[{"hash":"1302000007789815666","title":"Unknown","description":"The GO terms span highly diverse processes (autophosphorylation, telomerase holoenzyme assembly, DNA topology changes, chromosome segregation, xenobiotic response, IL-4 signaling, placenta development, etc.) with no clear shared pathway or function, and there are no edges connecting members. This lack of a cohesive theme makes it inappropriate to assign a specific, representative name.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901389","count":1},{"id":"GO:0046777","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0000160","count":1},{"id":"GO:0035690","count":1}]},{"hash":"410890624716845471","title":"Steroid signaling and male reproductive development","description":"The top GO terms cluster around steroid-related reproductive biology, with prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly indicating a focus on androgen/steroid signaling in male development. While there are additional terms for general cellular processes (cell division, mitochondrial translation, mRNA export) and immune response, the strongest common theme is steroid signaling linked to male reproductive biology.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0046661","count":2}]},{"hash":"2024332694263689168","title":"Potassium Ion Homeostasis and Membrane Excitability","description":"This cluster centers on potassium homeostasis and membrane potential regulation, with recurrent terms for intracellular potassium balance, potassium transport, membrane potential stabilization, resting potential regulation, and cardiac action potential repolarization. Additional signals like sodium import and cGMP-responsive pathways, plus mechanosensory and aerotaxis terms, suggest linked membrane signaling alongside ion balance.","confidence":"High","size":29,"edges":401,"triangles":3523,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030007","count":23},{"id":"GO:0050976","count":22},{"id":"GO:0071805","count":22},{"id":"GO:0098914","count":22},{"id":"GO:0030322","count":22}]},{"hash":"1820004076519081722","title":"Ciliogenesis and Centrosome/Cilia Organization","description":"The proteins cluster around centriole/centrosome biology and ciliogenesis (centrosome duplication, centriole replication, centriole cohesion, cilium assembly) with planar polarity and stereocilia organization; additional terms like Golgi localization and kidney development align with ciliopathy-related processes, indicating a ciliogenesis/centrosome module.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006810","count":1},{"id":"GO:0051298","count":1},{"id":"GO:0010457","count":1},{"id":"GO:0007099","count":1},{"id":"GO:0060271","count":1}]},{"hash":"1134130956461113318","title":"Hippocampal synapse formation and signaling","description":"This cluster centers on neuronal development and synaptic function in the hippocampus, with strong signals for excitatory postsynaptic potentials, dendrite morphogenesis, axon extension, and calcium-dependent exocytosis, plus dopamine responsiveness. Together these terms point to a module involved in establishing and modulating hippocampal synapses and activity-dependent signaling; other terms reflect broader neuronal signaling and protein regulation that support these processes.","confidence":"High","size":29,"edges":6,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":29},{"id":"GO:0021766","count":29},{"id":"GO:0045956","count":29},{"id":"GO:0046330","count":29},{"id":"GO:0034198","count":29}]},{"hash":"1456195997725966539","title":"Ribosome biogenesis and translation machinery","description":"This cluster\u2019s top GO terms are dominated by translation- and ribosome-related processes (translation, cytoplasmic translation, translational initiation, ribosome biogenesis, tRNA modification). A few terms pertain to cell cycle/division and stress responses, but the strongest pattern is assembly of ribosomes and protein synthesis, indicating a cohesive function in ribosome biogenesis and translation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0051301","count":5},{"id":"GO:1903833","count":4}]},{"hash":"1790878790122061169","title":"Unknown","description":"The Top Terms cover aerotaxis, cellular responses to cGMP and cAMP, receptor guanylyl cyclase signaling, ion transport (sodium and potassium), sarcomere organization, transcription, nuclear export, and mechanosensory touch detection. These terms span signaling, ion transport, muscle structure, and nuclear processes with no clear, single unifying function, so there isn\u2019t a cohesive theme to name a specific cluster. ","confidence":"","size":29,"edges":35,"triangles":1,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009454","count":7},{"id":"GO:0071321","count":7},{"id":"GO:0010754","count":7},{"id":"GO:0071320","count":7},{"id":"GO:0098719","count":7}]},{"hash":"2028123150491246732","title":"ER stress and ubiquitin-mediated protein degradation","description":"The dominant GO terms point to unfolded protein response, ER-associated degradation, and ubiquitin signaling (including K11-linked ubiquitination), with cadmium- and interferon-related stress responses also represented, suggesting a cluster tied to protein quality control under cellular stress.","confidence":"Medium","size":29,"edges":144,"triangles":127,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009938","count":21},{"id":"GO:0071276","count":21},{"id":"GO:0006986","count":21},{"id":"GO:1903071","count":21},{"id":"GO:0051348","count":21}]},{"hash":"1899303438954019559","title":"Transcriptional Regulation and RNA Processing","description":"The highest-weighted terms center on transcription and mRNA processing (DNA-templated transcription, positive regulation of transcription by RNA polymerase II, and nuclear-transcribed mRNA poly(A) tail shortening), indicating a core function in gene expression control. Some metabolic and developmental terms are present but less represented, so the dominant theme is transcriptional regulation and RNA processing.","confidence":"Medium","size":29,"edges":25,"triangles":5,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000023","count":5},{"id":"GO:0000289","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0045944","count":4},{"id":"GO:0050884","count":4}]},{"hash":"1307809766391101283","title":"Bacterial lipid and secondary metabolite biosynthesis","description":"The set centers on lipid and fatty acid metabolism (various chain lengths, transport, lipoteichoic acid biosynthesis) and on bacterial secondary metabolism (menaquinone biosynthesis, nonribosomal peptide biosynthesis, bioluminescence). These collectively suggest a module focused on membrane-associated lipid pathways and production of secondary metabolites typical of bacteria, including Gram-positive features. ","confidence":"High","size":29,"edges":148,"triangles":599,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":11},{"id":"GO:0008218","count":11},{"id":"GO:0070395","count":11},{"id":"GO:0001579","count":11},{"id":"GO:0009698","count":11}]},{"hash":"1969304002952013358","title":"Innate Immune Sensing and DC Antigen Presentation","description":"The proteins cluster around innate immune recognition (TLR9 and NOD2 signaling, MDP detection) and inflammasome activity (NLRP3), with downstream interferon signaling and dendritic cell antigen processing/presentation, including MHC class I biosynthesis. This points to a cohesive pathway from innate sensing to DC activation and antigen presentation, consistent with immune response and trafficking components.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":3},{"id":"GO:0030335","count":3},{"id":"GO:1902745","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0002830","count":3}]},{"hash":"35198813074078900","title":"Neuro-immune signaling and development","description":"This cluster shows prominent neural development terms (cerebellar cortex formation, cell morphogenesis, axon regeneration) alongside immune signaling (innate immune response, T cell receptor signaling). It also includes signaling-related processes like insulin receptor signaling and transcription, suggesting a broader theme of coordinated signaling and development across neural and immune contexts rather than a single, tight pathway. The label captures the main functional threads without overfitting to a single GO term.","confidence":"Medium","size":29,"edges":154,"triangles":486,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":20},{"id":"GO:0008286","count":20},{"id":"GO:0021697","count":20},{"id":"GO:2001275","count":20},{"id":"GO:0008285","count":20}]},{"hash":"18183807893115003","title":"Unknown","description":"The top GO terms span very different biology\u2014DNA replication and mitotic cell cycle point to proliferation, while visual perception, trachea formation, NK T cell differentiation, and Rho signaling/focal adhesion indicate development, immunity, and signaling. There is no single dominant functional theme linking the cluster's proteins, suggesting a mixed or noisy set rather than a cohesive module.","confidence":"","size":29,"edges":20,"triangles":1,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":28},{"id":"GO:0006260","count":28},{"id":"GO:0000278","count":28},{"id":"GO:1901214","count":27},{"id":"GO:0060440","count":27}]},{"hash":"1439564227711329899","title":"Ion transport and temperature-responsive signaling","description":"The terms indicate ion transport (sodium import, potassium transport) and signaling (cGMP and cAMP pathways) alongside environmental sensing features (aerotaxis, thermoception, cold response) and transcriptional regulation, suggesting a cluster of proteins that integrate ion movement with signaling and gene regulation in response to temperature and environmental cues.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":4},{"id":"GO:0010754","count":4},{"id":"GO:0009454","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0071321","count":4}]},{"hash":"2167409613544538762","title":"GTPase signaling and cardiac sarcomere regulation","description":"The top GO terms cluster around small GTPase-mediated signaling (including Ras and GPCR-related pathways) and modulation of cyclic nucleotide signaling (adenylate and guanylyl cyclase pathways), with supporting terms on sarcomere organization and cardiac muscle cell proliferation. This suggests a theme of signaling pathways that influence cardiac muscle structure and growth, even though a few outlier terms are present. ","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0007264","count":2}]},{"hash":"711821091132700143","title":"Unknown","description":"The listed GO terms span metal transport, hormone response, metabolic regulation, cardiac function, phospholipid translocation, ear development/mineralization, and calcium-dependent neurotransmitter exocytosis, with no clear shared function tying the proteins together. This heterogeneity makes it hard to assign a cohesive, specific label.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":2},{"id":"GO:0033574","count":2},{"id":"GO:1903249","count":2},{"id":"GO:0098736","count":2},{"id":"GO:0061092","count":2}]},{"hash":"1147597326997840863","title":"Unknown","description":"Top terms span RNA methylation (tRNA methylation, RNA (guanine-N7)-methylation) and a broad set of chemical/stress responses (response to cocaine, cellular response to xenobiotic stimulus, response to amine, cadmium, hyperosmotic response) plus a cell cycle term, with no clear unifying function or interactions. The lack of edges further suggests the terms do not define a cohesive module, so a concise, accurate label cannot be determined.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042220","count":4},{"id":"GO:0009236","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0036265","count":3}]},{"hash":"77169464949051834","title":"Xenobiotic Detoxification and Redox Response","description":"This cluster's top GO terms center on detoxification and redox processes: xenobiotic and camphor/propylene catabolic processes, along with oxygen metabolism, superoxide removal, and redox homeostasis. While there are some transcriptional regulation terms present, the dominant signal is detoxification and oxidative stress response.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0019430","count":5},{"id":"GO:0019383","count":5}]},{"hash":"2289151615781548080","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"The terms cluster around mitochondria: apoptotic mitochondrial changes, membrane potential regulation, and transport of key metabolites (alpha-ketoglutarate, thiamine pyrophosphate, CoA), plus the malate-aspartate shuttle. This supports a theme of mitochondrial metabolite transport and membrane potential control.","confidence":"High","size":29,"edges":15,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":6},{"id":"GO:0051881","count":6},{"id":"GO:0015742","count":6},{"id":"GO:0030974","count":6},{"id":"GO:0035349","count":6}]},{"hash":"1660485328899610283","title":"Protein Synthesis and Gene Expression Regulation","description":"The cluster is dominated by translation-related GO terms (formation of translation initiation complex, translation, preinitiation complex) and transcription regulation, with additional signals of differentiation and Golgi/ER pathways. This points to a cohesive theme of gene expression control and protein synthesis, rather than a single specialized process.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001732","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0002250","count":2}]},{"hash":"292114213570549644","title":"Unknown","description":"The Top Terms span skeletal muscle development, B cell signaling, renal morphogenesis, and ubiquitination processes with no clear shared function; the terms cover disparate biological areas (muscle, immune signaling, kidney, and protein ubiquitination), and there is no dominant pathway or cohesive theme.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0070294","count":2},{"id":"GO:0031397","count":2}]},{"hash":"1443421418664802042","title":"DNA replication and cell cycle checkpoint regulation","description":"The GO terms center on DNA replication, cell cycle progression, and checkpoint signaling, with related processes like replication fork dynamics, chromatid cohesion, and ubiquitination indicating coordinated replication stress response and regulation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0034087","count":1},{"id":"GO:0033262","count":1},{"id":"GO:0043111","count":1}]},{"hash":"1462076711222632726","title":"Unknown","description":"The GO terms are highly diverse: DNA-templated transcription and nuclear protein export; Ras and small GTPase signaling; sarcomere organization; ion transport; drug response; and aerotaxis. This mix lacks a single cohesive biological function or pathway to unify the cluster, so a specific functional label is not justifiable. ","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0046580","count":5},{"id":"GO:0007264","count":5},{"id":"GO:0051447","count":4}]},{"hash":"1701343922937561591","title":"Mitotic signaling and transcription regulation","description":"This cluster's top GO terms emphasize regulatory activities such as serine/threonine kinase activity, GTPase regulation, and protein autophosphorylation, together with DNA-templated transcription and mitotic cell cycle processes, suggesting a nucleus-centered program coordinating signaling with gene expression during cell division. Some terms are obsolete or peripheral (histone methylation, hypoxia, SREBP), but the dominant pattern is mitotic signaling linked to transcriptional control.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071902","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3}]},{"hash":"244718025418094233","title":"Neuronal development and synaptic signaling","description":"These proteins cluster around neuronal-centric processes: brain development and touch perception, regulation of synaptic vesicle exocytosis, MAPK/ERK signaling regulation, and cytoskeletal remodeling (stress fiber assembly), with ubiquitination as a modulator. Some terms may reflect broader or cross-species annotations (viral replication, mating projection growth), but the dominant pattern supports neuronal development and synaptic communication.","confidence":"Medium","size":28,"edges":175,"triangles":226,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043149","count":7},{"id":"GO:0070374","count":7},{"id":"GO:0050975","count":7},{"id":"GO:0033138","count":7},{"id":"GO:0016567","count":7}]},{"hash":"399732143727390993","title":"Cardiac muscle signaling and sarcomere organization","description":"This cluster predominantly maps to cardiac muscle biology: terms include sarcomere organization and cardiac muscle cell proliferation, plus signaling pathways involving cAMP and cGMP, and sodium ion transport, which are central to heart contraction and electronic signaling. The presence of DNA-templated transcription and protein tetramerization hints at transcriptional regulation and structural assembly of sarcomeric proteins. Despite a few outliers like aerotaxis and meiotic cell cycle regulation, the core theme centers on cardiac muscle contraction, signaling, and structural organization.","confidence":"High","size":28,"edges":132,"triangles":149,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009454","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0071321","count":6},{"id":"GO:0010754","count":6},{"id":"GO:0071320","count":6}]},{"hash":"1564314530476152395","title":"RNA processing and post-transcriptional regulation","description":"These proteins cluster around RNA metabolism and post-transcriptional control: mRNA splicing via the spliceosome, mRNA stabilization and regulation of stability under stress, regulatory ncRNA- and miRNA-mediated gene silencing, and assembly of translation-related complexes (eIF4F) and small-subunit processomes. The shared theme is processing, stability, silencing, and translation control of mRNA after transcription.","confidence":"High","size":28,"edges":36,"triangles":6,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048255","count":3},{"id":"GO:1902625","count":3}]},{"hash":"2061096511167659306","title":"Unknown","description":"The top GO terms are highly diverse (metabolism, autophagy/vesicle targeting, lipidation, cell cycle regulation, development) with little cohesive functional theme, and several terms are obsolete. This suggests no single clear function ties the proteins together, so it\u2019s best labeled Unknown.","confidence":"","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097755","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0019373","count":2},{"id":"GO:0060996","count":1}]},{"hash":"939788017146243989","title":"Mitochondrial import, lipid metabolism, and stress signaling","description":"Most representative terms point to mitochondria, including protein import into the mitochondrial matrix (GO:0030150) and regulation of mitochondrial membrane permeability (GO:0046902). The presence of metabolic and stress-related terms such as positive regulation of triglyceride biosynthetic process (GO:0010867) and cellular response to hydrogen peroxide (GO:0070301) suggests a cluster centered on mitochondrial function, metabolism, and stress signaling. A few cell cycle/DNA recombination terms appear, but they are less central to the core mitochondrial theme.","confidence":"Medium","size":28,"edges":30,"triangles":3,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":4},{"id":"GO:1903740","count":3},{"id":"GO:0046902","count":3},{"id":"GO:0030150","count":3},{"id":"GO:2000134","count":3}]},{"hash":"1557370023001237169","title":"Proteolysis and phytochelatin biosynthesis in plants","description":"The highest-frequency GO terms are proteolysis and phytochelatin biosynthetic process, with strong representation (15 and 14), pointing to a functional theme around protein turnover and metal detox via phytochelatins in plants. Other terms like DNA replication and transcription regulation are present but much less dominant, suggesting they are secondary annotations. Based on the dominant terms, the cluster likely groups proteins involved in proteolysis and phytochelatin-mediated detox pathways in plants.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":15},{"id":"GO:0046938","count":14},{"id":"GO:0043085","count":14},{"id":"GO:1904715","count":14},{"id":"GO:0042340","count":3}]},{"hash":"2025745665490246906","title":"Ubiquitin-Proteasome and Innate Immunity","description":"The prominent GO terms emphasize ubiquitin-dependent protein degradation and polyubiquitination (proteostasis) alongside innate immune signaling pathways (TLR9, NOD2, and type II interferon signaling) and related immune-regulatory processes such as cell migration. While RNA guanine-N7 methylation and brain development appear among the terms, they seem less central to the cluster\u2019s core theme. Overall, the cluster best fits a proteostasis-linked innate immunity theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0034162","count":1}]},{"hash":"1269553688422670057","title":"Kinase signaling and cell cycle regulation","description":"GO terms in this cluster emphasize regulation of GTPase activity, serine/threonine kinase activity and autophosphorylation, along with mitotic cell cycle and developmental processes. Together, they point to proteins that regulate signaling pathways and cell proliferation/differentiation, rather than a single siloed function, supporting this label.","confidence":"High","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:0000278","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0007205","count":4}]},{"hash":"710756632600635567","title":"Calcium-Dependent Stress Signaling","description":"This cluster is characterized by GO terms related to cellular response to xenobiotic stimulus, calcium ion transport and signaling, and regulation of the JNK cascade, indicating stress-activated pathways modulated by calcium. While some terms are more general, the prominent theme is calcium-linked stress signaling.","confidence":"Medium","size":28,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0000001","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0070588","count":2}]},{"hash":"1250234351734175535","title":"Nuclear DNA Replication and Developmental Cell Cycle","description":"The cluster is dominated by GO terms for DNA replication, transcription, and centrosome/mitotic cycle regulation, with additional embryonic development terms (cranial skeleton morphogenesis, trachea formation) suggesting a link between nuclear/nuclear-cytoplasmic processes and development. This combination supports a concise theme: nuclear DNA replication and cell cycle control in development.","confidence":"High","size":28,"edges":9,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":21},{"id":"GO:0046827","count":20},{"id":"GO:0048701","count":19},{"id":"GO:0006351","count":19},{"id":"GO:0007100","count":19}]},{"hash":"1160189792088860402","title":"Sterol and lipid biosynthesis cluster","description":"This cluster is dominated by terms for sterol and lipid metabolism (cholesterol biosynthesis via lathosterol, ergosterol regulation, unsaturated fatty acid biosynthesis, and sterol oxidation) with an ER unfolded protein response context that can arise from lipid imbalance, plus related membrane-associated processes, suggesting a lipid/membrane biosynthesis theme despite some outliers.","confidence":"Medium","size":28,"edges":27,"triangles":0,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":3},{"id":"GO:0032286","count":1},{"id":"GO:0033490","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0042128","count":1}]},{"hash":"1609115301724736218","title":"Oxidative Stress and Metabolism","description":"This cluster centers on responses to oxidative stress (hydrogen peroxide) and redox-related processes, while also highlighting diverse metabolic and signaling activities (retinol and pyridoxal biosynthesis, fructose and prostaglandin biosynthesis, calcium signaling, tissue homeostasis, and osmotic stress). The mixture suggests a broader theme of redox-regulated metabolism and signaling that supports cellular and tissue maintenance under stress. ","confidence":"Medium","size":28,"edges":348,"triangles":2667,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":26},{"id":"GO:0055114","count":25},{"id":"GO:0042572","count":25},{"id":"GO:0046370","count":25},{"id":"GO:0071277","count":24}]},{"hash":"1965144094291248723","title":"Detoxification, Metabolism, and DNA Repair","description":"The top GO terms show a strong emphasis on detoxification and xenobiotic metabolism (cellular oxidant detoxification; xenobiotic catabolic process; nitrobenzene metabolism) alongside DNA repair (nucleotide-excision repair) and related metabolic/inflammatory processes (prostaglandin biosynthesis; IL-1\u03b2 regulation; organ regeneration). This pattern suggests a cohesive cluster focused on managing chemical/oxidative stress through detoxification and metabolism while maintaining genome integrity and signaling for repair and regeneration.","confidence":"High","size":28,"edges":364,"triangles":2947,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":26},{"id":"GO:0042178","count":23},{"id":"GO:1904706","count":23},{"id":"GO:0018916","count":23},{"id":"GO:0032691","count":23}]},{"hash":"846548938394667367","title":"Innate antiviral response and mitotic regulation","description":"Based on the top GO terms, the cluster centers on innate antiviral defense (cellular response to type I interferon, dsRNA sensing, innate immune response, and defense against virus) together with cell cycle/mitotic processes (mitotic cell cycle, metaphase/anaphase transition, cell division). While a few terms are peripheral (e.g., GPCR signaling regulation, cadmium response, plant GA signaling), the dominant theme is antiviral response coupled to cell cycle control.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009938","count":23},{"id":"GO:0071357","count":23},{"id":"GO:0000278","count":23},{"id":"GO:0045087","count":23},{"id":"GO:0050689","count":23}]},{"hash":"2005323890819679396","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms center on translation, ribosome biogenesis, and translation initiation, with multiple entries for cytoplasmic translation and tRNA modification, indicating a cluster enriched for components of the protein-synthesis machinery. The presence of cell-cycle and cell-division terms suggests coordination of growth-related translation with division. Overall, the cluster represents ribosome- and translation-associated proteins, with some stress-response connections (antibiotic response, amino acid starvation) that can accompany translational control.","confidence":"High","size":28,"edges":26,"triangles":6,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0042254","count":8},{"id":"GO:0006413","count":7},{"id":"GO:0006400","count":7},{"id":"GO:1903833","count":6}]},{"hash":"1697542834019014204","title":"Antiviral innate immunity and xenophagy","description":"This cluster centers on innate immune activation in response to viral components, with terms like innate immune response, response to exogenous dsRNA, defense response to virus, and positive regulation of interferon-beta production. The inclusion of xenophagy and TLR9 signaling further supports a theme of antiviral sensing and autophagic clearance of pathogens, along with related immune signaling and cell migration.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0043330","count":5},{"id":"GO:1904417","count":5},{"id":"GO:0045359","count":5},{"id":"GO:0046827","count":5}]},{"hash":"1542276164084809354","title":"TLR9/NOD2-Driven Innate Immunity and Antigen Presentation","description":"The Top Terms cluster around TLR9 and NOD2 signaling, NLRP3 inflammasome assembly, interferon signaling, and enhanced dendritic cell antigen processing/presentation and MHC class I biosynthesis, indicating a coordinated innate sensing pathway that promotes dendritic cell activation and antigen presentation to adaptive immunity.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":28},{"id":"GO:0030335","count":28},{"id":"GO:1902745","count":28},{"id":"GO:0070431","count":28},{"id":"GO:0002830","count":28}]},{"hash":"97675598543505465","title":"DNA replication and mitotic cell cycle cluster","description":"This cluster is dominated by GO terms for DNA replication, mitotic cell cycle, and mitotic G1 DNA damage checkpoint signaling, suggesting proteins involved in genome duplication and cell division. Additional terms like septation initiation signaling and Rho protein signaling point to cytoskeletal dynamics and cytokinesis linked to division, with other terms touching morphogenesis and stress responses. Overall, the core theme is cell cycle control with related signaling pathways.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":27},{"id":"GO:0000278","count":27},{"id":"GO:0060440","count":26},{"id":"GO:0001403","count":26},{"id":"GO:0007266","count":26}]},{"hash":"2143737077229375904","title":"Strigolactone Biosynthesis and Plant Secondary Metabolism","description":"The top GO terms cluster around strigolactone biosynthesis (a key plant hormone) and related plant processes like secondary shoot formation, plus recurring themes of secondary metabolite biosynthesis and defense-related catabolism (stilbene, antibiotics, and responses to toxins). This suggests a cohesive theme of plant hormone production and defense metabolism, though some terms (e.g., bacterial catabolic processes) may reflect annotation noise. Overall, the dominant signal points to strigolactone-related biosynthesis and broader plant secondary metabolism.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009234","count":4},{"id":"GO:0010223","count":4},{"id":"GO:1901601","count":4},{"id":"GO:0046272","count":4}]},{"hash":"2069940881809735960","title":"Angiogenesis and immune response with RAS signaling","description":"The cluster brings together terms for blood vessel formation and blood pressure regulation (angiogenesis, renin-angiotensin system), inflammatory mediator production (leukotriene biosynthesis), and immune functions (adaptive immune response, MHC I antigen presentation). This pattern suggests a group of proteins involved in vascular remodeling that is closely linked to immune signaling and RAS-mediated regulation, though a few terms like symbiont entry and proteolysis indicate broader remodeling processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0002003","count":3},{"id":"GO:0045766","count":3},{"id":"GO:0019370","count":2},{"id":"GO:0006509","count":2}]},{"hash":"2288923602711283847","title":"Nuclear transport and meiotic chromosome dynamics","description":"The GO terms strongly point to nuclear import and pore assembly (NLS-bearing proteins, ribosomal protein import, nuclear pore complex assembly) alongside meiotic chromosome processes (meiotic sister chromatid cohesion and spindle elongation). This suggests a shared role in nuclear transport-related functions tied to meiotic chromosome dynamics, with supplementary regulatory activities (desumoylation, GTPase regulation).","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":6},{"id":"GO:0070262","count":6},{"id":"GO:0006607","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0051306","count":6}]},{"hash":"1973769975163999647","title":"Signaling and Trafficking Regulators","description":"The top GO terms cluster around cell signaling (ephrin receptor signaling, Wnt pathway, PKA signaling regulation) and membrane/vesicle trafficking (focal adhesion assembly regulation, endosome-to-melanosome transport, exosomal secretion). Also noted are protein complex formation and gene expression processes (protein heterooligomerization, spliceosome-mediated mRNA splicing, ribosomal subunit export). Together these suggest a group of proteins that act as regulators of signaling and intracellular trafficking, with broader roles in gene expression regulation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051893","count":3},{"id":"GO:0051291","count":3},{"id":"GO:0048013","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0010738","count":2}]},{"hash":"1427702522494579870","title":"Cell Proliferation and Mitosis","description":"The top GO terms are dominated by cell growth and division processes (cell population proliferation, cell division, mitotic cell cycle, mitotic spindle assembly) with supporting roles in ribosome biogenesis and vesicle trafficking (COPII budding, Golgi-ER transport), suggesting a cohesive theme of proliferative and mitotic machinery. This cluster appears to reflect core cellular growth and division functions rather than a specialized signaling pathway. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0008283","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0042254","count":3}]},{"hash":"1497769742845806047","title":"Cell Cycle Regulation and Development Signaling","description":"The top GO terms cluster around regulation of cell division and growth (mitotic cell cycle, positive regulation of cell proliferation, kinase activity, autophosphorylation), signaling pathways (PI-mediated signaling, GTPase activity), and development-related processes (skin development, multicellular organism development), with associated stress response (hypoxia) and mRNA transport, indicating a cohesive theme of growth and developmental signaling.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":8},{"id":"GO:0043547","count":8},{"id":"GO:0048015","count":7},{"id":"GO:0071902","count":7},{"id":"GO:0008284","count":7}]},{"hash":"1528783467639608365","title":"GTPase signaling and synaptic vesicle trafficking","description":"The cluster is dominated by terms about regulation of GTPase activity and Rho signaling, along with regulation and maturation/exocytosis of synaptic vesicles, suggesting a cohesive function in small GTPase\u2013driven vesicle trafficking. Some terms (ABA signaling, TNF regulation, apoptotic signaling, neuropeptide signaling) appear peripheral or cross-kingdom, but the core terms point to a theme of GTPase-mediated signaling controlling vesicle dynamics.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:1904468","count":1},{"id":"GO:2000300","count":1},{"id":"GO:0009738","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1848539462723721451","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:1901621","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0070389","count":1}]},{"hash":"153146165095619105","title":"Cell cycle and chromatin regulation","description":"Most terms cluster around mitosis, cell division, and chromatin modification (mitotic cell cycle, cell division, histone deacetylation, histone H3-K79 methylation), with supporting signals in cell proliferation and protein phosphorylation regulation. A few terms relate to translation initiation and vesicle transport, which are less central to this cluster but do not contradict the dominant cell-cycle/chromatin theme. Confidence reflects a solid but not perfect alignment due to the outlier terms.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0051301","count":2}]},{"hash":"923024422063252478","title":"Macrophage inflammatory activation with lipid regulation","description":"This cluster centers on macrophage-driven immune responses, evidenced by terms like positive regulation of macrophage activation, TNF production, and TLR4 signaling, along with lipid metabolism terms such as cholesterol efflux, reverse cholesterol transport, and triglyceride homeostasis. Together they suggest proteins coordinating inflammatory signaling in macrophages and associated lipid handling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044655","count":2},{"id":"GO:0010875","count":2},{"id":"GO:0034145","count":2},{"id":"GO:0071223","count":2},{"id":"GO:0043691","count":2}]},{"hash":"884456796386137715","title":"Plant translation and light-signaling cluster","description":"Dominant translation-related terms (translation, translational elongation, translational fidelity) point to a core of protein synthesis and its control. The presence of plant-specific light signaling and flowering terms (far-red signaling, short-day photoperiodism) suggests a broader plant photomorphogenesis context, but the obsolete terms and zero edges indicate limited current functional linkage among these proteins. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0007094","count":1},{"id":"GO:0032516","count":1},{"id":"GO:0032515","count":1},{"id":"GO:0006412","count":1}]},{"hash":"2299756665182069910","title":"Membrane Protein Proteolysis and Calcineurin-NFAT Signaling","description":"The cluster is enriched for membrane protein proteolysis terms (ectodomain, intracellular domain, and ER-to-cytosol related proteolysis) and regulation of immune signaling via the calcineurin-NFAT pathway, plus related membrane processing like GPI anchoring. This points to a theme of membrane remodeling coupled to NFAT signaling, with a few outliers (e.g., snoRNP assembly) that may be incidental. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046689","count":2},{"id":"GO:0070886","count":2},{"id":"GO:0051533","count":2},{"id":"GO:0006509","count":2},{"id":"GO:0050776","count":2}]},{"hash":"1877596704242504041","title":"Diverse biosynthesis pathways","description":"The top GO terms point to biosynthetic processes for a variety of metabolites (poly-hydroxybutyrate, lipopolysaccharide, antibiotics, retinal, phylloquinone, tropane alkaloids, etc.), suggesting the cluster groups enzymes involved in multiple biosynthetic steps rather than a single pathway. The presence of an obsolete redox term is less informative but redox chemistry commonly accompanies biosynthesis. Overall, this cluster appears to collect proteins participating in diverse biosynthetic processes across organisms.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0016311","count":2},{"id":"GO:0009244","count":2}]},{"hash":"2193922373634249340","title":"Lysine methylation and bacterial cell wall/sporulation","description":"The top terms include peptidyl-lysine methylation (monomethylation/dimethylation), tRNA wobble uridine modification, and cell envelope-related processes such as peptidoglycan biosynthesis, cell wall organization, and sporulation. This suggests a theme around protein lysine methylation coupled with bacterial cell wall remodeling and sporulation steps, with some additional general processes like endocytic recycling and cell growth providing context. Therefore the label reflects both PTM activity and cell envelope dynamics in bacteria.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":2},{"id":"GO:0018026","count":2},{"id":"GO:1990126","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0002098","count":2}]},{"hash":"1195603622343416768","title":"DNA Repair and Cell Cycle Regulation","description":"The top GO terms are dominated by DNA repair, error-prone translesion synthesis, and DNA-templated transcription, along with mitotic cell cycle and ubiquitin-proteasome\u2013dependent protein degradation. This combination points to genome maintenance and cell-cycle control as the core theme of the cluster, with other terms like bone development likely reflecting pleiotropy rather than a central function. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042276","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0051436","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1053583809381749512","title":"Unknown","description":"The top terms span diverse processes\u2014from kinase signaling and TORC1 to pattern formation, fungal cell wall biogenesis, and DNA repair\u2014without a unifying function. With no edges or cohesive prevalent GO terms, there isn\u2019t a clear common theme linking the cluster, so the label is Unknown with None confidence. ","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0061099","count":1},{"id":"GO:0034729","count":1},{"id":"GO:0032995","count":1}]},{"hash":"689197167508119719","title":"Neuronal development and axon guidance","description":"The cluster shows enrichment for neural development terms, including dendritic spine development, CNS projection neuron axonogenesis, fasciculation of sensory neuron axon, and ephrin receptor signaling, indicating a cohesive theme around neural differentiation and axon pathfinding. While some terms relate to other processes (immune function, iodide transport, nephric morphogenesis), they appear less central, so the neural development signal likely dominates the functional theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0060996","count":1},{"id":"GO:0072178","count":1},{"id":"GO:0097155","count":1},{"id":"GO:2000525","count":1}]},{"hash":"2037791401393780491","title":"NF-kappaB\u2013linked innate immune transcription","description":"The top GO terms include innate immune response and regulation of NF-kappaB transcription factor activity, suggesting a core theme of NF-kappaB\u2013mediated immune signaling and transcriptional regulation. While other terms touch on transcription, cell cycle, and development, the clearest and most represented connection is immune signaling via NF-kB. Confidence: Medium","confidence":"","size":27,"edges":33,"triangles":16,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051092","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0035372","count":5},{"id":"GO:0045719","count":4},{"id":"GO:0060079","count":4}]},{"hash":"445193343224576343","title":"Developmental morphogenesis and ECM remodeling","description":"Based on the top GO terms, the proteins cluster around extracellular matrix remodeling (basement membrane disassembly, collagen catabolic process) and morphogenetic processes (lung epithelial tube branching, intramembranous ossification). Additional terms hint at broader developmental signaling and cellular regulation, including Wnt- and thyroid hormone-related responses, neural precursor proliferation, and cytotoxicity. This combination suggests a cohesive theme of tissue morphogenesis and matrix remodeling rather than a single, narrow function.","confidence":"High","size":27,"edges":305,"triangles":2006,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":23},{"id":"GO:0034769","count":23},{"id":"GO:0010813","count":23},{"id":"GO:0097067","count":23},{"id":"GO:0001913","count":23}]},{"hash":"149928442679830096","title":"Meristem maintenance and BMP/TGF-\u03b2 signaling regulation","description":"This cluster centers on developmental signaling with terms for meristem identity maintenance and BMP/TGF-\u03b2/SMAD pathway regulation, aligning with growth signaling control; a few terms are unrelated or outdated (photosystem, vacuole fusion), but the dominant theme is regulation of developmental signals.","confidence":"Medium","size":27,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010074","count":9},{"id":"GO:0071560","count":9},{"id":"GO:0000173","count":9},{"id":"GO:0010991","count":9},{"id":"GO:0042006","count":9}]},{"hash":"1131993484119191144","title":"Lipid and carbohydrate catabolism","description":"The top GO terms show strong enrichment for lipid breakdown (triglyceride and diacylglycerol catabolic processes) and polysaccharide catabolism (cellulose, pectin), with additional signals related to signaling regulation and plant-specific responses (e.g., aerenchyma formation, salicylic acid signaling). This points to a cluster of proteins involved in broad metabolic catabolism of lipids and carbohydrates, with some regulatory or stress-related roles. ","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":7},{"id":"GO:0019433","count":7},{"id":"GO:0046340","count":7},{"id":"GO:0030245","count":7},{"id":"GO:0042136","count":7}]},{"hash":"1839271514815194882","title":"Defense Signaling and Immune Responses","description":"Top GO terms include plant-type hypersensitive response, defense response to tumor cell, callose deposition, and salicylic acid metabolism regulation, which point to a core theme of defense signaling and immunity. Some terms related to neural development and behavior appear as secondary annotations, suggesting possible cross-species annotations or pleiotropy; given the prominence of defense-related terms, the label is plausible but not exclusive. ","confidence":"Medium","size":27,"edges":121,"triangles":71,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":9},{"id":"GO:0002357","count":8},{"id":"GO:2000009","count":8},{"id":"GO:0048105","count":8},{"id":"GO:0001662","count":8}]},{"hash":"27023974897592002","title":"Xenobiotic Metabolism and Vitamin D Signaling","description":"The GO terms show a clear emphasis on detoxification and vitamin D-related pathways: xenobiotic catabolic processes, insecticide metabolism, and vitamin D response/catabolic processes cluster together, with prostaglandin biosynthesis adding a lipid signaling angle. Methylation and sex differentiation appear as ancillary regulatory themes, but the dominant pattern is metabolism and response to xenobiotics alongside vitamin D\u2013related activity.","confidence":"Medium","size":27,"edges":11,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":15},{"id":"GO:0035865","count":14},{"id":"GO:0032259","count":14},{"id":"GO:0001516","count":14},{"id":"GO:0042369","count":14}]},{"hash":"1843856788156302845","title":"Xenobiotic detoxification and metabolism","description":"These proteins show strong enrichment for detoxification and xenobiotic processing terms, including cellular oxidant detoxification, xenobiotic and toxin catabolic processes, nitrobenzene metabolism, and aromatic amino acid metabolism, suggesting a cohesive role in processing external compounds and managing oxidative stress. The additional terms relating to regulation of inflammation and DNA repair point to broader cellular stress responses triggered by toxin exposure, reinforcing the detox/metabolism theme. ","confidence":"Medium","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0098869","count":25},{"id":"GO:2000255","count":22},{"id":"GO:0042178","count":18},{"id":"GO:1904706","count":18},{"id":"GO:0018916","count":18}]},{"hash":"1487022015913911336","title":"RNA processing and translation initiation regulation","description":"These terms cluster around RNA-centric gene expression: processing events like mRNA splicing (spliceosome-related terms, regulatory splicing) and polyadenylation, together with multiple facets of translation initiation and reinitiation (preinitiation complex formation, translational initiation regulation, IRES-dependent and viral translation initiation). The mix suggests a module that coordinates RNA processing with translation control, including viral mechanisms. Therefore, RNA processing and translation initiation regulation is a concise, representative label.","confidence":"High","size":27,"edges":19,"triangles":1,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":11},{"id":"GO:1901407","count":11},{"id":"GO:0002188","count":11},{"id":"GO:0045292","count":10},{"id":"GO:0006378","count":10}]},{"hash":"852486166248043180","title":"Membrane Trafficking and Lipid Biosynthesis Regulation","description":"The strongest signals in the GO terms point to Golgi-to-plasma membrane protein transport and regulation of lipid biosynthesis (phosphatidylcholine and phosphatidylglycerol), with additional references to cell polarity maintenance. Some terms appear obscure or obsolete (placenta development, sporulation), likely annotation noise, but the core theme centers on membrane trafficking and lipid metabolism, suggesting these proteins function in vesicle transport and lipid biosynthesis regulation at cellular membranes.