.g., protein localization to the plasma membrane, post-translational modification) support membrane-related regulation, though a few annotations pertain to telomeres or broader signaling, which may be incidental. Overall, the dominant pattern points to muscle physiology and membrane-regulated contraction signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901187","count":1},{"id":"GO:0072660","count":1},{"id":"GO:0035994","count":1},{"id":"GO:0035508","count":1},{"id":"GO:0070198","count":1}]},{"hash":"650621513633859802","title":"Unknown","description":"The top GO terms span oxidative stress, aging, signaling related to vascular tone, pH response, selenium ion response, chromatin organization, and collagen catabolism, plus pigment differentiation. They do not converge on a single coherent biological function or pathway for this small cluster, so no clear common theme emerges.","confidence":"","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010447","count":1},{"id":"GO:0003069","count":1},{"id":"GO:0019430","count":1},{"id":"GO:0001320","count":1},{"id":"GO:0071291","count":1}]},{"hash":"1669368093465712894","title":"RNA splicing and post-transcriptional regulation","description":"This cluster\u2019s GO terms center on mRNA processing and spliceosome-mediated regulation of splicing (including splice site recognition and alternative splicing), with additional signals for ncRNA-mediated gene silencing and mRNA modification, indicating broader post-transcriptional mRNA control, including translation reinitiation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0000381","count":2}]},{"hash":"1475828346189358457","title":"Unknown","description":"The GO terms span many unrelated processes (glucose starvation response, gluconeogenesis, proton transport, GTP biosynthesis, cell-cycle regulation, transepithelial water transport, IL-4 response, protein tetramerization), and there is no clear shared function linking the five proteins. With no cohesive theme and no edges, a specific label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042149","count":1},{"id":"GO:0019343","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0006183","count":1},{"id":"GO:0030071","count":1}]},{"hash":"1715770022835324221","title":"Unknown","description":"The top GO terms are diverse, spanning mitotic cell cycle, transcription, neuronal development (hippocampus), kinase signaling, kinetochore localization, immune defense, exocytosis, and ER-stress\u2013related apoptosis. There isn't a single coherent biological theme that ties all proteins together, suggesting either heterogeneous functions or mixed annotations. Therefore a concise, meaningful label is not identifiable.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0021766","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0043366","count":2}]},{"hash":"530569028809620829","title":"Bacterial cell wall synthesis and division","description":"This cluster is dominated by GO terms for peptidoglycan biosynthesis and turnover, cell wall organization, and cell cycle/division, suggesting a group of proteins involved in bacterial growth and remodeling of the cell wall during division. The presence of carbohydrate-related terms like cellulose catabolic process adds metabolic context but does not override the core theme of cell wall dynamics.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0001302","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0009252","count":2},{"id":"GO:0071555","count":2}]},{"hash":"356408989082160527","title":"Environmental and Oxidative Stress Response","description":"These terms cluster around cellular responses to environmental and chemical stressors, notably oxidative stress (singlet oxygen, diamide, arsenite, cadmium) and radiation exposure (gamma radiation). The consistent theme is a general stress-response module rather than a single pathway, despite some obsolete terms; together they point to stress-adaptation functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":1},{"id":"GO:1900462","count":1},{"id":"GO:0072738","count":1},{"id":"GO:1903936","count":1},{"id":"GO:0043497","count":1}]},{"hash":"1392735096189271172","title":"RNA processing and splicing","description":"The cluster is dominated by GO terms for rRNA maturation, tRNA processing, spliceosome-related activities (snRNP and mRNA splicing), and P-body assembly, all pointing to RNA processing and post-transcriptional regulation. A few terms (chromatin-related or stress-related) are less central, but the core signal is RNA maturation and splicing machinery.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":3},{"id":"GO:0008033","count":2},{"id":"GO:0033962","count":2},{"id":"GO:0008334","count":2},{"id":"GO:0009414","count":2}]},{"hash":"2059235879632241796","title":"Unknown","description":"The GO terms span very different biological processes, including gas vesicle organization, peroxisome matrix protein import, PSII light-harvesting complex turnover, Golgi retention, SNARE disassembly, mitotic DNA replication checkpoint signaling, ATP biosynthesis regulation, centriole elongation, FAD catabolic process, and protein homooligomerization. There is no coherent functional theme linking these terms, suggesting diverse roles or non-representative annotations for this cluster, so a single descriptive label cannot be assigned.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0031412","count":1},{"id":"GO:0016558","count":1},{"id":"GO:0010304","count":1},{"id":"GO:0045053","count":1},{"id":"GO:0035494","count":1}]},{"hash":"2187037657698870395","title":"Plant Hormone Response Regulators","description":"The top GO terms cluster around plant hormone signaling and related development/defense processes, including responses to abscisic acid and salicylic acid and cytokinin-activated signaling, as well as regulation of leaf senescence and trichome patterning. This points to proteins that regulate hormone signaling pathways and their developmental outcomes, with a few outliers related to telomere regulation that may reflect broader regulatory roles or annotation noise.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010520","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1904792","count":1},{"id":"GO:1903086","count":1}]},{"hash":"807121650904830864","title":"Chromatin Modification and Silencing","description":"The top terms include histone H3K9/14/18 acetylation and heterochromatin organization, which together point to chromatin modification and silencing as a shared theme. Other terms reference signaling and protein regulation (NF-kappaB, estrogen receptor signaling, ufmylation), which may be incidental annotations rather than core cluster functions. Given the strongest, coherent signal is chromatin-related, this label is plausible, though the small, mixed term set and obsolete annotations limit certainty.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043971","count":1},{"id":"GO:0043970","count":1},{"id":"GO:0044154","count":1},{"id":"GO:0070868","count":1},{"id":"GO:1903721","count":1}]},{"hash":"1473396259488008056","title":"Mitochondrial ion transport and oxidative phosphorylation","description":"The top GO terms emphasize mitochondrial metal ion transport (magnesium and cobalt) and core energy metabolism processes (oxidative phosphorylation, aerobic electron transport chain, and complex IV assembly). This pattern points to a cluster of proteins involved in mitochondrial ion homeostasis and energy production, rather than cytosolic signaling. Other terms are less central and may reflect broader annotations, but the dominant theme is clear.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045016","count":2},{"id":"GO:1903830","count":2},{"id":"GO:0006824","count":2},{"id":"GO:0008535","count":1},{"id":"GO:1902600","count":1}]},{"hash":"812668467212631058","title":"Transcription initiation machinery (Pol I/II/III)","description":"The cluster\u2019s GO terms cluster around transcription initiation and RNA polymerase activities across Pol I, II, and III, including preinitiation complex assembly and nucleolar rRNA transcription, indicating a shared role in transcription initiation and ribosome biogenesis; the single N-terminal acetylation term appears incidental.