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060548","count":2},{"id":"GO:0043942","count":2},{"id":"GO:0046909","count":2},{"id":"GO:2001247","count":2},{"id":"GO:0007584","count":2}]},{"hash":"1294876127088794700","title":"Neuronal development and synaptic signaling","description":"This cluster is dominated by GO terms for hippocampus development, dendrite morphogenesis, excitatory postsynaptic potential, and dopamine response, together with Wnt signaling and cytoskeletal/adhesion processes that underpin neuronal differentiation, synapse formation, and neurotransmitter exocytosis. The convergence on developmental and synaptic functions suggests a neuronal development/synaptic regulation theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":21},{"id":"GO:0051893","count":20},{"id":"GO:0060079","count":20},{"id":"GO:0021766","count":20},{"id":"GO:0045956","count":20}]},{"hash":"1820060318285135490","title":"Developmental signaling and tissue morphogenesis","description":"This cluster shows strong enrichment for multicellular development and organ formation terms (mitotic cell cycle, multicellular organism development, trachea formation) plus signaling and adhesion/migration processes (Rho signaling, focal adhesion regulation, endothelial chemotaxis). Together these suggest proteins coordinating development, tissue remodeling, and cell movement during morphogenesis.","confidence":"Medium","size":27,"edges":257,"triangles":1250,"max_degree":25,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":26},{"id":"GO:0000278","count":26},{"id":"GO:0007275","count":24},{"id":"GO:2001028","count":24},{"id":"GO:1901214","count":23}]},{"hash":"1682803329381475815","title":"Proteostasis and Developmental Regulation","description":"The cluster centers on regulation of protein stability and turnover (proteasomal degradation, protein stability, CDK activity regulation) with components involved in precise localization (kinetochore) and broad developmental processes across tissues (neuron development, dendritic spine morphogenesis, muscle activity response, trachea formation). This suggests a set of proteins that govern proteostasis while modulating developmental signaling in multiple tissues, rather than a single, narrow pathway.","confidence":"Medium","size":27,"edges":7,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034501","count":21},{"id":"GO:0045736","count":21},{"id":"GO:0014850","count":19},{"id":"GO:0048666","count":19},{"id":"GO:0032435","count":19}]},{"hash":"1954882846199652952","title":"Neural development and synaptic signaling","description":"The enriched GO terms point to nervous system development and synaptic function, including excitatory postsynaptic potential, long-term potentiation, axonogenesis, Schwann cell development, and visual perception, indicating a cluster of proteins involved in neuronal differentiation and synaptic communication. While a few terms like heart development or ABA signaling appear, the dominant theme is neural development and synaptic activity.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060079","count":20},{"id":"GO:0060291","count":20},{"id":"GO:0007507","count":20},{"id":"GO:0014044","count":20},{"id":"GO:0043065","count":20}]},{"hash":"967401518009705975","title":"RNA processing, splicing, and translation initiation","description":"The cluster\u2019s top GO terms center on mRNA processing and splicing (regulation and cis/splicing via the spliceosome, small-subunit processome assembly, mRNA stabilization) and extend to translation initiation (eIF4F complex assembly). This suggests a cohesive role in RNA metabolism from transcription/splicing through to translation, despite some obsolete terms. ","confidence":"High","size":27,"edges":177,"triangles":419,"max_degree":23,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":14},{"id":"GO:0031047","count":13},{"id":"GO:0048026","count":13},{"id":"GO:0006378","count":11},{"id":"GO:0045292","count":10}]},{"hash":"4188543301215949","title":"Unknown","description":"The top GO terms cover a wide range of biological themes\u2014development (hippocampus, trachea), transcription, signaling, cell-cycle checkpoints, stress and metabolic regulation\u2014without a single connecting function. With no edges or interactions in the cluster, there isn\u2019t a cohesive shared pathway or process to name it after, so it fits an Unknown designation.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021766","count":25},{"id":"GO:0006351","count":25},{"id":"GO:0060440","count":24},{"id":"GO:0001403","count":24},{"id":"GO:0007266","count":24}]},{"hash":"232242573252640884","title":"JNK/MAPK stress signaling and apoptosis","description":"The cluster\u2019s prominent GO terms center on the JNK cascade, and on an intrinsic apoptotic pathway in response to DNA damage, highlighting a theme of stress-activated signaling leading to cell death. Additional terms such as response to lipopolysaccharide and response to absence of light suggest broader stress or immune signaling. Deneddylation and its regulation point to control of protein turnover and signaling, which can modulate MAPK pathways. Some germline development terms are present but appear less central to the main theme. Overall, the cluster is best described by stress-activated MAPK/JNK signaling and apoptosis.","confidence":"Medium","size":27,"edges":26,"triangles":0,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0000188","count":1},{"id":"GO:0000338","count":1},{"id":"GO:0060625","count":1},{"id":"GO:0048140","count":1},{"id":"GO:0034260","count":1}]},{"hash":"913227161602365039","title":"Actin Cytoskeleton Remodeling and Protrusions","description":"This cluster is dominated by GO terms for actin-based structures and remodeling\u2014microspike and filopodium assembly, nuclear migration along microfilaments, and dendritic spine maintenance\u2014coupled with regulation of Rho signaling, all pointing to actin-driven protrusive dynamics. The plant-related terms (chloroplast movement and ABA homeostasis) can also be tied to actin-mediated movements, reinforcing a cohesive theme of cytoskeletal remodeling. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030035","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0031022","count":1},{"id":"GO:1902265","count":1}]},{"hash":"300750691009480529","title":"DNA replication and chromatin assembly","description":"The top GO terms are dominated by nuclear DNA processes: DNA-templated transcription, DNA replication, and especially CENP-A containing chromatin assembly, with cell division also represented. This points to chromosome maintenance and cell-cycle roles as the core theme, despite some outlier terms related to other processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0061641","count":2}]},{"hash":"1272583192830596106","title":"Diverse membrane transporters","description":"This cluster is characterized by GO terms for transmembrane transport of a variety of substrates (sodium ions, arabinose, fucose, sialic acid, 4-hydroxyphenylacetate, xenobiotics) and related transporter activity, plus at least one vesicle loading term. The mix suggests a group enriched for membrane transport proteins handling multiple substrates. An outlier term on translational fidelity is present but does not outweigh the transport-focused theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":2},{"id":"GO:0098700","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0006004","count":1}]},{"hash":"1027782384333387553","title":"Vacuolar amino acid transport","description":"The top GO terms center on transmembrane transport of various amino acids (glutamate, lysine, arginine, proline, glutamine) into or out of the vacuole, plus related transport activities like sialic acid transport. This points to a cluster of proteins functioning as vacuolar amino acid transporters. The presence of an unrelated term like root cap development appears incidental noise. Confidence: High","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":4},{"id":"GO:0090515","count":4},{"id":"GO:1990818","count":4},{"id":"GO:0015824","count":4},{"id":"GO:0048829","count":4}]},{"hash":"2259884346804850001","title":"Bacterial biosynthesis and metabolism","description":"Top GO terms indicate diverse biosynthetic processes (antibiotic, biotin, menaquinone, cobalamin) and related metabolism (aerobic respiration, RNA methylation, cell division) plus stress responses. This points to a general bacterial metabolic/biosynthetic program rather than a single specialized function, hence the name.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0009102","count":6},{"id":"GO:0035902","count":5},{"id":"GO:0036265","count":5},{"id":"GO:0051301","count":5}]},{"hash":"1569202786890877960","title":"Growth signaling and cell-cycle regulation","description":"This cluster centers on terms describing positive regulation of signaling and cell growth processes: kinase activity, autophosphorylation, GTPase activity, and the mitotic cell cycle with promotion of cell proliferation. Supporting terms include thyroid hormone metabolism and cellular stress responses (hypoxia), along with mRNA transport and neuronal-related processes like dendritic spine development, suggesting broader regulation of gene expression and cellular behavior in growth contexts. Overall, the proteins likely participate in signaling networks that promote proliferation and growth, with auxiliary roles in metabolism and stress adaptation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042403","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0071902","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0008284","count":3}]},{"hash":"680689891848132986","title":"Macromolecular Complex Assembly","description":"The top GO terms point to assembly of large protein complexes (RNA polymerases I/II/III, RNA Pol II core complex, and tubulin complex), suggesting a shared function in assembling major molecular machines; a couple of outliers (protein folding and lipid metabolism) are less central. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990113","count":1},{"id":"GO:0032968","count":1},{"id":"GO:1990114","count":1},{"id":"GO:0031137","count":1},{"id":"GO:0006457","count":1}]},{"hash":"747734489716225275","title":"TLR9/NOD2 Innate Immunity and Inflammasome Activation","description":"It centers on innate sensing (TLR9, NOD2), cytokine upregulation (IL-6, type II IFN), dendritic cell maturation/presentation, and NLRP3 inflammasome assembly, with concurrent dendritic cell migration and lamellipodium dynamics, pointing to a coordinated innate immune activation and inflammasome-mediated inflammation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":25},{"id":"GO:0032755","count":25},{"id":"GO:0030335","count":25},{"id":"GO:1902745","count":25},{"id":"GO:0070431","count":25}]},{"hash":"163330711270620342","title":"Glutamatergic Synaptic Signaling","description":"The GO terms point most strongly to neuronal communication at glutamatergic synapses, including synaptic transmission and receptor recycling, with additional signals related to receptor trafficking, endosomal regulation, and kinase activity. This suggests the cluster centers on glutamatergic synaptic signaling and receptor turnover, rather than non-neuronal pathways.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0001881","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0034968","count":1}]},{"hash":"1494374850626507229","title":"Innate antiviral sensing and inflammasome activation","description":"This cluster centers on innate immune detection and response to viral infection. Top GO terms include innate immune response, defense against virus, TLR9 and NOD2 signaling, type II interferon pathways, and NLRP3 inflammasome assembly, indicating coordinated sensing and inflammatory responses; plus regulation of cell migration and lamellipodium organization consistent with immune cell movement. The proteasomal ubiquitin-dependent turnover supports regulation of these signaling components. Overall, a cohesive theme of antiviral innate sensing with inflammasome activation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":15},{"id":"GO:0045087","count":14},{"id":"GO:0051607","count":14},{"id":"GO:0034162","count":12},{"id":"GO:0030335","count":12}]},{"hash":"2245127907633757698","title":"Unknown","description":"The GO terms span xenobiotic response, lung and plant development, tRNA processing, metabolism, immune signaling, and DNA replication, with no single cohesive function uniting the proteins.","confidence":"","size":26,"edges":18,"triangles":0,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0030324","count":4},{"id":"GO:0090502","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0019358","count":3}]},{"hash":"1040255328079419736","title":"Ubiquitin-regulated signaling and gene expression","description":"This cluster centers on deubiquitination and regulation of ubiquitin-related processes, with associated signaling pathways (TNF, TCR, Wnt/PCP) and regulation of mRNA stability and transcription, indicating a cohesive module of ubiquitin-dependent control of signaling and gene expression.","confidence":"Medium","size":26,"edges":255,"triangles":1601,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":11},{"id":"GO:0006521","count":9},{"id":"GO:0061418","count":9},{"id":"GO:0009651","count":9},{"id":"GO:0043488","count":9}]},{"hash":"1253547168546012634","title":"RNA processing and translation regulation","description":"The cluster centers on RNA maturation and regulation of translation, with GO terms for mRNA splicing, polyadenylation, mRNA stabilization, small-subunit processome assembly, eIF4F complex assembly, and miRNA-mediated silencing, indicating a cohesive RNA metabolism and translational control module (with a minor insulin-responsive signaling note).","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0032869","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0048255","count":2}]},{"hash":"1919232376586061886","title":"Golgi-ER trafficking in development","description":"The proteins in this cluster show strong representation of vesicle transport between the ER and Golgi and onward to the plasma membrane, plus regulation of intracellular protein transport, alongside several development-related GO terms (nerve, kidney, spermatid development). This suggests a theme of Golgi-ER trafficking that supports developmental processes.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0006888","count":2}]},{"hash":"368124723860076988","title":"Intracellular Membrane Trafficking","description":"The top terms cluster around placing and moving proteins within cells\u2014targeting to mitochondria, insertion into the mitochondrial inner membrane, Golgi localization and Golgi-to-ER retrograde transport, endocytosis, and general organelle trafficking. Although some terms are obsolete or outliers, the common theme is intracellular membrane trafficking and organelle targeting.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0048313","count":1},{"id":"GO:0043473","count":1}]},{"hash":"711259682008514519","title":"Organogenesis and Developmental Signaling","description":"The top GO terms cover multiple organ development processes (genitalia, kidney, neural tube, skin) and include JAK-STAT signaling, suggesting a cohesive theme of organogenesis and developmental signaling rather than a single molecular activity. Thus, Organogenesis and Developmental Signaling is an apt label for this cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031659","count":2},{"id":"GO:0048806","count":2},{"id":"GO:0060674","count":2},{"id":"GO:0007259","count":2},{"id":"GO:0001822","count":2}]},{"hash":"711340558382117872","title":"Signaling and transcription regulation cluster","description":"This cluster includes GO terms for cAMP and cGMP signaling responses, Ras pathway regulation, DNA-templated transcription, and nuclear export, indicating a core theme of signal transduction linked to gene expression. Additional terms like aerotaxis and sarcomere organization hint at broader roles in cell movement and cytoskeletal organization, but the predominant connection appears to be proteins that relay signals and modulate transcription.","confidence":"Medium","size":26,"edges":174,"triangles":366,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0046827","count":9},{"id":"GO:0010754","count":8},{"id":"GO:0009454","count":8}]},{"hash":"1329697003277421222","title":"Kinase signaling and chromatin regulation","description":"The top GO terms point to regulation of kinase activity (serine/threonine and tyrosine), TORC1 signaling, and the SREBP pathway, along with ubiquitination and histone methylation, suggesting a broad regulatory module coordinating signaling with chromatin-level control. The set appears heterogeneous with no strong connectivity, so a general regulatory label is most appropriate.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0061099","count":1},{"id":"GO:0034729","count":1},{"id":"GO:0032995","count":1}]},{"hash":"2282719395686851944","title":"Unknown","description":"The Top Terms are highly diverse, spanning sarcomere organization, transcription regulation (including RNA polymerase II/III preinitiation complex assembly), protein ubiquitination and degradation, and a few unrelated processes. This scattered mix makes it hard to identify a single, cohesive biological function for the cluster, so it should be labeled Unknown.","confidence":"","size":26,"edges":34,"triangles":0,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070893","count":2}]},{"hash":"2058021559739911136","title":"Unknown","description":"This set mixes many unrelated GO terms (phytochelatin biosynthesis, proteolysis, chaperone autophagy regulation, heart morphogenesis, neuromuscular control, glycan processing, metabolism, diaphragm contraction), with no single function or pathway common to most proteins. The absence of edges supports a lack of cohesive functional theme, so a unified label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0006508","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0003007","count":1}]},{"hash":"1170484995568917524","title":"Amino acid catabolism and central energy metabolism","description":"The terms cohere around amino acid breakdown (alanine, kynurenine, lysine) and the tricarboxylic acid cycle, signaling a metabolism-centric cluster focused on energy production from amino acids. Additional lipid metabolism hints (sphingomyelin biosynthesis, fatty acid transport) suggest broader metabolic roles, while Notch signaling appears more peripheral. Overall, a metabolism-focused cluster with strongest emphasis on amino acid catabolism and energy generation.","confidence":"Medium","size":26,"edges":239,"triangles":1344,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006099","count":11},{"id":"GO:0019878","count":10},{"id":"GO:0042853","count":10},{"id":"GO:0097053","count":10},{"id":"GO:0007219","count":10}]},{"hash":"435903492915714173","title":"Proteostasis and Gene Expression Regulation","description":"This cluster combines GO terms pointing to transcription and translation control (DNA-templated transcription, formation of translation preinitiation complex, translation reinitiation) with protein homeostasis processes (autophagy, negative regulation of proteasomal degradation) and stress-response signaling (PI3K/AKT pathway, oxidative detoxification). The shared theme appears to be coordinating gene expression with protein quality control under stress.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006914","count":3},{"id":"GO:0046826","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2}]},{"hash":"414721659690330876","title":"Adhesion signaling and cytoskeletal remodeling","description":"The cluster is dominated by terms tied to focal adhesion assembly regulation, Rho protein signaling, and extracellular matrix disassembly, pointing to roles in cell adhesion and cytoskeletal dynamics; developmental and immune differentiation terms may reflect broader signaling connections within this cluster, rather than a separate module.","confidence":"Medium","size":26,"edges":150,"triangles":408,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":26},{"id":"GO:0060440","count":26},{"id":"GO:0051893","count":26},{"id":"GO:0001403","count":26},{"id":"GO:0007266","count":26}]},{"hash":"1724744045326781566","title":"Apoptosis and Cell-Cycle Regulators with Transport Roles","description":"These proteins show a mix of regulatory GO terms spanning apoptosis (extrinsic pathway regulation), mitosis (sister chromatid separation), growth signaling (TORC1), and regulation of GTPase activity, plus nucleocytoplasmic transport (NLS-bearing import) and ciliary docking. The common thread appears to be regulators that coordinate cell fate, growth, and intracellular trafficking rather than a single enzyme or direct effector function, suggesting a broad regulatory module rather than a narrow pathway. ","confidence":"Medium","size":26,"edges":18,"triangles":1,"max_degree":14,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:2001241","count":9},{"id":"GO:0070262","count":9},{"id":"GO:0045945","count":9},{"id":"GO:0060561","count":9},{"id":"GO:0006607","count":9}]},{"hash":"1504001423885390598","title":"Proteostasis under Stress","description":"The cluster is enriched for proteostasis and stress-response terms: ER unfolded protein response, autophagosome maturation, aggresome and inclusion body assembly, oxidative stress response, and oxidation-dependent protein catabolic processes, all pointing to a cohesive network maintaining protein homeostasis under stress.","confidence":"High","size":26,"edges":16,"triangles":0,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":10},{"id":"GO:0034599","count":9},{"id":"GO:0030968","count":9},{"id":"GO:0001824","count":9},{"id":"GO:0097352","count":9}]},{"hash":"798752059846182277","title":"Ion transport and membrane potential regulation","description":"The top GO terms point to ion transport (sodium import, potassium transport/export, potassium homeostasis) and activities that affect membrane potential (membrane depolarization in cardiac cells). Also, signaling-related terms (cAMP/cGMP responses, guanylyl cyclase regulation) suggest coupling between ion flux and signaling. Taken together, the cluster likely represents proteins involved in ion homeostasis and control of membrane excitability.","confidence":"High","size":26,"edges":307,"triangles":2189,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":14},{"id":"GO:0009454","count":13},{"id":"GO:0071805","count":13},{"id":"GO:0071321","count":13},{"id":"GO:0010754","count":13}]},{"hash":"2187134007110134726","title":"Plant secondary metabolism and hormone biosynthesis","description":"This cluster centers on plant secondary metabolism and hormone biosynthesis. Terms such as 3-phenylpropionate catabolic process, stilbene catabolic process, strigolactone biosynthetic process, and secondary shoot formation point to phenylpropanoid metabolism and strigolactone-driven growth regulation, with additional terms reflecting antibiotic biosynthesis and responses to toxic substances. While a few terms (e.g., menaquinone biosynthesis) are less plant-specific, the dominant theme is plant metabolite biosynthesis and hormone-related pathways.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019380","count":5},{"id":"GO:0009234","count":4},{"id":"GO:0010223","count":4},{"id":"GO:1901601","count":4},{"id":"GO:0046272","count":4}]},{"hash":"1714365235156703608","title":"Endocannabinoid lipid signaling and triglyceride catabolism","description":"The top GO terms point to regulation of endocannabinoid signaling and multiple lipid catabolic processes (triglyceride, monoacylglycerol, diacylglycerol, phosphatidylserine), plus acyl-chain remodeling, suggesting a core function in lipid signaling and metabolism. Some terms may reflect annotation noise (e.g., cellulose catabolic process), but the dominant theme is endocannabinoid-related lipid signaling and lipid breakdown.","confidence":"Medium","size":26,"edges":31,"triangles":6,"max_degree":22,"top_function":"autophagy","top_go_terms":[{"id":"GO:2000124","count":9},{"id":"GO:0019433","count":9},{"id":"GO:0036155","count":7},{"id":"GO:0098869","count":6},{"id":"GO:0052651","count":6}]},{"hash":"1017992593739964638","title":"Cell cycle and stress response cluster","description":"Most frequently enriched GO terms describe fundamental cellular processes and stress responses (DNA replication, centrosome cycle, apoptotic process, ER stress\u2013related translation regulation and protein folding). Some terms touch on development and immune signaling, but they are less central. Overall, the cluster aligns with regulators of cell cycle progression and cellular stress responses, supporting this label.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0007098","count":2}]},{"hash":"1485703767410998968","title":"Nuclear transcription and cell cycle regulation","description":"This cluster\u2019s top GO terms are dominated by nuclear processes: DNA-templated transcription, mitotic cell cycle, cell division, and positive regulation of protein export from the nucleus, suggesting a core theme of transcriptional and cell cycle control. The presence of immune/stress-related terms (innate immune response, defense against Gram-positive bacteria, cadmium response) alongside a few peripheral terms (cilium assembly, renin secretion) implies these proteins may be involved in broader regulatory networks that couple transcription and cell cycle with stress responses. Overall, the nuclear-centric theme best describes the cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051301","count":3}]},{"hash":"763712325795558507","title":"GPCR- and Cytokine-Mediated Signaling","description":"The top GO terms predominantly point to signaling processes, particularly GPCR-related pathways (regulation of GPCR signaling, bitter taste perception, IP3 biosynthesis) and immune cytokine signaling (IL-1, IL-12, IL-15) along with T cell receptor signaling, suggesting a cluster centered on diverse signal transduction mechanisms. A couple of terms (meiotic activation, monocyte extravasation) are less core but don\u2019t override the overall theme.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008277","count":2},{"id":"GO:0060466","count":1},{"id":"GO:0032959","count":1},{"id":"GO:0070498","count":1},{"id":"GO:2000438","count":1}]},{"hash":"604942854807400717","title":"Endomembrane trafficking and vesicle transport","description":"The cluster shows GO terms tied to membrane trafficking within the endomembrane system\u2014ER-to-Golgi transport, endosome localization, vesicle budding, vacuole organization, and phospholipid translocation\u2014indicating a cohesive role in vesicle transport. Some terms like pigmentation and locomotory behavior may reflect broader cellular contexts but do not override the core vesicle-trafficking theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0044088","count":2},{"id":"GO:0010570","count":2},{"id":"GO:0036010","count":2},{"id":"GO:0045332","count":2}]},{"hash":"1513185838620587217","title":"Endosome trafficking and receptor recycling","description":"The top GO terms center on endosome size regulation and receptor recycling, pointing to a core theme of intracellular membrane trafficking. Additional terms for Rho signaling and transcriptional regulation suggest broader regulation, but the recurring motif appears to be endosomal processing and membrane receptor handling, with some terms being obsolete or less specific.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0034968","count":2}]},{"hash":"1768899232648299119","title":"Regulation of transcription and signaling","description":"This cluster\u2019s top GO terms emphasize nuclear processes (DNA-templated transcription and nuclear protein export) alongside multiple signaling-related terms (small GTPase signaling, Ras signaling, and receptor signaling pathways). Although a few terms refer to other processes (sarcomere organization, aerotaxis, sodium transport), the prevailing pattern points to coordinated regulation of gene expression and signal transduction. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2}]},{"hash":"1883350369561650630","title":"Cyclic nucleotide signaling and sensory perception","description":"The top GO terms indicate strong enrichment for cellular responses to cGMP and cAMP and regulation of guanylyl cyclase signaling, with sensory perception of smell and heart-rate regulation also represented. This points to a coherent theme centered on cyclic nucleotide signaling pathways and their sensory/physiological outputs, with supplementary links to transcription regulation and broader signaling processes.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071321","count":8},{"id":"GO:0010754","count":8},{"id":"GO:0007608","count":8},{"id":"GO:0009454","count":7},{"id":"GO:0071320","count":7}]},{"hash":"796534744055128889","title":"Unknown","description":"The terms cover a highly diverse set of processes (DNA-templated transcription, vacuole fusion regulation, meiotic cell cycle control, Ras signaling, sarcomere organization, sodium import, small GTPase signaling, antipsychotic response, receptor guanylyl cyclase signaling, aerotaxis) with no clear, single biological theme. Additionally, there are no edges or strong connections in the cluster (Edges: 0, Triangles: 0, Max Degree: 0), supporting the lack of a cohesive function among the proteins.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0032889","count":4},{"id":"GO:0051447","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0045214","count":3}]},{"hash":"678518766332413510","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0036269","count":1}]},{"hash":"2089908642719856048","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0015937","count":1},{"id":"GO:0006432","count":1},{"id":"GO:0051290","count":1},{"id":"GO:0008033","count":1}]},{"hash":"1537546130965294953","title":"Antiviral Innate Immune Signaling","description":"Dominant GO terms center on defense response to virus and innate immunity, with connections to TLR signaling (MyD88-independent), NF-kappaB regulation, IL-18/IL-1 cytokine modulation, and antigen processing/presentation via MHC class I, plus proteasomal degradation. This combination points to a cohesive antiviral innate immune response cluster.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":19},{"id":"GO:0031146","count":19},{"id":"GO:0045087","count":19},{"id":"GO:0030335","count":18},{"id":"GO:0002830","count":18}]},{"hash":"163139108351609257","title":"Unknown","description":"The top GO terms are a mix of signaling (aerotaxis; cellular response to cGMP and cAMP; regulation of guanylyl cyclase signaling), ion transport (sodium import), and core gene expression processes (RNA transcription/termination and ribosome biogenesis). The absence of a coherent, single functional theme and the presence of both signaling/regulatory and housekeeping processes suggest there isn\u2019t a unifying function for this cluster. ","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009454","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0010754","count":2},{"id":"GO:0048265","count":2},{"id":"GO:0071320","count":2}]},{"hash":"213377451639498197","title":"NOD-like receptor signaling and cytokine production","description":"The top GO terms point to innate immune sensing of bacterial components (detection of muramyl dipeptide and cellular response to muramyl dipeptide) and downstream inflammatory signaling (negative regulation of NF-kappaB, IL-1\u03b2, IL-8, and IFN-\u03b1 production), along with modulation of Th17 differentiation. There is also evidence of cytoskeletal remodeling (barbed-end actin uncapping, lamellipodium organization) that often accompanies immune activation. This combination suggests a coherent theme of NOD-like receptor\u2013driven innate sensing with cytokine production and associated cytoskeletal changes.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043124","count":8},{"id":"GO:2000321","count":8},{"id":"GO:0051638","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0050718","count":8}]},{"hash":"2143319884830740311","title":"Innate Immunity Activation and DC Antigen Presentation","description":"The terms point to innate immune sensing (TLR9 signaling, NOD2 signaling, muramyl dipeptide detection) and inflammasome assembly (NLRP3), with downstream promotion of type II interferon signaling and overall immune activation. This is coupled with dendritic cell\u2013mediated antigen processing and MHC class I biosynthesis, and even cell migration features relevant to DC trafficking, suggesting a cohesive theme of innate immune activation that feeds into adaptive antigen presentation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":3},{"id":"GO:0030335","count":3},{"id":"GO:1902745","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0002830","count":3}]},{"hash":"1519049389579629734","title":"Vesicle trafficking and actin remodeling","description":"The top GO terms cluster around intracellular transport (plasma membrane to endosome transport, regulation of synaptic vesicle exocytosis), endocytic/cytoskeletal processes (actin filament branching, focal adhesion assembly), and signaling pathways (EGFR signaling, regulation of gene expression). This points to a cohesive theme where membrane trafficking is coupled with actin dynamics and signaling, rather than a single isolated process. Some terms like brain development or viral replication appear broader or incidental but do not override the dominant trafficking/cytoskeletal signal.","confidence":"Medium","size":25,"edges":215,"triangles":887,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0010796","count":6},{"id":"GO:2000300","count":5},{"id":"GO:0039694","count":5}]},{"hash":"1641804812738156403","title":"Developmental signaling and vesicle trafficking","description":"The top GO terms point to developmental processes in skin (hair follicle morphogenesis) and brain (midbrain dopaminergic neuron differentiation, cortical migration), along with cellular trafficking and signaling activities (exosomal secretion, endosome-to-Golgi transport, regulation of protein kinase activity, protein heterooligomerization). This suggests a cluster of proteins involved in coordinating development with vesicle trafficking and signaling rather than a single linear function.","confidence":"Medium","size":25,"edges":190,"triangles":582,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":4},{"id":"GO:0045859","count":4},{"id":"GO:0031069","count":3},{"id":"GO:1990182","count":3},{"id":"GO:0007174","count":3}]},{"hash":"793153192369850254","title":"Immune signaling and cytoskeletal remodeling","description":"The cluster features multiple immune-related terms (positive regulation of ERK1/ERK2 cascade, T cell activation via TCR-MHC interaction, complement activation) alongside signals of cytoskeletal dynamics (stress fiber assembly, mechanosensation) and post-translational modifications (protein ubiquitination, peptidyl-serine phosphorylation) and vesicle trafficking (endosome to Golgi). Together, this points to integrated signaling modules governing immune responses and cytoskeletal rearrangements, with some involvement in protein processing and trafficking. ","confidence":"Medium","size":25,"edges":82,"triangles":30,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070374","count":4},{"id":"GO:0043149","count":4},{"id":"GO:0050975","count":4},{"id":"GO:0034498","count":4},{"id":"GO:0033138","count":4}]},{"hash":"1030061620166507464","title":"Mitotic Cell Cycle and Chromosome Segregation","description":"This cluster includes GO terms for mitotic spindle assembly, mitotic chromosome segregation, mitotic cell cycle, and Okazaki fragment processing in mitotic DNA replication, which together point to mitosis and chromosome handling during cell division. Additional terms include TORC1 signaling, heat-stress\u2013related mRNA export, and COPII vesicle budding, suggesting broader growth and trafficking roles, but the core signal is mitotic cell division.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031990","count":2},{"id":"GO:0090344","count":2},{"id":"GO:0090307","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1931065031890406961","title":"Neural signaling and development","description":"This cluster\u2019s top GO terms point to neural-related functions: Schwann cell development, regulation of synaptic vesicle exocytosis, and clustering of voltage-gated potassium channels, all core to neural signaling and development. Additional terms reflect shared excitability and signaling mechanisms (calcium/calmodulin pathways, kinase activity) that can appear in excitable tissues. While some terms (e.g., cardiac contraction) are broader, the strongest, most recurrent signals are neural in nature, supporting a neural signaling and development theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008360","count":6},{"id":"GO:0060316","count":6},{"id":"GO:0071902","count":5},{"id":"GO:0050665","count":5},{"id":"GO:0045163","count":5}]},{"hash":"1891829759089714216","title":"ECM Remodeling in Development","description":"This cluster centers on extracellular matrix remodeling and morphogenesis, with bone resorption and intramembranous ossification indicating mineralized tissue remodeling, basement membrane disassembly and lung morphogenesis branching showing ECM restructuring during organ development, and broader developmental signals such as thyroid hormone response and neural precursor regulation that can coordinate growth with remodeling.","confidence":"High","size":25,"edges":296,"triangles":2214,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":25},{"id":"GO:2000179","count":24},{"id":"GO:0034769","count":24},{"id":"GO:0010813","count":24},{"id":"GO:0097067","count":24}]},{"hash":"589777168069970715","title":"Nuclear RNA processing and transcription regulation","description":"The top GO terms cluster around mRNA lifecycle in the nucleus\u2014export, splicing, decay, and transcriptional regulation by RNA polymerase II\u2014along with related processes like translational initiation regulation and ribosome biogenesis, suggesting a cohesive theme of nuclear RNA processing and control of gene expression.","confidence":"High","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006406","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4}]},{"hash":"2294575617729714049","title":"Antiviral Innate Immune Signaling and Xenophagy","description":"Proteins in this cluster revolve around sensing foreign nucleic acids and triggering antiviral defenses, notably dsRNA response, innate immunity, and interferon-\u03b2 production, with positive regulation of xenophagy. Signaling pathways such as TLR9, NOD2, and lipopolysaccharide responses support a theme of pathogen recognition and autophagic/immune activation rather than a single metabolic role. Confidence in this label is High.","confidence":"","size":25,"edges":4,"triangles":0,"max_degree":4,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043330","count":7},{"id":"GO:0045087","count":7},{"id":"GO:1904417","count":7},{"id":"GO:0045359","count":7},{"id":"GO:0046827","count":7}]},{"hash":"729605190002323711","title":"Developmental growth and chromatin regulation","description":"The cluster is enriched for developmental and growth control terms (positive regulation of stem cell proliferation, positive regulation of cell size, cerebral cortex development) and gene expression regulation (DNA-templated transcription, nucleosome density), suggesting a theme of growth/development regulated by chromatin state; some other terms (lipopolysaccharide response, thiamine biosynthesis) may reflect background noise.","confidence":"Medium","size":25,"edges":18,"triangles":7,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2000648","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0045793","count":8},{"id":"GO:0048240","count":8},{"id":"GO:0021987","count":8}]},{"hash":"1003000316961631319","title":"Developmental ECM Remodeling and Morphogenesis","description":"The terms point to extracellular matrix remodeling (basement membrane disassembly, collagen catabolic process) and morphogenesis (lung tube branching, ossification), suggesting roles in developmental tissue remodeling and organ formation. Other terms reflect developmental signaling and regulation, supporting a theme of ECM-guided morphogenesis, though a few immune-related terms are present.","confidence":"Medium","size":25,"edges":47,"triangles":12,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":2},{"id":"GO:0034769","count":2},{"id":"GO:0010813","count":2},{"id":"GO:0097067","count":2},{"id":"GO:0001913","count":2}]},{"hash":"1147340545067499516","title":"Male Germline Meiosis and Spermatogenesis","description":"The top GO terms are dominated by male germ cell development, including meiosis cytokinesis, germ-line cyst formation, spermatocyte division, and spermatid differentiation, plus the G1/S transition, indicating coordinated spermatogenesis. Additional terms suggest regulatory processes in germ cells (negative regulation of autophagy and translation) and stress or hormonal responses (dexamethasone stimulus), with stem cell maintenance supporting germline stem cell regulation. An outlier term (behavioral fear response) may reflect annotation noise, but overall the cluster centers on male germline development and meiosis.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007112","count":1},{"id":"GO:0048136","count":1},{"id":"GO:0000082","count":1},{"id":"GO:0010507","count":1},{"id":"GO:0017148","count":1}]},{"hash":"2114363228482742085","title":"Specialized metabolite and lipid metabolism","description":"The top GO terms cluster around biosynthetic and metabolic pathways for specialized metabolites and lipids, including tropane alkaloid biosynthesis, antibiotic biosynthesis, steroid hormone biosynthesis (glucocorticoids, estrogen), sphingolipid (3-keto-sphinganine) metabolism, very long-chain fatty acid biosynthesis, retinal metabolism, and phylloquinone turnover. This pattern points to a functional group centered on lipid- and secondary-metabolite pathways rather than core cellular processes.","confidence":"High","size":25,"edges":128,"triangles":338,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009710","count":11},{"id":"GO:0042574","count":11},{"id":"GO:0042376","count":11},{"id":"GO:0055114","count":11},{"id":"GO:0017000","count":11}]},{"hash":"566712169248346818","title":"Unknown","description":"The top terms cover a highly diverse set of biology: protein heterooligomerization, Schwann cell development, histone dephosphorylation (obsolete), morphine response, DNA replication, meiotic cell cycle, unfolded protein response, kinetochore localization, lead ion response, and excitatory postsynaptic potential. There is no single cohesive function or pathway uniting these terms, so a specific, meaningful label for this cluster cannot be determined.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051291","count":4},{"id":"GO:0014044","count":3},{"id":"GO:0016576","count":3},{"id":"GO:0043278","count":3},{"id":"GO:0006260","count":3}]},{"hash":"2114092430767680231","title":"Signaling, migration, and cytoskeleton regulation","description":"The cluster\u2019s GO terms span signaling pathways (TORC2, Ras, stress-activated MAPK), actin cytoskeleton polarity, cell migration, stress granule assembly, and synaptic/neuromuscular junction assembly. While no single function dominates, the common thread appears to be signaling-driven cytoskeletal remodeling and migratory/structural organization, with touches of stress response and synaptic assembly. This suggests a cohesive theme of signaling and cytoskeleton dynamics rather than a strict metabolic role.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008152","count":1},{"id":"GO:1902475","count":1},{"id":"GO:0090116","count":1},{"id":"GO:0038203","count":1},{"id":"GO:0030950","count":1}]},{"hash":"1350767067049330475","title":"Unknown","description":"The top GO terms cover disparate areas (amino acid biosynthesis, bacterial LPS biosynthesis, cell cycle progression and cilium assembly, ER-stress\u2013related translation, ubiquitination, interferon signaling, protein sulfation, and steroid receptor assembly). There is no single cohesive theme uniting the proteins, so a meaningful specific label is not apparent.","confidence":"","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006564","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0009103","count":7},{"id":"GO:0007091","count":6},{"id":"GO:1905515","count":6}]},{"hash":"1299020477599093660","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":214,"triangles":882,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0044205","count":4},{"id":"GO:0015976","count":4},{"id":"GO:2000122","count":4},{"id":"GO:0071244","count":4},{"id":"GO:0045214","count":3}]},{"hash":"2010935845480087362","title":"Innate immune sensing and DC antigen presentation","description":"The cluster centers on innate immune sensing pathways (TLR9, NOD2, NLRP3 inflammasome, muramyl dipeptide detection) and downstream activation of dendritic cells with increased antigen processing and MHC class I presentation, plus interferon signaling. This suggests a coherent theme of innate sensing driving adaptive antigen presentation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":25},{"id":"GO:0030335","count":25},{"id":"GO:1902745","count":25},{"id":"GO:0070431","count":25},{"id":"GO:0002830","count":25}]},{"hash":"920929440023214232","title":"Unknown","description":"The terms span neural signaling, immune response, cell cycle, and development with no single dominant function, making it hard to assign a cohesive label. Therefore, Unknown with no confidence.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903351","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0001889","count":4},{"id":"GO:0071320","count":4}]},{"hash":"766300689466072111","title":"Metal Ion Homeostasis and Transcription","description":"The top GO terms mainly point to metal ion handling (manganese, cadmium, zinc) and transport, paired with DNA-templated transcription, suggesting a core theme of metal ion regulation coupled with transcriptional control. A few cardiovascular-related terms appear but are much less represented, so the dominant signal is metal ion homeostasis with transcription regulation.","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:0071287","count":2},{"id":"GO:0070574","count":1},{"id":"GO:0033574","count":1},{"id":"GO:1903249","count":1}]},{"hash":"1133048765699393032","title":"Cerebellar development and neural signaling","description":"This cluster is strongly anchored by cerebellum-specific terms: cerebellar cortex formation and Bergmann glial cell differentiation, with related neural processes such as regulation of axon regeneration and various signaling pathways (including insulin and T cell receptor signaling) that can occur in neural tissue. While other terms touch on general cell cycle and protein stability, the cerebellar development and neural communication themes dominate, suggesting a functional grouping around cerebellar development and neural signaling networks.","confidence":"Medium","size":25,"edges":211,"triangles":840,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008286","count":25},{"id":"GO:0021697","count":25},{"id":"GO:2001275","count":25},{"id":"GO:0008285","count":25},{"id":"GO:0050852","count":25}]},{"hash":"1532077645689728162","title":"Regulatory signaling and transcription","description":"This cluster\u2019s top GO terms point to transcriptional regulation and diverse signaling/regulatory processes (Rho signaling, osmotic stress response, development signals, and immune-related stimulus response), suggesting a set of proteins that coordinate responses rather than a single pathway.","confidence":"Medium","size":25,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097011","count":22},{"id":"GO:0006351","count":22},{"id":"GO:0046827","count":21},{"id":"GO:0060440","count":20},{"id":"GO:0001403","count":20}]},{"hash":"1137902118156567414","title":"Unknown","description":"The top GO terms span cytolysis, metal ion homeostasis, signaling, immune regulation, morphogenesis, and defense, with little overlap pointing to a single cohesive theme. The mixture suggests diverse or poorly characterized proteins rather than a clear functional module, so a reliable label cannot be assigned.","confidence":"","size":25,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019835","count":1},{"id":"GO:0006882","count":1},{"id":"GO:0033211","count":1},{"id":"GO:1901223","count":1},{"id":"GO:0061042","count":1}]},{"hash":"1187097651656433784","title":"Unknown","description":"The Top Terms span disparate biological themes (ascospore formation, inflammatory regulation, morphine response, lung development, neuron differentiation, apoptotic signaling, mitotic checkpoints, xenobiotic response, and glycogen metabolism) with no clear shared function or pathway. The lack of a cohesive signal, plus zero edges and triangles, suggests the proteins do not form a single coherent functional cluster.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":2},{"id":"GO:0050728","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0030182","count":1}]},{"hash":"737759132125325594","title":"Neural development and DNA damage response","description":"The top GO terms strongly point to neural development (neuron differentiation; Schwann cell development) while also highlighting genome maintenance processes (DSB repair processing, intra-S checkpoint signaling, and trinucleotide repeat maintenance) and stress-related responses (apoptosis regulation, xenobiotic response). This suggests a cohesive theme where proteins participate in neural development alongside DNA damage response pathways, even though a few terms (like ascospore formation or glycogen regulation) are less directly connected.","confidence":"Medium","size":25,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":2},{"id":"GO:2001241","count":2},{"id":"GO:1905213","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0031573","count":2}]},{"hash":"2046998740636897663","title":"Neuronal vesicle trafficking","description":"This cluster shows terms related to vesicle movement between ER, Golgi, endosomes, and plasma membrane, including ER-to-Golgi transport, COPII cargo loading, endosome-to-Golgi transport, and Rab-regulated trafficking. The presence of brain development hints at neuronal context, suggesting these proteins participate in neuronal secretory and recycling pathways. Overall, the common theme is vesicle trafficking in neurons.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0010800","count":2},{"id":"GO:0007205","count":2},{"id":"GO:1902018","count":1},{"id":"GO:0071955","count":1}]},{"hash":"336047529841119381","title":"Schwann cell development and neural crest differentiation","description":"The terms point to peripheral nervous system glia and neural crest\u2013driven neural development, with emphasis on Schwann cell maturation, axon ensheathment, and neural crest\u2013related migration, supporting a cohesive PNS neural development theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014068","count":1},{"id":"GO:0035310","count":1},{"id":"GO:0032285","count":1},{"id":"GO:0048146","count":1},{"id":"GO:1905208","count":1}]},{"hash":"430935124733292018","title":"Limb joint morphogenesis and adhesion signaling","description":"This cluster is dominated by terms related to embryonic skeletal limb joint morphogenesis, calcium-dependent cell-cell adhesion, and regulation of actin cytoskeleton organization by adhesion, suggesting a core role in developmentally controlled cell adhesion and cytoskeletal remodeling during limb morphogenesis. Additional signals point to GTPase activity regulation and cell-cycle control that often accompany dynamic morphogenetic processes. Some terms are housekeeping or obsolete, but the central theme appears to be adhesion-mediated cytoskeletal dynamics in developmental morphogenesis. ","confidence":"Medium","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":8},{"id":"GO:0006607","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0007050","count":7},{"id":"GO:0016339","count":6}]},{"hash":"132142819452378567","title":"Mitochondrial Respiration and Energy Transport","description":"The top GO terms center on mitochondrial electron transport (ubiquinol to cytochrome c), aerobic respiration, and proton transmembrane transport, all core to ATP production. While there are some peripheral terms related to transcription regulation and host interactions, the strongest signal is mitochondrial energy metabolism, justifying this label. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":3},{"id":"GO:0000973","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0009060","count":2}]},{"hash":"1324715661359888272","title":"Unknown","description":"The top GO terms are diverse and singletons (epithelial maturation in salivary gland, NK cell cytotoxicity, triglyceride homeostasis, ER stress response, cytokine production, IL-4 response, osteoblast differentiation, dorsal identity), with no shared pathway or interaction (edges/triangles = 0, max degree 0). This lack of cohesion makes it impossible to assign a concise biological label.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060691","count":1},{"id":"GO:0042267","count":1},{"id":"GO:0035356","count":1},{"id":"GO:0010691","count":1},{"id":"GO:1990440","count":1}]},{"hash":"552043050858987329","title":"Mitotic cell cycle regulation via APC/C ubiquitination","description":"The top GO terms point strongly to mitosis and cell division (mitotic cell cycle, cell division, mitotic spindle assembly, APC-dependent catabolic process), with several entries about K11-linked ubiquitination, which is characteristic of APC/C-regulated protein turnover during mitosis. A few vesicle trafficking terms appear but don\u2019t outweigh the prevailing mitotic theme. This cluster likely represents proteins involved in regulating mitotic progression through ubiquitin-mediated turnover and chromatin-related control. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0070979","count":3},{"id":"GO:2001162","count":3}]},{"hash":"822854350143797665","title":"Neural development and axonogenesis with innate immunity","description":"The top GO terms are dominated by neural development signals (corpus callosum development, axonogenesis) and dopaminergic signaling (cellular response to dopamine), suggesting a neural development-focused cluster. Concurrent immune-related terms (innate immune response, LPS signaling, interferon-beta production, defense against Gram-positive bacteria) imply potential cross-talk between neural development and immune pathways. Some terms are more general (DNA-templated transcription) or unrelated (heart development), but the neural development axis appears strongest. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0046827","count":4},{"id":"GO:0007507","count":3},{"id":"GO:0045359","count":3},{"id":"GO:0022038","count":3}]},{"hash":"899442342473305613","title":"Unknown","description":"The GO terms span neuronal signaling, immune regulation, development, cytoskeletal organization, apoptosis, and transcription, with no single cohesive function or pathway dominating the cluster. Therefore a consistent, specific label is not apparent.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032226","count":1},{"id":"GO:0032691","count":1},{"id":"GO:1900136","count":1},{"id":"GO:0090327","count":1},{"id":"GO:0060613","count":1}]},{"hash":"1493746781745390935","title":"TLR/NLR Innate Immunity Signaling and Inflammasome","description":"The cluster is dominated by GO terms for MyD88-dependent TLR signaling, TLR9 signaling, NOD-like receptor pathways (NOD2 and detection of MDP), and NLRP3 inflammasome complex assembly, indicating a coherent innate immune signaling module. Additional terms point to regulation of type II interferon signaling, type 2 immune responses, and processes linked to immune cell migration and lamellipodium organization, all supporting activation and recruitment of immune cells. Altogether, this set represents innate immune receptor signaling converging on inflammasome activation and effector responses.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":16},{"id":"GO:0031146","count":16},{"id":"GO:0034162","count":15},{"id":"GO:0030335","count":15},{"id":"GO:1902745","count":15}]},{"hash":"132013759860572822","title":"TLR/NLR Innate Immune Signaling and Inflammasome Assembly","description":"The cluster centers on Toll-like receptor signaling (MyD88-dependent and TLR9), NOD2 signaling, and NLRP3 inflammasome assembly, with muramyl dipeptide detection and downstream interferon signaling. Several terms also note leukocyte migration and lamellipodium organization, suggesting roles in immune cell recruitment during innate responses. Together these terms point to an innate immune sensing and inflammatory program.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":9},{"id":"GO:0031146","count":9},{"id":"GO:0034162","count":8},{"id":"GO:0030335","count":8},{"id":"GO:1902745","count":8}]},{"hash":"620588370191035407","title":"Unknown","description":"The GO terms are highly diverse, spanning transcription (DNA-templated transcription), plant signaling (cytokinin-activated signaling pathway), cardiac electrophysiology (positive regulation of membrane depolarization during cardiac muscle cell action potential), sensory biology (thermoception, response to heat), cell division (spindle assembly), neuronal development (cerebellar granule cell differentiation, negative regulation of dendrite development), and prostate/gland maturation, with no clear shared function tying the proteins together. The lack of a coherent theme and zero edges suggest this cluster does not reflect a single biological concept.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1900827","count":2},{"id":"GO:0050955","count":2},{"id":"GO:0009408","count":2}]},{"hash":"905189134922664055","title":"Regulated GTPase and cAMP signaling","description":"The Top GO terms emphasize modulation of signaling pathways, featuring positive regulation of adenylate cyclase (cAMP) and small GTPase\u2013mediated signaling with negative regulation of Ras signaling, indicating a cluster of proteins that tune intracellular signal transduction.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045762","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0051447","count":1},{"id":"GO:0046580","count":1}]},{"hash":"1072770603494248616","title":"Genome maintenance and protein quality control","description":"The top GO terms cluster around core genome tasks (DNA replication, nucleotide-excision repair, transcription regulation) alongside protein homeostasis and stress responses (autoubiquitination, proteasomal regulation, deglycosylation, ER stress-related signaling, and mitochondrial fusion regulation), suggesting a cohesive theme of genome integrity maintenance together with cellular protein quality control under stress.","confidence":"Medium","size":24,"edges":69,"triangles":58,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006412","count":6},{"id":"GO:0010636","count":5},{"id":"GO:1902236","count":5},{"id":"GO:0006289","count":5}]},{"hash":"1669509582503615333","title":"Ion Transport and cAMP/cGMP Signaling Regulation","description":"This cluster is dominated by GO terms for ion transport (sodium and potassium), potassium homeostasis, and cellular responses to cAMP and cGMP, with additional signals related to regulation of Ras and guanylyl cyclase pathways. The common thread appears to be modulation of ion homeostasis and intracellular signaling, rather than a single metabolic pathway, making this a coherent theme despite the inclusion of DNA-templated transcription terms plus a aerotaxis hint.","confidence":"Medium","size":24,"edges":247,"triangles":1461,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0098719","count":10},{"id":"GO:0046827","count":10},{"id":"GO:0009454","count":9},{"id":"GO:0071805","count":9}]},{"hash":"1407257877229886284","title":"Developmental Signaling and Tissue Remodeling","description":"These proteins show enrichment in neural development signals (neural precursor proliferation, neuropeptide turnover) alongside extracellular matrix remodeling (basement membrane disassembly, bone ossification) and broad developmental pathways (thyroid hormone response, Wnt signaling) with ancillary immune and tissue-specific processes (T cell cytotoxicity, surfactant homeostasis). The common thread appears to be involvement in development and remodeling across tissues, rather than a single cohesive pathway.","confidence":"Medium","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":24},{"id":"GO:0034769","count":24},{"id":"GO:0010813","count":24},{"id":"GO:0097067","count":24},{"id":"GO:0001913","count":24}]},{"hash":"495186455800447387","title":"Chromatin Regulation and Genome Maintenance","description":"This cluster is dominated by GO terms tied to chromatin state control (rDNA heterochromatin formation, histone H3-K9 modification), transcription (DNA-templated transcription), and genome maintenance (base-excision repair). While some terms touch on growth-factor signaling and apoptosis, the common thread is regulation of gene expression through chromatin remodeling and DNA repair processes.","confidence":"High","size":24,"edges":247,"triangles":1466,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":8},{"id":"GO:0006351","count":8},{"id":"GO:1902237","count":7},{"id":"GO:0061647","count":7},{"id":"GO:0045950","count":7}]},{"hash":"1049684206933653558","title":"Diverse metabolite and lipid biosynthesis","description":"The proteins show enrichment for a range of biosynthetic processes (antibiotic, alkaloid, retinal, and very long\u2011chain fatty acid/lipid biosynthesis), pointing to a general theme of metabolite and lipid production rather than a single specific pathway.","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042619","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0009710","count":4},{"id":"GO:0042574","count":4}]},{"hash":"1341183695304170472","title":"RNA processing and post-transcriptional regulation","description":"The top GO terms cluster around RNA maturation and control of gene expression after transcription: spliceosome-mediated mRNA splicing, mRNA stabilization, polyadenylation regulation, small-subunit processome and eIF4F complex assembly, and ncRNA/miRNA\u2013mediated silencing. These collectively point to RNA processing and post-transcriptional regulatory roles for the proteins in this cluster, despite some obsolete annotations. ","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:0009190","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048255","count":2},{"id":"GO:1902625","count":2}]},{"hash":"2096385069764779660","title":"Unknown","description":"The top GO terms cover transcription, multiple developmental processes (forebrain development, neural tube closure, skeletal system development, multicellular organism development), and various stress responses (ER stress-induced apoptosis, cadmium response, defense against Gram-positive bacteria), indicating a broad and divergent set of functions with no single cohesive theme. Therefore, a coherent, specific label could not be determined.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0001403","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0001501","count":4}]},{"hash":"1643793653676739361","title":"Unknown","description":"Top terms are diverse: protein ubiquitination, innate immune signaling (TLR7, LPS response), mRNA export, chromatin remodeling, plus developmental morphogenesis terms. With no edges and a mix of unrelated topics, there is no clear shared function tying the proteins together. Therefore Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0071222","count":3},{"id":"GO:0006406","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0034154","count":1}]},{"hash":"25325208593803501","title":"Post-transcriptional Regulation of Translation and RNA Processing","description":"Most frequent GO terms center on translation initiation and reinitiation, including formation of translation preinitiation complex, IRES-dependent initiation, and overall regulation of translational initiation, plus translation reinitiation. Additionally, there are RNA-level regulatory processes such as spliceosome-mediated alternative splicing regulation, ncRNA-mediated gene silencing, and mRNA stabilization, implying a broader post-transcriptional control of gene expression. The xenobiotic response and transformation competence terms may reflect cellular stress responses that couple to translation and RNA regulation.","confidence":"High","size":24,"edges":33,"triangles":8,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1688078796851547806","title":"GPCR Signaling and Lipid Mediator Biosynthesis","description":"The terms cluster around GPCR-driven signaling: sensory perception of smell points to olfactory GPCR activity, and there are cellular responses to cAMP and cGMP with regulation of guanylyl cyclase signaling. In addition, prostaglandin and steroid biosynthetic processes (aldosterone, cortisol) tie into lipid mediator and hormone biosynthesis, suggesting a shared theme of signal transduction and signaling-molecule production, even though some terms (like lipopolysaccharide response) broaden the scope. Overall, a cohesive label is GPCR signaling and lipid mediator biosynthesis.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007608","count":4},{"id":"GO:0071320","count":3},{"id":"GO:0055119","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0010754","count":3}]},{"hash":"2296160339628612841","title":"Gram-positive cell wall biosynthesis","description":"The top GO terms point to teichoic acid and lipoteichoic acid biosynthesis, as well as general cell wall organization, which are hallmark features of Gram-positive bacterial cell wall construction. While some translation-related terms appear, the dominant signal is clearly tied to cell wall biosynthesis, particularly teichoic acid pathways.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":2},{"id":"GO:0046898","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0071353","count":1}]},{"hash":"835802149863250217","title":"Developmental signaling and differentiation","description":"These GO terms cluster around developmental processes and differentiation (neural tube patterning, myotube differentiation, trachea formation) with related signaling (p38 MAPK), adhesion, and some stress/apoptosis components, suggesting a group of proteins involved in developmental signaling and cell differentiation plus coordinated remodeling cues.","confidence":"Medium","size":24,"edges":85,"triangles":74,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032435","count":23},{"id":"GO:0044565","count":22},{"id":"GO:1901621","count":22},{"id":"GO:0035729","count":22},{"id":"GO:0014902","count":22}]},{"hash":"327220128904017777","title":"Unknown","description":"The Top Terms cover immunoregulation, yeast bud-neck localization, meiotic and Ras/GTPase signaling, sarcomere organization, ion transport, aerotaxis, and drug response. These functions are diverse and not cohesively linked, so there is no clear shared function to name a single, representative cluster label.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046007","count":3},{"id":"GO:0097271","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2}]},{"hash":"130685658527223864","title":"Ubiquitin-regulated signaling and immune responses","description":"This cluster is enriched for ubiquitination (protein polyubiquitination), innate immune response, and regulators of NF-kappaB signaling, plus related signaling controls (GTPase activity regulation, estrogen response). While there are some outliers (neuron development, prospore membrane formation, sterol transport), the dominant theme centers on regulation of signaling pathways and immune-related processes via ubiquitin-dependent mechanisms.","confidence":"Medium","size":24,"edges":73,"triangles":21,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0048666","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0032366","count":1}]},{"hash":"1471321110189016497","title":"Transcriptional Regulation and Ras Signaling","description":"This cluster is enriched for DNA-templated transcription and modulation of Ras/small GTPase signaling, plus related regulation of PKA activity, suggesting a core theme of transcriptional control intertwined with Ras/PKA pathways. Other terms like nuclear export regulation, sarcomere organization, and ion transport appear as supporting processes within a broader signaling/transcription context, rather than defining a single cohesive pathway.","confidence":"Medium","size":24,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0046827","count":5},{"id":"GO:2000480","count":4},{"id":"GO:0034638","count":4},{"id":"GO:0051447","count":3}]},{"hash":"1359123319638218056","title":"Excitable tissue signaling and ion-channel regulation","description":"This cluster centers on ion-channel\u2013mediated electrical signaling and calcium-dependent regulation, with terms such as cellular response to calcium ion, clustering of voltage-gated potassium channels, cardiac muscle contraction, and regulation of synaptic vesicle exocytosis. These point to mechanisms of excitability and rapid intercellular communication in heart and neural tissues. Some development-related terms (Schwann cell, collecting duct) and xenobiotic responses appear ancillary but do not override the core theme of ion-channel\u2013driven electrical signaling.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":3},{"id":"GO:0071902","count":2},{"id":"GO:0050665","count":2},{"id":"GO:0045163","count":2},{"id":"GO:0060048","count":2}]},{"hash":"2257058300987325291","title":"Cholesterol transport and steroid biosynthesis","description":"The terms show a strong emphasis on cholesterol handling and steroid hormone production: intracellular cholesterol transport, cholesterol transport involved in cholesterol storage, and progesterone biosynthetic process. This suggests the cluster comprises proteins involved in lipid transport and steroid metabolism. Additional terms related to heart morphogenesis, integument development, and endothelial tube lumen extension may reflect broader developmental contexts or annotations, but the prevailing signal is cholesterol transport and steroid biosynthesis.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":1},{"id":"GO:0071373","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0006701","count":1},{"id":"GO:0032367","count":1}]},{"hash":"1633273542450489181","title":"Cilia/Flagella Assembly and Movement","description":"The cluster is dominated by GO terms for ciliogenesis and motility, including sperm axoneme assembly, flagellated sperm motility, epithelial cilium movement, and regulation of cilium movement, plus microtubule-related processes like microtubule severing and post-translational modifications (polyglycylation, polyglutamylation) that support axoneme dynamics and axon extension. Although one term (short-term memory) is not aligned, the overall pattern points to a cohesive theme of ciliary/flagellar structure and movement across cell types.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007614","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0007288","count":2},{"id":"GO:0003351","count":2},{"id":"GO:1905419","count":2}]},{"hash":"1553740164541590044","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006303","count":2},{"id":"GO:0071480","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0071481","count":2}]},{"hash":"2169840445523385054","title":"Unknown","description":"The Top GO terms are scattered across diverse cellular processes (cell division, left/right development, NK cell degranulation, dephosphorylation, apoptotic signaling, vasculature development, protein complex assembly, tRNA clustering, ER-Golgi transport, and synaptonemal complex assembly). There is no clear, cohesive biological theme or pathway linking these terms, and the zero edges suggest no tight clustering of a single function. Therefore, a specific, representative label cannot be determined with confidence.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007368","count":2},{"id":"GO:0043323","count":1},{"id":"GO:0070262","count":1},{"id":"GO:2001241","count":1}]},{"hash":"689993404382944229","title":"Innate immune sensing and inflammasome signaling","description":"This cluster is dominated by GO terms for innate immune response, defense against virus, TLR9 signaling, NOD2 signaling, NLRP3 inflammasome assembly, and muramyl dipeptide detection, all pointing to pathogen sensing and inflammasome activation. The presence of type II interferon signaling and positive regulation of immune cell migration further supports a cohesive innate-immune signaling theme rather than a single enzymatic function. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":20},{"id":"GO:0051607","count":20},{"id":"GO:0034162","count":19},{"id":"GO:0030335","count":19},{"id":"GO:1902745","count":19}]},{"hash":"1571487725330312722","title":"Innate immune signaling and cytoskeletal remodeling","description":"The terms cluster around innate immune sensing and inflammatory signaling (muramyl dipeptide detection, NF-kappaB regulation, IL-1\u03b2 and IL-8 production, Th17 differentiation) along with actin cytoskeleton reorganization (lamellipodium organization, barbed-end actin uncapping). This supports a cohesive theme of immune activation with concurrent cytoskeletal remodeling, rather than a single narrow function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0046827","count":6},{"id":"GO:0043124","count":5},{"id":"GO:2000321","count":5},{"id":"GO:0051638","count":5},{"id":"GO:0031146","count":5}]},{"hash":"9698268312143093","title":"Leukocyte Activation and ECM Remodeling","description":"Based on the top GO terms, the cluster is enriched for immune-related processes (T cell activation via TCR-MHC interaction and complement activation) as well as extracellular matrix remodeling and cell adhesion/migration (negative regulation of ECM assembly, metallopeptidase activity, heterotypic cell-cell adhesion, substrate-dependent migration, extravasation). The presence of GTPase activity regulation and protein heterotrimerization suggests coordination of signaling and cytoskeletal changes necessary for cell movement. Together, these terms indicate a theme of immune cell activation coupled with ECM remodeling and migration through tissues.","confidence":"High","size":23,"edges":14,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0002291","count":2},{"id":"GO:0006956","count":2},{"id":"GO:0003429","count":2}]},{"hash":"2214572044967068177","title":"Membrane trafficking and signaling","description":"This cluster is characterized by terms pointing to vesicle dynamics and membrane-associated signal transduction, such as regulation of synaptic vesicle exocytosis, plasma membrane to endosome transport, and EGFR signaling. While other terms (brain development, osteoclast differentiation, viral RNA replication) appear less connected, the strongest shared theme across the terms is membrane trafficking coupled with signaling processes. The low connectivity suggests a broad, somewhat diffuse grouping rather than a tight functional module, but the core appears to be vesicle trafficking and related signaling. ","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0031384","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0045670","count":1}]},{"hash":"902887037993163199","title":"Unknown","description":"This cluster's terms come from many unrelated biological areas (cell cycle, protein modification, cilium assembly, plant signaling, metal response, ER stress, ubiquitination, interferon signaling, sulfation). Because there is no clear shared function or pathway tying the proteins together, there is no confident cohesive label.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007091","count":2},{"id":"GO:0000413","count":2},{"id":"GO:1905515","count":2},{"id":"GO:0009938","count":2},{"id":"GO:0010288","count":2}]},{"hash":"1815547025593949073","title":"Neuronal vesicle trafficking and filopodium dynamics","description":"This cluster centers on vesicle trafficking (endocytosis, ER-Golgi transport, retrograde transport) and filopodium assembly/regulation, with neural context signals (substantia nigra development, GABAergic synaptic transmission), suggesting a cohesive theme of neuronal membrane trafficking coupled with actin-driven filopodial remodeling and neurite/synapse formation.","confidence":"High","size":23,"edges":22,"triangles":0,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0006897","count":4},{"id":"GO:0046847","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0006890","count":4}]},{"hash":"510841744583515513","title":"Ubiquitin-Proteasome Degradation and TNF-NF-\u03baB Signaling","description":"The terms are dominated by ubiquitin-dependent protein catabolic processes (including autoubiquitination and SCF-dependent degradation) and components of the TNF signaling and NF-\u03baB pathways, suggesting a cluster of proteins involved in ubiquitin-tagged protein turnover linked to inflammatory signaling. This makes a cohesive label focusing on the ubiquitin-proteasome system and its connection to NF-\u03baB activation appropriate.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0090073","count":6}]},{"hash":"1095965248283036553","title":"Sterol biosynthesis and lipid metabolism","description":"The top GO terms are dominated by sterol biosynthesis and oxidation (ergosterol biosynthetic process, lathosterol, multiple sterol oxidations, and related lipid metabolism terms). While there are a few terms related to neural or immune functions, the strongest signal is sterol/lipid biosynthesis and modification, suggesting the cluster centers on sterol metabolism. ","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042619","count":7},{"id":"GO:0032286","count":6},{"id":"GO:0033490","count":6},{"id":"GO:0035754","count":6}]},{"hash":"630833792310159167","title":"RNA Methylation and RNA Modification","description":"This cluster is dominated by RNA methylation-related terms (tRNA methylation, tRNA wobble modification, rRNA methylation, peptidyl-glutamine methylation), suggesting a core function in RNA modification. Additional terms touch on cofactor biosynthesis and mitochondrial respiration, which may reflect related enzymatic activities but do not overshadow the RNA modification signal. Confidence: Medium","confidence":"","size":23,"edges":52,"triangles":38,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0055114","count":3}]},{"hash":"578279344318870609","title":"Diverse biosynthetic and metabolic processes","description":"The top GO terms point to multiple, distinct biosynthetic and metabolic pathways (retinol/retinal metabolism, androgen/testosterone biosynthesis, phylloquinone catabolism, tropane alkaloid and antibiotic biosynthesis) with a lone transcription-regulation term, suggesting a cluster of proteins involved in a variety of biosynthetic/metabolic activities rather than a single coherent pathway.","confidence":"Medium","size":23,"edges":41,"triangles":16,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0042572","count":9},{"id":"GO:0042574","count":8},{"id":"GO:0042619","count":8},{"id":"GO:0061370","count":8}]},{"hash":"651446722218664221","title":"Unknown","description":"Top GO terms are highly varied, spanning membrane repair, deubiquitination regulation, development and morphogenesis, nervous system and cardiac physiology, and antiviral responses. There is no coherent, shared biological process that ties these terms together, suggesting the proteins do not reflect a single functional module. Therefore, a concise single-label interpretation is not evident.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":2},{"id":"GO:0090086","count":1},{"id":"GO:0007275","count":1},{"id":"GO:0071641","count":1},{"id":"GO:1902187","count":1}]},{"hash":"239183915641980788","title":"DNA replication and cell cycle regulation","description":"The top GO terms cluster around core cell cycle and genome maintenance processes (DNA replication, DNA damage response/p53-mediated arrest, mitotic centrosome separation), with additional signals for translation regulation and development/morphogenesis that often accompany proliferation and growth. This suggests a cohesive group of proteins focused on DNA replication and cell-cycle control, with developmental context as a secondary theme.","confidence":"High","size":23,"edges":81,"triangles":144,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0048701","count":11},{"id":"GO:0045727","count":11},{"id":"GO:0006977","count":11},{"id":"GO:0007100","count":11}]},{"hash":"1193793540116703387","title":"Ubiquitin-Dependent Cell Cycle Regulation","description":"The cluster centers on ubiquitin-related processes (K11-linked ubiquitination; ubiquitin-dependent protein catabolic process) and cell-cycle terms (cell cycle, mitotic cell cycle, cell division), suggesting ubiquitin\u2011mediated protein turnover as a core regulator of cell progression; additional signals in DNA damage response and signaling pathways (NF-kappaB signaling; response to corticosterone) indicate coordinated control linking ubiquitination, cell cycle, and stress responses.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0051412","count":2}]},{"hash":"1072721979727410127","title":"Mitochondrial energy metabolism and dynamics","description":"This cluster centers on mitochondrial metabolism and membrane dynamics, with GO terms for amino acid starvation response, apoptotic mitochondrial changes, regulation of mitochondrial membrane potential, and transport of key metabolites (alpha-ketoglutarate, thiamine pyrophosphate, coenzyme A) across membranes, plus the malate-aspartate shuttle. Some terms are marked obsolete, but the core signal is mitochondrial energy metabolism and membrane transport.","confidence":"High","size":23,"edges":78,"triangles":108,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034198","count":10},{"id":"GO:0008637","count":8},{"id":"GO:0051881","count":8},{"id":"GO:0015742","count":8},{"id":"GO:0030974","count":8}]},{"hash":"70305115373834132","title":"Cellular Stress Responses and Protein Homeostasis","description":"This cluster centers on cellular stress responses and protein quality control pathways\u2014unfolded protein response, ER stress\u2013driven translation initiation, and ER-associated degradation\u2014alongside various stress-related signaling (cadmium response, interferon response, morphine response) and translation regulation. Some plant- or tissue-specific terms appear (gibberellin signaling, photosynthesis, photoreceptor localization), but the dominant signal is stress response and protein folding/degradation management.","confidence":"Medium","size":23,"edges":162,"triangles":538,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009938","count":15},{"id":"GO:0016570","count":15},{"id":"GO:0035457","count":15},{"id":"GO:0071276","count":15},{"id":"GO:0043278","count":15}]},{"hash":"2180697406682663110","title":"Unknown","description":"The GO terms span immune response (type I interferon, defense against virus), cilium assembly, and steroid-related development (prostate gland development, male sex differentiation, steroid hormone receptor complex assembly), plus other processes (ER stress translation, ubiquitination). This wide mix suggests no single, coherent function characterizes all proteins in the cluster, and there are no network edges to support a shared role.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071357","count":12},{"id":"GO:0006463","count":12},{"id":"GO:0046661","count":12},{"id":"GO:0030850","count":12},{"id":"GO:0007091","count":10}]},{"hash":"1515396466197935716","title":"Multisystem Development and Gene Regulation","description":"The terms point to developmental processes across tissues (salivary gland, skeletal muscle, nervous system) and regulatory activities (DNA-templated transcription, nuclear export regulation), with a few general DNA repair terms. This pattern suggests a broad, multi-tissue developmental and regulatory program rather than a single, narrow function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007435","count":2},{"id":"GO:0006297","count":2},{"id":"GO:0051402","count":2},{"id":"GO:0006288","count":2},{"id":"GO:0007519","count":2}]},{"hash":"1442365445642292340","title":"TLR9 and NLRP3-Driven DC Activation and Antigen Presentation","description":"Based on the top GO terms, the cluster centers on innate immune sensing (TLR9 signaling, NOD2/NLR pathways, and NLRP3 inflammasome assembly) and downstream dendritic cell functions, including antigen processing and presentation (MHC class I biosynthesis) and IFN-\u03b3 signaling. The lamellipodium organization and cell migration terms align with dendritic cell maturation and migration to lymph nodes, supporting antigen presentation. Overall, the data point to a coherent theme of innate detection leading to DC activation and antigen presentation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":22},{"id":"GO:0030335","count":22},{"id":"GO:1902745","count":22},{"id":"GO:0070431","count":22},{"id":"GO:0002830","count":22}]},{"hash":"2220422504735390619","title":"Antiviral Innate Immune Signaling","description":"This cluster centrally features GO terms for defense response to virus and innate immune response, with components of TLR signaling (including MyD88-independent pathway), non-canonical NF-kappaB regulation, and modulation of cytokines such as IL-18 and IL-1. It also includes positive regulation of MHC class I biosynthetic process and cell migration, suggesting coordinated antiviral sensing with antigen presentation and immune cell trafficking. Overall, the terms converge on a core antiviral innate immune program.