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017196","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0006352","count":1},{"id":"GO:0045893","count":1},{"id":"GO:1903357","count":1}]},{"hash":"2264383373840031961","title":"Mitotic cell division and vesicle trafficking","description":"The top GO terms center on mitotic cell cycle and cell division, complemented by vesicle docking and protein secretion, suggesting a cluster combining cell-division machinery with trafficking processes.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006478","count":2},{"id":"GO:0033144","count":2}]},{"hash":"1309993323644488582","title":"Cerebral Cortex Development and Transcriptional Regulation","description":"The dominant GO terms are about DNA-templated transcription and brain development (cerebral cortex development, embryonic cranial skeleton morphogenesis) with supporting notes on cortical actin organization, suggesting neuronal morphogenesis and transcriptional control during brain development. Other terms point to broader signaling and developmental processes, but the brain-development theme remains strongest.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0046827","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0000160","count":3},{"id":"GO:0060440","count":2}]},{"hash":"850413503716080315","title":"Fungal Secretory Pathway & Cell Wall Synthesis","description":"The cluster centers on GO terms for membrane targeting and translocation, including SRP-dependent cotranslational and post-translational protein targeting to membranes, which points to secretory pathway involvement. The presence of fungal-type beta-glucan biosynthetic process supports a link to cell wall synthesis in fungi. However, several other terms (ER stress-related apoptosis regulation, DNA replication, iron-sulfur cluster assembly) seem less connected, making the overall theme somewhat mixed. Therefore, moderate confidence that this label reflects the cluster\u2019s representative function.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070880","count":2},{"id":"GO:1903382","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1903751","count":2},{"id":"GO:1900035","count":2}]},{"hash":"1511399099864103680","title":"Growth regulation and synaptic signaling","description":"These proteins touch on growth control (Wnt and Hippo pathways, negative regulation of cardiac muscle cell proliferation), differentiation (keratinocyte differentiation), and apoptosis, together with ubiquitin-mediated proteolysis, plus neural/synaptic organization (neuroligin clustering and synaptic vesicle clustering). The shared theme appears to be signaling-based regulation of growth/differentiation, with links to synaptic assembly and protein turnover.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060044","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0035329","count":3}]},{"hash":"511234058119461142","title":"Cytoskeletal dynamics and GPCR signaling","description":"The terms center on cytoskeletal remodeling (filopodium assembly, regulation of cell diameter) and diverse signaling pathways (G protein-coupled acetylcholine receptor signaling, VEGF response, and related cAMP signaling), suggesting a function in coordinating cell shape changes with signal transduction rather than a single metabolic process. Some muscle-contractility-related terms also align with cytoskeletal regulation of contraction. ","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045988","count":2},{"id":"GO:0035924","count":1},{"id":"GO:0007213","count":1},{"id":"GO:0006924","count":1},{"id":"GO:0043951","count":1}]},{"hash":"572552843500520328","title":"TORC1-Driven Growth and Ribosome Biogenesis","description":"Top GO terms center on TORC1 signaling and its positive regulation, plus LSU-rRNA maturation, indicating a growth/translation control theme governed by TORC1. Additional terms point to cytoskeletal remodeling and developmental regulation that may accompany growth but are less directly tied. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0007064","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0071902","count":1}]},{"hash":"221779030317662664","title":"Golgi Vesicle Trafficking and Organization","description":"This cluster is dominated by GO terms describing vesicle transport to, from, and within the Golgi apparatus (ER-to-Golgi, intra-Golgi, Golgi-to-vacuole) and Golgi ribbon formation. Together, these indicate a cohesive function in Golgi-mediated vesicle trafficking and structural organization. A few low-frequency terms appear unrelated (e.g., meiotic processes, histone modification), likely noise.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0090161","count":2},{"id":"GO:0006888","count":2}]},{"hash":"31313961151020773","title":"Developmental signaling and differentiation","description":"Most terms point to signaling and development (intracellular signal transduction, cell migration, fat cell differentiation, trachea formation, response to muscle stretch). Telomere maintenance and RNA processing appear but are less central. Overall, the cluster seems best described by developmental signaling and differentiation rather than a single narrow function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904355","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0045444","count":2},{"id":"GO:2001275","count":2}]},{"hash":"2207351501443477146","title":"Unknown","description":"The GO terms are very diverse, including ubiquitination, vitamin D response, imprinting regulation, NF-kappaB signaling, immune defense, transcription, MAPK signaling, ER-stress\u2013induced apoptosis, phorbol ester response, and mitotic cell cycle, with no single dominant theme. This breadth suggests the cluster does not reflect a cohesive, specific function, so a definite label cannot be assigned beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0033280","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0050830","count":2}]},{"hash":"1343952939110596682","title":"Wnt signaling and cell cycle regulation","description":"The cluster\u2019s shared terms include canonical Wnt signaling (GO:0060070) and cell cycle-related processes (G2/M transition GO:0000086, GO:0051301), along with liver regeneration (GO:0097421) and meiosis-related pairing (GO:0007129), suggesting a core theme of signaling pathways that drive cell proliferation and tissue regeneration. Some terms such as regulation of insulin signaling and early viral transcription are less directly connected, but the dominant pattern points to Wnt-mediated control of cell division and regenerative processes. ","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032026","count":3},{"id":"GO:0046626","count":3},{"id":"GO:0030857","count":3},{"id":"GO:0060070","count":3},{"id":"GO:0019085","count":3}]},{"hash":"1288658465347838876","title":"Chromatin remodeling and mitotic cohesion","description":"The cluster's top GO terms center on chromatin-related processes: CENP-A chromatin assembly, mitotic sister chromatid cohesion, and nucleosome mobilization, with supporting hints from histone modification and chromatin dynamics. While there are a few terms pointing to growth signaling and development (TORC1 signaling, TGF-beta response, cytokine production), the dominant pattern is chromatin remodeling tied to chromosome segregation during mitosis.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0038202","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0007064","count":1}]},{"hash":"1685655899321037635","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006189","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0032958","count":1},{"id":"GO:0071524","count":1},{"id":"GO:0017000","count":1}]},{"hash":"1856499684942011185","title":"Amino Acid Biosynthesis and Cofactor Generation","description":"The top GO terms show biosynthesis of amino acids (tyrosine, proline; isoleucine is obsolete) and pantothenate, plus NADPH regeneration, pointing to amino acid and cofactor biosynthesis and maintenance. Additional catabolic processes (inositol, galactarate) suggest broader metabolic activity. With no specific pathway linkage beyond general metabolism, this label captures the overall function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019310","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0098706","count":1},{"id":"GO:0046392","count":1}]},{"hash":"2254872917812609159","title":"Membrane signaling and trafficking","description":"These proteins appear linked by membrane-associated signaling and cargo transport: GPCR acetylcholine signaling, Ras pathway regulation, VEGF response, and transport processes such as ceramide transport between ER and Golgi, plus glucose transmembrane transport. Filopodium assembly suggests cytoskeletal changes accompanying membrane dynamics. The terms point to a general theme of membrane signaling and trafficking rather than a single specific pathway, supporting the label \u201cMembrane signaling and trafficking.