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":21},{"id":"GO:0045087","count":21},{"id":"GO:0030335","count":20},{"id":"GO:0002830","count":20},{"id":"GO:0045345","count":20}]},{"hash":"903794423416922072","title":"Neuronal development and signaling regulators","description":"The top terms cluster around neural development and morphology (hippocampus development, dendrite morphogenesis, regulation of axonogenesis) along with cytoskeletal dynamics (focal adhesion assembly regulation, actin cytoskeleton reorganization) and key signaling pathways (ERK1/ERK2 and JNK cascades) that influence calcium-dependent exocytosis. This pattern suggests a set of proteins involved in neurite outgrowth, dendrite formation, and synaptic signaling rather than a single linear process.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051893","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0031532","count":2}]},{"hash":"449497144287769942","title":"Strigolactone biosynthesis and secondary shoot formation","description":"This cluster centers on plant-specific functions: the strigolactone biosynthetic process and secondary shoot formation suggest hormone signaling controlling shoot architecture.Additional terms point to plant secondary metabolism and defense compounds (stilbene catabolism, antibiotic biosynthesis) and core metabolism (malate), which fits a broader plant metabolism theme. The presence of a few obsolete GO terms and lack of direct interactions (edges/triangles) keeps the label at a confident, but not certain, level.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0007155","count":3},{"id":"GO:0010223","count":2},{"id":"GO:0006108","count":2},{"id":"GO:1901601","count":2}]},{"hash":"492515892173064850","title":"Signal transduction and potassium homeostasis","description":"The top GO terms point to diverse signaling pathways (cAMP/cGMP signaling, receptor signaling) alongside potassium ion transport and homeostasis, plus DNA-templated transcription. This suggests a cluster of proteins coordinating cellular signaling with ionic balance, potentially linking sensory or cardiac contexts to transcriptional responses. The terms are somewhat broad and multi-context, so the label is a best-fit overview rather than a single precise function.","confidence":"Medium","size":23,"edges":241,"triangles":1541,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":20},{"id":"GO:0046827","count":20},{"id":"GO:0009454","count":20},{"id":"GO:0050976","count":20},{"id":"GO:0071805","count":20}]},{"hash":"1967154899722966048","title":"Transcriptional and metabolic control of angiogenesis","description":"This cluster centers on transcriptional regulation (DNA-templated transcription) and signaling pathways that modulate angiogenesis and metabolic responses. The presence of NFAT-related regulation, cytoskeletal remodeling, and glucose-responsive processes suggests a coordinated program linking gene expression, cytoskeleton dynamics, and metabolic cues in angiogenic contexts.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":16},{"id":"GO:0046826","count":15},{"id":"GO:0030866","count":14},{"id":"GO:0033138","count":14},{"id":"GO:0008542","count":14}]},{"hash":"157823632520988610","title":"Renin-angiotensin regulation and kidney development","description":"The GO terms cluster around the renin-angiotensin system, aldosterone production, blood volume regulation, angiotensin maturation, and mesonephros development, pointing to a kidney/endocrine signaling theme. Other terms (ER-to-Golgi transport, membrane proteolysis, protein autoprocessing) reflect general cellular processing but do not override the renal-RA focus.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0050435","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0002018","count":2},{"id":"GO:0001823","count":2}]},{"hash":"2061788951174821921","title":"Developmental morphogenesis and ECM remodeling","description":"The terms point to tissue formation and remodeling across organs: branching morphogenesis in lung, epithelial tube branching, basement membrane and collagen remodeling, and ossification/remodeling of bone; these reflect a cohesive theme of developmental morphogenesis coupled with extracellular matrix dynamics. A few terms (neural precursor proliferation, thyroid hormone response) tie into developmental signaling, while others (neuropeptide catabolic, T cell cytotoxicity) are tangential but do not overturn the core pattern.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":1},{"id":"GO:0034769","count":1},{"id":"GO:0010813","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0060448","count":1}]},{"hash":"1635267057694756451","title":"Chromatin remodeling and RNA processing","description":"The proteins cluster around nuclear gene-expression regulation, with strong signals for chromatin remodeling and multiple RNA-centric processes: ncRNA-mediated gene silencing, mRNA splicing via the spliceosome (and its positive regulation), nonsense-mediated decay, and mRNA stability in stress response. This suggests a cohesive module coordinating chromatin state with RNA maturation and surveillance, rather than isolated pathways.","confidence":"Medium","size":23,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0000184","count":2},{"id":"GO:0048026","count":2}]},{"hash":"1063627937957743479","title":"Unknown","description":"The top GO terms span diverse processes (DNA-templated transcription, mRNA processing, protein degradation, cell cycle checkpoints) and broad developmental and immune contexts (bronchus/trachea formation, T cell differentiation, neuron death regulation), with no clear single functional theme tying the cluster together. The lack of a cohesive pathway or tissue-specific signature suggests the proteins are heterogeneous rather than a cohesive, interpretable group, hence Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031571","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0032435","count":3}]},{"hash":"245988064674554189","title":"Unknown","description":"The top GO terms span transcription, development, cell cycle, and a mix of stress and immune responses (e.g., DNA-templated transcription; multicellular development; mitotic cell cycle; neural tube closure; skeletal system development; ER-stress\u2013related apoptosis; cadmium response; defense against Gram-positive bacteria; invasive growth under glucose limitation). This diversity suggests no single cohesive biological function or pathway tying the cluster together, and the lack of edges supports this lack of connectivity. Therefore no concise, representative label can be assigned beyond Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0046827","count":5},{"id":"GO:0007275","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0001403","count":3}]},{"hash":"1535446162919993411","title":"Unknown","description":"The top terms span diverse processes (transcription regulation, chromosome segregation, telomerase assembly, phosphorylation, xenobiotic response, immune signaling) with no clear shared function or pathway, and several terms are obsolete. The lack of a cohesive theme or interactions among proteins suggests no single representative function for this cluster.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":2},{"id":"GO:0006355","count":2},{"id":"GO:1901389","count":1},{"id":"GO:0046777","count":1},{"id":"GO:1905323","count":1}]},{"hash":"1699492392060081909","title":"Unknown","description":"The terms mix ribosome biogenesis and rRNA maturation with innate immune and various development-related processes, plus cell cycle activities. There is no clear, single function tying these terms together, and the lack of edges supports the absence of a cohesive theme. Therefore, Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0007275","count":3}]},{"hash":"2246417318048007264","title":"Prostate development and cell cycle control","description":"The top GO terms cluster around male reproductive development (male sex differentiation, prostate gland development, steroid hormone receptor complex assembly) together with core cell cycle processes (cell division, metaphase/anaphase transition). This suggests a coordinated program linking prostate development with cell-cycle regulation, with additional signals from ubiquitination, interferon response, and ciliogenesis that may reflect broader regulatory roles. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":13},{"id":"GO:0006463","count":12},{"id":"GO:0046661","count":12},{"id":"GO:0030850","count":12},{"id":"GO:0007091","count":11}]},{"hash":"2047010865621953813","title":"Developmental Signaling and Trafficking","description":"The GO terms show enrichment for development (brain and male gonad development, pattern formation) together with signaling regulation (kinase activity, dephosphorylation, SREBP pathway) and vesicle transport (ER to Golgi). This suggests the cluster represents proteins that regulate development through signaling and intracellular trafficking, justifying the label Developmental Signaling and Trafficking.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0008584","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0071902","count":2}]},{"hash":"967023693110967032","title":"Cardiac muscle signaling and sarcomere organization","description":"This cluster is enriched for sarcomere organization and cardiac muscle cell proliferation, suggesting a focus on heart muscle structure and growth. The presence of small GTPase-mediated signaling and Ras pathway regulation supports a signaling module linked to cardiac muscle function. Some terms appear unrelated (aerotaxis, drug response), likely reflecting annotation noise, but the core pattern points to muscle architecture and signaling.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0098719","count":2}]},{"hash":"1294579259071084061","title":"TLR-NF-\u03baB Innate Immune Signaling","description":"The GO terms cluster around Toll-like receptor signaling and NF-kB\u2013driven regulation of cytokines (TNF, IL-18, IL-1), LPS response, and MHC I biosynthesis, with links to cell migration in inflammation. This suggests a cohesive innate immune signaling module.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":5},{"id":"GO:0002830","count":5},{"id":"GO:0045345","count":5},{"id":"GO:0032741","count":5},{"id":"GO:0002756","count":5}]},{"hash":"1600747279560412790","title":"Innate Antiviral Signaling","description":"The top GO terms cluster around innate immunity and antiviral defense, including defense response to virus, suppression of viral release and transcription, negative regulation of viral processes, and NOD2 signaling, with NF-kappaB and LPS pathway regulation as supporting immune-regulatory signals. Vitamin D response and microtubule localization appear as auxiliary notes, but the dominant theme is innate antiviral signaling.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0033280","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0070431","count":3}]},{"hash":"2039092413342048992","title":"Vertebrate development and ciliogenesis","description":"The top GO terms point to diverse vertebrate developmental processes (skin, spinal cord, genitalia, placental vasculature) and ciliogenesis (cilium assembly) plus microtubule remodeling, suggesting this cluster contains proteins coordinating development with ciliary/microtubule machinery. Some terms are obsolete or broad, but the shared theme appears to be developmental programs linked to ciliary organization.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0043588","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0060271","count":2},{"id":"GO:0030433","count":2}]},{"hash":"2265729172723405497","title":"Cdc42-driven signaling and actin remodeling","description":"The top GO terms cluster around signaling pathways that regulate the cytoskeleton and membrane dynamics\u2014especially Cdc42 signaling, actin filament branching, focal adhesion regulation, and EGFR signaling\u2014along with endosomal transport and phagocytic signaling. This points to a cohesive theme of cytoskeleton remodeling governed by receptor- and small GTPase\u2013mediated signaling, with vesicle trafficking as a connected process; the viral replication term may be incidental noise in this context.","confidence":"Medium","size":22,"edges":82,"triangles":141,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0039694","count":21},{"id":"GO:0010628","count":21},{"id":"GO:0048227","count":21},{"id":"GO:0007173","count":21},{"id":"GO:0051893","count":21}]},{"hash":"2006929575539119547","title":"Innate Immune Activation and Inflammatory Signaling","description":"Top GO terms indicate strong enrichment for innate immune response, NF-kappaB signaling, LPS response, TNF- and IL-1\u2013mediated pathways, and interferon-beta production. The cluster also includes terms related to angiogenesis and nitric oxide response, which can accompany inflammatory processes. Overall, the proteins seem to participate in innate immune sensing and cytokine-driven signaling cascades. ","confidence":"High","size":22,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051092","count":4},{"id":"GO:0071222","count":4},{"id":"GO:0033209","count":4},{"id":"GO:0001525","count":3}]},{"hash":"1047903147790213997","title":"Germline chromatin remodeling and transcription regulation","description":"The top GO terms converge on chromatin assembly/remodeling (CENP-A chromatin, DNA replication-dependent chromatin assembly, heterochromatin formation) and transcription control (negative regulation of RNAP II, transcription initiation-coupled remodeling), with germline context indicated by spermatogenesis and male gonad development, suggesting a cohesive chromatin-regulatory theme in germ cells.","confidence":"High","size":22,"edges":110,"triangles":279,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0030466","count":8},{"id":"GO:0050830","count":7},{"id":"GO:0008584","count":7},{"id":"GO:0000183","count":7}]},{"hash":"1990731703457315169","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":22,"triangles":13,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:1901621","count":5},{"id":"GO:1900035","count":5},{"id":"GO:0036494","count":5},{"id":"GO:0070389","count":5}]},{"hash":"563165587937449379","title":"Membrane Transporters and Secretion Proteins","description":"Dominated by transmembrane transport terms (vitamin/xenobiotic transport, amino acid and lipoprotein transport, cobalt ion transport, doxorubicin transport) and a secretion system term, suggesting this cluster mainly groups membrane transport/secretion proteins; a single nucleotide-excision repair term is an outlier.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0035461","count":22},{"id":"GO:0006855","count":22},{"id":"GO:0006289","count":17},{"id":"GO:0006824","count":17},{"id":"GO:0042760","count":17}]},{"hash":"2106016687347350630","title":"Meristem vegetative-to-reproductive transition","description":"This cluster is characterized by the single GO term GO:0010228 describing vegetative to reproductive phase transition of the meristem, suggesting a plant developmental timing/phase-change theme among the proteins; with no additional terms or interactions, the label captures the apparent function but is supported by limited evidence.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010228","count":1}]},{"hash":"1927898044698202296","title":"Membrane Transport and Secretion","description":"The top GO terms are dominated by various transport processes across membranes and secretion (oligosaccharide, cobalt ion, methionine, vitamin, phospholipid transport; very long-chain fatty acid catabolism; doxorubicin transport; and protein secretion via the Type I system). This suggests the cluster mainly comprises transporters or secretion-related proteins. A few non-transport terms (nucleotide-excision repair, pigment biosynthesis) are present but not dominant, so they do not override the main theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":4},{"id":"GO:0015772","count":4},{"id":"GO:0006727","count":4},{"id":"GO:0006824","count":4},{"id":"GO:0042760","count":4}]},{"hash":"782311484907839429","title":"Neuronal mitochondrial energy and synaptic regulation","description":"GO terms converge on mitochondrial function (membrane permeability regulation, import into mitochondrial matrix) and metabolism (hydrogen peroxide biosynthesis, triglyceride biosynthetic regulation) with neural activity and autonomic regulation clues (memory, synaptic potentiation, heart rate). The cluster likely represents mitochondrial involvement in neuronal energy production and synaptic signaling, hence the name.  ","confidence":"Medium","size":22,"edges":27,"triangles":0,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:1903740","count":4},{"id":"GO:0046902","count":4},{"id":"GO:0070940","count":4},{"id":"GO:0030150","count":4},{"id":"GO:2000134","count":4}]},{"hash":"293143629835030325","title":"Unknown","description":"The top GO terms span transcription, metabolism, sensory perception, chemotaxis, plant signaling, and proteasomal regulation with no single shared function, and the cluster has no edges or cohesive enrichment, making a specific label unreliable.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033160","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0006935","count":2}]},{"hash":"1825615087718202877","title":"Bacterial metabolism and quinone biosynthesis","description":"The cluster\u2019s top GO terms are dominated by metabolic and biosynthetic processes: antibiotic biosynthesis, various amino acid catabolic pathways (valine, alanine, kynurenine), fatty acid beta-oxidation, and quinone biosynthesis (menaquinone, phylloquinone). This points to bacterial primary/secondary metabolism and energy-related pathways as the unifying theme. The presence of an outlier term like Notch signaling may reflect annotation noise rather than a true functional link. Overall, the label captures the core functional theme of the cluster.","confidence":"Medium","size":22,"edges":230,"triangles":1520,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":12},{"id":"GO:0010124","count":11},{"id":"GO:0009234","count":11},{"id":"GO:0042372","count":11},{"id":"GO:0006574","count":11}]},{"hash":"2096224971314914404","title":"Ribosome biogenesis and translation","description":"Frequent GO terms center on translation and ribosome biogenesis (including cytoplasmic translation, ribosomal small subunit biogenesis, and tRNA modification), indicating a cluster of proteins involved in ribosome production and protein synthesis. The presence of cell cycle and cell division terms suggests coordination with cell growth, but the dominant signal is ribosome assembly and translational machinery.","confidence":"High","size":22,"edges":202,"triangles":1084,"max_degree":21,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0051301","count":7},{"id":"GO:0006400","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0007049","count":6}]},{"hash":"1584312709865287847","title":"Xenobiotic and lipid metabolism","description":"The top GO terms cluster around metabolic processing of foreign compounds and lipids\u2014xenobiotic/carbazole/insecticide catabolism, plus prostaglandin and vitamin D\u2013related lipid metabolism\u2014suggesting detoxification and lipid-signaling roles. A few terms (e.g., sex differentiation) are less connected, so the theme is moderate in strength.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046232","count":9},{"id":"GO:0035865","count":8},{"id":"GO:0032259","count":8},{"id":"GO:0001516","count":8},{"id":"GO:0042369","count":8}]},{"hash":"2301126840252586358","title":"Unknown","description":"Terms point to multiple, loosely related activities (redox metabolism, amino acid biosynthesis, translation, and developmental/response terms) with little overlap. The cluster lacks a dominant shared pathway and shows minimal connectivity, so a single descriptive function label is not evident.","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0001701","count":3},{"id":"GO:0097171","count":2},{"id":"GO:0006740","count":2},{"id":"GO:0009099","count":2}]},{"hash":"392658644279250233","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0000398","count":9},{"id":"GO:0000472","count":9},{"id":"GO:0051301","count":9}]},{"hash":"490704360477033017","title":"Membrane Lipid Biosynthesis","description":"This cluster is best described by a lipid and membrane biogenesis theme: several top GO terms point to sterol synthesis (ergosterol), fatty acid biosynthesis, GPI anchor formation, dolichol metabolism, and sphingolipid metabolism, all of which relate to building and modifying membranes. Some terms also reflect tissue contexts rich in lipids (myelin maintenance, sebaceous gland differentiation), reinforcing this lipid/membrane focus. A few terms (mitochondrial inheritance, nitrate assimilation, nitric oxide biosynthesis) are not clearly linked to lipid processes, suggesting a dominant lipid/membrane signal with some outliers. Overall, \u201cMembrane Lipid Biosynthesis\u201d captures the central tendency of the cluster.","confidence":"Medium","size":22,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0006636","count":2}]},{"hash":"1212444332702676241","title":"Mitochondrial energy metabolism and ROS signaling","description":"Proteins in this cluster are dominated by annotations tied to mitochondrial electron transport (cytochrome c, ubiquinol pathways) and oxidative stress responses (hydrogen peroxide metabolism, ROS signaling) as well as apoptotic processes, suggesting a theme of energy production coupled with ROS-mediated signaling or PCD. Though a plant-specific term like photosynthesis appears, the core pattern points to mitochondrial energetics and ROS. ","confidence":"Medium","size":22,"edges":21,"triangles":0,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0008635","count":1},{"id":"GO:0042743","count":1},{"id":"GO:0010730","count":1},{"id":"GO:0034465","count":1},{"id":"GO:0006470","count":1}]},{"hash":"818407047098284800","title":"Signaling and stress-response pathways","description":"The cluster\u2019s terms point to a broad mix of signaling functions (Rho signaling, insulin receptor signaling) and stress or damage responses (osmotic stress, cadmium ion response, DNA damage checkpoint). There isn\u2019t a single cohesive process, but the common theme is participation in cellular signaling and stress-related responses across diverse contexts, making a general label appropriate.","confidence":"Medium","size":22,"edges":218,"triangles":1298,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":22},{"id":"GO:0001403","count":22},{"id":"GO:0007266","count":22},{"id":"GO:0010614","count":22},{"id":"GO:0047484","count":22}]},{"hash":"1284361386197523492","title":"Regulation of cell adhesion and signaling","description":"The prominent terms center on focal adhesion assembly, ECM disassembly, and Rho signaling, pointing to control of adhesion, cytoskeletal dynamics, and cell movement. While there are developmental and immune-related terms present (e.g., trachea formation, NK T cell differentiation), the core theme across the cluster appears to be regulation of cell adhesion and signaling pathways, which ties together several top GO terms.","confidence":"Medium","size":22,"edges":186,"triangles":1022,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":22},{"id":"GO:0060440","count":22},{"id":"GO:0051893","count":22},{"id":"GO:0001403","count":22},{"id":"GO:0007266","count":22}]},{"hash":"1872963541635184435","title":"Rho-driven Adhesion and ECM Remodeling","description":"The cluster\u2019s top terms center on signaling that regulates cell adhesion and cytoskeletal dynamics (Rho signaling, focal adhesion regulation, ECM disassembly) and invasive/migratory contexts, with a few immune differentiation terms as ancillary. This suggests a common theme of signaling-driven adhesion and extracellular matrix remodeling governing cell movement.","confidence":"Medium","size":22,"edges":230,"triangles":1520,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":22},{"id":"GO:0060440","count":22},{"id":"GO:0051893","count":22},{"id":"GO:0001403","count":22},{"id":"GO:0007266","count":22}]},{"hash":"803810711377709310","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":228,"triangles":1482,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0042273","count":5},{"id":"GO:0000463","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0000480","count":3}]},{"hash":"785327792958396092","title":"Calcium signaling and smooth/cardiac muscle contraction","description":"This cluster shows enrichment in GO terms tied to calcium signaling and muscle function: membrane depolarization in atrial cardiac muscle, response to calcium ion, and smooth muscle contraction involved in micturition, plus regulation of ion transport and Mg2+ homeostasis. While some terms like aerotaxis or hypoxia are less directly linked to muscle activity, the preponderance of calcium- and ion-transport related terms suggests a cohesive theme around ion dynamics governing muscle excitability and contraction.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098912","count":3},{"id":"GO:0001666","count":3},{"id":"GO:0009454","count":3},{"id":"GO:0050955","count":3},{"id":"GO:0051592","count":3}]},{"hash":"611989633880219879","title":"Plant stress responses and vesicle trafficking","description":"The cluster\u2019s top GO terms are dominated by plant stress-related processes (salicylic acid signaling, UV-B response, trehalose stimulus response, aerenchyma formation) and vesicle/autophagy-related activities (multivesicular body disassembly, vacuolar protein processing, piecemeal autophagy of the nucleus), suggesting a coherent role in stress adaptation via cell-wall remodeling and vacuolar/autophagic pathways.","confidence":"Medium","size":22,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002003","count":3},{"id":"GO:0034496","count":3},{"id":"GO:0010618","count":3},{"id":"GO:0045490","count":3},{"id":"GO:0080151","count":3}]},{"hash":"259064134352963197","title":"Unknown","description":"The top GO terms are scattered and many are obsolete, covering host-symbiont interactions (symbiont induction of host processes), cell adhesion, mitotic centrosome separation, cadmium transport, hormone response, and heart contraction regulation, with no clear common function. Because there is no cohesive biological theme linking these terms, and the connections are weak, I cannot assign a precise, representative label to this protein cluster.","confidence":"","size":22,"edges":4,"triangles":0,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0052014","count":5},{"id":"GO:0036523","count":5},{"id":"GO:1902769","count":5},{"id":"GO:0007155","count":5},{"id":"GO:0007100","count":5}]},{"hash":"887444052162503200","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":9},{"id":"GO:0002188","count":9},{"id":"GO:0000398","count":7},{"id":"GO:0000472","count":7},{"id":"GO:0048568","count":7}]},{"hash":"1205998162845191574","title":"Leukocyte adhesion and phagocytosis signaling","description":"The non-obsolete terms cluster around leukocyte adhesion/rolling and engulfment of apoptotic cells, pointing to immune cell interactions and phagocytic signaling, with supporting hints from calcium signaling and proteolytic shedding. However, the presence of outlier terms (neuronal spine maintenance, mitotic centrosome separation) and obsolete GO terms weakens the cohesion.","confidence":"Low","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052014","count":1},{"id":"GO:0036523","count":1},{"id":"GO:1902769","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0007100","count":1}]},{"hash":"2011656273242270088","title":"Muscle sarcomere organization and signaling","description":"The top GO terms are dominated by muscle-related processes such as sarcomere organization and cardiac muscle cell proliferation, complemented by several signaling pathways (small GTPase signaling, adenylate cyclase, and guanylyl cyclase pathways). While there are a few outliers, the overall theme points to proteins involved in muscle structure and its signaling regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045214","count":4},{"id":"GO:0051447","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0007264","count":3}]},{"hash":"2140491280450599641","title":"Unknown","description":"The top GO terms are highly diverse, spanning transcription (DNA-templated transcription, mRNA processing), signaling/regulation (phosphorylation, positive regulation of protein export from nucleus, cell-matrix adhesion), and distinct biological processes (sensory perception of smell, xylan catabolic process, defense responses, apoptotic cell clearance). There is no clear, shared functional theme or a cohesive pathway connecting these terms, and the absence of edges suggests a loosely related or noisy set of annotations. ","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0007608","count":3},{"id":"GO:0016310","count":2},{"id":"GO:0045493","count":2}]},{"hash":"1991433642539943242","title":"Ion and xenobiotic transmembrane transport","description":"The top GO terms are dominated by various transmembrane transport processes for ions (Na+, K+, nitrite) and a range of substrates (vitamins, xenobiotics, arabinose, 4-hydroxyphenylacetate), indicating a cluster of membrane transport proteins with broad substrate specificity. There is one outlier term on replicative senescence that likely reflects noise rather than a core function. ","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035461","count":17},{"id":"GO:0042908","count":17},{"id":"GO:0006855","count":17},{"id":"GO:0071805","count":17},{"id":"GO:0070715","count":16}]},{"hash":"1009731810781748210","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000209","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0001403","count":4}]},{"hash":"2161637916777518282","title":"Developmental Signaling and Cytoskeletal Remodeling","description":"The cluster centers on GO terms for multicellular and skin development, with multiple entries involving regulation of kinase activity, GTPase activity, and phosphorylation, plus Arp2/3-mediated actin nucleation. This points to proteins coordinating developmental signaling with dynamic cytoskeletal remodeling and intracellular transport, rather than a single pathway. The lack of edges suggests no direct interactions captured here, but the GO terms collectively imply a developmental signaling/cytoskeletal remodeling theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0043588","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0000278","count":7}]},{"hash":"106655404321472509","title":"Synaptic vesicle trafficking and neurotransmitter release","description":"The top terms cluster around neuronal communication, including receptor recycling, glutamatergic synaptic transmission, and acetylcholine biosynthesis/secretion, all pointing to vesicle cycling and neurotransmitter release at synapses. Although there are a few outliers (e.g., obsolete or plant-specific terms), the dominant theme ties vesicle trafficking with synaptic signaling.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001881","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0034968","count":2},{"id":"GO:0035023","count":2}]},{"hash":"574447800423042930","title":"Neural development and axon guidance","description":"This cluster is driven by neural development terms such as dendritic spine development, CNS projection neuron axonogenesis, axon fasciculation, and ephrin receptor signaling, indicating a theme around neuronal differentiation and connectivity. Although there are unrelated terms (nephric duct morphogenesis, iodide transport, immune processes), the neural development signals seem to dominate, making this a moderately cohesive neuronal development cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060996","count":5},{"id":"GO:0072178","count":5},{"id":"GO:0097155","count":5},{"id":"GO:2000525","count":5},{"id":"GO:0048013","count":5}]},{"hash":"1858930925900777577","title":"Innate Antiviral Signaling and NF-\u03baB Modulation","description":"The cluster is enriched for innate immune and antiviral terms, including innate immune response, defense against virus, TLR9 signaling, NOD2 signaling, and type II interferon pathways, plus proteasomal ubiquitin-dependent protein catabolism linked to NF-\u03baB regulation. It also shows positive regulation of cell migration and lamellipodium organization, suggesting coordinated immune signaling with cytoskeletal remodeling for cell movement. This points to a cohesive innate antiviral signaling module with nuanced NF-\u03baB control.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":15},{"id":"GO:0032088","count":14},{"id":"GO:0031146","count":14},{"id":"GO:0051607","count":14},{"id":"GO:0034162","count":13}]},{"hash":"2226387747263359110","title":"Ubiquitin-dependent proteolysis","description":"The top GO terms cluster around ubiquitination events (autoubiquitination, K6- and K48-linked ubiquitination) and ubiquitin-dependent protein catabolic processes, pointing to proteasomal degradation and protein turnover; additional terms touch ubiquitin\u2019s roles in signaling (TNF) and chromatin dynamics (histone catabolism), supporting a label focused on ubiquitin-mediated regulation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":14},{"id":"GO:1903265","count":13},{"id":"GO:0042787","count":13},{"id":"GO:1903762","count":11},{"id":"GO:1901253","count":11}]},{"hash":"1824566787457619691","title":"Antiviral Innate Immunity and Antigen Presentation","description":"The proteins cluster around innate immune signaling and antiviral defense, with GO terms for innate immune response, defense against virus, TLR9 and NOD2 signaling, and type II interferon pathways. Additionally, MHC class I biosynthesis and SCF-dependent proteasomal degradation link to antigen processing/presentation, while cell migration and lamellipodium organization reflect immune cell trafficking. Overall, these terms together indicate a coherent antiviral innate response coupled with antigen presentation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":8},{"id":"GO:0045345","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0051607","count":7},{"id":"GO:0034162","count":6}]},{"hash":"634599863858487","title":"T cell tolerance and apoptotic signaling","description":"The terms center on T cell immune regulation, including central tolerance to self antigen, peripheral T cell tolerance, thymocyte migration, and apoptotic signaling, suggesting a cluster enriched for proteins involved in T cell development and tolerance. Some terms are labeled obsolete, but the remaining signals collectively point to a T cell tolerance/apoptosis theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000584","count":1},{"id":"GO:0002509","count":1},{"id":"GO:0090308","count":1},{"id":"GO:1901726","count":1},{"id":"GO:0043972","count":1}]},{"hash":"2048818769236524766","title":"Nuclear deubiquitination and transcription regulators","description":"The cluster\u2019s top GO terms are dominated by nuclear deubiquitination activities (histone H2B deubiquitination, K6/K29-linked deubiquitination, and linear deubiquitination) and DNA-templated transcription, pointing to a shared role in chromatin-associated regulation and transcription in the nucleus. While some obsolete terms and unrelated behavioral terms appear, the cohesive theme is ubiquitin-dependent regulation of nuclear processes.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903070","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035616","count":1},{"id":"GO:0060013","count":1},{"id":"GO:0035523","count":1}]},{"hash":"510502785006275136","title":"Chromatin modification and transcription regulation","description":"Most terms point to chromatin regulation and transcription: histone modifications and deubiquitination, plus DNA-templated transcription and ubiquitin\u2013proteasome\u2013dependent turnover. Retina development appears but is not central. Overall, the cluster centers on chromatin modification controlling transcription.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034729","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070537","count":2},{"id":"GO:0035871","count":2},{"id":"GO:0035522","count":2}]},{"hash":"296359375127660516","title":"Unknown","description":"The top terms point to a highly heterogeneous mix of processes (plant glucosinolate metabolism, DNA-damage\u2013related apoptosis, mRNA stability, endoreduplication, proliferation and transcription regulation, xenobiotic response, and lens-specific apoptosis), with no single coherent function uniting them. Hence no clear cluster theme can be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019760","count":2},{"id":"GO:0008630","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0042023","count":2},{"id":"GO:0070345","count":2}]},{"hash":"728238187727029154","title":"Unknown","description":"The GO terms are diverse, spanning gravity sensing, otolith development, bone resorption, and general cellular processes like stress response and gene expression. There is no clear, shared function tying these proteins together, so a single intuitive label cannot be confidently assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072553","count":1},{"id":"GO:0009590","count":1},{"id":"GO:0048840","count":1},{"id":"GO:1990451","count":1},{"id":"GO:0050665","count":1}]},{"hash":"406801188978652349","title":"Mitotic progression and growth signaling","description":"This cluster is dominated by mitosis-related GO terms (mitotic cell cycle, mitotic spindle assembly, cell division) and growth-related processes (ribosome biogenesis, TORC1 signaling). Additional terms for GTPase activity regulation and vesicle transport align with cellular remodeling during division, while brain development and cellular fusion are peripheral. Overall, the core theme is proliferative mitosis coupled with growth signaling. ","confidence":"High","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0008283","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0090307","count":3}]},{"hash":"244348897757720952","title":"Mitotic cell cycle and vesicle trafficking","description":"The cluster is enriched for mitosis-related terms (cell division, mitotic cell cycle, mitotic spindle assembly) and for vesicle transport processes (ER-to-Golgi trafficking, protein targeting to vacuole). While neuronal development terms and signaling appear, the strongest and most coherent signal centers on cell division and intracellular transport, suggesting proteins involved in mitotic machinery and vesicle trafficking. ","confidence":"High","size":21,"edges":17,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0007420","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0007173","count":4}]},{"hash":"169566892875328688","title":"Osteogenesis and limb morphogenesis","description":"The GO terms show a strong emphasis on bone formation (osteoblast differentiation, bone mineralization) and limb/appendage development (forelimb/hindlimb morphogenesis, dorsal fin development, nail development), suggesting a cluster tied to skeletal development. Some terms related to general transcription/translation and ER-Golgi transport appear as background cellular processes, but the dominant pattern is skeletal development.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006888","count":2}]},{"hash":"585832493455295769","title":"RNA splicing and post-transcriptional regulation","description":"The cluster shows enrichment across RNA processing and post-transcriptional control: spliceosome-mediated mRNA splicing, small-subunit processome assembly, mRNA modification and stabilization, translation initiation complex assembly, and miRNA/ncRNA-mediated silencing. These together indicate a cohesive theme of RNA maturation and regulation of gene expression after transcription, including translational control under stress.","confidence":"High","size":21,"edges":177,"triangles":865,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0048255","count":3},{"id":"GO:1902625","count":3},{"id":"GO:1903586","count":3}]},{"hash":"267241068752704379","title":"Innate immune signaling and cytokine production","description":"This cluster centers on ubiquitin-proteasome\u2013mediated degradation, innate antiviral defense, and regulation of NF-kB signaling, coupled with production of pro-inflammatory cytokines (IL-1\u03b2, IL-8) and factors promoting Th17 differentiation, as well as actin cytoskeleton remodeling for a migratory immune response. The cohesive themes point to innate immune activation and inflammatory signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0045087","count":8},{"id":"GO:0051607","count":8},{"id":"GO:0042787","count":6},{"id":"GO:0043124","count":6}]},{"hash":"555797657393179730","title":"Redox Homeostasis and Chemical Stress Responses","description":"This cluster is dominated by GO terms for redox balance (cell redox homeostasis) and diverse chemical/stress responses (ethanol, corticosterone, aluminum ions, lipopolysaccharide), plus related catabolic/biosynthetic processes. The common theme appears to be maintaining redox homeostasis while adapting to varied chemical stimuli, justifying this label.","confidence":"High","size":21,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0045454","count":7},{"id":"GO:0008283","count":6},{"id":"GO:0042420","count":6},{"id":"GO:0045471","count":6}]},{"hash":"827497802289013959","title":"Mitotic progression and DNA repair","description":"The GO terms center on cell division (G2/M transition, mitotic spindle elongation) and DNA repair (NHEJ and homologous recombination), with additional notes on meiosis-related synaptonemal complex organization and ubiquitination regulation. This points to a cohesive module coordinating mitosis and genome maintenance, justifying the label.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0006303","count":1},{"id":"GO:0070193","count":1},{"id":"GO:1901487","count":1}]},{"hash":"628981916034706333","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":1},{"id":"GO:0090086","count":1},{"id":"GO:0071641","count":1},{"id":"GO:2000637","count":1},{"id":"GO:1902187","count":1}]},{"hash":"31744749126542064","title":"Renin-angiotensin signaling and peptide processing","description":"This cluster is clearly enriched for renin-angiotensin system functions (aldosterone production, regulation of blood volume, angiotensin maturation) and for proteolytic maturation processes (membrane protein proteolysis, protein autoprocessing), pointing to peptide signaling and maturation in kidney/vascular contexts. Supporting terms like mesonephros development and digestion align with renal and digestive roles, though a few terms (amyloid-beta metabolism, antibacterial peptide production) are less central. Overall, the dominant theme ties peptide hormone signaling and proteolysis to renal regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050435","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0002018","count":2},{"id":"GO:0001823","count":2},{"id":"GO:0016540","count":2}]},{"hash":"845378982843874462","title":"Chromatin acetylation and centromeric cohesion","description":"The top GO terms cluster around acetylation events (N-terminal glutamic acid acetylation, peptidyl-lysine N6 acetylation, putrescine acetylation) and chromatin-related processes (subtelomeric heterochromatin formation, centromeric sister chromatid cohesion), pointing to a theme of chromatin modification linked to chromosome segregation, despite some peripheral biosynthetic terms.","confidence":"Medium","size":21,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006348","count":7},{"id":"GO:0045150","count":6},{"id":"GO:0030187","count":5},{"id":"GO:0019491","count":5},{"id":"GO:0018002","count":5}]},{"hash":"2003119481653782806","title":"Mitochondrial fission and fusion regulators","description":"Most of the top GO terms point to mitochondrial dynamics, including positive regulation of mitochondrial fusion, mitochondrial fission, and positive regulation of mitochondrial fission, along with mitochondrial membrane organization. This suggests the cluster centers on proteins that govern mitochondrial morphology and membrane integrity. Some neuron-associated terms appear (adult locomotory behavior, synaptic vesicle budding), which could reflect tissue-specific roles or pleiotropy, but do not override the core mitochondrial dynamics signal.