\u201d ","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035924","count":1},{"id":"GO:0007213","count":1},{"id":"GO:0006924","count":1},{"id":"GO:0030259","count":1},{"id":"GO:0046847","count":1}]},{"hash":"769664600438676547","title":"Oxidative Stress Response","description":"Most of the top GO terms describe cellular responses to oxidative stress or related insults (gamma radiation, diamide, arsenite, singlet oxygen, cadmium). Even though several entries are obsolete or less related, the prevailing theme is cellular defense against oxidative damage, so a concise label \"Oxidative Stress Response\" best captures the cluster.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":2},{"id":"GO:1900462","count":2},{"id":"GO:0072738","count":2},{"id":"GO:1903936","count":2},{"id":"GO:0043497","count":2}]},{"hash":"626955078338801904","title":"Acetylation and Small Molecule Metabolism","description":"This cluster centers on acetylation-related processes (spermidine/spermine acetylation and N-terminal acetylation) and includes several small-molecule biosynthetic/catabolic pathways (mycothiol, ectoine, melatonin, acetoin), suggesting a theme of acetylation-linked metabolism across diverse substrates.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":2},{"id":"GO:0010125","count":2},{"id":"GO:2000025","count":2},{"id":"GO:0046208","count":2},{"id":"GO:0045150","count":2}]},{"hash":"1295114557294273110","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034475","count":1},{"id":"GO:0036450","count":1},{"id":"GO:0036416","count":1},{"id":"GO:0071036","count":1},{"id":"GO:0035044","count":1}]},{"hash":"239011320298048362","title":"Cellular stress response to radiation and oxidative stress","description":"The cluster is dominated by GO terms for cellular responses to gamma radiation, diamide, singlet oxygen, and cadmium ion, indicating a shared function in sensing and responding to oxidative and environmental stress. Some terms are obsolete or less relevant, but the core pattern supports a general stress-response role.","confidence":"Medium","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071480","count":3},{"id":"GO:1900462","count":3},{"id":"GO:0072738","count":3},{"id":"GO:1903936","count":3},{"id":"GO:0043497","count":3}]},{"hash":"1370183911490603659","title":"N-terminal and Polyamine Acetylation","description":"Most GO terms are centered on acetylation events, including spermidine acetylation, spermine acetylation, and N-terminal peptidyl acetylations, indicating a common theme of acetylation-related protein modifications. There are also related small-molecule biosynthesis/catabolism terms (mycothiol, ectoine, acetoin, melatonin), which fit within a broader metabolic context, though a few terms appear as annotation noise (e.g., leaf formation). Overall, the acetylation signal dominates, justifying a label focused on acetylation and related metabolism.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":4},{"id":"GO:0010125","count":4},{"id":"GO:2000025","count":4},{"id":"GO:0046208","count":4},{"id":"GO:0045150","count":4}]},{"hash":"325418867174981240","title":"Unknown","description":"The GO terms are scattered across chromatin organization, neural development and learning, metabolism, extracellular matrix remodeling, and platelet/coagulation processes, with no single dominant function linking the proteins. There is no meaningful network-connected theme to label, and the limited connectivity suggests a non-specific or heterogeneous set. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034724","count":1},{"id":"GO:0070527","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034396","count":1}]},{"hash":"275342076542007730","title":"ESCRT-Mediated Endosomal/MVB Trafficking","description":"The top terms cluster around ESCRT-dependent sorting and trafficking through endosomes and multivesicular bodies, including endosome transport, MVB assembly, vesicle targeting to the vacuole/lysosome, and ubiquitin-dependent degradation. This points to a cohesive function in ESCRT-driven cargo sorting and trafficking rather than a broader or unrelated process.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903772","count":1},{"id":"GO:0045022","count":1},{"id":"GO:0036258","count":1},{"id":"GO:0045053","count":1},{"id":"GO:0007567","count":1}]},{"hash":"996304450187832492","title":"Unknown","description":"The GO terms are a mix of membrane potential changes (depolarization/hyperpolarization), transcription regulation, and general protein processing (proteolysis, deglycosylation), with several entries labeled obsolete. There is no clear, single theme uniting these functions for the four proteins, making it difficult to assign a specific, representative label. ","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006517","count":1},{"id":"GO:0060081","count":1},{"id":"GO:2000679","count":1},{"id":"GO:1903168","count":1},{"id":"GO:0006508","count":1}]},{"hash":"396180813582961829","title":"Cytokine signaling and stress response with proteostasis","description":"GO terms are dominated by cytokine production regulation (IL-6, TNF), heat and general stress responses, and proteostasis-related activities (protein stabilization, chaperone-dependent refolding). This points to a module balancing inflammatory signaling with cellular stress management, with a minor outlier in sperm\u2013zona pellucida binding that does not define the cluster\u2019s core theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000778","count":4},{"id":"GO:0033198","count":4},{"id":"GO:0007339","count":4},{"id":"GO:0014823","count":4},{"id":"GO:0050821","count":4}]},{"hash":"1267355984406604305","title":"Ubiquitin-Dependent Protein Degradation","description":"Top terms include several ubiquitination-related processes (K48-linked ubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process), suggesting a link to proteasomal degradation. However other terms point to tRNA modification, Wnt signaling, and NF-kappaB activation, with no clear unifying function or demonstrated interactions among the four proteins. This makes the assignment provisional; the strongest theme is ubiquitin-mediated degradation, but not all terms fit neatly.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":1},{"id":"GO:0017183","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0038018","count":1},{"id":"GO:0070936","count":1}]},{"hash":"2037388012562863683","title":"Neurodevelopment and Apoptosis Regulation","description":"This cluster includes terms tied to brain development (cerebral cortex development, embryonic cranial skeleton morphogenesis) and regulation of apoptotic signaling, suggesting proteins involved in neural development with control of cell death. Additional terms concerning actin cytoskeleton organization and innate immune response hint at structural remodeling and immune-related processes in neural contexts, supporting a theme of development coupled with apoptosis regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0060440","count":1},{"id":"GO:2001233","count":1},{"id":"GO:0061368","count":1}]},{"hash":"232050383971913919","title":"Cell cycle control and DNA replication","description":"The strongest and most frequent GO terms center on regulation of cyclin-dependent kinase activity, the broader cell cycle, and DNA replication, as well as kinetochore localization. Together these point to a module focused on cell division and genome duplication. Some additional terms touch on development or signaling, which might reflect broader roles of these proteins, but the core theme is cell cycle regulation and replication.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0034501","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0001707","count":2}]},{"hash":"1946835060486238039","title":"Unknown","description":"The GO terms are highly diverse (gland development, thrombocyte differentiation, androgen signaling, histone modification, glucose signaling, IL-6 production, and tubulin deacetylation) and include obsolete annotations, providing no clear shared function across the cluster. This suggests no cohesive biological theme, so the label Unknown with no confidence is appropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903709","count":1},{"id":"GO:0002574","count":1},{"id":"GO:0060765","count":1},{"id":"GO:0097676","count":1},{"id":"GO:1903699","count":1}]},{"hash":"1612333035095823280","title":"Meiosis, chromatin silencing, and mitotic control","description":"The key GO terms point to meiotic DNA double-strand break formation and silencing of mating-type loci via heterochromatin, coupled with cell-cycle transitions such as G2/M and exit from mitosis. Ubiquitin-dependent degradation pathways (N-end rule and K29-linked ubiquitination) likely regulate these processes, reinforcing a theme of coordinated meiosis, epigenetic regulation, and mitotic control. The sperm axoneme assembly term is less aligned but may reflect shared cytoskeletal components in certain contexts. Overall, the cluster appears to group proteins involved in meiosis and chromatin silencing linked to cell-cycle regulation.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0043951","count":4},{"id":"GO:0007288","count":4},{"id":"GO:0071596","count":4},{"id":"GO:0035519","count":4},{"id":"GO:0000086","count":4}]},{"hash":"623173632570404052","title":"TORC1-Driven Ribosome Biogenesis","description":"The dominant terms are ribosome biogenesis and TORC1 signaling, with supporting terms for rRNA maturation and kinase activity, pointing to a growth- and protein-synthesis\u2013oriented module. Some inflammatory/apoptotic and developmental terms appear as possible secondary roles or annotation noise.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0038202","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0007064","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1492542127759398640","title":"Unknown","description":"Top GO terms point to neural synapse assembly and vesicle clustering, but there are also muscle regulation, cell migration, ubiquitination, ribosome export, histone modification, and other processes. Because these signals do not converge on a single, coherent function for the protein set, a concise functional label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097118","count":1},{"id":"GO:2000809","count":1},{"id":"GO:0035519","count":1},{"id":"GO:0016203","count":1},{"id":"GO:0035441","count":1}]},{"hash":"2001935859081416944","title":"Ubiquitin-Proteasome Regulation of DNA Repair and Cell Cycle","description":"This cluster is enriched for ubiquitin-related proteolysis and cell-cycle processes: SCF- and APC/C-mediated ubiquitination, various ubiquitin linkages (K48, K11), neddylation, proteasomal degradation, plus nucleotide-excision repair and cell division, indicating a cohesive theme of regulated protein turnover coordinating DNA repair and cell-cycle progression. The presence of viral process terms may reflect host-virus interactions with the UPS but does not override the core UPS/DNA repair/cell-cycle signal.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0070936","count":2},{"id":"GO:0051865","count":2}]},{"hash":"2181610763100349412","title":"Meiosis-related chromatin silencing and ubiquitin regulation","description":"The cluster\u2019s GO terms center on meiosis, including meiotic DNA double-strand break formation and silent mating-type cassette heterochromatin formation, along with G2/M transition and exit from mitosis, and ubiquitin-dependent protein turnover (N-end rule pathway, K29-linked ubiquitination). Together these indicate a theme of meiosis-specific chromatin regulation and coordinated protein degradation, with noise terms like sperm axoneme assembly likely incidental. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0043951","count":4},{"id":"GO:0007288","count":4},{"id":"GO:0071596","count":4},{"id":"GO:0035519","count":4},{"id":"GO:0000086","count":4}]},{"hash":"2010616031259453186","title":"MAPK signaling in immune cell responses","description":"The GO terms show prominent MAPK involvement (ERK1/ERK2 cascade and p38MAPK cascade) with stimuli like GM-CSF and EGF, pointing to MAPK-driven signaling in immune/growth-factor contexts; other immune differentiation terms may reflect downstream effects of this pathway.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:1904628","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0038066","count":2},{"id":"GO:0071364","count":1}]},{"hash":"2199029759314141875","title":"Neuronal Development and Synaptic Organization","description":"The GO terms point to neural development (hippocampus development, cortex migration) as well as synaptic architecture and membrane trafficking (presynaptic active zone maintenance, endosome/vesicle transport), suggesting proteins involved in neural development and synaptic maintenance.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050885","count":1},{"id":"GO:0045022","count":1},{"id":"GO:0050919","count":1},{"id":"GO:0021799","count":1},{"id":"GO:0038027","count":1}]},{"hash":"2268003799817085618","title":"Meiotic DSB Formation and Repair","description":"The proteins in this cluster are enriched for GO terms related to meiotic double-strand break formation and subsequent processing/repair (including synthesis-dependent strand annealing) and even mitochondrial HR repair, indicating a core role in meiotic DNA damage response and recombination. Some calcium signaling and developmental terms appear as secondary associations, but the meiotic repair signal is dominant.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010780","count":4},{"id":"GO:0051037","count":4},{"id":"GO:0010791","count":4},{"id":"GO:0033173","count":4},{"id":"GO:0005513","count":4}]},{"hash":"332467316096136419","title":"Unknown","description":"The GO terms for this cluster are highly diverse, spanning bacterial catabolic/biosynthetic pathways (beta-ketoadipate, menaquinone, antibiotic/alkaloid biosynthesis) and plant/human signaling (strigolactone response, endocannabinoid regulation) with no single unifying function. Obsolete terms further muddy interpretation, and there are no network connections among the proteins. There isn\u2019t a cohesive theme to label a specific, representative function beyond \u201cunknown/diverse metabolism.\u201d","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1990577","count":1},{"id":"GO:0042952","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0017000","count":1}]},{"hash":"1842421876130668577","title":"Neddylation and Ubiquitin Regulation","description":"The cluster is dominated by GO terms related to protein neddylation (including positive and negative regulation) and ubiquitin-protein transferase activity, pointing to a core theme of post-translational modification by NEDD8/ubiquitin systems. Some stress-response terms (response to UV-C, gamma radiation) and protein catabolic process further suggest cellular responses and turnover, but the central motif remains regulation of neddylation/ubiquitination. A few amino-acid biosynthesis terms appear unrelated and may be noise. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000435","count":1},{"id":"GO:0010225","count":1},{"id":"GO:0051443","count":1},{"id":"GO:2000436","count":1},{"id":"GO:0044254","count":1}]},{"hash":"457591013497675795","title":"Membrane protein localization and ubiquitin-mediated turnover","description":"The strongest signals in this cluster point to membrane-related processes and ubiquitin-driven turnover: maintenance of protein location in the plasma membrane, ubiquitin-dependent degradation via the multivesicular body pathway, and synaptic organization (neuroligin clustering and synaptic vesicle clustering). These together suggest a shared theme of membrane protein localization and ubiquitin-mediated turnover, with a possible synaptic organization angle. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0043162","count":2},{"id":"GO:0097118","count":1},{"id":"GO:2000809","count":1}]},{"hash":"84284674086623301","title":"Cell signaling and membrane trafficking","description":"The top GO terms indicate membrane-initiated signaling (GPCR signaling, VEGF response) alongside membrane trafficking and lipid transport (ceramide transport, glucose transmembrane transport), plus cytoskeletal remodeling (filopodium assembly) and Ras pathway regulation, pointing to a cluster centered on membrane-associated signaling and trafficking functions.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035924","count":2},{"id":"GO:0007213","count":2},{"id":"GO:0006924","count":2},{"id":"GO:0030259","count":2},{"id":"GO:0046847","count":2}]},{"hash":"1906086199097088715","title":"Ubiquitin-Dependent Regulation and Chromatin Modification","description":"The cluster is dominated by ubiquitination-related GO terms (autoubiquitination, ubiquitin-dependent proteolysis, various histone ubiquitinations) and signaling components (NF-kappaB activation, I-kappaB phosphorylation) that tie protein turnover to transcriptional/chromatin regulation and apoptosis. This points to a cohesive role in ubiquitin-mediated regulation affecting both protein degradation and chromatin dynamics.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0007250","count":3},{"id":"GO:0033151","count":3},{"id":"GO:1903721","count":3}]},{"hash":"1586647776540634653","title":"Spermatogenesis and intraciliary transport","description":"The terms strongly point to male reproductive biology, with spermatid development and seminiferous tubule development, plus intraciliary retrograde transport linking to sperm flagellar/ciliary function. While some generic signaling terms appear, the dominant theme ties to reproductive cell development and ciliary transport.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033674","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0038202","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0007064","count":1}]},{"hash":"1516845830860608624","title":"Meiotic DNA Repair and Recombination","description":"The cluster is dominated by GO terms related to double-strand break (DSB) repair and recombination processes, especially in the context of meiosis (meiotic joint molecule formation, recombinase assembly, SSA/BIR repair pathways, and telomere maintenance via recombination). This suggests the proteins function together in meiotic DNA repair and recombination machinery rather than unrelated pathways.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000819","count":1},{"id":"GO:0006277","count":1},{"id":"GO:0000709","count":1},{"id":"GO:0000727","count":1},{"id":"GO:0000730","count":1}]},{"hash":"1507088162276310272","title":"Ciliary motility and microtubule transport","description":"The top GO terms point strongly to ciliary function and microtubule-based transport (cilium movement, outer dynein arm assembly, intraciliary/anterograde and retrograde transport) and related developmental processes (left/right symmetry, lateral ventricle development, spindle localization, nuclear migration along microtubules). A couple of terms about P-body and stress granule assembly suggest some RNA-processing associations, but the dominant signal is ciliary motility and microtubule-driven transport.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":1},{"id":"GO:0030473","count":1},{"id":"GO:0034063","count":1},{"id":"GO:0036158","count":1},{"id":"GO:0003341","count":1}]},{"hash":"1091588557261083181","title":"Calcium signaling and ion homeostasis","description":"Based on the GO terms, the common theme is calcium signaling and ion homeostasis: several terms describe regulation of cytosolic and ER Ca2+ levels, and the calcineurin-NFAT axis, while others involve ion transport and membrane repolarization. Additional terms point to Ca2+-dependent processes such as contraction regulation and biomineralization, and even pheromone-related signaling that can engage calcium fluxes. Taken together, these terms suggest a cluster of proteins that function in calcium signaling and related ion transport pathways rather than a single narrow function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070885","count":2},{"id":"GO:0051599","count":2},{"id":"GO:0051481","count":2},{"id":"GO:1990938","count":2},{"id":"GO:0070574","count":2}]},{"hash":"619175154813134714","title":"Golgi-ER trafficking and mitosis","description":"The cluster shows strong signals for secretory pathway processes (COPII-coated vesicle budding; ER to Golgi and Golgi to ER transport) together with cell division activities (mitotic cell cycle, mitotic spindle assembly, cell division). This suggests a cohesive function in coordinating vesicle trafficking with mitosis, possibly within developmental contexts reflected by brain development and organismal growth terms.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0000278","count":4}]},{"hash":"2250477256397386013","title":"Unknown","description":"The top GO terms span diverse, seemingly unrelated processes (mitotic spindle assembly, karyogamy, plant stamen formation, immune activation, coagulation, various aspects of cell migration and adhesion, and tissue morphogenesis) with no clear, single biological theme connecting the four proteins. This suggests there isn\u2019t a cohesive, well-supported functional cluster to name beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0048455","count":1},{"id":"GO:0006471","count":1},{"id":"GO:0002291","count":1}]},{"hash":"955844453259772344","title":"Embryonic Morphogenesis and Neural Development","description":"The top GO terms cluster around embryonic development and tissue morphogenesis, especially cranial skeleton and cerebral cortex formation, with several neural-related terms (e.g., brain development, cortical actin organization) and related signaling. While some terms about cell cycle and apoptosis are present, the dominant theme is developmental morphogenesis with a neural emphasis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0060440","count":3},{"id":"GO:2001233","count":3},{"id":"GO:0061368","count":3}]},{"hash":"2017811768211158651","title":"Stimulus-Triggered Transcription Signaling","description":"The top GO terms point to cellular response to external stimuli (such as TGF-beta) and signaling through immune receptors, paired with DNA-templated transcription, suggesting these proteins participate in signaling pathways that regulate gene expression. Some terms appear unrelated (e.g., phototransduction, sugar phosphotransferase), but the core theme seems to be signaling cascades converging on transcriptional control.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0032754","count":1},{"id":"GO:0032743","count":1},{"id":"GO:0086004","count":1}]},{"hash":"941528271649527605","title":"Neuronal GTPase-driven cytoskeletal dynamics","description":"The cluster is enriched for small GTPase-mediated signaling and filopodium-related actin remodeling (positive regulation of substrate adhesion-dependent cell spreading; filopodium assembly; regulation of filopodium assembly), which points to actin-driven protrusions. Additional terms like GABAergic synaptic transmission and neuromuscular balance suggest a neuronal/synaptic context, while endosome transport and mitochondrial fission indicate broader trafficking and organelle dynamics relevant to neurites. Together, these terms support a focus on neuronal cytoskeletal remodeling and related trafficking driven by GTPase signaling.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0000266","count":3},{"id":"GO:0043497","count":3},{"id":"GO:0046847","count":3}]},{"hash":"2023370608037105752","title":"DNA Damage Response and Chromatin Regulation","description":"The top GO terms cluster around mitotic/intra-S and G1 DNA damage checkpoint signaling, nucleotide-excision repair, and chromatin-related processes like histone modification and heterochromatin formation, suggesting a cohesive role in genome maintenance during the cell cycle.