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010636","count":7},{"id":"GO:0008344","count":7},{"id":"GO:0000266","count":7},{"id":"GO:0090141","count":6},{"id":"GO:0001300","count":5}]},{"hash":"1394033130885078936","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":20,"triangles":0,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0035690","count":2}]},{"hash":"1092040307791074508","title":"Mitotic Spindle Organization and Cytokinesis","description":"The top GO terms cluster around cell division and mitosis, including cell cycle, mitotic spindle assembly and midzone formation, and division site positioning, indicating proteins involved in mitotic processes and cytokinesis. Some terms like interleukin-4 response and viral genome replication appear less connected and may reflect broader annotation, but the dominant theme is mitotic machinery and cytokinesis. ","confidence":"High","size":21,"edges":20,"triangles":6,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0007049","count":7},{"id":"GO:0090529","count":5},{"id":"GO:2000767","count":5},{"id":"GO:0071353","count":5}]},{"hash":"234036873346654085","title":"Unknown","description":"This cluster lists GO terms from diverse processes (mitotic cell cycle transition; protein peptidyl-prolyl isomerization; lipopolysaccharide metabolism; non-motile cilium assembly; gibberellin signaling regulation; RNA polymerase III transcription; response to lead ions; GPCR signaling regulation; regulation of protein modification; defense response to virus) with no clear shared function. The terms span different organisms and contexts, suggesting heterogeneous or non-specific annotations rather than a single coherent biological theme. Therefore, no interpretable, unified function can be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007091","count":6},{"id":"GO:0000413","count":6},{"id":"GO:0008653","count":6},{"id":"GO:1905515","count":6},{"id":"GO:0009938","count":6}]},{"hash":"703179573496640438","title":"Cell surface receptor signaling","description":"This cluster is enriched for GO terms around cell surface receptor signaling, including T cell and B cell receptor signaling, serine/threonine kinase signaling, and VEGF receptor pathways, plus downstream processes like angiogenesis and developmental events driven by these signals. The pollen recognition term is less coherent, but overall the common theme is receptor-mediated signal transduction governing immune responses and development.","confidence":"High","size":21,"edges":109,"triangles":265,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048544","count":20},{"id":"GO:0001525","count":20},{"id":"GO:0022038","count":20},{"id":"GO:0051092","count":20},{"id":"GO:0007178","count":20}]},{"hash":"988730072784090885","title":"Wnt/Hippo signaling and transcriptional regulation","description":"This cluster's top GO terms cluster around canonical Wnt signaling regulation and Hippo pathway activity, both key regulators of development and cell growth. The presence of DNA-templated transcription and positive regulation of cell size supports a theme of transcriptional control downstream of these growth signals, with placenta development and apoptosis reflecting developmental and cell fate outcomes. While terms like chemotaxis and cocaine response are more peripheral, the core signal-transduction and transcriptional themes tie the set together.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090263","count":16},{"id":"GO:0035329","count":16},{"id":"GO:0006351","count":16},{"id":"GO:0045793","count":16},{"id":"GO:0001890","count":16}]},{"hash":"1126833993088851704","title":"Protein and amine acetylation","description":"The top GO terms are centered on acetylation events, including N-terminal acetylation and various peptidyl-lysine/glutamic acid acetylations, as well as putrescine acetylation and related catabolic processes, suggesting a cohesive theme around protein and amine acetylation with some auxiliary regulatory terms.","confidence":"Medium","size":21,"edges":72,"triangles":67,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":1},{"id":"GO:0006474","count":1},{"id":"GO:0019491","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0018002","count":1}]},{"hash":"773318956670762762","title":"Proteolysis and peptide hormone processing","description":"This cluster centers on proteolytic processing events and peptide hormone pathways: amyloid-beta metabolic process, protein autoprocessing, angiotensin maturation, renin-angiotensin\u2013regulated aldosterone production, and membrane protein proteolysis, with digestion and drinking-behavior terms supporting systemic peptide regulation.","confidence":"Medium","size":21,"edges":101,"triangles":236,"max_degree":19,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0050435","count":4},{"id":"GO:0007586","count":4},{"id":"GO:0002018","count":4},{"id":"GO:0001823","count":4},{"id":"GO:0016540","count":4}]},{"hash":"2300975347348031116","title":"ER Stress and Vesicle Trafficking in Host-Virus Interaction","description":"This cluster is driven by GO terms centering on the endoplasmic reticulum stress/UPR (ER unfolded protein response), ER localization, and vesicle trafficking (COPII-coated vesicles), with supporting hints from calcium homeostasis and autophagy-related processes. The presence of host-virus interaction terms suggests the cluster reflects a coordinated antiviral stress response that engages ER membrane dynamics and trafficking pathways to influence viral replication.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044828","count":1},{"id":"GO:0006987","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0070972","count":1}]},{"hash":"1404007353276243556","title":"ER-Golgi transport and ER quality control","description":"The top terms point to ER-to-Golgi vesicle transport and ER-associated degradation, with related signaling and lipid biosynthesis context (SREBP). This suggests proteins functioning in the secretory pathway and ER quality control, with some terms that may reflect related regulation or noise.","confidence":"Medium","size":21,"edges":20,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0071902","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0061099","count":2}]},{"hash":"216070526288224335","title":"Osteoblast differentiation and adipose development","description":"The top GO terms center on bone formation (bone development, osteoblast fate commitment) and adipose tissue development, with supporting signals and membrane remodeling processes; a secondary thread involves regulation of cellular fusion and proteolysis. Together these suggest a cluster of proteins involved in mesenchymal lineage decisions toward bone and fat tissue, plus related signaling pathways.","confidence":"Medium","size":21,"edges":20,"triangles":0,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0051044","count":3},{"id":"GO:0031139","count":3},{"id":"GO:0060348","count":3},{"id":"GO:0060378","count":3}]},{"hash":"1881433429227935667","title":"Embryonic organ development","description":"The top GO terms cluster around development of multiple organs during embryogenesis (placenta, kidney, neural tube, liver, genitalia, etc.), with some involvement in JAK-STAT signaling. This points to a broad organogenesis theme rather than a tissue-specific function, so a concise label that captures embryonic organ development fits well.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001892","count":2},{"id":"GO:0031659","count":1},{"id":"GO:0048806","count":1},{"id":"GO:0060674","count":1},{"id":"GO:0007259","count":1}]},{"hash":"1651220367299484478","title":"Metabolic and vascular regulation","description":"The top GO terms cluster around energy and glucose homeostasis, blood pressure-related pathways (plasma kallikrein-kinin cascade, regulation of systemic arterial blood pressure), endothelial cell migration, and thyroid hormone signaling, with supporting notes on proteolysis and autophagy regulation. While not all terms point to a single unified function, the recurring theme centers on regulation of metabolic states and vascular signaling, suggesting a cluster of proteins involved in coordinating metabolism with cardiovascular and endocrine signals. Some terms (e.g., phytochelatin biosynthesis) may reflect annotation noise, but the core grouping aligns with metabolic and vascular regulatory processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0046938","count":1},{"id":"GO:0043085","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0003085","count":1}]},{"hash":"17117717126029594","title":"Autophagy and Ubiquitin-Mediated Proteolysis","description":"Most of the top GO terms describe autophagy processes (phagophore assembly, Cvt pathway transport, peroxisome autophagy) and protein turnover via ubiquitination and proteolysis (K11-linked ubiquitination, autoubiquitination). This clustering suggests a cohesive functional group centered on autophagy-related degradation regulated by ubiquitin signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034497","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0046938","count":1},{"id":"GO:0043085","count":1}]},{"hash":"2013627472445175008","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":21,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:1990414","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0010520","count":2},{"id":"GO:0035066","count":2},{"id":"GO:0000480","count":2}]},{"hash":"2236168797715542251","title":"Aminoacyl-tRNA synthetases and translational fidelity","description":"The cluster prominently features translation and specific aminoacyl-tRNA synthetase activities (LeuRS, ValRS, IleRS, MetRS) along with regulation of translational fidelity, indicating a cohesive translation machinery module with fidelity control; oxidative stress and redox terms suggest linked stress responses affecting translation, with a possible incidental DNA-binding regulation term.","confidence":"High","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006429","count":2},{"id":"GO:0006438","count":2},{"id":"GO:0006428","count":2}]},{"hash":"1715188749804651090","title":"Membrane transport and secretion","description":"The terms cluster around proton-driven transport and ATP synthesis, exocytosis, SNARE regulation, and peptide hormone secretion, with some membrane biogenesis references; together these point to a core membrane transport/secretion machinery rather than a single tissue-specific function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042777","count":1},{"id":"GO:0007430","count":1},{"id":"GO:0007034","count":1},{"id":"GO:0035675","count":1},{"id":"GO:0039022","count":1}]},{"hash":"1637229332581755465","title":"Unknown","description":"The GO terms are highly diverse, spanning transcription, cell cycle, morphogenesis, xenobiotic response, placenta development, chemotaxis, and metabolism, with no clear shared pathway or function tying the proteins together. Because there are no cohesive edges or dominant themes to define a specific cluster function, the appropriate label is Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0046827","count":3},{"id":"GO:0000902","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0035690","count":2}]},{"hash":"23940559180394614","title":"Muscle signaling and sarcomere organization","description":"Top terms show a strong focus on muscle structure (sarcomere organization, cardiac muscle cell proliferation) and signaling pathways (small GTPase signaling, adenylate cyclase activity) with related ion transport. While a couple terms are less directly tied (aerotaxis, meiotic cell cycle regulation), the dominant theme revolves around muscle-related signaling and organization. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051447","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0007264","count":3}]},{"hash":"1510683826977045500","title":"Ras/GTPase and cAMP signaling regulators","description":"This cluster is dominated by GO terms for small GTPase-mediated signal transduction and negative regulation of Ras signaling, with involvement in adenylate cyclase activity, pointing to modulation of GTPase and cAMP signaling pathways. Some terms like hair follicle maturation and sarcomere organization are less directly related, suggesting a primary theme of signal transduction with a few outliers. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007264","count":3},{"id":"GO:0045762","count":3},{"id":"GO:0048820","count":2},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2}]},{"hash":"2072660307521416678","title":"Innate Antiviral Defense and Inflammasome Signaling","description":"GO terms center on antiviral innate immunity (defense response to virus, innate immune response), with TLR9 and NOD2 signaling, and interferon pathways, plus NLRP3 inflammasome assembly. The inclusion of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process suggests antigen processing, while positive regulation of type II immune responses and lamellipodium organization points to downstream effector activation and cytoskeletal remodeling during antiviral responses. Overall, these terms depict a coherent innate antiviral defense and inflammasome activation module.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":12},{"id":"GO:0045087","count":12},{"id":"GO:0031146","count":12},{"id":"GO:0034162","count":10},{"id":"GO:0030335","count":10}]},{"hash":"167754155758032718","title":"Innate immune signaling and cytokine production","description":"The proteins in this cluster are strongly enriched for GO terms involving TLR signaling (MyD88-independent), LPS-mediated signaling, non-canonical NF-kappaB pathways, and cytokine production (TNF, IL-18, IL-1), as well as processes related to MHC class I biosynthesis. This pattern points to innate immune activation and inflammatory signaling with links to antigen presentation and immune cell trafficking. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":18},{"id":"GO:0002830","count":18},{"id":"GO:0045345","count":18},{"id":"GO:0032741","count":18},{"id":"GO:0002756","count":18}]},{"hash":"1161097903639678681","title":"Mitotic cell cycle and vesicle trafficking","description":"Top GO terms indicate roles in mitosis and cytokinesis, with concurrent involvement in translation and multiple intracellular trafficking pathways (endosome-Golgi transport, Cvt/autophagy), plus cell morphogenesis and development. The common theme ties cell division with membrane remodeling and transport, suggesting a coordination between proliferative processes and trafficking/morphogenesis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0036089","count":1},{"id":"GO:0051044","count":1}]},{"hash":"1147831366594502215","title":"Unknown","description":"The top GO terms are pulled from several unrelated themes (transcription/regulation, biotin/lipoylation metabolism, chromatin modification, and separate processes like thermoception and spindle assembly). With no connections among the proteins, there is no cohesive function tying the cluster together, so a single interpretable label isn\u2019t supported.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070781","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0009107","count":1},{"id":"GO:0071110","count":1}]},{"hash":"218719838989087633","title":"Membrane trafficking and mitochondrial dynamics","description":"The top GO terms point to endocytic recycling and receptor internalization, plus mitochondrial membrane organization, fusion/fission, and autophagy, indicating a set of proteins coordinating membrane trafficking with mitochondrial quality control, relevant to neural synapses and muscle cell fusion.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":2},{"id":"GO:0010636","count":1},{"id":"GO:0016236","count":1},{"id":"GO:0051932","count":1},{"id":"GO:1901741","count":1}]},{"hash":"1316188712806786161","title":"Vesicle trafficking and neural development","description":"This cluster is enriched for endoplasmic reticulum to Golgi vesicle transport and regulation of synaptic vesicle exocytosis, with several terms linking to brain and dendrite development, suggesting proteins involved in vesicle trafficking in neuronal contexts. Some outliers (mating projection growth, liver/kidney development, viral replication) may reflect broader or cross-species roles or annotation noise, but the central theme is vesicle transport linked to neural development.","confidence":"Medium","size":20,"edges":161,"triangles":702,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:2000300","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0031384","count":4},{"id":"GO:0010796","count":4}]},{"hash":"1046858763516879102","title":"Developmental Growth and ER-Golgi Vesicle Trafficking","description":"The top GO terms indicate developmental processes (brain development, multicellular organism growth, osteoclast development) alongside intracellular vesicle trafficking between the endoplasmic reticulum and Golgi (ER-to-Golgi and retrograde Golgi-to-ER transport), as well as synaptic vesicle exocytosis regulation and mitotic cell cycle. This suggests a cluster of proteins involved in developmental programs with active vesicle trafficking and some cell-cycle functions, with ER-Golgi transport as the most coherent shared feature.","confidence":"Medium","size":20,"edges":27,"triangles":1,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0035264","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0006623","count":4}]},{"hash":"130545886384786206","title":"Stress Response and Proteostasis","description":"The top GO terms cluster around cellular stress responses (unfolded protein response, lead ion response, morphine response) and protein quality control (ubiquitination, ER-associated degradation) with links to glucocorticoid signaling. While a few terms touch on other processes (lipid catabolism, plant hormone signaling), the dominant theme ties to stress management and proteostasis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016576","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0010288","count":2},{"id":"GO:2000324","count":2}]},{"hash":"243522108276088778","title":"Potassium Transport and Membrane Potential Regulation","description":"These proteins cluster around potassium handling and the control of membrane potential\u2014potassium ion transmembrane transport, intracellular potassium homeostasis, stabilization and regulation of resting membrane potential, and cardiac repolarization. While some sensory and signaling terms appear (touch, pain, aerotaxis, cGMP response), the core theme is ion transport linked to cellular excitability, making this a concise, representative label for the cluster.","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050976","count":14},{"id":"GO:0071805","count":14},{"id":"GO:0030007","count":14},{"id":"GO:0098914","count":14},{"id":"GO:0030322","count":14}]},{"hash":"1961995566378756444","title":"Ciliary and Flagellar Motility with Tubulin Modifications","description":"This cluster is dominated by GO terms related to axoneme/ciliary movement, especially sperm flagellum function, and post-translational tubulin modifications (polyglycylation, polyglutamylation), along with microtubule severing and axon extension regulation. These features point to a cohesive theme of microtubule-based motility in cilia/flagella, particularly in sperm, with PTMs of tubulin playing a key regulatory role. Some amyloid-related terms appear, but they seem incidental to the main motif.","confidence":"High","size":20,"edges":166,"triangles":768,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0007288","count":1},{"id":"GO:0003351","count":1},{"id":"GO:1905419","count":1},{"id":"GO:0018094","count":1},{"id":"GO:0003353","count":1}]},{"hash":"697432052023797104","title":"Pyrimidine nucleotide salvage and metabolism","description":"The cluster is dominated by salvaging pyrimidine nucleotides (CMP/CTP/UMP salvage) and pyrimidine nucleobase metabolic processes, indicating a coherent nucleotide-recycling/metabolism module; other terms like phosphorylation and translation are broader processes that may accompany this core function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":6},{"id":"GO:0006238","count":3},{"id":"GO:0006206","count":3},{"id":"GO:0044211","count":3},{"id":"GO:0044206","count":3}]},{"hash":"1386743334463752870","title":"Ubiquitin-Regulated Development and Cell Death","description":"Top GO terms include ubiquitin-mediated processes (polyubiquitination and ERAD) along with developmental and cell-fate regulation (neural tube closure, asymmetric neuroblast division, TLR signaling, necroptosis, apoptosis, and organ growth), suggesting a theme of ubiquitin-dependent regulation that influences development and cell death rather than a single pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0048312","count":1},{"id":"GO:0055059","count":1}]},{"hash":"1167777309927433663","title":"Organogenesis and tissue development","description":"These GO terms cover development and morphogenesis across multiple organs (cartilage condensation, kidney, neural tube, liver, placenta, genitalia) and include JAK-STAT signaling, suggesting a broad developmental role rather than tissue-specific function. The cluster appears to group proteins involved in organogenesis processes, hence the general label. Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001502","count":3},{"id":"GO:0032092","count":3},{"id":"GO:0031659","count":2},{"id":"GO:0048806","count":2},{"id":"GO:0060674","count":2}]},{"hash":"409100685852965245","title":"Potassium Ion Transport and Membrane Potential Regulation","description":"Most of the top GO terms point to ion transport and maintenance of membrane potential, especially potassium ion transport and homeostasis, along with related processes like stable/resting membrane potential and cardiac repolarization. A few terms related to sodium import, mechanosensation, and signaling (cGMP) are present but appear secondary. The overall theme is ion gradients and membrane excitability.","confidence":"High","size":20,"edges":145,"triangles":488,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030007","count":11},{"id":"GO:0098719","count":9},{"id":"GO:0050976","count":8},{"id":"GO:0071805","count":8},{"id":"GO:0098914","count":8}]},{"hash":"1108847710900081027","title":"Cell signaling and stress response","description":"The top GO terms emphasize signal transduction and hormone-related responses (cellular response to cAMP, regulation of mRNA stability, cellular response to peptide hormone stimulus, phosphatidylinositol dephosphorylation), alongside stress-related outcomes (apoptotic process, base-excision repair, corneocyte development). This pattern suggests a module of proteins involved in transmitting signals and managing cellular stress, with connections to genome maintenance and differentiation. While diverse, the terms collectively point to signaling-driven control of cell fate under stress. ","confidence":"Medium","size":20,"edges":23,"triangles":2,"max_degree":16,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0071320","count":5},{"id":"GO:0006284","count":4},{"id":"GO:0043488","count":3},{"id":"GO:0014912","count":3},{"id":"GO:0006915","count":3}]},{"hash":"927517565604135360","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":165,"triangles":786,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":19},{"id":"GO:0007601","count":19},{"id":"GO:0060271","count":16},{"id":"GO:0035330","count":16},{"id":"GO:1905608","count":16}]},{"hash":"607095802419552072","title":"Unknown","description":"The top GO terms cover DNA replication/repair, reproduction, development, immune differentiation, and signaling/adhesion, with no single coherent function tying them all together. The proteins appear to participate in diverse, unrelated processes rather than one shared role, so a specific, representative label isn\u2019t supported.","confidence":"","size":20,"edges":63,"triangles":173,"max_degree":11,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006281","count":5},{"id":"GO:0048240","count":5},{"id":"GO:1901214","count":4},{"id":"GO:0060440","count":4}]},{"hash":"1493961058368213753","title":"Pollen exine formation and anther dehiscence","description":"The top terms clearly point to pollen wall biosynthesis (pollen exine formation) and anther dehiscence, indicating a plant reproductive development theme. While nucleotide-sugar metabolism and glycosylation appear as supporting processes, the strongest cluster signal is toward pollen wall formation and anther opening.","confidence":"Medium","size":20,"edges":153,"triangles":660,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046032","count":6},{"id":"GO:0046706","count":6},{"id":"GO:0071405","count":6},{"id":"GO:0006256","count":6},{"id":"GO:0009901","count":6}]},{"hash":"1393654088282076640","title":"Signaling and receptor trafficking regulation","description":"GO terms indicate involvement in diverse signaling pathways (e.g., TNF-mediated signaling, calcium-release regulation) and membrane trafficking processes (receptor recycling, endosome size regulation), with hints of neuronal signaling (glutamatergic synaptic transmission) and regulatory modules like Rho signaling and transcription regulation. This points to a cohesive theme of controlling signaling dynamics and membrane trafficking rather than a single specific pathway.","confidence":"Medium","size":20,"edges":15,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0033209","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0035249","count":1}]},{"hash":"2255644773187946005","title":"Sperm flagellum assembly and motility","description":"The cluster is dominated by GO terms related to cilium/axoneme assembly and movement, especially in sperm: sperm axoneme assembly, flagellated sperm motility, epithelial cilium movement, and positive regulation of cilium movement, with an additional nod to gamete-related processes like oocyte construction and protein polyglycylation. Copper ion transport and redox/homeostasis terms may support general cellular energy and metal balance, but the core signal points to the assembly and motility of flagella/cilia in reproductive cells.","confidence":"High","size":20,"edges":88,"triangles":254,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0008535","count":1},{"id":"GO:0006825","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0007308","count":1}]},{"hash":"505956604443369973","title":"Nuclear RNA Processing and Transcription Regulation","description":"The top GO terms cluster around nuclear RNA processing and transcription control (mRNA export, polyadenylation, ta-siRNA processing, transcription elongation, replication fork processing). Some terms are plant-specific or immunology/ storage-related and appear as noise, but the dominant theme ties to RNA handling and transcription in the nucleus.","confidence":"Medium","size":20,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0031990","count":1},{"id":"GO:0046784","count":1},{"id":"GO:0010267","count":1},{"id":"GO:0031297","count":1}]},{"hash":"1610457268581313789","title":"Genome Maintenance and Transcription Regulation","description":"The terms cluster around nuclear DNA processes: regulation of DNA-templated transcription, DNA topology changes, and chromosome segregation, plus telomerase holoenzyme assembly, all pointing to genome maintenance and transcription control. Some signaling-related terms (phosphorelay, autophosphorylation) and stress responses (xenobiotic, IL-4) may reflect regulatory layers that influence these core DNA processes. Overall, the group appears to represent proteins involved in genome integrity and transcription regulation rather than a single signaling pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:1901389","count":1},{"id":"GO:0046777","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0000160","count":1}]},{"hash":"1699685178695226832","title":"Podocyte and glomerular filtration barrier development","description":"The GO terms include podocyte development, glomerular basement membrane development, tight junction assembly, actin cytoskeleton organization, and VEGF signaling\u2014all key components of the kidney glomerulus filtration barrier and podocyte-endothelial interactions. Although a few immune-related terms appear, the dominant signal points to barrier formation and podocyte biology, justifying this label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019236","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0072015","count":1},{"id":"GO:2000810","count":1},{"id":"GO:0000147","count":1}]},{"hash":"1738524721063736179","title":"Regulatory signaling and development","description":"This cluster centers on a mix of GO terms related to regulation (e.g., GTPase activity regulation, kinase activity regulation), as well as several development- and signaling-associated terms (retina development, adaxial/abaxial patterning, SREBP signaling). The proteins appear to participate in broad regulatory processes rather than a single cohesive pathway, so the label reflects a general theme of regulatory signaling and developmental control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0071902","count":1},{"id":"GO:0032933","count":1}]},{"hash":"1323486505615167564","title":"Diverse metabolite biosynthesis and xenobiotic response","description":"This cluster is enriched for multiple biosynthetic processes (antibiotic, biotin, poly-hydroxybutyrate, polyamine, strigolactone) and for stress/xenobiotic response terms (response to toxic substance, cellular response to xenobiotic stimulus). The presence of RNA guanine-N7 methylation and secondary shoot formation suggests broader metabolic and developmental roles, not a single, cohesive pathway. Overall, it points to diverse metabolite production with associated detox/response capabilities. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0009102","count":9},{"id":"GO:0009636","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0042619","count":6}]},{"hash":"560248916588896478","title":"Redox-Linked Energy Metabolism","description":"This cluster is dominated by GO terms tied to redox balance (cell redox homeostasis, response to oxygen radical, removal of superoxide) and mitochondrial energy production (NADH to ubiquinone). Cofactor-related processes (dihydrolipoamide, tetrahydrofolate metabolism) further connect to mitochondrial metabolism and energy generation, with a minor signal of ER-to-Golgi transport; overall, redox and energy metabolism best explain the cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0019430","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006120","count":1},{"id":"GO:0046653","count":1}]},{"hash":"1992997237624693219","title":"Innate inflammatory signaling and cytoskeletal remodeling","description":"Top terms converge on innate immune signaling and cytokine production (NF-kappaB regulation, IL-1\u03b2 and IL-8, interferon-\u03b1) and muramyl dipeptide sensing. It also includes actin cytoskeleton remodeling (lamellipodium dynamics), supporting immune cell migration. Together, this cluster represents innate inflammatory signaling with cytoskeletal reorganization.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043124","count":8},{"id":"GO:2000321","count":8},{"id":"GO:0051638","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0050718","count":8}]},{"hash":"1872617476945765531","title":"Cytoskeleton Regulation and Microtubule Transport","description":"GO terms point to microtubule-based movement, intracellular transport, and cytoskeleton regulation, with links to nervous system and spermatid development, mitotic cell cycle, and viral transport\u2014together indicating a cluster of proteins involved in microtubule-dependent transport and cytoskeletal remodeling across development and cell division.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048812","count":1},{"id":"GO:0008340","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0019060","count":1}]},{"hash":"1712904137781227091","title":"Growth signaling, transcription, and protein turnover","description":"The top GO terms cluster around nutrient-sensing and growth pathways (TORC1 signaling, SREBP signaling), transcription/translation control (mRNA splicing, IRES-dependent translation), and proteostasis (SCF-proteasomal ubiquitin-dependent protein catabolic process, regulation of kinase activity). These collectively point to coordinated regulation of gene expression and cell growth rather than a single, narrow function, with some terms like digestion and immune defense appearing ancillary. Overall, the cluster seems to reflect growth signaling and protein homeostasis control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":3},{"id":"GO:0038202","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0031146","count":2}]},{"hash":"963715808317079697","title":"APC/C-Driven Mitotic Proteolysis","description":"This cluster's prominent terms\u2014mitotic cell cycle, cell division, anaphase-promoting complex-dependent catabolic process, and K11-linked ubiquitination\u2014highlight APC/C-mediated ubiquitin proteolysis as the core mechanism driving mitotic progression. Additional stress-response terms are present but likely secondary to this central theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010288","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0000278","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0051301","count":2}]},{"hash":"494794887915684574","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031564","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0006362","count":1},{"id":"GO:0097190","count":1},{"id":"GO:0051123","count":1}]},{"hash":"1950846822514314514","title":"Cell Cycle and Signaling Regulators","description":"The top GO terms point to transcriptional control (DNA-templated transcription), cell cycle regulation (mitotic and meiotic), and various signaling processes (Ras, small GTPases, receptor pathways) along with some structural and ion transport activities. This suggests a broad theme of coordinating gene expression with cell cycle and signal transduction, rather than a single specific pathway, so a label reflecting regulators of these processes fits best.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0046827","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0051447","count":3},{"id":"GO:0046580","count":3}]},{"hash":"1145389000605171289","title":"Unknown","description":"The top GO terms are very diverse (transcription, chromosome segregation, telomerase assembly, sporulation, signaling, transport, xenobiotic response), with no single dominant function linking the proteins. This makes it hard to assign a cohesive, specific label.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006893","count":1},{"id":"GO:1901389","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0046777","count":1}]},{"hash":"2207783530625370602","title":"Mitotic spindle organization and microtubule nucleation","description":"The top GO terms cluster around microtubule organization and mitotic processes (cytoplasmic microtubule organization, spindle pole body duplication, spindle midzone assembly, microtubule nucleation), indicating a core theme of cytoskeletal dynamics during cell division. A couple of outliers touch on neuron differentiation and cytokine responses, but they are minor relative to the dominant mitotic/microtubule signals.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0031122","count":1},{"id":"GO:0030182","count":1},{"id":"GO:0071353","count":1},{"id":"GO:1902408","count":1}]},{"hash":"535791683111476094","title":"Transcription & RNA Processing","description":"Genes in this cluster are enriched for DNA-templated transcription, transcription elongation regulation, DNA repair, and RNA processing/maintenance. This pattern suggests a shared role in controlling gene expression at both transcriptional and post-transcriptional levels. A few immune-related terms appear but seem contextual rather than defining the primary function. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0035196","count":1},{"id":"GO:0009190","count":1},{"id":"GO:0051237","count":1}]},{"hash":"1702991411786817521","title":"Nuclear transcription and cell-cycle stress signaling","description":"The terms point to transcriptional regulation in the nucleus (DNA-templated transcription, nuclear export regulation) and cell-cycle checkpoints, coupled with signaling pathways (Rho signaling) and stress responses (osmotic stress, invasive growth under glucose limitation). Together they suggest a theme of coordinating transcription, growth, division, and stress adaptation, though a few terms (e.g., trachea formation, pancreatic secretion) appear less directly connected, likely representing annotation noise. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0046827","count":4},{"id":"GO:0060440","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007266","count":3}]},{"hash":"1035909365089985882","title":"Ubiquitin-Dependent Degradation and Antiviral Immunity","description":"The top GO terms cluster around ubiquitin-dependent protein catabolic processes (including K48-linked ubiquitination and ERAD), ubiquitin-mediated regulation, and aspects of innate immunity, defense against virus, MHC class I biosynthesis, and TNF signaling. This points to a functional theme where ubiquitin-proteasome\u2013driven protein turnover intersects with antiviral and inflammatory immune pathways, suggesting roles in antigen processing and immune signaling. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0045087","count":6},{"id":"GO:0051607","count":6},{"id":"GO:0070936","count":5}]},{"hash":"83730972112480632","title":"Unknown","description":"The Top Terms span diverse biosynthetic and metabolic processes (menaquinone, strigolactone, stilbene, antibiotic biosynthesis) plus catabolic and developmental terms (secondary shoot formation, toxic substance response) across different kingdoms, with no single cohesive function tying all proteins together.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":1},{"id":"GO:0010223","count":1},{"id":"GO:1901601","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0097755","count":1}]},{"hash":"1369445753453996677","title":"TLR/NOD signaling and antigen presentation","description":"GO terms cluster around innate immune sensing (TLR9 and NOD2 signaling) and inflammasome-related processes (NLRP3 assembly), complemented by downstream immune activation such as type II interferon signaling and dendritic cell antigen processing and presentation, including MHC class I biosynthesis. The inclusion of lamellipodium organization and positive regulation of cell migration also points to immune cell movement. Together, these terms define a coherent function group in innate pathogen sensing and antigen presentation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":8},{"id":"GO:0030335","count":8},{"id":"GO:1902745","count":8},{"id":"GO:0070431","count":8},{"id":"GO:0002830","count":8}]},{"hash":"395473569641029546","title":"DNA/RNA Repair and tRNA Modification","description":"The GO terms cluster around nucleic acid maintenance, including DNA and RNA repair, mRNA processing, and tRNA wobble/translation-modifying processes, suggesting a cohesive role in RNA/DNA biology; plus some death-related terms indicating potential links to stress responses and mitochondrial involvement.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042245","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0035552","count":1},{"id":"GO:0006307","count":1}]},{"hash":"861264603349798103","title":"Iron and manganese ion homeostasis","description":"This cluster is dominated by GO terms for manganese ion transmembrane transport and manganese ion homeostasis, with a cellular response to iron ion as a supporting signal, pointing to a shared role in metal ion handling. Additional terms related to ER-to-Golgi vesicle transport and ethylene response are present but far less specific, likely reflecting broader trafficking or context-specific annotations. With only a few occurrences and no apparent strong interactions, the strongest common theme is metal ion balance and transport.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071421","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0030026","count":1},{"id":"GO:0071281","count":1},{"id":"GO:0071369","count":1}]},{"hash":"908223785201954902","title":"Skeletal muscle satellite cell activation and regeneration","description":"This cluster shows enrichment for terms tied to skeletal muscle regeneration and satellite cell activation (e.g., positive regulation of satellite cell activation involved in skeletal muscle regeneration, and negative regulation of skeletal muscle differentiation), supplemented by related signaling pathways (kinase and GTPase activity) and cell cycle/proliferation processes. The combined cues suggest a theme around muscle progenitor activation and repair.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051281","count":2},{"id":"GO:2001015","count":2},{"id":"GO:0014718","count":2},{"id":"GO:0033234","count":2},{"id":"GO:0070315","count":2}]},{"hash":"1573455945547057689","title":"DNA replication and chromatin maintenance","description":"This cluster centers on DNA replication machinery (e.g., MCM complex assembly, mitotic DNA replication, replication fork protection) and chromatin regulation (heterochromatin formation, chromatin silencing at telomeres). The presence of repair and recombination terms (double-strand break repair via break-induced replication, late meiotic recombination nodule assembly) reinforces a genome stability theme. A plant-related term (root meristem growth) appears as a minor outlier, but the dominant motif ties to replication and chromatin state control.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006343","count":1},{"id":"GO:0042140","count":1},{"id":"GO:0000727","count":1},{"id":"GO:0048478","count":1},{"id":"GO:0042127","count":1}]},{"hash":"814404347546510158","title":"Golgi trafficking and GTPase signaling","description":"The top GO terms cluster around Golgi-related processes\u2014Golgi inheritance, Golgi localization, and retrograde Golgi-to-ER transport\u2014along with endocytosis and regulation of Rho GTPase activity, suggesting a shared theme in vesicle trafficking governed by small GTPases; a few terms like pigmentation and tissue development appear more peripheral.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:1904179","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0048313","count":1},{"id":"GO:0043473","count":1}]},{"hash":"1736113594447482160","title":"Centrosome and centriole duplication regulators","description":"This cluster is strongly characterized by GO terms around centrosome duplication, centriole replication, and centriole-centriole cohesion, pointing to a shared role in centrosome/centriole biogenesis and cell-cycle\u2013related events. A few other terms (neuronal development, placental formation) appear as less central outliers, but do not alter the core theme. Therefore, the label centering on centrosome/centriole duplication best fits the predominant functional signal.