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034729","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0031573","count":1},{"id":"GO:0070911","count":1}]},{"hash":"581437261200316131","title":"Unknown","description":"The top terms span lipid transport, defense and inflammatory signaling, TORC1 signaling, cell division, rRNA maturation, protein kinase regulation, and intraciliary transport, with no clear single function tying all proteins together. The mix, plus obsolete terms and lack of interactions, suggests no cohesive theme for a precise label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006869","count":1},{"id":"GO:0034053","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0038202","count":1}]},{"hash":"642391049942180654","title":"Unknown","description":"Top Terms are not provided, and with only four proteins and minimal connectivity, there is no clear shared function to deduce a meaningful label. Without GO terms or domain signals, the cluster cannot be reliably named.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"1719402192572643402","title":"Unknown","description":"The proteins point to a highly diverse set of biosynthetic and developmental processes (steroid, inositol, antibiotic, alkaloid, lipopolysaccharide biosynthesis, plus neural development and sporulation) with no clear, shared pathway or function. Because there is no cohesive theme or interaction pattern, a specific label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010264","count":1},{"id":"GO:0052746","count":1},{"id":"GO:0021915","count":1},{"id":"GO:0032957","count":1},{"id":"GO:0030435","count":1}]},{"hash":"1459322404096595630","title":"Lipid Metabolism and Lipoprotein Homeostasis","description":"This cluster shows strong enrichment for lipid-related processes: triglyceride and diacylglycerol biosynthesis, ceramide and long-chain fatty-acyl-CoA metabolism, acyl-chain remodeling, lipid storage, and regulation of plasma lipoprotein particle levels, plus intestinal lipid absorption and responses to fatty acids. The combined themes point to coordinated lipid biosynthesis, remodeling, storage, and lipoprotein handling.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":3},{"id":"GO:0006672","count":2},{"id":"GO:0036155","count":2},{"id":"GO:0034383","count":2},{"id":"GO:0050892","count":2}]},{"hash":"393170190572792371","title":"Golgi and Vesicle Trafficking","description":"The top GO terms include protein retention in the Golgi, SNARE complex disassembly, intralumenal vesicle formation, and maintenance of protein location at the plasma membrane, all of which point to membrane trafficking and Golgi-associated transport. Although a few entries are obsolete, the core signal is a vesicle trafficking/localization module, especially related to Golgi function and vesicle formation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":2},{"id":"GO:0045053","count":1},{"id":"GO:0035494","count":1},{"id":"GO:2001171","count":1},{"id":"GO:0072660","count":1}]},{"hash":"858874400585819444","title":"Unknown","description":"The GO terms are highly diverse (ubiquitination, cilium assembly, interferon response, transcriptional regulation of metabolism, protein folding, secretion, cell cycle regulation, chlorophyll biosynthesis, viral replication, GPCR signaling). There isn\u2019t a single coherent theme or shared function tying these four proteins together, so a concise, representative label cannot be determined.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:1905515","count":1},{"id":"GO:0035457","count":1},{"id":"GO:2000531","count":1},{"id":"GO:1903646","count":1}]},{"hash":"2121095679783504143","title":"Unknown","description":"The terms are highly heterogeneous, including metabolism (thymidine, pyrimidine bases, AMP, tryptophan), regulation of myelination and gastric motility, angiogenesis, and chemotaxis, with several obsolete GO annotations. There is no clear, shared biological process or function linking the four proteins (no edges or triangles), so a cohesive cluster label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000746","count":1},{"id":"GO:0006627","count":1},{"id":"GO:1905333","count":1},{"id":"GO:0046104","count":1},{"id":"GO:0031641","count":1}]},{"hash":"510352119391542681","title":"T cell differentiation and RNA regulation","description":"Top GO terms include multiple immune differentiation processes (T follicular helper cell differentiation, T cell homeostasis, positive regulation of monocyte differentiation) alongside RNA processing terms (mRNA splicing via spliceosome, deadenylation-dependent decay, polyadenylation). This blend suggests a loose link between immune cell differentiation and RNA metabolism, but the set is sparse and lacks a tight cohesive function. Therefore, this label is a best-fit representation rather than a strongly cohesive cluster. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0071364","count":1},{"id":"GO:0045657","count":1},{"id":"GO:0046782","count":1},{"id":"GO:0061470","count":1}]},{"hash":"1736612123886128303","title":"Unknown","description":"The top GO terms are a mix of membrane trafficking (endocytic recycling, maintenance of protein localization at the plasma membrane), cell movement, muscle-related remodeling (skeletal muscle tissue regeneration, cell growth), and even a cold-response term, with several terms marked obsolete. There is no single cohesive biological process or function that clearly ties all four proteins together, and the presence of obsolete terms further diminishes interpretability. Therefore, a reliable, specific label cannot be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0007205","count":2},{"id":"GO:2001275","count":2},{"id":"GO:1990126","count":2},{"id":"GO:0072660","count":1}]},{"hash":"1259677020719328414","title":"Ubiquitin-regulated muscle sarcomere organization","description":"The core GO terms point to ubiquitination processes (K33-linked ubiquitination, ubiquitin-dependent proteolysis, and regulation of ubiquitination) and muscle-specific architecture (sarcomere organization, skeletal muscle development), suggesting a module tied to ubiquitin signaling controlling muscle structure. Some broader terms appear, but the muscle-related signals dominate.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990390","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0036268","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0019046","count":1}]},{"hash":"2019702984840000617","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034475","count":1},{"id":"GO:0000378","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0042766","count":1},{"id":"GO:1903241","count":1}]},{"hash":"137065984256657548","title":"Nuclear transport and protein complex assembly","description":"The GO terms point to nuclear processes (protein import into nucleus, tRNA export from nucleus, mitotic nuclear membrane disassembly) along with protein complex formation and turnover (oligomerization, ubiquitin-dependent degradation). This combination suggests a role in coordinating nuclear transport with protein assembly/degradation. The signal is present but limited (single terms), so the label is plausible but not definitive.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007077","count":1},{"id":"GO:0042306","count":1},{"id":"GO:0006409","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0075733","count":1}]},{"hash":"646349904397234652","title":"Intracellular protein trafficking and maturation","description":"The top GO terms cluster around movement and processing of proteins within the cell, including import into the peroxisome matrix, ER-to-Golgi vesicle transport, Golgi retention, and SNARE complex disassembly, all pointing to trafficking and maturation of proteins across organelles. While a few terms touch on unrelated areas (cell cycle checkpoints, centriole elongation, and metabolism), the dominant theme is intracellular protein trafficking and maturation, justifying the label. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":1},{"id":"GO:0045053","count":1},{"id":"GO:0035494","count":1},{"id":"GO:0033314","count":1},{"id":"GO:2001171","count":1}]},{"hash":"634890571370051877","title":"Dopaminergic Signaling and AKT Pathway","description":"This cluster shows dopaminergic synaptic transmission and neuronal excitability signals (GO:0001963, GO:0060081) combined with AKT/PI3K pathway activation (GO:0051897, GO:0032148) and transcription-related terms (GO:0006351, GO:2000679), suggesting a cohesive role in dopamine-mediated neuronal signaling with AKT-dependent transcriptional regulation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046826","count":2},{"id":"GO:0032148","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001963","count":2},{"id":"GO:0033138","count":2}]},{"hash":"1439257540188455278","title":"Actin Cytoskeleton and Migration Signaling","description":"The cluster includes GO terms about cell migration (mesendoderm), actin cytoskeleton polarity, and TORC2 signaling, all pointing to cytoskeletal regulation and associated signaling pathways that govern cell movement and structural remodeling. Other terms like stress granule assembly and mRNA processing may be less connected, but the strongest common theme is actin dynamics and migration-related signaling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090134","count":1},{"id":"GO:0038203","count":1},{"id":"GO:0051124","count":1},{"id":"GO:0030950","count":1},{"id":"GO:0034063","count":1}]},{"hash":"1283424378217747089","title":"Unknown","description":"The listed GO terms are very diverse, including translation, gamma radiation response, blastocyst growth, meiosis cohesion, DNA repair, circadian regulation, development, and broad protein regulation. There is no single, cohesive theme uniting these functions for this cluster, so a definite label cannot be assigned with confidence.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0071480","count":1},{"id":"GO:0001832","count":1},{"id":"GO:1990426","count":1},{"id":"GO:0042754","count":1}]},{"hash":"58503451769209617","title":"RNA Pol II Transcription Initiation and Regulation","description":"These proteins predominantly tie to RNA polymerase II\u2013mediated transcription initiation and its regulation, including promoter open complex formation and initiation at RNAP II promoters. While a few other terms (viral process, membrane protein localization, etc.) appear, the core signal is transcription initiation/regulation by RNAP II, making this label representative of the cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001113","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0072660","count":1}]},{"hash":"960657115718248829","title":"Unknown","description":"There are no GO terms or connections to bind these proteins into a common function; with zero edges/triangles and no top terms, a cohesive theme cannot be determined from the data provided.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1265087301128586133","title":"Unknown","description":"There are no shared GO terms or network connections (Edges 0, Triangles 0, Max Degree 0) and no clear functional theme among the few proteins, so a coherent cluster label cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1816668355344667129","title":"Protein quality control and degradation pathways","description":"The top GO terms point to cellular protein quality control, including mitophagy, ERAD-related unfolded protein maintenance, deglycosylation, and sumoylation, as well as stress responses and vesicle formation regulation. These collectively suggest a function in detecting and disposing of damaged or misfolded proteins via autophagic/ERAD routes and related trafficking. Some terms are obsolete or less directly connected, but the core theme is protein quality control and turnover.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000423","count":3},{"id":"GO:1904378","count":3},{"id":"GO:0030474","count":3},{"id":"GO:1905366","count":3},{"id":"GO:1902283","count":3}]},{"hash":"1370757821170102197","title":"Mitochondrial ATP synthase assembly","description":"The top GO term is mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615), indicating these proteins are linked to assembling the mitochondrial ATP synthase complex. With no other interactions highlighted, the cluster appears to represent a small assembly-focused group, supporting the label.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033615","count":1}]},{"hash":"966692372406758811","title":"Actin cytoskeleton dynamics","description":"The cluster is enriched for GO terms related to actin organization and dynamics, including Arp2/3 complex-mediated actin nucleation, actin motor activity, phagocytosis, and mitotic actomyosin ring assembly, indicating a core function in actin cytoskeleton regulation and cellular movement. A few terms are less clearly linked (e.g., retina homeostasis, aggressive behavior), but the dominant theme is actin-based processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904623","count":3},{"id":"GO:0002121","count":3},{"id":"GO:0032508","count":3},{"id":"GO:0001895","count":3},{"id":"GO:0070527","count":3}]},{"hash":"482491777503418282","title":"Unknown","description":"The top GO terms span both basic cellular processes (tRNA processing, ribosome disassembly) and a wide range of energy metabolism pathways (photosynthesis, electron transport chain, formate metabolism, methanogenesis, sulfate reduction) plus motility, with no single cohesive function linking them all. The cluster appears heterogeneous, so a definite label is not attainable.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:0009773","count":1},{"id":"GO:0032790","count":1},{"id":"GO:0022900","count":1},{"id":"GO:0015944","count":1}]},{"hash":"543370188059880563","title":"Triglyceride catabolism and lipid remodeling","description":"This cluster is dominated by GO terms for triglyceride catabolic processes, triglyceride mobilization, and acyl-chain remodeling of triglycerides and phospholipids (lipid catabolism/remodeling). While a couple of terms like brain development and regulation of PKA activity appear, the strongest shared signal is lipid breakdown and remodeling, justifying the label. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034638","count":2},{"id":"GO:0036153","count":2},{"id":"GO:0046338","count":2},{"id":"GO:0006642","count":2},{"id":"GO:2000480","count":2}]},{"hash":"1993913300023990114","title":"Unknown","description":"The GO terms span meiotic regulation, various hormone responses (ABA, cytokinin, SA), telomere assembly, and development, with no single shared function across the proteins. There is no coherent theme to label this cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010520","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1904792","count":1},{"id":"GO:1903086","count":1}]},{"hash":"226752450996528273","title":"Diverse Transmembrane Transport","description":"GO terms here cluster around transport across membranes for a variety of substrates, including ions (sodium, phosphate), sugars (galactose, arabinose, fucose), vitamins, and even neurotransmitter loading into synaptic vesicles, plus other transport-related processes. This suggests the proteins in this cluster are primarily involved in membrane transport of diverse solutes rather than a single, narrow pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0015757","count":1}]},{"hash":"587240423509023447","title":"Ubiquitin-Dependent Signaling and NF-\u03baB Regulation","description":"The top terms are dominated by various ubiquitination processes (K48, K63, and K6 linked; autoubiquitination; ubiquitin-dependent protein catabolic process) and pathways that feed into NF-\u03baB signaling (activation of NIK, I-\u03baB phosphorylation, regulation of apoptotic processes). This pattern points to a cohesive theme of ubiquitin-mediated regulation that influences NF-\u03baB activity and downstream responses like apoptosis, with some terms touching chromatin modification (histone ubiquitination) and immune gene rearrangement (V(D)J recombination). Despite the small cluster size, the common thread is clearly ubiquitin-driven signaling and NF-\u03baB pathway modulation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0007250","count":2},{"id":"GO:0033151","count":2}]},{"hash":"2175769442131874798","title":"Multisystem Development","description":"The top GO terms indicate development across multiple tissues and organs (skin, renal/genital systems, cartilage) plus a general cell cycle regulatory term, suggesting proteins clustered under broad developmental programs rather than a single pathway. While sensory terms appear, the dominant signal points to multisystem organ development, making a label like Multisystem Development appropriate and interpretable.