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0051298","count":1},{"id":"GO:0010457","count":1},{"id":"GO:0007099","count":1},{"id":"GO:0042068","count":1}]},{"hash":"480084596742988143","title":"Cytoskeletal dynamics and ERK-GTPase signaling in development","description":"The top GO terms cluster around actin cytoskeleton remodeling (stress fiber assembly), signaling pathways (ERK cascade, GTPase activity), and cell-cycle processes (mitotic spindle assembly, ubiquitination, proliferation), with development-related terms such as brain development and sensory perception of touch. This suggests a cohesive program where cytoskeletal dynamics are coordinated with signaling during development, particularly neural development. ","confidence":"Medium","size":19,"edges":10,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070208","count":3},{"id":"GO:0043149","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0050975","count":3}]},{"hash":"206270721483848060","title":"DNA damage response and stress signaling","description":"This cluster shows strong representation of base-excision repair and apoptosis, along with responses to xenobiotic stimuli and peptide hormone signaling, indicating a cohesive DNA damage response and stress-signaling module. Regulation of mRNA stability and phosphatidylinositol dephosphorylation suggest links to post-transcriptional control and signaling cross-talk, while corneocyte development hints at tissue-specific aspects; a couple obsolete GO terms appear as noise.","confidence":"Medium","size":19,"edges":20,"triangles":6,"max_degree":7,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006284","count":8},{"id":"GO:0007568","count":8},{"id":"GO:0042493","count":8},{"id":"GO:0043488","count":7},{"id":"GO:0014912","count":7}]},{"hash":"1533470788088048096","title":"Antiviral innate immune signaling cluster","description":"The top GO terms cluster around innate immunity and antiviral responses (innate immune response, defense response to virus, LPS signaling, and interferon-beta production), suggesting proteins involved in early pathogen sensing and type I IFN induction. Additional terms for transcription, mRNA processing, and ubiquitin-proteasome turnover fit downstream gene expression and protein turnover in immune signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":9},{"id":"GO:0000278","count":8},{"id":"GO:0071276","count":8},{"id":"GO:0051607","count":8},{"id":"GO:0006351","count":7}]},{"hash":"1771170374122771786","title":"Growth signaling and ribosome biogenesis","description":"This cluster centers on growth and proliferation machinery, highlighted by TORC1 signaling, ribosome biogenesis, and transcription, along with mitotic spindle assembly and GTPase-regulated signaling. While brain development and vesicle trafficking appear among the terms, the dominant theme ties to cellular growth, protein synthesis capacity, and cell-cycle functions that drive proliferation. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0090307","count":2}]},{"hash":"2003698448590952105","title":"Membrane Transport and Substrate Uptake","description":"The cluster is characterized by a broad representation of transport-related GO terms across membranes, including cobalt ion transport, amino acid and vitamin transport, lipoprotein transport, and even drug transport (doxorubicin). There is also metabolism-related activity (very long-chain fatty acid catabolic process). The commonality appears to be membrane-associated uptake and trafficking of diverse substrates, with nucleotide-excision repair seemingly unrelated to the core theme. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":19},{"id":"GO:0006824","count":19},{"id":"GO:0042760","count":19},{"id":"GO:1900753","count":19},{"id":"GO:0030253","count":19}]},{"hash":"1788602190812398125","title":"Plant secondary metabolite and lipid biosynthesis","description":"The cluster is enriched for diverse biosynthetic processes, including tropane alkaloid, phylloquinone, very long-chain fatty acid, sphinganine (lipid) metabolism, and steroid hormone biosynthesis, pointing to production of plant-derived metabolites and lipids. Some terms like regulation of transcription or obsolete redox are less specific, but the predominant theme is biosynthesis of plant secondary metabolites and lipids. ","confidence":"Medium","size":19,"edges":49,"triangles":36,"max_degree":12,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":14},{"id":"GO:0009710","count":13},{"id":"GO:0042574","count":13},{"id":"GO:0042376","count":13},{"id":"GO:0055114","count":13}]},{"hash":"1874615671398938573","title":"Unknown","description":"This cluster has no GO terms and no interactions (Edges: 0, Triangles: 0), so there is no clear shared function to identify a label. Despite 20 proteins re-added by ReCIPE, the lack of functional terms or connections prevents defining a coherent theme, hence Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"881805136275879351","title":"Endomembrane Trafficking and Sphingolipid Homeostasis","description":"The top GO terms cluster around intracellular transport pathways (endocytic recycling, retrograde transport endosome to Golgi, lysosomal transport, dense core granule transport) and regulation of sphingolipid homeostasis, implying a shared role in membrane trafficking and lipid regulation. A few terms related to reproduction appear as outliers, but the dominant theme is endomembrane transport and lipid homeostasis.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007290","count":1},{"id":"GO:0060052","count":1},{"id":"GO:0060378","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0050881","count":1}]},{"hash":"689417339483288356","title":"Axon fasciculation and cell adhesion","description":"This cluster is dominated by terms tied to neural development, especially fasciculation of sensory neuron axons and cell adhesion, with supporting signals from proteolysis and responses to growth factors and hormones, suggesting a neural adhesion/guidance theme. Confidence: Medium","confidence":"","size":19,"edges":19,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0097155","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0044344","count":1},{"id":"GO:0014075","count":1}]},{"hash":"870760837278353898","title":"Xenobiotic Metabolism and Detoxification","description":"This cluster is dominated by GO terms related to detoxification and metabolism of xenobiotics (xenobiotic catabolic process, nitrobenzene metabolic process, aromatic amino acid metabolism) and broad responses to toxic substances, suggesting a core function in processing and defending against foreign compounds. Additional terms like prostaglandin biosynthesis and negative regulation of interleukin-1 beta production point to linked inflammatory and signaling roles, while nucleotide-excision repair indicates cellular stress responses; together, these terms paint a cohesive picture of detoxification with associated stress and repair responses.","confidence":"High","size":19,"edges":167,"triangles":905,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0042178","count":19},{"id":"GO:1904706","count":19},{"id":"GO:0018916","count":19},{"id":"GO:0032691","count":19},{"id":"GO:0006289","count":19}]},{"hash":"1615586610395664592","title":"Innate Immune Sensing and Antigen Presentation","description":"The GO terms cluster around pathogen sensing (TLR9 and NOD2 signaling), inflammasome assembly (NLRP3), detection of muramyl dipeptide, interferon signaling, and dendritic cell\u2013driven antigen processing/presentation (including MHC I biosynthesis). This suggests a cohesive role in innate immune activation of dendritic cells and subsequent antigen presentation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":19},{"id":"GO:0030335","count":19},{"id":"GO:1902745","count":19},{"id":"GO:0070431","count":19},{"id":"GO:0002830","count":19}]},{"hash":"1506700849028898893","title":"ECM Remodeling and Adhesion Signaling","description":"The proteins cluster around regulation of focal adhesion assembly, ECM disassembly, and Rho-mediated signaling, pointing to roles in cell adhesion dynamics and extracellular matrix remodeling. Peripheral terms touch on development and immune differentiation, but the core appears to be adhesion and signaling in matrix interactions.","confidence":"Medium","size":19,"edges":47,"triangles":34,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":18},{"id":"GO:0060440","count":18},{"id":"GO:0051893","count":18},{"id":"GO:0001403","count":18},{"id":"GO:0007266","count":18}]},{"hash":"2050757823777990203","title":"Neural development and innate immune signaling","description":"The top GO terms cluster around neural development and synaptic plasticity (axonogenesis, long-term potentiation, corpus callosum development) and innate immune signaling (innate immune response, LPS-mediated signaling, interferon-beta production, defense against Gram-positive bacteria). While DNA replication and cadmium response appear as outliers, the dominant theme ties brain development with immune communication.","confidence":"Medium","size":19,"edges":86,"triangles":168,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0071276","count":5},{"id":"GO:0060291","count":5},{"id":"GO:0045359","count":5},{"id":"GO:0022038","count":5}]},{"hash":"627967333637081605","title":"Unknown","description":"The top GO terms span diverse biological areas (bacterial lipopolysaccharide biosynthesis, metal transport, hormone response, heart function, lipid translocation, plant metabolism, and inner ear development), with no single cohesive function uniting the cluster. This makes it hard to assign a specific, representative label, so Unknown is appropriate.","confidence":"","size":19,"edges":80,"triangles":153,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":7},{"id":"GO:0070574","count":6},{"id":"GO:0033574","count":6},{"id":"GO:1903249","count":6},{"id":"GO:0098736","count":6}]},{"hash":"1500929509229082057","title":"TNF-NF-\u03baB Innate Immunity and Apoptosis","description":"This cluster is dominated by GO terms related to innate immune response, TNF-mediated signaling, and I-kappaB phosphorylation, pointing to NF-\u03baB\u2013driven inflammatory signaling and regulation of apoptosis. Although some terms are miscellaneous (e.g., histone modification), the core theme centers on immune signaling and cell fate decisions.","confidence":"High","size":19,"edges":15,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":2},{"id":"GO:0090073","count":2},{"id":"GO:2000620","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0033209","count":2}]},{"hash":"2063305676129111158","title":"Cilium/Flagellum assembly and motility","description":"Top terms point to ciliary and flagellar processes: sperm axoneme assembly, flagellated sperm motility, and epithelial cilium movement, suggesting the cluster centers on the structure and movement of cilia/flagella. Additional terms related to receptor recycling and endosome size imply trafficking functions that can support cilium formation and maintenance, while regulatory terms for Rho signaling and transcription may reflect broader coordination of cell morphology. Overall, the strongest cohesive theme is cilium/flagellum biology with related trafficking.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001881","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0060316","count":1},{"id":"GO:0034968","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1879722808342622942","title":"Cardiac potassium transport and membrane potential regulation","description":"This cluster is driven by membrane potential regulation and potassium transport in cardiac tissue (atrial repolarization, resting potential maintenance, potassium ion homeostasis), suggesting involvement in cardiac electrical activity. Some unrelated terms appear (heart morphogenesis, glucose response, T cell proliferation) but do not outweigh the core ion-transport theme.","confidence":"High","size":19,"edges":18,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0098914","count":1},{"id":"GO:0060075","count":1},{"id":"GO:0030322","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0030007","count":1}]},{"hash":"1793431140820339468","title":"Gene Expression Regulation Under Stress and Development","description":"This cluster centers on gene expression control, combining DNA-templated transcription and chromatin-related processes (nucleosome assembly, histone H3-K9 methylation) with translation initiation and reinitiation. It also includes stress- and development-related terms (ER stress\u2013triggered apoptotic signaling; cadmium response; invasive growth under glucose limitation; skeletal and multicellular development). The shared theme appears to be regulation of gene expression in response to cellular stress and developmental programs, rather than a single pathway.","confidence":"Medium","size":19,"edges":64,"triangles":51,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006334","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001403","count":2}]},{"hash":"1700934534030106327","title":"Diverse membrane solute transporters","description":"The top GO terms show transmembrane transport across membranes for a wide range of substrates (vitamins, xenobiotics, organic cations, arabinose, nitrite, dehydroascorbic acid, sodium ions) and even neurotransmitter loading into synaptic vesicles, pointing to a cluster of membrane transport proteins with broad substrate specificity. There is one outlier term related to replicative senescence that seems unrelated and may be noise. ","confidence":"High","size":19,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035461","count":16},{"id":"GO:0006855","count":16},{"id":"GO:0070715","count":15},{"id":"GO:0015751","count":15},{"id":"GO:0035725","count":15}]},{"hash":"1324415486516610187","title":"RNA Pol II Transcription Regulation","description":"The cluster's proteins are predominantly linked to RNA Polymerase II\u2013driven transcription, with GO terms for DNA-templated transcription, transcription initiation and promoter assembly (preinitiation complex formation, transcription start site selection, and open complex formation) indicating a coherent role in transcription initiation and regulation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0001113","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0051123","count":1}]},{"hash":"2293800832128855343","title":"Mitochondrial transport and energetics","description":"The top GO terms cluster around mitochondrial function: transport of key metabolic substrates (alpha-ketoglutarate, thiamine pyrophosphate, coenzyme A) across the mitochondrial membrane; malate-aspartate shuttle; regulation of mitochondrial membrane potential and apoptotic changes, indicating involvement in energy production and apoptosis. Together these terms suggest a coherent theme of mitochondrial transport and energy metabolism in the proteins.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0030974","count":1},{"id":"GO:0035349","count":1}]},{"hash":"1351189592212149776","title":"Unknown","description":"The Top Terms are highly heterogeneous, with only a couple pointing clearly to muscle biology (sarcomere organization and cardiac muscle cell proliferation) and many others spanning signaling regulation, ion transport, transport/export processes, and even processes like aerotaxis and drug response. There is no single unifying function or pathway that ties the majority of these GO terms together, so a concise, representative label cannot be assigned. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0098719","count":2}]},{"hash":"642659923903313563","title":"Muscle sarcomere organization and signaling","description":"The cluster\u2019s top GO terms center on sarcomere organization and cardiac/muscle-related processes, plus signaling pathways such as small GTPase-mediated signaling, Ras regulation, and adenylate cyclase/cAMP and cGMP signaling. This points to a cohesive theme of muscle structure (sarcomere) and its regulation by signaling networks. A few terms (aerotaxis, meiotic cell cycle regulation) seem unrelated and may reflect annotation noise, but the dominant pattern supports muscle organization and signaling. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051447","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0007264","count":3}]},{"hash":"1888160193381804324","title":"Antiviral Innate Immune Signaling","description":"The cluster is dominated by GO terms tied to innate immunity and antiviral responses, including defense response to virus, innate immune response, TLR9 and NOD2 signaling, and type II interferon\u2013mediated pathways, plus IL-6 production and immune cell migration. This cohesive pattern points to a coordinated antiviral innate immune signaling role, with some involvement in antigen processing via ubiquitin-proteasome\u2013mediated degradation.","confidence":"High","size":19,"edges":111,"triangles":347,"max_degree":17,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":17},{"id":"GO:0051607","count":14},{"id":"GO:0045087","count":14},{"id":"GO:0034162","count":12},{"id":"GO:0032755","count":12}]},{"hash":"923255450818280983","title":"Unknown","description":"The GO terms are very heterogeneous across phosphorylation, proteoglycan biosynthesis, lipid metabolism, signaling, and neural development with no single dominant function tying the proteins together. Because there isn't a clear, common biological theme among the top terms, a concise, representative label cannot be confidently assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0050650","count":1},{"id":"GO:0016036","count":1},{"id":"GO:0060168","count":1},{"id":"GO:2001311","count":1}]},{"hash":"161766297090957988","title":"Unknown","description":"The terms mix lipid droplet/storage functions with several viral lifecycle processes (latency, entry/fusion, genome replication) and a few unrelated terms, with no observed interactions among the proteins. Since there is no coherent, single theme linking the GO terms, this cluster is best labeled Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034389","count":2},{"id":"GO:0010344","count":1},{"id":"GO:0019915","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0000413","count":1}]},{"hash":"993840585972119035","title":"Glycophagy and carbohydrate catabolism","description":"The GO terms point strongly to autophagy-related processing of carbohydrate substrates: glycophagy, positive regulation of macroautophagy, starch and maltose catabolism, and carbon utilization regulation. This suggests a coherent theme around autophagy-linked breakdown of glycogen and other carbohydrates, with some broader carbon metabolism context. The presence of a lipid catabolic term is a minor outlier within an overall carbohydrate/autophagy-focused cluster.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061723","count":1},{"id":"GO:0046959","count":1},{"id":"GO:0016239","count":1},{"id":"GO:0005983","count":1},{"id":"GO:0046475","count":1}]},{"hash":"1933076781728429620","title":"Unknown","description":"There are no GO terms or network connections to reveal a shared function among the 19 proteins. With 0 edges, 0 triangles, and no top terms, the cluster lacks a clear functional theme; the mention of \"1 proteins re-added by ReCIPE (degree, 0.75)\" does not provide a cohesive property. Therefore the label is Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"784969474139419477","title":"TLR/NLR-Mediated Antiviral Innate Immunity","description":"The cluster is driven by innate immune signaling terms, including defense response to virus and innate immune response, with specific engagement of TLR9 signaling and NLR/NLRP3 inflammasome pathways, Muramyl dipeptide detection, and regulation of interferon signaling. Additional terms about cell migration and lamellipodium organization suggest recruitment and movement of immune cells during activation, supporting a cohesive antiviral innate-immunity theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":8},{"id":"GO:0045087","count":8},{"id":"GO:0034162","count":7},{"id":"GO:0030335","count":7},{"id":"GO:1902745","count":7}]},{"hash":"1863200895072087556","title":"Neuronal development and axon guidance","description":"Based on the GO terms, several entries point to neural development and connectivity: dendritic spine development, CNS projection neuron axonogenesis, fasciculation of sensory neuron axon, and ephrin receptor signaling, with retinoic acid response also supporting developmental signaling. A few terms (iodide transport, nephric duct morphogenesis, T cell costimulation, type IV hypersensitivity) are less related and may reflect annotation noise. Overall, the dominant theme is neuronal development and axon guidance.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071300","count":2},{"id":"GO:0060996","count":1},{"id":"GO:0072178","count":1},{"id":"GO:0097155","count":1},{"id":"GO:2000525","count":1}]},{"hash":"682710195928822281","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070979","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0071560","count":2}]},{"hash":"2095456543042089197","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":1},{"id":"GO:0090086","count":1},{"id":"GO:0071641","count":1},{"id":"GO:2000637","count":1},{"id":"GO:1902187","count":1}]},{"hash":"66250004008593020","title":"Tyrosine phosphatases regulating MAPK and T cell signaling","description":"The cluster is dominated by GO terms tied to dephosphorylation of tyrosine residues and the negative regulation of signaling pathways, especially MAPK/ERK cascades and T cell receptor signaling, plus inhibition of PI3K/AKT signaling. This points to protein tyrosine phosphatases and related regulators dampening key signaling networks. Some mitosis-related terms suggest additional roles for certain members, but the unifying theme appears to be phosphatase-mediated signal attenuation.","confidence":"High","size":18,"edges":149,"triangles":756,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0000200","count":18},{"id":"GO:0070373","count":18},{"id":"GO:0050860","count":18},{"id":"GO:0035335","count":16},{"id":"GO:0051898","count":15}]},{"hash":"792498738894479650","title":"Mitochondrial Respiration and Proton Transport","description":"Enrichment for mitochondrial electron transport (ubiquinol to cytochrome c) and aerobic respiration, plus proton transmembrane transport, points to a core function in mitochondrial energy production. Additional terms touch on regulatory and neuronal processes, but the dominant signal is respiration-related proteins.","confidence":"High","size":18,"edges":67,"triangles":127,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0009060","count":2},{"id":"GO:2000146","count":1},{"id":"GO:2000749","count":1}]},{"hash":"1887802922808292806","title":"Mitotic Cell Cycle and Protein Modification Regulation","description":"This cluster is dominated by terms tied to mitosis and cell division (mitotic cell cycle, cell division, metaphase/anaphase transition), with related roles in protein regulation (protein ubiquitination, isomerization, and heterooligomerization). Together these terms point to a cohesive theme of mitotic progression and control of protein state during division, even though a few outlier terms appear that relate to other signaling or stress responses. ","confidence":"High","size":18,"edges":12,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051291","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0007091","count":4},{"id":"GO:0000413","count":4}]},{"hash":"1781136703191829346","title":"Neural signaling and sensory function","description":"The cluster\u2019s top GO terms include anterograde synaptic vesicle transport, olfactory learning, and eye pigment granule organization, all pointing to neural signaling and sensory processing. Additional terms like protein transport and kinase activity regulation also fit into neuronal signaling contexts. Some terms appear unrelated (e.g., fungal cell wall biogenesis, plant patterning), but the core theme centers on nervous system function and sensory perception, justifying this label.  ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048490","count":1},{"id":"GO:0008355","count":1},{"id":"GO:0008057","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0015031","count":1}]},{"hash":"2042898765118170228","title":"Endocytic trafficking and membrane remodeling regulators","description":"The top GO terms center on membrane trafficking and surface receptor processing, including plasma membrane to endosome transport, early endosome to Golgi transport, and regulation of protein localization to the cell surface, as well as ectodomain proteolysis and TNF signaling components. The set is somewhat heterogeneous, but the shared theme appears to be regulators of membrane trafficking and surface receptor processing rather than a single, cohesive pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":1},{"id":"GO:1902306","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0033209","count":1},{"id":"GO:1902072","count":1}]},{"hash":"534421039953536348","title":"RNA transcription machinery and ribosome biogenesis","description":"The top GO terms are strongly centered on transcription by RNA polymerases I, II, and III (including initiation, elongation, and termination), RNA-templated transcription, and tRNA transcription by Pol III, plus ribosome biogenesis, which together define core RNA synthesis and ribosome assembly processes. A couple of outlier terms related to inflammatory response and dendrite morphogenesis are incidental. Overall, the cluster seems to reflect transcriptional machinery and ribosome biogenesis functions.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0006386","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0042797","count":1}]},{"hash":"322728423100665824","title":"Unknown","description":"The GO terms cover diverse processes (mitotic cell cycle transition, protein folding, ciliogenesis, plant hormone signaling regulation, metal ion response, translation regulation under ER stress, ubiquitination, interferon response, and posttranslational modifications like sulfation), with no single cohesive function tying the proteins together. Therefore there isn\u2019t a specific, representative label beyond Unknown.","confidence":"","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007091","count":5},{"id":"GO:0000413","count":5},{"id":"GO:1905515","count":5},{"id":"GO:0009938","count":5},{"id":"GO:0010288","count":5}]},{"hash":"686339690834073185","title":"Unknown","description":"The top GO terms cover a wide range of processes from DNA damage response and repair to telomere maintenance, RNA processing, chromatin methylation, and various signaling/trafficking activities (receptor recycling, synaptic transmission, calcium signaling) plus mechanosensing (response to muscle stretch). This lack of a single cohesive biological theme makes it difficult to assign a specific, representative function to the cluster. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007095","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0006397","count":2}]},{"hash":"1833806293990223132","title":"Ribosome biogenesis and translation","description":"The top GO terms point to core ribosome-related processes, including translation, ribosomal subunit biogenesis, and maturation of rRNA transcripts (both SSU and LSU). This combination indicates a cluster of proteins involved in ribosome assembly and protein synthesis, with some peripheral links to rRNA processing.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0042254","count":4},{"id":"GO:0006407","count":4},{"id":"GO:0000027","count":4},{"id":"GO:0046677","count":3}]},{"hash":"2069342437590683129","title":"Innate immune signaling and cytokine production","description":"This cluster is dominated by GO terms related to innate immune activation, including TLR signaling (MyD88-independent), NF-kappaB pathways, and cytokine production (TNF, IL-18, IL-1), as well as related processes like MHC biosynthesis and cell migration. The close grouping of these immune-related functions suggests a coherent innate immune signaling module.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":18},{"id":"GO:0002830","count":18},{"id":"GO:0045345","count":18},{"id":"GO:0032741","count":18},{"id":"GO:0002756","count":18}]},{"hash":"168178056578626154","title":"Signaling and Stress Response Network","description":"The top GO terms show a mix of signal transduction (Rho), insulin signaling, cell-cycle checkpoint signaling, developmental processes (trachea formation, septation), and stress responses (osmotic stress, cadmium exposure), suggesting a cluster of proteins involved in broad signaling and stress-response pathways rather than a single, cohesive module.","confidence":"Medium","size":18,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":18},{"id":"GO:0001403","count":18},{"id":"GO:0007266","count":18},{"id":"GO:0010614","count":18},{"id":"GO:0047484","count":18}]},{"hash":"2104008715429977725","title":"Regulation of adhesion and ECM remodeling signaling","description":"The dominant terms point to cell\u2013matrix interactions and cytoskeletal signaling: regulation of focal adhesion assembly, regulation of extracellular matrix disassembly, and Rho protein signal transduction. These reflect signaling that governs adhesion dynamics and ECM remodeling. While there are outliers related to development and immune differentiation, the shared theme centers on adhesion and matrix remodeling processes.","confidence":"Medium","size":18,"edges":14,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":18},{"id":"GO:0060440","count":18},{"id":"GO:0051893","count":18},{"id":"GO:0001403","count":18},{"id":"GO:0007266","count":18}]},{"hash":"924955392097122239","title":"Neural development and synaptic signaling","description":"The proteins are strongly associated with nervous system processes, including excitatory postsynaptic potential, long-term synaptic potentiation, and visual perception, along with developmental terms like Schwann cell development and embryonic cranial skeleton morphogenesis, suggesting a cluster focused on neural development and synaptic function, with some broader developmental context reflected by other terms.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":17},{"id":"GO:0060291","count":17},{"id":"GO:0007507","count":17},{"id":"GO:0014850","count":17},{"id":"GO:0014044","count":17}]},{"hash":"1212406071748712827","title":"Neuronal development and synaptic trafficking","description":"This cluster is dominated by terms related to glutamatergic synaptic transmission, nervous system development, and receptor recycling, pointing to proteins involved in neuronal synapse function and endosomal trafficking. Additional terms about transcription regulation and histone methylation suggest concurrent roles in gene expression control relevant to neurons. The combination supports a cohesive theme around neuronal signaling and endosomal/via trafficking processes, with a secondary layer of transcriptional regulation.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035249","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0060316","count":3}]},{"hash":"1653628282002942873","title":"Cardiac signaling and sarcomere organization","description":"The top GO terms point to cardiac muscle function (heart rate regulation and sarcomere organization) with additional signaling modulation (Ras/small GTPases and guanylyl cyclase pathways) and transcription, suggesting a cohesive theme of cardiac signaling coupled to muscle structure.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0046827","count":5},{"id":"GO:0002027","count":4},{"id":"GO:0051447","count":3},{"id":"GO:0046580","count":3}]},{"hash":"486487364046656712","title":"Liver Hormone and Metabolic Response","description":"The GO terms cluster around hepatic-regulated responses to hormones and nutrients: dexamethasone and growth hormone responses, oleic acid and ethanol-related metabolic adaptation, and liver development, plus nutrition-related cues like response to food. Together these suggest a liver-centered hormonal and metabolic signaling theme. A few terms (e.g., 4-aminobenzoate biosynthesis) may reflect annotation noise but do not change the overall liver/hormonal focus.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":2},{"id":"GO:0071400","count":2},{"id":"GO:0044344","count":1},{"id":"GO:0014075","count":1},{"id":"GO:0008153","count":1}]},{"hash":"1746476743412927397","title":"Cardiac signaling and sarcomere organization","description":"This cluster is dominated by GO terms tied to heart function and muscle structure: regulation of heart rate, cardiac muscle cell proliferation, and sarcomere organization. Supporting signaling layers include small GTPase signaling, negative regulation of Ras signaling, and receptor guanylyl cyclase pathway regulation. Sodium ion import aligns with excitable cardiac cells, reinforcing a cardiac signaling theme. A few terms appear less central (aerotaxis, antipsychotic response), which may reflect annotation breadth, but the core pattern points to cardiovascular signaling and contractile apparatus organization.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":7},{"id":"GO:0007264","count":6},{"id":"GO:0002027","count":6},{"id":"GO:0051447","count":5},{"id":"GO:0046580","count":5}]},{"hash":"1692720549591066657","title":"Heat-stress response and protein quality control","description":"This cluster centers on heat response and protein quality control, with emphasis on detecting misfolded proteins and chaperone-mediated assembly, indicating proteostasis under stress. Additional terms for cell cycle and telomere maintenance suggest broader cellular responses to stress that influence proliferation and genome integrity, plus ischemia and TNF signaling as general stress indicators.","confidence":"Medium","size":18,"edges":21,"triangles":4,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0002236","count":3}]},{"hash":"2142133364195648116","title":"Oxidative metabolism and stress response","description":"The terms cluster around oxidative and catabolic metabolism (ethanol and fatty acid oxidation, furaldehyde metabolism, Ehrlich pathway) and various stress/defense responses (response to copper ion, response to lipopolysaccharide) plus extracellular regulation of signaling. The lignin biosynthesis term hints a plant phenylpropanoid context, but overall the proteins seem tied to oxidative metabolism with associated stress-response signaling rather than a single precise pathway. ","confidence":"Medium","size":18,"edges":108,"triangles":343,"max_degree":17,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0009809","count":17},{"id":"GO:0046688","count":17},{"id":"GO:0045777","count":17},{"id":"GO:0032496","count":17},{"id":"GO:0033859","count":17}]},{"hash":"1167475608329176432","title":"RNA splicing and silencing machinery","description":"The terms cluster around RNA processing and regulation: spliceosome-driven splicing (splice site recognition, alternative splicing, cis splicing, small-subunit processome), mRNA stabilization, and ncRNA/miRNA-mediated gene silencing, with additional signals for translation initiation complex assembly. This points to a cohesive group of proteins involved in RNA maturation and post-transcriptional control.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0048255","count":2},{"id":"GO:1902625","count":2}]},{"hash":"391662583013164863","title":"Membrane Transporters","description":"Most of the top GO terms center on transport across membranes for ions, sugars, vitamins, and other small molecules (e.g., sodium-dependent organic cation transport, arabinose and nitrite transport, vitamin and dehydroascorbic acid transport, neurotransmitter loading into vesicles). This suggests a cluster of proteins specialized in transmembrane transport rather than a single substrate. A non-transport term appears (positive regulation of replicative senescence), but the dominant signal is membrane transport. ","confidence":"High","size":18,"edges":26,"triangles":12,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0070715","count":17},{"id":"GO:0015751","count":17},{"id":"GO:0035725","count":17},{"id":"GO:1900754","count":17},{"id":"GO:0015707","count":17}]},{"hash":"1051116127256911060","title":"Translation Initiation and Reinitiation","description":"The top GO terms are centered on translation initiation and reinitiation, including formation of the translation preinitiation complex, translation reinitiation, and IRES-dependent viral translational initiation, which together suggest a cohesive role in ribosome assembly and re-use during translation, even though a few RNA processing terms appear among the results. Confidence in this being representative is Medium.","confidence":"","size":18,"edges":22,"triangles":6,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0075525","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0075522","count":4}]},{"hash":"1142644342439867288","title":"Unknown","description":"The top GO terms span plant signaling, muscle development, immune signaling, viral latency, chromosomal organization, flower development, and renal processes with no shared pathway or interaction pattern, and there are no edges in the cluster, indicating no cohesive biological theme.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009742","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0019046","count":1},{"id":"GO:0048741","count":1},{"id":"GO:0045214","count":1}]},{"hash":"1198118933896628564","title":"Unknown","description":"The top terms are highly diverse and include histone methylation, hypoxia response, salt stress response, development and differentiation terms, calcium signaling, proteolysis, digestion, and some obsolete or species-specific terms, with no edges connecting proteins. This lack of a cohesive functional theme makes a meaningful, concise label untenable.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0071472","count":1},{"id":"GO:0001824","count":1},{"id":"GO:0007520","count":1}]},{"hash":"164720576780020208","title":"Unknown","description":"The terms show a mix of ribosome-related processes (rRNA processing; translation preinitiation complex; regulation of translational initiation; viral translation-termination/reinitiation), RNA export, and vesicle trafficking/endocytosis (intracellular protein transport; synaptic vesicle coating; clathrin-dependent endocytosis). SREBP signaling and ubiquitin ligase activity add additional, unrelated signals. This lack of a single coherent biological theme across the cluster makes it difficult to assign a concise, representative function. Therefore label Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0016183","count":1},{"id":"GO:0072583","count":1},{"id":"GO:0001731","count":1}]},{"hash":"629968838119057219","title":"Cell Cycle Regulation and Nuclear Transport","description":"This cluster centers on GO terms related to cell division (meiotic spindle elongation, mitotic cell cycle), protein turnover (K11-linked ubiquitination), and nuclear trafficking (NLS-bearing protein import into nucleus), with supportive signals from TORC1 and transcription regulation. Together these terms suggest a coherent theme of coordinating cell cycle progression with protein regulation and nuclear localization, rather than a single narrowly defined process, hence a label focusing on cell cycle control and nuclear transport is most representative.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051232","count":5},{"id":"GO:0070979","count":3},{"id":"GO:0000278","count":3},{"id":"GO:2001241","count":3},{"id":"GO:0070262","count":3}]},{"hash":"1944695183490679368","title":"N-acetyltransferases and polyamine metabolism","description":"The top GO terms are dominated by various acetylation processes (N-terminal and peptidyl acetylation across multiple residues) and polyamine catabolic pathways (putrescine and spermine). This suggests a cluster centered on N-acetyltransferase activity and polyamine metabolism, with melatonin biosynthesis terms likely reflecting AANAT-like acetyltransferase function. A cohesive label that captures these themes is thus appropriate.","confidence":"High","size":18,"edges":87,"triangles":251,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0017198","count":10},{"id":"GO:0030187","count":9},{"id":"GO:0019491","count":9},{"id":"GO:0018002","count":9},{"id":"GO:0046208","count":9}]},{"hash":"231080046016923494","title":"Unknown","description":"The top terms cover a mix of hypoxia sensing, oxidative modification, lactation, epithelial differentiation, viral transcription/replication interactions, ER unfolded protein response, and cell cycle regulation. There isn\u2019t a single coherent function or pathway tying these terms together, so a specific, representative label cannot be assigned beyond Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070483","count":1},{"id":"GO:0018171","count":1},{"id":"GO:0007595","count":1},{"id":"GO:0030857","count":1},{"id":"GO:0044828","count":1}]},{"hash":"1215108219628905559","title":"Innate Immune Sensing and Antigen Presentation","description":"This cluster is dominated by innate immune recognition and signaling pathways (TLR9, NOD2, NLRP3 inflammasome) and microbial detection (muramyl dipeptide), with downstream enhancement of dendritic cell antigen processing/presentation and MHC class I biosynthesis, plus type II interferon signaling and cell migration. The cohesive theme is immune sensing leading to antigen presentation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":8},{"id":"GO:0030335","count":8},{"id":"GO:1902745","count":8},{"id":"GO:0070431","count":8},{"id":"GO:0002830","count":8}]},{"hash":"632829046678323978","title":"Innate Antiviral Signaling and Antigen Presentation","description":"This cluster centers on innate antiviral defense (defense response to virus, innate immune response, MyD88-independent TLR signaling) and coordinates proteasome/SCF-driven protein degradation for MHC class I antigen processing, with cytokine regulation (IL-18, IL-1) and NF-\u03baB pathway modulation; the inclusion of cell migration regulation supports immune cell trafficking. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":13},{"id":"GO:0031146","count":13},{"id":"GO:0045087","count":13},{"id":"GO:0030335","count":12},{"id":"GO:0002830","count":12}]},{"hash":"1074838441768651788","title":"Plant hormone biosynthesis and shoot development","description":"This cluster is dominated by plant-specific processes: strigolactone biosynthesis and secondary shoot formation, both key to plant hormonal control of branching and architecture. Additional terms like stilbene catabolic process and antibiotic biosynthetic process point to plant secondary metabolism, while oxidant detoxification reflects stress responses. The shared thread is plant metabolism linked to hormone signaling and development, though the mix of terms suggests a broad metabolic/defense context rather than a single narrow function. Confidence: Medium.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0055114","count":16},{"id":"GO:0010223","count":14},{"id":"GO:1901601","count":14},{"id":"GO:0046272","count":14},{"id":"GO:0097755","count":14}]},{"hash":"1489385498725360546","title":"TLR-NF-\u03baB Driven Cytokine Signaling","description":"The top terms point to innate immune signaling via Toll-like receptors, including MyD88-independent pathways, with NF-\u03baB regulation and cytokine production (IL-1, IL-18, TNF) plus MHC class I biosynthesis, all indicating a coordinated TLR-NF-\u03baB\u2013driven inflammatory and antigen-presenting response.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":18},{"id":"GO:0002830","count":18},{"id":"GO:0045345","count":18},{"id":"GO:0032741","count":18},{"id":"GO:0002756","count":18}]},{"hash":"777042266539289266","title":"Innate immune sensing and dendritic cell activation","description":"The GO terms cluster around pattern-recognition and innate sensing (TLR9, NOD-like receptor signaling, NLRP3 inflammasome assembly, muramyl dipeptide detection) and the subsequent activation of antigen processing/presentation pathways in dendritic cells, including MHC class I biosynthesis, plus interferon signaling. This cohesive theme centers on initiating innate immune responses and preparing adaptive immunity via DCs.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":17},{"id":"GO:0030335","count":17},{"id":"GO:1902745","count":17},{"id":"GO:0070431","count":17},{"id":"GO:0002830","count":17}]},{"hash":"1027753481062104755","title":"Plant chromatin remodeling and telomere regulation","description":"The top GO terms center on chromatin dynamics (chromatin remodeling) and telomere-associated processes (subtelomeric heterochromatin formation, shelterin complex assembly), pointing to chromatin state and telomere maintenance as the core theme. Plant hormone responses (ABA and gibberellin) may reflect regulatory layers linked to chromatin, while a confusing viral process annotation likely represents annotation noise rather than a shared function. Overall, the cluster appears to reflect nuclear/chromatin regulation with telomere safeguards in plants.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035390","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0009737","count":1},{"id":"GO:1904792","count":1}]},{"hash":"741191745902830204","title":"Innate antiviral immunity and inflammasome assembly","description":"The terms show a cohesive antiviral innate immune theme, with defense against virus, innate immune responses, TLR and NOD2 signaling, NLRP3 inflammasome assembly, and regulation of interferon signaling and MHC I processing, alongside leukocyte migration components.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":13},{"id":"GO:0045087","count":13},{"id":"GO:0045345","count":12},{"id":"GO:0034162","count":11},{"id":"GO:0030335","count":11}]},{"hash":"492663675082205767","title":"Antiviral Innate Immunity and Antigen Presentation","description":"The terms cluster around innate immune defense and antiviral signaling (TLR9, NOD2, interferon pathways), plus antigen processing/presentation (MHC I biosynthesis and proteasomal degradation), and immune cell migration, indicating a coordinated antiviral response with antigen presentation readiness.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":9},{"id":"GO:0051607","count":9},{"id":"GO:0045345","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0034162","count":7}]},{"hash":"1762264746460914499","title":"Innate Antiviral Signaling and Inflammasome Activation","description":"The top GO terms cluster around innate immune sensing (TLR9 signaling, NOD2 signaling), defense against virus, and assembly of the NLRP3 inflammasome, with downstream interferon signaling and detection of microbial motifs (e.g., muramyl dipeptide). The inclusion of positive regulation of cell migration and lamellipodium organization aligns with immune cell recruitment during innate responses. Altogether, these terms point to a cohesive innate immune signaling/inflammasome module rather than a different specialized process.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0034162","count":4},{"id":"GO:0030335","count":4},{"id":"GO:1902745","count":4}]},{"hash":"691322613370724805","title":"Cilium and flagellum motility and assembly","description":"The cluster is driven by GO terms tied to cilium/axoneme structure and movement (axoneme assembly, flagellated sperm motility, cilium movement, microtubule severing, and tubulin post-translational modifications like polyglycylation and polyglutamylation), with a couple of outliers (ubiquitin-dependent proteolysis and RNA polymerase II promoter clearance). ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0007288","count":1},{"id":"GO:0003351","count":1},{"id":"GO:1905419","count":1},{"id":"GO:0018094","count":1}]},{"hash":"1370446016467235893","title":"TLR-NF-\u03baB innate immune signaling","description":"GO terms cluster around TLR signaling, NF-\u03baB activation, cytokine production (TNF, IL-18), LPS response, and MHC class I biosynthesis, plus regulation of IL-1. Together these indicate innate immune activation and antigen presentation, justifying a label of an innate immune signaling module.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":9},{"id":"GO:0002830","count":9},{"id":"GO:0045345","count":9},{"id":"GO:0032741","count":9},{"id":"GO:0002756","count":9}]},{"hash":"1030779205478162750","title":"Neuronal Differentiation and Vesicle Trafficking","description":"This cluster\u2019s top terms center on neuronal signaling and development (neurotrophin TRK signaling, regulation of synaptic depression, tau-related processes) combined with intracellular transport and trafficking (ER-to-Golgi transport, exit from ER, endosome transport). Although individual terms are diverse and not strongly enriched, the recurring theme appears to link neural differentiation/signaling with secretory/vesicle trafficking pathways, suggesting a coherent functional group at the intersection of neural development and protein trafficking.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014902","count":1},{"id":"GO:0032460","count":1},{"id":"GO:1900452","count":1},{"id":"GO:1902997","count":1},{"id":"GO:0048227","count":1}]},{"hash":"657432423461806219","title":"Unknown","description":"The top terms span trafficking (receptor recycling, endosome size) and various nuclear/regulatory processes (chromatin regulation, transcription, DNA repair, ncRNA-mediated heterochromatin), plus signaling (Rho) and a neuronal/synaptic term. The mix shows no single cohesive function or module tying all proteins together, and there are no interactions (Edges 0), so a confident, representative label cannot be inferred.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001881","count":3},{"id":"GO:0051036","count":3},{"id":"GO:0035249","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0034968","count":2}]},{"hash":"295327973818392331","title":"NOD2/TLR9 sensing and inflammasome activation","description":"The GO terms center on innate immune sensing via NOD2 (muramyl dipeptide detection) and TLR9 signaling, leading to NLRP3 inflammasome complex assembly. They also reflect regulation of inflammatory signaling (negative regulation of NF-kappaB and IL-6 production) and promotion of type II interferon signaling and cell migration, indicating a coordinated innate immune response that integrates pathogen detection with inflammasome-driven cytokine maturation and feedback control.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0032715","count":5},{"id":"GO:0034162","count":4},{"id":"GO:0030335","count":4},{"id":"GO:1902745","count":4}]},{"hash":"1673724691553466647","title":"Vesicle trafficking and cell morphogenesis","description":"The top GO terms cluster around vesicular transport and membrane remodeling (endosome to lysosome, endosome to Golgi, Cvt pathway targeting to vacuole) and processes underlying cell shape changes (cleavage furrow formation, cell morphogenesis). There are also related membrane-related activities (regulation of ectodomain proteolysis, phosphatidic acid biosynthesis) and broader developmental processes (bone development, brood size), all pointing to a theme of vesicle trafficking coupled with morphological development. Confidence: Medium.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0036089","count":1},{"id":"GO:0051044","count":1},{"id":"GO:0031139","count":1},{"id":"GO:0034498","count":1}]},{"hash":"1642907555205487654","title":"Vesicle trafficking and exocytosis regulation","description":"The cluster's GO terms cluster around regulated transport and exocytosis, including ER-to-Golgi and Golgi vesicle trafficking (COPI-coated vesicles), endosome-to-plasma membrane transport, and calcium-dependent exocytosis. Small GTPase signaling supports these processes, while acrosome assembly and epithelial polarity reflect specialized secretory and polarized trafficking. Together, these point to a cohesive theme of vesicle trafficking and exocytosis control.","confidence":"High","size":17,"edges":72,"triangles":148,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":3},{"id":"GO:1905751","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0007624","count":2}]},{"hash":"2061244043551489488","title":"Autophagy core and protein modifications","description":"This cluster is dominated by autophagy-related GO terms (macroautophagy, Cvt pathway, piecemeal microautophagy of the nucleus) and post-translational modification processes (sumoylation, neddylation, C-terminal lipidation), suggesting a cohesive theme around autophagy regulation and protein processing. Other terms (amygdala development, tRNA modification, cyclic threonylcarbamoyladenosine biosynthesis) appear secondary but do not override the central autophagy/PTM motif.","confidence":"High","size":17,"edges":22,"triangles":6,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0016236","count":2},{"id":"GO:0018192","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0006501","count":2},{"id":"GO:0051726","count":2}]},{"hash":"178984223213158955","title":"Lung branching morphogenesis and ECM remodeling","description":"This cluster is enriched for GO terms centered on branching morphogenesis in the lung (epithelial tube branching in lung morphogenesis, dichotomous subdivision of terminal units in lung branching) and extracellular matrix remodeling (basement membrane disassembly, collagen catabolic process). Additional terms point to broader developmental regulation (neural precursor proliferation, cellular response to thyroid hormone) and ECM-related bone development processes (bone resorption, intramembranous ossification), suggesting a cohesive theme of developmental morphogenesis coordinated with matrix remodeling across tissues, with a focus on lung branching. ","confidence":"Medium","size":17,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":4},{"id":"GO:0034769","count":4},{"id":"GO:0010813","count":4},{"id":"GO:0097067","count":4},{"id":"GO:0060448","count":4}]},{"hash":"1206759150398150743","title":"mRNA decay and P-body regulation","description":"This cluster centers on nuclear mRNA deadenylation-dependent decay, decapping, poly(A) tail shortening, P-body assembly, and miRNA-mediated post-transcriptional silencing, pointing to a module of post-transcriptional regulation and RNA turnover.","confidence":"High","size":17,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0033962","count":1},{"id":"GO:0035195","count":1},{"id":"GO:0090503","count":1}]},{"hash":"679786967516870355","title":"Unknown","description":"The top GO terms are highly diverse, including short-term memory, digestion, protein autoprocessing, nuclear membrane organization, defense responses, protein homooligomerization, and even plant- and behavior-related terms. There is no coherent biological theme tying all proteins together, making it inappropriate to assign a single, representative function label. Therefore, the cluster is best described as Unknown.","confidence":"","size":17,"edges":121,"triangles":493,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0007614","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0071763","count":1},{"id":"GO:0002357","count":1}]},{"hash":"1906369977432806642","title":"Membrane trafficking and cell morphogenesis","description":"The enriched terms center on membrane trafficking and morphogenetic processes (endosome-Golgi transport, Cvt/vacuolar targeting, cleavage furrow formation, and prospore membrane formation) and membrane lipid biosynthesis, suggesting a cluster of proteins involved in membrane remodeling and cell shape changes. Some non-membrane terms appear, but the dominant theme is vesicle trafficking and morphogenesis.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036089","count":1},{"id":"GO:0051044","count":1},{"id":"GO:0031139","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0032258","count":1}]},{"hash":"228490730390297839","title":"Protein Regulation and Degradation","description":"The top GO terms point to control of protein turnover and signaling (SCF-dependent ubiquitin-proteasome degradation, dephosphorylation, and cellular response to TGF-beta), plus regulation of nuclear export. While some biosynthetic/catabolic terms are present, the recurrent theme centers on how proteins are processed and their activity coordinated in signaling pathways.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0046295","count":1}]},{"hash":"1356446312331088661","title":"Embryonic organ development","description":"The GO terms cluster around development of multiple organs and tissues (genitalia, placenta, kidney, liver, neural tube, skin) and include a developmental signaling pathway (JAK-STAT), suggesting a shared role in embryonic organogenesis 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:0031659","count":1},{"id":"GO:0048806","count":1},{"id":"GO:0060674","count":1},{"id":"GO:0007259","count":1},{"id":"GO:0001822","count":1}]},{"hash":"482819212941626838","title":"Mitotic Regulation and Ubiquitination","description":"This cluster's strongest signals are cell division and mitotic cell cycle, along with protein K11-linked ubiquitination and protein heterooligomerization, suggesting a theme of mitotic control and ubiquitin-dependent assembly of protein complexes. Some peripheral terms (innate immunity, retinal development, plant hormone signaling, redox homeostasis) may reflect multifunctional proteins or broad cellular maintenance roles rather than a single pathway. Overall, the dominant theme points to mitotic regulation tied to ubiquitination.","confidence":"Medium","size":17,"edges":25,"triangles":0,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":10},{"id":"GO:0051291","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0045087","count":6},{"id":"GO:0009938","count":5}]},{"hash":"1810902397743812035","title":"Apoptosis and innate immune signaling","description":"This cluster centers on stress-response signaling: intrinsic apoptotic pathways in response to DNA damage (p53-mediated), TNF-mediated signaling, and cellular responses to lipopolysaccharide, along with oxidative stress management. While a few plant-specific terms appear, the dominant pattern is apoptosis and inflammatory/innate immune signaling, suggesting proteins that mediate stress-induced cell fate decisions and immune responses across species.","confidence":"Medium","size":17,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001302","count":2},{"id":"GO:0042771","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0034051","count":2},{"id":"GO:0042347","count":2}]},{"hash":"154506746580259404","title":"Potassium transport and membrane excitability","description":"This cluster is dominated by GO terms for potassium ion transport and membrane potential regulation, including transmembrane transport, intracellular potassium homeostasis, membrane stabilization, and cardiac action potential repolarization. These together point to proteins that control cellular excitability via potassium flux and membrane potential, with a secondary nod to a mechanosensory term likely representing peripheral or multifunctional roles.","confidence":"High","size":17,"edges":130,"triangles":597,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050976","count":14},{"id":"GO:0071805","count":14},{"id":"GO:0030007","count":14},{"id":"GO:0098914","count":14},{"id":"GO:0030322","count":14}]},{"hash":"73735886191090732","title":"Membrane transporters for ions and small molecules","description":"This cluster is characterized by GO terms tied to transmembrane transport across a range of substrates, including sodium-dependent organic cation transport, sodium ion transport, arabinose and nitrite transport, vitamin transport, dehydroascorbic acid transport, and related transport processes, plus a vesicular neurotransmitter loading term. The dominant pattern is diverse transporter activity across membranes, suggesting a cohesive theme of membrane transport proteins. A single outlier term on replicative senescence is unlikely to redefine the cluster\u2019s function.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070715","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0035725","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0015707","count":1}]},{"hash":"6441557889911084","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2014857025282019595","title":"Potassium transport and membrane potential regulation","description":"The top GO terms cluster around maintaining and changing membrane potential and regulating potassium ions, including resting potential regulation, membrane stabilization, repolarization/depolarization in cardiac cells, and potassium ion transport/homeostasis. A secondary signal pathway (glutamate GPCR signaling) and occasional hypoxia/aerotaxis hints are present but do not define the core theme.","confidence":"High","size":17,"edges":23,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098914","count":2},{"id":"GO:0060075","count":2},{"id":"GO:0030322","count":2},{"id":"GO:0050976","count":2},{"id":"GO:0030007","count":2}]},{"hash":"1932154196098672331","title":"Metal Ion Homeostasis and Transport","description":"The cluster shows enrichment for metal ion-related terms, including cellular response to manganese ion, intracellular zinc ion homeostasis, and cadmium ion transmembrane transport, suggesting a core theme around metal ion handling. Yet several unrelated terms (testosterone response, heart contraction regulation, nerve formation) imply broader or multifunctional annotations, so the theme is present but not exclusive. ","confidence":"Medium","size":17,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":2},{"id":"GO:0070574","count":1},{"id":"GO:0033574","count":1},{"id":"GO:1903249","count":1},{"id":"GO:0098736","count":1}]},{"hash":"895780871480385472","title":"ER Protein Folding and Redox Stress Response","description":"Most terms point to ER-based protein quality control (folding, ER stress response, repair) and redox regulation (deglutathionylation, oxidative stress detoxification). This suggests a cluster centered on ER protein folding and redox stress management; a couple of terms (chromatin localization, viral process) may reflect broader regulatory roles but do not define the core theme.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0030091","count":1},{"id":"GO:0080058","count":1},{"id":"GO:0034599","count":1}]},{"hash":"2091249835163284687","title":"Regulation of Gene Expression under Nutrient Stress","description":"The cluster includes terms centered on transcription and translation control (DNA-templated transcription; formation of translation preinitiation complex; translation reinitiation), signaling modulation (positive/negative regulation of kinase activity; SREBP signaling), and stress responses (invasive growth in response to glucose limitation; nucleotide-excision repair). These together suggest coordinated regulation of gene expression and signaling in response to nutrient limitation and cellular stress.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001403","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0002188","count":3}]},{"hash":"464707090062324465","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolism, SCF-dependent ubiquitination, K48-linked ubiquitination, autoubiquitination, and proteasome- and ERAD-related degradation, indicating a cohesive function in ubiquitin-proteasome\u2013driven proteolysis; a couple of older or incidental terms appear, but the central theme remains proteolysis via ubiquitination.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":7},{"id":"GO:0042787","count":6},{"id":"GO:1900095","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0046621","count":5}]},{"hash":"1837250019473055924","title":"Glycogen, lipid, and steroid biosynthesis","description":"The dominant GO terms point to biosynthesis of glycogen, fatty acids/fatty-acyl-CoA, and steroids, with related energy/metabolism processes. Tissue development terms like liver and cardiac differentiation hint at expression context rather than a dedicated signaling role, but overall the cluster centers on metabolic biosynthesis pathways. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0051793","count":1},{"id":"GO:0006694","count":1},{"id":"GO:0046949","count":1}]},{"hash":"6181935130490536","title":"Membrane protein maturation and signaling","description":"Top GO terms cluster around membrane-associated processes: GPI anchor biosynthesis, glycosylation/mannosylation, ER quality control (ERAD), and regulation of small GTPase and Ras signaling, along with a note of sodium transport. This combination implies a group of proteins involved in preparing membrane proteins for function and modulating signaling pathways, rather than a single cohesive function. Some terms appear noisy or unrelated, so the connection is moderate rather than strong.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0097502","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0051447","count":1}]},{"hash":"1314148627091068033","title":"NOD2/TLR/NLRP3 Innate Immune Signaling","description":"Several top GO terms center on recognition-and-signal pathways in innate immunity: NOD2 signaling (muramyl dipeptide sensing), TLR9 signaling, and NLRP3 inflammasome assembly. Additional terms point to enhanced dendritic cell antigen processing/presentation and type II interferon signaling, as well as positive regulation of immune cell migration, which fits migratory dendritic cell activation during an innate immune response.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0070431","count":5},{"id":"GO:0032088","count":5},{"id":"GO:0034162","count":4},{"id":"GO:0030335","count":4},{"id":"GO:1902745","count":4}]},{"hash":"2233545869517747776","title":"TLR9/NLRP3 Innate Immune Activation and Antigen Presentation","description":"This cluster shows strong enrichment for TLR9 signaling, NLRP3 inflammasome assembly, interferon signaling, and dendritic cell antigen processing/presentation, including MHC class I biosynthesis and muramyl dipeptide detection. Together these terms depict a coordinated innate immune sensing program that drives inflammation, cell recruitment, and bridging to adaptive immunity via antigen presentation.  ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":9},{"id":"GO:0030335","count":9},{"id":"GO:1902745","count":9},{"id":"GO:0070431","count":9},{"id":"GO:0002830","count":9}]},{"hash":"1947666076484884333","title":"Hormone signaling and development","description":"The top GO terms point to hormonal regulation and developmental processes, notably steroid hormone receptor complex assembly, male sex differentiation, and prostate gland development, suggesting a shared theme around hormonal signaling influencing development. Other terms like cellular response to type I interferon and response to morphine imply additional signaling or immune-related roles, and general processes such as mitotic transitions and protein modification are broadly regulatory. Overall, the strongest common thread appears to be hormone signaling tied to development, with some broader signaling context; thus a broad Hormone signaling and development label is appropriate given the mix. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071357","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0046661","count":6},{"id":"GO:0030850","count":6},{"id":"GO:0043278","count":6}]},{"hash":"1040169205796231909","title":"Mitochondrial Metabolic Transport and Membrane Potential","description":"The top GO terms center on transport of metabolites and cofactors across the mitochondrial membrane (e.g., alpha-ketoglutarate, thiamine pyrophosphate, coenzyme A) and the malate-aspartate shuttle, along with regulation of mitochondrial membrane potential and apoptotic mitochondrial changes. This points to a cohesive theme of mitochondrial metabolite transport and energy metabolism, with linked regulatory and stress-related functions.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":16},{"id":"GO:0051881","count":16},{"id":"GO:0015742","count":16},{"id":"GO:0030974","count":16},{"id":"GO:0035349","count":16}]},{"hash":"651616165351960269","title":"Golgi vesicle trafficking and localization","description":"Top GO terms cluster around Golgi apparatus functions and vesicular transport, including Golgi localization, Golgi-to-ER retrograde transport, Golgi-to-vacuole transport, and endocytosis, plus Golgi inheritance. A few unrelated terms (pigmentation, cerebellar Purkinje maturation, virus response) are present but do not define the main theme. Thus the cluster can be best described as proteins involved in Golgi trafficking and localization.","confidence":"Medium","size":17,"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:0048313","count":1},{"id":"GO:0043473","count":1},{"id":"GO:0021691","count":1}]},{"hash":"368122345133549752","title":"TLR/NOD2\u2013NLRP3 Innate Immune Activation","description":"The terms cluster around innate immune sensing and inflammatory signaling: TLR9 and NOD2 pathways, NLRP3 inflammasome assembly, IL-6 production, dendritic cell antigen processing/presentation, and detection of muramyl dipeptide, all pointing to coordinated innate immune activation and inflammation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":17},{"id":"GO:0032755","count":17},{"id":"GO:0030335","count":17},{"id":"GO:1902745","count":17},{"id":"GO:0070431","count":17}]},{"hash":"1813708794525142663","title":"Innate TLR-NF-kB Immune Signaling","description":"These GO terms cluster around innate immune signaling via TLRs and NF-kB, including MyD88-independent TLR signaling, LPS response, cytokine production (TNF, IL-18), and MHC I biosynthesis, pointing to a cohesive TLR/NF-kB\u2013driven immune response cluster.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":16},{"id":"GO:0002830","count":16},{"id":"GO:0045345","count":16},{"id":"GO:0032741","count":16},{"id":"GO:0002756","count":16}]},{"hash":"1198897274428710012","title":"Innate antiviral immune signaling and inflammasome assembly","description":"This cluster groups proteins involved in innate immunity, antiviral defense, TLR9 and NOD2 signaling, interferon pathways, and NLRP3 inflammasome assembly. The recurring GO terms point to coordinated innate immune activation and inflammasome-related responses, with ubiquitin-proteasome\u2013mediated regulation supporting signaling. Overall, the terms cohere around antiviral innate immune signaling and inflammasome formation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":11},{"id":"GO:0051607","count":11},{"id":"GO:0031146","count":10},{"id":"GO:0034162","count":9},{"id":"GO:0030335","count":9}]},{"hash":"1347624944606444618","title":"TLR-mediated inflammatory and antiviral response","description":"The cluster is dominated by GO terms related to Toll-like receptor signaling (TLR4, TLR9, MyD88-independent pathways), LPS signaling, and upregulation of interferon-beta and inflammatory defenses against viruses, indicating a cohesive innate immune signaling theme. Some terms about protein localization and chromatin exist but do not outweigh the antiviral/inflammatory signaling pattern.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0032741","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0002756","count":2},{"id":"GO:0031663","count":2}]},{"hash":"2223262291979749557","title":"Mitotic spindle and cytokinesis regulation","description":"The top GO terms center on mitosis (mitotic cell cycle, mitotic spindle assembly, cleavage furrow formation) and Rho-mediated control of actin dynamics, pointing to coordinated roles in spindle function and cytokinesis, with a few outliers likely reflecting broader developmental signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007375","count":1},{"id":"GO:0036089","count":1}]},{"hash":"1389539974803898780","title":"Telomere and Chromatin Regulation","description":"These proteins show GO terms focused on chromatin remodeling and telomere biology\u2014chromatin remodeling (GO:0043044), subtelomeric heterochromatin formation (GO:0035390), and positive regulation of shelterin complex assembly (GO:1904792)\u2014suggesting a theme of chromatin organization at telomeres. Some terms (like SA node action potential and certain hormone responses) may be annotations from broader datasets and appear as noise, but the core signal points to telomere-associated chromatin maintenance.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0035390","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0072362","count":2}]},{"hash":"1241877455714466575","title":"DNA replication and cell cycle regulation","description":"The top GO terms point to control of DNA replication initiation and progression through meiosis and mitosis (e.g., positive regulation of DNA replication initiation, premeiotic replication, meiosis I, mitotic cohesion), suggesting a core theme of genome duplication and chromosomal maintenance. A few terms relate to lipid metabolism or other pathways, likely representing annotation breadth or multifunctional proteins, but the central cluster appears to center on cell-cycle regulation and DNA replication. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903468","count":1},{"id":"GO:0001100","count":1},{"id":"GO:0060903","count":1},{"id":"GO:0007307","count":1},{"id":"GO:0071960","count":1}]},{"hash":"174111972588476324","title":"Muscle signaling and sarcomere organization","description":"This cluster centers on signaling pathways (positive regulation of adenylate cyclase activity; small GTPase-mediated signaling; Ras pathway regulation) and muscle-related processes (sarcomere organization; cardiac muscle cell proliferation), suggesting a group of proteins coordinating signaling with muscle structure and growth. Some terms like aerotaxis or drug response are peripheral, but the core theme is signaling linked to muscle function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045762","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0098719","count":2}]},{"hash":"1152532755718621331","title":"Tyrosine Phosphatase\u2013Mediated Signaling Inhibition","description":"Top GO terms center on peptidyl-tyrosine dephosphorylation and broad negative regulation of signaling pathways, including MAPK/ERK and PI3K-AKT, across immune and neuronal contexts. This suggests a core function in dephosphorylation-driven downregulation of signaling, likely involving protein tyrosine phosphatases or their regulators, with additional links to focal adhesion and synaptic signaling. Therefore, the label captures the unifying theme of phosphatase-mediated attenuation of signaling across diverse cellular processes.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000200","count":14},{"id":"GO:0070373","count":14},{"id":"GO:0050860","count":14},{"id":"GO:0051898","count":13},{"id":"GO:0035335","count":13}]},{"hash":"1270787993340338799","title":"Neuronal development and synaptic signaling","description":"The top GO terms converge on neuronal growth and function: dendrite morphogenesis, hippocampus development, axon extension, excitatory postsynaptic potential, calcium-dependent exocytosis, and dopamine response, all signaling processes underlying synaptic formation and plasticity. While a single term refers to T cell receptor signaling, the strongest signal is clearly neuronal, supporting a label focused on neuronal development and synaptic communication.","confidence":"High","size":16,"edges":10,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0045956","count":3},{"id":"GO:0046330","count":3},{"id":"GO:0048813","count":3}]},{"hash":"1198277949716435294","title":"Mitochondrial Fe-S cluster assembly and respiration","description":"This cluster's GO terms cluster around iron handling and Fe-S cluster biosynthesis (response to iron(II) ion; iron incorporation into metallo-sulfur clusters; regulation of Fe-S cluster assembly) and mitochondrial respiration (mitochondrial electron transport from succinate to ubiquinone; succinate dehydrogenase activity; regulation of cytochrome c release), indicating a coherent role in mitochondrial Fe-S biogenesis and respiratory chain function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010040","count":1},{"id":"GO:0046621","count":1},{"id":"GO:0040015","count":1},{"id":"GO:1904234","count":1},{"id":"GO:0006121","count":1}]},{"hash":"1397703635219441155","title":"Neural membrane trafficking and myelination regulation","description":"This cluster centers on neural membrane dynamics: endocytic and receptor recycling, phosphatidylinositol dephosphorylation, and vacuole organization, alongside myelin assembly/regulation. These GO terms together suggest a module where membrane trafficking and signaling influence neural myelination and related neuronal remodeling. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901300","count":2},{"id":"GO:0031642","count":1},{"id":"GO:0032288","count":1},{"id":"GO:0001921","count":1},{"id":"GO:2001135","count":1}]},{"hash":"9661487258442988","title":"RNA processing and transcription regulation","description":"Dominant GO terms center on DNA-templated transcription, mRNA processing and various steps of RNA splicing, including regulation of alternative splicing via the spliceosome and related transcriptional control. A few outliers (heart morphogenesis, hormone response, ceramide transport) appear incidental; overall the cluster reflects nuclear RNA metabolism and transcription regulation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0008380","count":1},{"id":"GO:1903507","count":1},{"id":"GO:0048025","count":1}]},{"hash":"1429251587455774592","title":"Neuronal ubiquitination and vesicle trafficking","description":"The cluster centers on protein ubiquitination and vesicle/secretory trafficking (ER-to-Golgi transport, Golgi organization, exosomal secretion) with several neural-context terms (excitatory postsynaptic potential, hippocampus development), suggesting a cohesive role in neuronal protein processing and synaptic transport. Additional terms like mitochondrial fission and autophagy-related targeting support a broader cellular trafficking theme that is particularly relevant in neurons.","confidence":"High","size":16,"edges":6,"triangles":0,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0006888","count":5},{"id":"GO:0043124","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0021766","count":4}]},{"hash":"1364174853105975875","title":"Endocytosis and EGFR signaling","description":"This cluster is dominated by endocytosis and membrane trafficking terms (endocytosis; plasma membrane to endosome transport; extracellular transport) and includes an EGFR signaling pathway term, suggesting a theme of receptor internalization coupled to signaling. The liver and kidney development annotations may reflect broader developmental roles of signaling pathways or annotation noise, but the core pattern points to endocytic trafficking and RTK signaling.","confidence":"Medium","size":16,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0010738","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0001822","count":2}]},{"hash":"1652158882839323303","title":"Lipid biosynthesis and adipogenesis","description":"This cluster is dominated by GO terms related to lipid production and fatty acid metabolism (sphingosine/sphinganine biosynthesis, monounsaturated fatty acid biosynthesis, response to fatty acid) and adipocyte development (white fat cell differentiation), suggesting a cohesive theme of lipid metabolism and adipogenesis. A few outlier terms (photoinhibition, tarsal gland development) may be less informative for this cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046512","count":5},{"id":"GO:0010205","count":5},{"id":"GO:1903966","count":5},{"id":"GO:0050872","count":5},{"id":"GO:0070542","count":5}]},{"hash":"470306506877588387","title":"Chromatin Regulation and Proteostasis","description":"The terms cluster around chromatin dynamics and transcription regulation (DNA-templated transcription, rDNA heterochromatin formation, histone deacetylation) together with protein quality control processes (aggresome assembly, polyubiquitinated misfolded protein transport, regulation of protein stability) and stress-related responses (abscisic acid response, hydrogen peroxide\u2013driven programmed cell death). This suggests a cohesive module where chromatin remodeling and transcription are linked to proteostasis under cellular stress.","confidence":"High","size":16,"edges":25,"triangles":10,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0070933","count":4},{"id":"GO:0000183","count":4},{"id":"GO:0070842","count":3},{"id":"GO:0009737","count":3}]},{"hash":"802970904837844270","title":"Mitochondrial matrix protein import","description":"This cluster is defined by the GO term protein import into mitochondrial matrix (GO:0030150), suggesting a shared role in targeting and importing proteins into the mitochondrial matrix. Despite no reported edges or interactions, the single strong functional annotation points to a cohesive theme around matrix import.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":1}]},{"hash":"639190545688602110","title":"Actin dynamics and endocytic signaling","description":"Based on the GO terms, the cluster is centered on actin cytoskeleton remodeling (actin filament branching, regulation of focal adhesion assembly) and Cdc42 signaling, together with endocytic trafficking and receptor-mediated signaling (plasma membrane to endosome transport, EGFR pathway). These themes point to a module coordinating cytoskeletal changes with endocytosis and surface receptor signaling, with a few outlier terms (viral replication, Pol I transcription) that are less connected to the core function. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039694","count":1},{"id":"GO:0010628","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0007173","count":1},{"id":"GO:0051893","count":1}]},{"hash":"1932507047765856720","title":"Plant TOR-Mediated Growth and Meristem Development","description":"These proteins seem tied to plant growth signaling and development. The GO terms point to TOR signaling regulated by amino acid status, along with positive regulation of GTPase activity and a plant-specific meristem transition, suggesting roles in coordinating growth with developmental timing. While the terms are not perfectly cohesive, TOR-related growth control in plants provides the most coherent unifying theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010228","count":1},{"id":"GO:0071230","count":1},{"id":"GO:0032008","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0000186","count":1}]},{"hash":"1483865298578041536","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":66,"triangles":117,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":7},{"id":"GO:1901621","count":5},{"id":"GO:1900035","count":5},{"id":"GO:0036494","count":5},{"id":"GO:0070389","count":5}]},{"hash":"1302251173026148080","title":"Axon guidance and synapse development","description":"This cluster is dominated by neural development terms: axon fasciculation, CNS projection neuron axonogenesis, dendritic spine development, and ephrin receptor signaling, all pointing to axon pathfinding and synaptic maturation. A few immune-related terms appear, but they are sparse relative to the neuronal terms, so the primary theme is neural development and synaptic connectivity.","confidence":"Medium","size":16,"edges":82,"triangles":215,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0060996","count":3},{"id":"GO:0072178","count":3},{"id":"GO:0097155","count":3},{"id":"GO:2000525","count":3},{"id":"GO:0048013","count":3}]},{"hash":"1424214670718130639","title":"Histone deubiquitination and neural development","description":"This cluster shows strong signals for deubiquitination activities (various lysine linkages and histone modifications) linked to regulation of DNA-templated transcription, plus neural development and behavior terms (CNS morphogenesis, adult feeding behavior, righting reflex). Together these suggest a chromatin-regulation axis via histone deubiquitination that influences neural development and related behaviors.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0035616","count":3},{"id":"GO:0060013","count":3},{"id":"GO:0035523","count":3},{"id":"GO:0044313","count":3}]},{"hash":"56011542798180575","title":"Xenobiotic and vitamin D metabolism","description":"The top GO terms revolve around processing and modifying small molecules and signaling lipids: xenobiotic and insecticide metabolism, xenobiotic catabolic, vancomycin biosynthesis, prostaglandin biosynthesis, and vitamin D\u2013related responses and catabolism. A methylation term hints at regulatory or epigenetic modulation that often accompanies metabolic pathways. While a couple terms (sex differentiation, potassium ion response) are less central, the dominant theme is metabolism and detoxification of xenobiotics and vitamin D\u2013related signaling molecules.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035865","count":14},{"id":"GO:0032259","count":14},{"id":"GO:0001516","count":14},{"id":"GO:0042369","count":14},{"id":"GO:0033280","count":14}]},{"hash":"899592356667863923","title":"Innate Immune Sensing and Antigen Presentation","description":"The cluster is enriched for GO terms centered on innate immune sensing (TLR9 and NOD2 pathways), inflammasome assembly (NLRP3), interferon signaling, and dendritic cell antigen processing and presentation, including MHC class I biosynthesis. There is also support for associated processes like positive regulation of cell migration and lamellipodium organization, which fits dendritic cell movement during antigen presentation. Overall, these terms point to a cohesive role in bacterial component detection and subsequent adaptive immune readiness.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":13},{"id":"GO:0030335","count":13},{"id":"GO:1902745","count":13},{"id":"GO:0070431","count":13},{"id":"GO:0002830","count":13}]},{"hash":"1878523735312370199","title":"Innate Immune Sensing and DC Antigen Presentation","description":"The cluster is dominated by terms for innate immune sensing (TLR9, NOD2, NLRP3 inflammasome) and downstream activation of dendritic cell antigen processing and MHC class I presentation, plus interferon signaling, suggesting coordinated innate recognition and DC-driven antigen presentation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":9},{"id":"GO:0030335","count":9},{"id":"GO:1902745","count":9},{"id":"GO:0070431","count":9},{"id":"GO:0002830","count":9}]},{"hash":"1595600543955775049","title":"Potassium Transport and Membrane Potential Regulation","description":"Top GO terms show a clear emphasis on ion transport and membrane potential dynamics: potassium ion transmembrane transport, intracellular potassium homeostasis, sodium import, and membrane stabilization, together with events tied to membrane repolarization in cardiac muscle cells. Additional signals related to cGMP and cAMP suggest regulatory pathways that tune excitability and signaling thresholds. Although a few terms touch on mechanosensation and aerotaxis, the central shared theme is control of ionic flux and membrane potential in excitable cells, justifying a label centered on ion transport and membrane excitability.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009454","count":12},{"id":"GO:0050976","count":12},{"id":"GO:0071805","count":12},{"id":"GO:0071321","count":12},{"id":"GO:0010754","count":12}]},{"hash":"2202612306641745976","title":"Unknown","description":"The GO terms span development, immune differentiation, sensory perception, signaling, and structural processes (e.g., multicellular development, NK T cell differentiation, Rho signaling, focal adhesion regulation) with no single dominant function. The lack of edges and the presence of diverse, somewhat unrelated terms suggest there isn\u2019t a cohesive biological theme to label, so Unknown is appropriate with no confidence.