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0050960","count":2},{"id":"GO:2000134","count":1},{"id":"GO:0072001","count":1}]},{"hash":"1422976766475874049","title":"Unknown","description":"The top GO terms cover a broad and disparate set of processes (light response/photomorphogenesis, miRNA processing, endosomal transport, hormone signaling, and various developmental/behavioral terms) with no clear shared function or interaction among the proteins (no edges or triangles). There isn\u2019t a cohesive theme to tie these together reliably.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010099","count":1},{"id":"GO:0009637","count":1},{"id":"GO:0035196","count":1},{"id":"GO:0010114","count":1},{"id":"GO:0009873","count":1}]},{"hash":"76482573653454005","title":"Unknown","description":"The GO terms span immune signaling (T cell costimulation, cytokine production), neuronal development (dendritic spine morphogenesis, behavior), vascular differentiation (pericyte differentiation), and general signaling/cell processes (TORC1 signaling, adenosine receptor signaling, ribosome maturation, mitotic cohesion, slit diaphragm assembly); there is no single unifying function evident among the proteins, so a concise, representative cluster name cannot be assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000525","count":1},{"id":"GO:0060997","count":1},{"id":"GO:0038202","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0044708","count":1}]},{"hash":"1648268991457247238","title":"Inflammation and Heat-Stress Response","description":"The proteins cluster around cytokine regulation (positive regulation of IL-6 and TNF production), heat response, and proteostasis (protein stabilization and chaperone-assisted refolding). While a few terms like sperm binding and telomere maintenance are less coherent with this theme, the dominant signals point to inflammatory signaling linked to cellular stress and protein homeostasis.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000778","count":3},{"id":"GO:0033198","count":3},{"id":"GO:0007339","count":3},{"id":"GO:0014823","count":3},{"id":"GO:0050821","count":3}]},{"hash":"1820801273817038246","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033317","count":1},{"id":"GO:0000162","count":1},{"id":"GO:0046391","count":1},{"id":"GO:0070981","count":1},{"id":"GO:0006189","count":1}]},{"hash":"1440855370927160486","title":"Amino Acid Catabolism and Quinone Biosynthesis","description":"This cluster\u2019s top GO terms center on amino acid catabolic processes (phenylacetate, valine) and quinone biosynthesis (menaquinone, phylloquinone), with additional signals for lipid metabolism and antibiotic biosynthesis, suggesting a microbial metabolic module. The label emphasizes the two core themes: amino acid degradation and quinone biosynthesis.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":3},{"id":"GO:0006574","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006635","count":3}]},{"hash":"1717850165784006097","title":"Endocannabinoid signaling and regulation","description":"Top GO terms indicate a cohesive theme around endocannabinoid signaling, including endocannabinoid signaling pathway, retrograde trans-synaptic signaling by endocannabinoid, and regulation of endocannabinoid signaling pathway. A few other terms (arginine biosynthesis, urea cycle, cellulose catabolic process) appear only once and likely reflect annotation noise or incidental associations. Overall, the most representative function of this cluster is endocannabinoid signaling and its regulation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":1},{"id":"GO:0071499","count":1},{"id":"GO:0000050","count":1},{"id":"GO:0000053","count":1},{"id":"GO:0000052","count":1}]},{"hash":"110232682674002286","title":"Meiotic Chromatin Silencing and Cell Cycle Regulation","description":"This cluster centers on meiotic processes and chromatin at mating-type loci (meiotic DSB formation, silent/heterochromatin at mating-type cassette) with concurrent links to cell cycle transitions (G2/M, exit from mitosis) and ubiquitin-mediated protein regulation, suggesting a coordinated role in meiosis and chromatin control.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0043951","count":3},{"id":"GO:0007288","count":3},{"id":"GO:0071596","count":3},{"id":"GO:0035519","count":3},{"id":"GO:0000086","count":3}]},{"hash":"848244249506160967","title":"Protein and polyamine acetylation","description":"The Top Terms are dominated by acetylation-related processes (spermidine acetylation, spermine acetylation, N-terminal peptidyl acetylation), with additional biosynthetic/catabolic terms that may involve acetylation steps. This suggests a theme centered on acetylation modifications of proteins and polyamines, rather than a single cohesive pathway. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":2},{"id":"GO:0010125","count":2},{"id":"GO:2000025","count":2},{"id":"GO:0046208","count":2},{"id":"GO:0045150","count":2}]},{"hash":"1921499610773887011","title":"Transmembrane transporters","description":"The top GO terms are dominated by transmembrane transport activities (ions like Na+ and K+, and various sugars and nutrients), with one term related to neurotransmitter loading into synaptic vesicles. This pattern points to proteins that move substrates across membranes rather than a single metabolic pathway, suggesting a cluster of membrane transporter proteins. Overall, the label captures the shared function suggested by the GO annotations.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0015757","count":1}]},{"hash":"1998286316383114781","title":"Wnt Secretion and ER-Golgi Trafficking","description":"The GO terms point to secretory pathway components (COPI vesicles, Golgi ribbon, ER retention and exit) and regulation of Wnt secretion, with some development-related terms that may reflect downstream effects. This makes a cohesive theme around intracellular trafficking of secreted proteins, especially Wnt, rather than other unrelated processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061357","count":1},{"id":"GO:0002121","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0007311","count":1},{"id":"GO:0090161","count":1}]},{"hash":"1175320895408414642","title":"Exocyst-Mediated Vesicle Transport","description":"The top GO terms cluster around exocytosis, vesicle tethering, exocyst assembly, and Golgi-to-plasma membrane transport, all characteristic of the exocyst complex coordinating vesicle docking and release at the plasma membrane. This suggests the proteins function in exocytosis and targeted secretion, with some peripheral transport terms but the dominant theme is vesicle trafficking via the exocyst.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0090522","count":1},{"id":"GO:0001927","count":1},{"id":"GO:0006893","count":1},{"id":"GO:0006887","count":1}]},{"hash":"1823078098756661248","title":"TLR2-driven inflammatory signaling","description":"The cluster is dominated by GO terms related to innate immune activation, specifically TLR2 signaling, macrophage activation, I-kappaB phosphorylation (NF-\u03baB pathway), and inflammatory responses. While there are a few neuronal development terms present, the inflammatory and immune signaling themes prevail, supporting a label centered on TLR2-mediated inflammation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061368","count":1},{"id":"GO:0034134","count":1},{"id":"GO:0090394","count":1},{"id":"GO:0042116","count":1},{"id":"GO:0007252","count":1}]},{"hash":"525868550030153478","title":"GPI-anchored fungal cell wall proteins","description":"The strongest signals are GPI anchor biosynthesis and attachment to proteins, plus fungal-type cell wall organization, suggesting these proteins may be cell-surface, GPI-anchored components involved in fungal cell wall structure. Other terms appear more general or incidental, so the link is best explained by GPI-anchored cell wall proteins in fungi.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904715","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0043085","count":2},{"id":"GO:0046938","count":2},{"id":"GO:0031505","count":1}]}]