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0019233","count":4},{"id":"GO:1901214","count":3},{"id":"GO:0060440","count":3},{"id":"GO:0051893","count":3}]},{"hash":"1590062763487216249","title":"Cardiac Muscle Signaling and Sarcomere Regulation","description":"The cluster's terms center on muscle structure and cardiac-associated processes (sarcomere organization; cardiac muscle cell proliferation) and signaling pathways (small GTPase-mediated signaling, Ras regulation, adenylate cyclase activity, receptor guanylyl cyclase signaling). Sodium import across the plasma membrane aligns with ion handling in excitation-contraction coupling. Some outliers (aerotaxis, meiotic cell cycle, drug response) may reflect annotation noise, but the dominant theme points to cardiac muscle signaling and sarcomere dynamics. ","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":7},{"id":"GO:0051447","count":5},{"id":"GO:0046580","count":5},{"id":"GO:0045214","count":5},{"id":"GO:0007264","count":5}]},{"hash":"1337255810261590215","title":"DNA Replication and Transcription Machinery","description":"This cluster is dominated by core growth-related processes: DNA-templated transcription, DNA replication, ribosome biogenesis, and cell division, indicating a module of genes supporting genome duplication and protein synthesis. The additional terms (development and stress/immune responses) may reflect broader roles of some proteins or annotation cross-terms, but the central theme remains fundamental gene expression and cell cycle machinery.","confidence":"High","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0001403","count":3}]},{"hash":"669835187061547643","title":"Unknown","description":"The GO terms span signaling, transcription, nuclear transport, cell cycle, detoxification, metabolism, digestion, and kidney development/hormonal regulation, with no single dominant function linking the proteins. This lack of a cohesive theme makes a precise label unreliable.","confidence":"","size":16,"edges":115,"triangles":492,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1268141515835036712","title":"Stress-Responsive Signaling and Rho Pathways","description":"The cluster's GO terms include cellular response to lipopolysaccharide, responses to osmotic stress and cadmium ion, and Rho protein signal transduction, suggesting a cohesive theme of stress-sensing and signaling that governs cytoskeletal dynamics and growth. While there are some development-related terms (trachea formation, septation initiation signaling), the majority point to signaling networks activated by external stressors. This supports a label focused on stress-responsive signaling with Rho pathway involvement.","confidence":"Medium","size":16,"edges":9,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071222","count":4},{"id":"GO:0060440","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007266","count":3},{"id":"GO:0010614","count":3}]},{"hash":"942656334757628700","title":"Ubiquitin-Dependent Protein Turnover","description":"GO terms point to ubiquitination and proteolysis as the strongest shared theme (ubiquitin-dependent protein catabolic process, protein K33-linked ubiquitination, regulation of ubiquitination). Other terms are diverse (muscle development, renal morphogenesis, immune signaling), but the ubiquitin-related processes are the most coherent across the cluster, supporting this label.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0070294","count":2},{"id":"GO:0031397","count":2}]},{"hash":"538089429017183683","title":"Ubiquitin-Proteostasis and Mitotic Regulation","description":"The cluster\u2019s top terms center on ubiquitin-related processes (ubiquitin-dependent ERAD, K11-linked ubiquitination) and mitosis (mitotic spindle assembly, preblastoderm mitotic cell cycle), suggesting a theme of protein quality control that supports cell division. While a few terms touch synaptic development or intraciliary transport, the strongest signal ties ubiquitin-mediated proteostasis to mitotic regulation.","confidence":"Medium","size":16,"edges":23,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0050773","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0090344","count":2},{"id":"GO:0031915","count":2}]},{"hash":"474452842406277358","title":"Proteostasis and stress response regulators","description":"These proteins collectively touch on stress responses (salt stress, xenobiotic stimulus), proteostasis (chaperone-mediated protein complex assembly, translational attenuation), and growth/metabolic adjustments (regulation of cell cycle, downregulation of cellular respiration). The common thread is maintaining protein homeostasis and modulating translation and metabolism under stress, rather than a single narrowly defined pathway.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":1},{"id":"GO:1901389","count":1},{"id":"GO:1901856","count":1},{"id":"GO:0043524","count":1},{"id":"GO:0009651","count":1}]},{"hash":"2163571741366911569","title":"ER-Golgi and endosomal vesicle trafficking","description":"This cluster is dominated by GO terms related to intracellular transport and vesicle trafficking in the secretory and endocytic pathways (ER-to-Golgi, recycling endosome to Golgi, late endosome to Golgi, COPII cargo loading, and Rab signaling), indicating a cohesive function in vesicle movement and trafficking regulation. Some terms about cilium assembly and virus-host interactions appear but do not outweigh the trafficking signal.","confidence":"High","size":16,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:1902018","count":1},{"id":"GO:0071955","count":1},{"id":"GO:0032483","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0034499","count":1}]},{"hash":"503776901403214602","title":"Unknown","description":"The top GO terms span plant hormone biosynthesis (strigolactone), various secondary metabolite pathways (stilbene, antibiotic biosynthesis, poly-hydroxybutyrate), along with shoot formation and redox/detoxification processes. The collection is too heterogeneous to define a single cohesive function for the cluster, and some terms are obsolete, so a specific, representative label cannot be confidently assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0019433","count":4},{"id":"GO:0010223","count":3}]},{"hash":"685706058030066827","title":"Unknown","description":"There are no GO terms or interactions linking these 16 proteins (Edges: 0, Triangles: 0, Max Degree: 0), so no common function can be inferred. Without a theme, the safest label is Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1387983568370936595","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning glucose response, transcription, nuclear export, development (trachea formation), invasive growth in response to glucose limitation, Rho signaling, stress/osmotic regulation, septation signaling, and regulation of organ functions. There is no clear single biological theme uniting these terms across the proteins, making a specific, representative label inappropriate. Therefore the cluster is best described as Unknown with no confidence. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071333","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0046827","count":4},{"id":"GO:0060440","count":3},{"id":"GO:0001403","count":3}]},{"hash":"1139422696404742931","title":"Lipid metabolism and lipoprotein regulation","description":"The GO terms cluster around lipid biosynthesis and handling, including fatty-acyl-CoA, triglyceride/diacylglycerol and ceramide metabolism, intracellular triglyceride homeostasis, lipoprotein particle clearance and regulation, plus intestinal lipid absorption and fat pad development. This combination points to a theme of lipid synthesis and lipoprotein/adipose regulation, rather than a single signaling or catabolic pathway. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035336","count":1},{"id":"GO:0034383","count":1},{"id":"GO:0050892","count":1},{"id":"GO:0060613","count":1},{"id":"GO:0006651","count":1}]},{"hash":"3356963232513711","title":"Vesicle trafficking and protein localization","description":"The strongest signal among the terms centers on intracellular membrane trafficking: synaptic vesicle endocytosis, endocytic recycling, and regulation of Rab signaling, plus basal protein localization. These sales point to a cohesive theme of vesicle transport and subcellular localization. Other terms (SREBP signaling, cell division, various apoptosis-related terms) are less tightly connected to this core function, likely reflecting broader regulatory roles or incidental annotations. Confidence reflects a moderate, trafficking-focused interpretation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0048488","count":1},{"id":"GO:0035745","count":1}]},{"hash":"243242318548728177","title":"Innate immune sensing and DC antigen presentation","description":"The terms point to pattern-recognition receptor signaling (TLR9, NOD2), inflammasome assembly, and muramyl dipeptide detection, driving type II interferon signaling and dendritic cell antigen processing and MHC class I biosynthesis. This suggests a cohesive module of innate immune sensing that activates dendritic cells to process and present antigens.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":7},{"id":"GO:0030335","count":7},{"id":"GO:1902745","count":7},{"id":"GO:0070431","count":7},{"id":"GO:0002830","count":7}]},{"hash":"860580860727087395","title":"Ubiquitin-Proteasome Regulation and NF-\u03baB Signaling","description":"The top GO terms point to ubiquitin-dependent protein degradation (and autoubiquitination), combined with TNF-mediated signaling and regulation of I-kappaB phosphorylation, all of which are core components of NF-\u03baB signaling and apoptosis regulation. This suggests the cluster centers on ubiquitin-proteasome\u2013mediated control of NF-\u03baB\u2013related pathways, with some chromatin remodeling context via histone turnover. Confidence: High","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:1903762","count":4},{"id":"GO:0090073","count":4},{"id":"GO:2000620","count":4},{"id":"GO:0051865","count":4}]},{"hash":"15381782873677676","title":"Unknown","description":"The top GO terms span immune antigen processing, vesicle transport, amyloid metabolism, digestion, development, hormonal regulation, neural behavior, and even plant-specific metabolism, showing no single cohesive function tying all proteins together.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019886","count":2},{"id":"GO:0006893","count":1},{"id":"GO:0050435","count":1},{"id":"GO:0042985","count":1},{"id":"GO:0007586","count":1}]},{"hash":"1217262871508442168","title":"Unknown","description":"The top GO terms include cholesterol and choline metabolism and neural-related processes (glutamatergic synaptic transmission and learning), but also terms like floral organ morphogenesis and obsolete cocaine metabolism, suggesting a mixed, cross-kingdom set with no single cohesive function. There are no edges or interactions (Edges: 0, Triangles: 0), so a clear, unified biological theme cannot be inferred. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0019695","count":1}]},{"hash":"780079176007028735","title":"TLR-NF-\u03baB driven innate immune signaling","description":"This cluster is dominated by GO terms for innate immune response and regulation of NF-\u03baB signaling, including MyD88-independent TLR pathways, cytokine production (TNF, IL-18, IL-1), and MHC class I biosynthesis, indicating coordinated innate sensing and inflammatory regulation. The mix of positive and negative regulatory terms suggests a balance of activation and restraint in innate immunity.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":13},{"id":"GO:0032088","count":13},{"id":"GO:0030335","count":12},{"id":"GO:0002830","count":12},{"id":"GO:0045345","count":12}]},{"hash":"228082435028872485","title":"Innate Immune Activation and Cytokine Production","description":"This cluster is enriched for GO terms related to innate immunity (innate immune response, defense against virus, muramyl dipeptide detection) and inflammatory signaling (NF-kappaB regulation) as well as cytokine production (IL-1\u03b2, IL-8) and cell migration (lamellipodium organization). The inclusion of Th17 differentiation hints at broader adaptive-immune crosstalk. The proteasomal degradation term suggests regulation of signaling pathways. Overall, the proteins appear to coordinate innate immune activation with inflammatory responses.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":15},{"id":"GO:0045087","count":15},{"id":"GO:0051607","count":15},{"id":"GO:0043124","count":14},{"id":"GO:2000321","count":14}]},{"hash":"1870632901587307526","title":"Actin Cytoskeleton Remodeling and Adhesion Regulation","description":"Top GO terms indicate regulation of actin dynamics (fragmentation, depolymerization), modulation of cell motility and focal adhesion assembly, and inflammatory signaling (IL-6, TNF), suggesting these proteins coordinate cytoskeletal remodeling and adhesion in response to cytokines. This cohesive theme justifies a label focused on actin-based remodeling and adhesion control.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000146","count":1},{"id":"GO:0030043","count":1},{"id":"GO:0051894","count":1},{"id":"GO:1905875","count":1},{"id":"GO:0007162","count":1}]},{"hash":"1994629771867746695","title":"Innate Immune Signaling and Antigen Presentation","description":"These terms point to innate immune sensing and signaling (TLR9, NOD2) with inflammasome engagement (NLRP3) and bacterial component detection (muramyl dipeptide), together with dendritic cell activation and adaptive antigen presentation (MHC I biosynthesis and antigen processing). The inclusion of positive regulation of cell migration and lamellipodium organization suggests DC trafficking to lymph nodes, coordinating innate sensing with antigen presentation to T cells.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":15},{"id":"GO:0030335","count":15},{"id":"GO:1902745","count":15},{"id":"GO:0070431","count":15},{"id":"GO:0002830","count":15}]},{"hash":"890029603886466926","title":"Regulatory Signaling and Development Across Tissues","description":"This cluster centers on regulatory processes across diverse biological contexts: regulation of GTPase activity, ubiquitination, synaptic transmission, cytokine and chemokine activity, and locomotion, plus development terms (retina and prostate gland) and general protein interactions. The GO terms indicate broad, cross-tissue regulatory roles rather than a single, cohesive pathway, suggesting a label that reflects overall regulatory signaling across multiple tissues. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0031397","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0060770","count":2}]},{"hash":"1491565773729347671","title":"Redox Homeostasis and NF-\u03baB Signaling","description":"The top GO terms are dominated by redox-related processes (removal of superoxide radicals, redox homeostasis, peptidyl-cysteine oxidation) and I-kappaB phosphorylation, pointing to redox-regulated signaling and NF-\u03baB pathway involvement. A few terms related to immune cytotoxicity and gonad development appear less central and there are no protein-protein interactions, so the core theme is redox signaling with potential NF-\u03baB link. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019430","count":1},{"id":"GO:0042267","count":1},{"id":"GO:2000255","count":1},{"id":"GO:0008584","count":1},{"id":"GO:0018171","count":1}]},{"hash":"585052612040913909","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0009408","count":1}]},{"hash":"1595697756905897671","title":"TLR-mediated innate immune signaling and xenophagy","description":"Based on the prominence of GO terms for Toll-like receptor signaling (MyD88-dependent and TLR9), dsRNA response, interferon-beta production, LPS signaling, and xenophagy, the proteins appear to function together in innate immune sensing and antiviral/autophagy pathways; a few terms are peripheral but do not change the main theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0043330","count":3},{"id":"GO:0002755","count":3},{"id":"GO:1904417","count":3},{"id":"GO:0045359","count":3}]},{"hash":"1299991583024429939","title":"Mitotic cell cycle and ER-Golgi transport","description":"Most represented GO terms center on mitosis (mitotic spindle assembly, cell division, mitotic cell cycle, cell population proliferation) and vesicle trafficking between the ER and Golgi (COPII budding, ER-to-Golgi and Golgi-to-ER transport). This combination suggests a functional theme where cell division processes are coupled with intracellular transport mechanisms, characteristic of proteins involved in mitosis that rely on vesicular trafficking. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0090114","count":2}]},{"hash":"2174464137865520488","title":"Cholesterol transport and steroid biosynthesis","description":"The top GO terms cluster around cholesterol transport (intracellular cholesterol transport, cholesterol transport involved in cholesterol storage) and lipid-related processes (ER to Golgi ceramide transport, progesterone biosynthetic process, cholesterol esterification), pointing to a lipid metabolism theme with emphasis on cholesterol handling and steroid hormone production. While there are some developmental terms included, the lipid-centered terms are most representative of the cluster's function. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":1},{"id":"GO:0071373","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0006701","count":1},{"id":"GO:0032367","count":1}]},{"hash":"254085588917096623","title":"Cerebellar development and synaptic plasticity","description":"The top GO terms point to cerebellar cortex formation and Bergmann glial differentiation, plus markers of synaptic activity and plasticity (excitatory postsynaptic potential, long-term potentiation). While insulin signaling and angiogenesis appear, the core signal centers on cerebellar development, glial support, and neuronal synaptic maturation. Confidence: High","confidence":"","size":15,"edges":93,"triangles":324,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008286","count":14},{"id":"GO:0021697","count":14},{"id":"GO:2001275","count":14},{"id":"GO:0014850","count":14},{"id":"GO:0050852","count":14}]},{"hash":"1899601958741447596","title":"Developmental morphogenesis and ECM remodeling","description":"The top GO terms point clearly to tissue development and morphogenesis, with multiple entries on organogenesis and morphogenetic processes (lung branching, ossification, neural precursor proliferation) alongside extracellular matrix remodeling (basement membrane disassembly, collagen catabolic process) and developmental signaling (Wnt, thyroid hormone response). While there is a lone immune term, the dominant signal is developmental remodeling of tissues and ECM, justifying this label.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":15},{"id":"GO:0034769","count":15},{"id":"GO:0010813","count":15},{"id":"GO:0097067","count":15},{"id":"GO:0001913","count":15}]},{"hash":"266237763849407546","title":"Nematode Development and Endocytosis Regulation","description":"This cluster co-occurs with GO terms tied to nematode development (dauer larval development, pharyngeal pumping) and multiple entries on endocytosis and its negative regulation (clathrin- and caveolin-mediated), suggesting a theme where nematode developmental processes are linked to regulation of endocytic pathways and related signaling. While a few terms reference other organisms or broader signaling (protein tyrosine kinase activity, response to stimulus), the dominant signal is development in nematodes coupled with endocytosis regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040024","count":1},{"id":"GO:1900186","count":1},{"id":"GO:0016319","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0034260","count":1}]},{"hash":"1321821254421487280","title":"Unknown","description":"TheTopTerms are highly diverse, spanning signaling (Ras, GTPase, adenylate/guanylyl cyclase), muscle structure and growth (sarcomere organization, cardiac muscle proliferation), ion transport, and even meiosis and drug response, with no clear, singular function tying all proteins together. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051447","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0045214","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0007264","count":1}]},{"hash":"2128520703341807461","title":"Sterol and Lipid Metabolism & Transport","description":"Based on the GO terms, the cluster is dominated by lipid-related processes such as lipid storage, unsaturated fatty acid biosynthesis, intracellular cholesterol transport, and ergosterol/sphingolipid metabolism, suggesting a shared role in lipid/sterol biosynthesis and transport. Some terms (nitrate assimilation, nitric oxide synthesis, sebaceous gland differentiation) are less directly tied, possibly reflecting broader metabolic or organism-specific connections, but the overall pattern points to lipid/sterol metabolism as the core theme.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0019915","count":2},{"id":"GO:0032286","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0032443","count":1}]},{"hash":"531668958530841901","title":"Developmental transcription and stress response","description":"This cluster centers on development-related GO terms (multicellular organism development, forebrain development, neural tube closure) along with DNA-templated transcription and nuclear export regulation, suggesting transcriptional programs driving development. The presence of stress-related terms (intrinsic apoptotic signaling in ER stress, cellular response to cadmium) and defense responses hints that these developmental regulators also integrate cellular stress and defense signals, forming a cohesive module linking development with stress responses.","confidence":"Medium","size":15,"edges":72,"triangles":171,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0001403","count":5},{"id":"GO:0070059","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0007275","count":5}]},{"hash":"2178286251905792237","title":"Innate Immune Sensing and Antigen Presentation","description":"The cluster is dominated by innate immune signaling terms (TLR9 and NOD2 pathways, NLRP3 inflammasome) and dendritic cell\u2013driven antigen processing/presentation (MHC I biosynthesis), plus interferon signaling, pointing to a cohesive module of pathogen recognition leading to adaptive immune activation.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":14},{"id":"GO:0030335","count":14},{"id":"GO:1902745","count":14},{"id":"GO:0070431","count":14},{"id":"GO:0002830","count":14}]},{"hash":"1628717744900578226","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":16,"triangles":10,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000467","count":3}]},{"hash":"1488572566352529420","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":76,"triangles":219,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006283","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0042769","count":3}]},{"hash":"262418388410676772","title":"Rho signaling and ECM remodeling","description":"The cluster\u2019s top terms center on Rho protein signaling, regulation of focal adhesion assembly, and regulation of extracellular matrix disassembly, all of which tie to cytoskeletal dynamics, cell adhesion, and migration; while some terms touch on development or immune differentiation, the shared theme is adhesion/movement signaling.","confidence":"Medium","size":15,"edges":79,"triangles":198,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":15},{"id":"GO:0060440","count":15},{"id":"GO:0051893","count":15},{"id":"GO:0001403","count":15},{"id":"GO:0007266","count":15}]},{"hash":"740245536698431428","title":"Rho-driven adhesion and ECM remodeling","description":"The top GO terms cluster around cytoskeletal signaling and cell-matrix interactions: Rho protein signal transduction, regulation of focal adhesion assembly, and regulation of extracellular matrix disassembly. This suggests a module focused on adhesion, migration, and ECM remodeling. Some immune-related terms are present, but the dominant theme is cytoskeleton\u2013ECM dynamics.","confidence":"High","size":15,"edges":51,"triangles":51,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":14},{"id":"GO:0060440","count":14},{"id":"GO:0051893","count":14},{"id":"GO:0001403","count":14},{"id":"GO:0007266","count":14}]},{"hash":"2143606366685167048","title":"Innate Immune Signaling and Antiviral Response","description":"The top GO terms cluster around pathogen sensing and antiviral defense, including innate immune response, interferon-beta production, dsRNA response, LPS signaling, and TLR/NOD2 pathways, with xenophagy as a host defense mechanism. This indicates a cohesive theme of innate immune activation and antiviral/autophagic responses, justifying the label.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045359","count":6},{"id":"GO:0045087","count":6},{"id":"GO:0031663","count":6},{"id":"GO:0043330","count":6},{"id":"GO:1904417","count":6}]},{"hash":"2087003996242751656","title":"Ion Transport and Cyclic Nucleotide Signaling","description":"The cluster is dominated by GO terms related to ion movement across membranes (sodium import, potassium homeostasis, potassium transmembrane transport) and responses to cyclic nucleotides (cAMP and cGMP), pointing to a cohesive theme of ion transport coupled to cyclic nucleotide signaling. Some transcription-related terms are present but less central, suggesting ancillary roles or annotations. ","confidence":"Medium","size":15,"edges":27,"triangles":3,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":6},{"id":"GO:0030007","count":5},{"id":"GO:0010754","count":4},{"id":"GO:0009454","count":4},{"id":"GO:0006351","count":4}]},{"hash":"647665898197158087","title":"Plant immune signaling","description":"Several GO terms indicate plant innate immunity, including plant-type hypersensitive response, defense response by callose deposition, and regulation of salicylic acid metabolism, suggesting a plant defense signaling module. Additional terms about GPCR signaling and protein homooligomerization may reflect general signaling or cross-species annotations, but the plant immunity signals dominate. ","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0007216","count":2},{"id":"GO:0002357","count":1},{"id":"GO:2000009","count":1},{"id":"GO:0048105","count":1}]},{"hash":"1682660062757468022","title":"Ras/GTPase Signaling and Transcription in Muscle","description":"This cluster centers on transcriptional regulation (DNA-templated transcription) and multiple small GTPase\u2013driven signaling pathways (Ras signaling, receptor guanylyl cyclase pathways) with muscle-related processes (sarcomere organization, cardiac muscle proliferation). While there are a few peripheral terms, the overarching theme appears to be transcription coupled with Ras/GTPase signaling in a muscular context.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0098719","count":2}]},{"hash":"1780825793080082230","title":"Cyclic Nucleotide Signaling and Membrane Excitability","description":"The dominant GO terms point to cyclic nucleotide signaling (cGMP and cAMP), including cellular responses and regulation of guanylyl cyclase pathways, and a term about membrane depolarization in cardiac muscle, plus sodium ion transport. Together, these suggest a cluster of proteins involved in signaling pathways that modulate membrane potential and ion flux via cyclic nucleotides, with peripheral terms like aerotaxis, transcription, development, and pain being less central. ","confidence":"Medium","size":15,"edges":12,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009454","count":5},{"id":"GO:0071321","count":5},{"id":"GO:0010754","count":5},{"id":"GO:0071320","count":5},{"id":"GO:0098719","count":5}]},{"hash":"41466877595774729","title":"Cyclic nucleotide signaling and GTPase pathways","description":"This cluster centers on membrane-associated signaling and ion transport. It includes cellular responses to cAMP and cGMP, small GTPase\u2013mediated signaling (including Ras), and regulation of receptor guanylyl cyclase, alongside transmembrane sodium and potassium transport. Sarcomere organization and meiotic regulation appear as peripheral terms but do not dominate. Overall, the proteins seem to participate in cyclic-nucleotide signaling linked to membrane ion transport via GTPase pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":3},{"id":"GO:0010754","count":3},{"id":"GO:0009454","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0071320","count":3}]},{"hash":"573673866937204522","title":"TNF/NF-kB signaling and apoptosis regulation","description":"The top GO terms cluster around TNF-mediated signaling, I-kappaB phosphorylation, and regulation of apoptosis, with protein autoubiquitination tying signaling to protein turnover; related histone modification terms suggest parallel chromatin regulation. Some entries are obsolete, but the core theme remains a NF-kB\u2013driven survival/apoptosis module with ubiquitin-mediated control.","confidence":"High","size":15,"edges":36,"triangles":20,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":3},{"id":"GO:0090073","count":3},{"id":"GO:2000620","count":3},{"id":"GO:1900095","count":3},{"id":"GO:0051865","count":3}]},{"hash":"1426424362318613042","title":"Cardiac muscle signaling and sarcomere regulation","description":"The cluster\u2019s top GO terms include sarcomere organization, cardiac muscle cell proliferation, small GTPase-mediated signaling, Ras pathway regulation, and adenylate cyclase activity, which together point to signaling pathways that regulate cardiac muscle structure and function. Some terms are unrelated (e.g., aerotaxis, antipsychotic response), but the core appears to be signaling linked to cardiac muscle regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051447","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0045214","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0007264","count":1}]},{"hash":"1021905585698888911","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":11,"triangles":10,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0034247","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0017038","count":3},{"id":"GO:0034476","count":3},{"id":"GO:0048026","count":3}]},{"hash":"2020653682612035464","title":"Vacuolar amino acid and ion transport","description":"Top GO terms indicate import of several amino acids (glutamate, arginine, proline, lysine, glutamine) into the vacuole and transmembrane transport of ions (lithium, potassium), suggesting a cohesive role in vacuolar transporter activity and nutrient ion homeostasis. The pattern is strongly transport-focused with little evidence for other processes, supporting a specific label of vacuolar amino acid and ion transport.","confidence":"High","size":15,"edges":29,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090515","count":4},{"id":"GO:1990818","count":4},{"id":"GO:0015824","count":4},{"id":"GO:0048829","count":4},{"id":"GO:0061402","count":4}]},{"hash":"1097708907165477667","title":"Unknown","description":"The terms are scattered across sensory, developmental, neural, metabolic, and stress-response processes with no clear shared function or interaction pattern (edges are zero), so there isn\u2019t a cohesive theme to label beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050909","count":2},{"id":"GO:0060157","count":1},{"id":"GO:0060134","count":1},{"id":"GO:0032526","count":1},{"id":"GO:2001245","count":1}]},{"hash":"355967486354925103","title":"Phospholipid biosynthesis and sperm motility","description":"This cluster is dominated by GO terms for biosynthesis of phospholipids (phosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine, platelet activating factor) and related membrane lipid processes, alongside terms related to sperm flagellum assembly and motility. The combination suggests proteins involved in membrane lipid production that supports flagellar/ciliary function in sperm, making this a cohesive, if dual-nocused, functional theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006663","count":1},{"id":"GO:0006655","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0010512","count":1},{"id":"GO:0006659","count":1}]},{"hash":"225719463333135267","title":"Transmembrane Transporters for Ions, Sugars, and Neurotransmitters","description":"The shared functions are membrane transport activities across diverse substrates: ions (sodium, phosphate), sugars (arabinose), sialic acid, and xenobiotics, with a note on neurotransmitter loading into synaptic vesicles indicating vesicular transporter activity. Taken together, these proteins appear to be broadly specialized transmembrane transporters.","confidence":"High","size":15,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0098700","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0006004","count":2}]},{"hash":"1140975878773263853","title":"Stress-induced apoptosis and cell cycle control","description":"Top GO terms point to immune and stress-related signaling (cellular response to lipopolysaccharide; T cell receptor signaling), together with intrinsic apoptosis triggered by ER stress and various mitotic checkpoints (G1 DNA damage checkpoint signaling, G2/M transition). The mix suggests proteins involved in coordinating cellular stress responses with cell cycle regulation, rather than a single cohesive pathway. Therefore, a label like Stress-induced apoptosis and cell cycle control captures the overarching theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":3},{"id":"GO:0070059","count":2},{"id":"GO:0031571","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0006348","count":2}]},{"hash":"2298517378696931368","title":"Unknown","description":"There are no GO terms or enrichment signals to tie these proteins to a common function; the cluster has no edges or shared terms, so no clear theme can be inferred.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1253714649387331894","title":"Meiosis and Genome Maintenance","description":"Top terms cluster around meiotic processes (spermatogenesis, synaptonemal complex organization), chromosome segregation (mitotic spindle elongation), and DNA repair (NHEJ), with additional RNA processing and ubiquitination terms that are secondary. This suggests the cluster labels proteins involved in meiotic chromosome maintenance and genome stability.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0006303","count":1},{"id":"GO:0070193","count":1}]},{"hash":"1214398832670538278","title":"Innate immune sensing and DC antigen presentation","description":"The GO terms cluster around innate immune sensing (TLR9, NOD2, muramyl dipeptide detection) and inflammasome/IFN signaling, plus dendritic cell antigen processing/presentation, pointing to a unified theme of innate detection leading to DC-driven antigen presentation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":5},{"id":"GO:0030335","count":5},{"id":"GO:1902745","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0002830","count":5}]},{"hash":"837692074456798339","title":"Innate immune sensing and DC antigen presentation","description":"The terms cluster around innate immune recognition (TLR9, NOD2, NLRP3 inflammasome, muramyl dipeptide detection), cytokine signaling (IFN-\u03b3/type II interferon pathways), and enhanced dendritic cell antigen processing/presentation, plus increased dendritic cell migration. This suggests a cohesive theme of sensing pathogens and activating dendritic cells to present antigens to T cells, with some cytoskeletal changes supporting cell movement. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":9},{"id":"GO:0030335","count":9},{"id":"GO:1902745","count":9},{"id":"GO:0070431","count":9},{"id":"GO:0002830","count":9}]},{"hash":"2201169678370696865","title":"Innate immune sensing and antigen presentation","description":"GO terms indicate Toll-like receptor 9 signaling, NLRP3 inflammasome assembly, muramyl dipeptide detection, dendritic cell antigen processing and presentation, MHC class I biosynthesis, and type II interferon signaling, plus lamellipodium organization and cell migration. This collective pattern points to proteins coordinating pathogen sensing and subsequent antigen presentation/maturation of antigen-presenting cells, aligning with innate immune activation and adaptive response initiation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":12},{"id":"GO:0030335","count":12},{"id":"GO:1902745","count":12},{"id":"GO:0070431","count":12},{"id":"GO:0002830","count":12}]},{"hash":"704045299216154854","title":"TLR9/NOD2-Inflammasome Immune Signaling","description":"The GO terms point to innate immune sensing via TLR9 and NOD2, assembly of the NLRP3 inflammasome, detection of muramyl dipeptide, and regulation of dendritic cell antigen processing and presentation and MHC class I biosynthesis, along with type II interferon signaling, all consistent with a dendritic cell\u2013mediated immune activation module. In short, it reflects innate sensing leading to antigen presentation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":6},{"id":"GO:0030335","count":6},{"id":"GO:1902745","count":6},{"id":"GO:0070431","count":6},{"id":"GO:0002830","count":6}]},{"hash":"350395273704772795","title":"Innate immune signaling and morphogenesis","description":"This cluster combines terms for innate immune signaling (cellular response to lipopolysaccharide; Toll-like receptor signaling) with developmental/morphogenesis processes (Wnt signalosome assembly; various tissue- and organ-specific morphogenesis terms). The shared thread appears to be involvement in signaling pathways that regulate both immune responses and developmental morphogenesis, albeit with diverse tissue contexts. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0034154","count":1},{"id":"GO:0060658","count":1},{"id":"GO:0034123","count":1}]},{"hash":"805158537482321059","title":"Unknown","description":"The top GO terms are highly diverse, spanning plant brassinosteroid signaling and flower development, animal skeletal muscle development and sarcomere organization, B cell receptor signaling, chromosome passenger complex localization, protein homooligomerization, renal sodium absorption, and viral latency release. With only single-term representations and no shared biological theme or connectivity (and no edges), there is no coherent function tying the cluster together.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009742","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0019046","count":1},{"id":"GO:0048741","count":1},{"id":"GO:0045214","count":1}]},{"hash":"2000195846186486117","title":"Membrane signaling and actin cytoskeleton remodeling","description":"The cluster centers on signaling pathways at the plasma membrane (EGFR, Cdc42, Fc receptor signaling) and cytoskeletal dynamics (actin branching, focal adhesion regulation, endosome transport, nerve branching), suggesting a cohesive theme of membrane-associated signal transduction driving cytoskeletal remodeling. A few terms (cell cycle, viral RNA replication) are less aligned and may be incidental noise.","confidence":"High","size":14,"edges":22,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0039694","count":2},{"id":"GO:0010628","count":2},{"id":"GO:0048227","count":2},{"id":"GO:0007173","count":2}]},{"hash":"1989262636898582386","title":"Neuronal microtubule dynamics and axon maintenance","description":"These proteins show strong enrichment for microtubule dynamics terms (plus-end and cytoplasmic depolymerization, plus-end directed sliding, spindle elongation/assembly) and neuronal context (neuron projection maintenance, Purkinje cell layer organization). The cluster likely represents components regulating microtubule remodeling in neurons to preserve axonal structure and projections.","confidence":"High","size":14,"edges":77,"triangles":232,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":9},{"id":"GO:0060404","count":5},{"id":"GO:0070462","count":5},{"id":"GO:0021693","count":5},{"id":"GO:0000022","count":5}]},{"hash":"550307865543410724","title":"Neural development and cortical neuron differentiation","description":"The strongest signals are neural development: forebrain radial glial cell differentiation, midbrain dopaminergic neuron differentiation, and cortex radially oriented cell migration, indicating a brain development theme. Other terms like exosomal secretion, endosome-to-Golgi transport, hair follicle morphogenesis, and trabecula morphogenesis are present but less central, suggesting auxiliary cellular processes accompanying development.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021861","count":2},{"id":"GO:0031069","count":1},{"id":"GO:1990182","count":1},{"id":"GO:0007174","count":1},{"id":"GO:1904948","count":1}]},{"hash":"601897229211671353","title":"Neuronal vesicle trafficking and membrane transport","description":"This cluster is dominated by GO terms related to neuronal processes and vesicle trafficking, including regulation of synaptic vesicle endocytosis and nervous system development, as well as several membrane transport activities (sodium-dependent cation transport, sodium ion transport, arabinose transmembrane transport, nitrite transport, and 4-hydroxyphenylacetate transport). The common theme appears to be proteins involved in neuronal intracellular transport and membrane transport functions. Some terms like cell cycle and replicative senescence are less aligned, possibly representing broader or overlapping annotations, but the core signal points to neuronal vesicle trafficking and transporter activity.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900242","count":3},{"id":"GO:0035646","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0070715","count":3}]},{"hash":"1954365940915646223","title":"ER-Golgi-Vacuole Vesicle Trafficking","description":"The proteins cluster around intracellular transport routes within the secretory pathway, with GO terms for ER-to-Golgi (COPII) vesicle budding, Golgi-related transport, endosome-to-Golgi and Golgi-to-vacuole trafficking, and vacuolar targeting pathways (including the Cvt pathway). This indicates a cohesive role in vesicle trafficking and protein localization between the ER, Golgi, endosomes, and vacuole.","confidence":"High","size":14,"edges":12,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0090114","count":2},{"id":"GO:0006623","count":2},{"id":"GO:1903078","count":2},{"id":"GO:0032258","count":2}]},{"hash":"1431080302534167691","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0000467","count":1},{"id":"GO:0002107","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0000738","count":1}]},{"hash":"950446357382645989","title":"TLR/NOD2-driven innate immune activation","description":"The cluster centers on innate immune sensing and inflammatory signaling, with strong links to TLR9 signaling, NOD2 detection of muramyl dipeptide, and NLRP3 inflammasome assembly, driving IL-6 production and type II interferon pathways, as well as processes related to dendritic cell antigen presentation and immune-cell migration. This points to a cohesive theme of innate immune recognition leading to inflammation and antigen presentation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":13},{"id":"GO:0032755","count":13},{"id":"GO:0030335","count":13},{"id":"GO:1902745","count":13},{"id":"GO:0070431","count":13}]},{"hash":"1409408305221482739","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":82,"triangles":280,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0006269","count":7},{"id":"GO:0071894","count":7},{"id":"GO:0071031","count":7}]},{"hash":"1217817761230033977","title":"P53-Linked cell cycle and proteostasis regulation","description":"Explanation: The terms indicate a regulatory program coordinating cell cycle control, p53 signaling, and proteostasis. The mix of translation, protein stabilization, ubiquitin pathway modulation, and RNA decay points to coupling of protein synthesis, turnover, and RNA quality control in a stress/DNA-damage context (actinomycin D response).","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1901798","count":1},{"id":"GO:0071158","count":1},{"id":"GO:0071157","count":1},{"id":"GO:1904667","count":1}]},{"hash":"675680209344818496","title":"Endosomal trafficking and MVB formation","description":"The top GO terms cluster around endosome biology\u2014early endosome to Golgi/late endosome transport and multivesicular body assembly\u2014pointing to vesicle trafficking within the endosomal system as the core function. Other terms like xenobiotic response or brain development appear ancillary, but the dominant theme is endosomal sorting and transport.","confidence":"Medium","size":14,"edges":17,"triangles":1,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034498","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0042832","count":3},{"id":"GO:0036258","count":3},{"id":"GO:0043547","count":3}]},{"hash":"800637620887161093","title":"Unknown","description":"The GO terms point to divergent biological processes across multiple species (lipid catabolism, development, autophagy, plant defense and stress responses), giving no single shared function to unify the cluster.","confidence":"","size":14,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046338","count":1},{"id":"GO:0046843","count":1},{"id":"GO:0031161","count":1},{"id":"GO:0034496","count":1},{"id":"GO:0010618","count":1}]},{"hash":"1902707154855770153","title":"Pyroglutamate biosynthesis","description":"This cluster is annotated with GO:0017186, describing peptidyl-pyroglutamic acid biosynthesis via glutaminyl-peptide cyclotransferase, i.e., formation of N-terminal pyroglutamate. The shared function centers on pyroglutamate formation, justifying the label.","confidence":"Medium","size":14,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0017186","count":1}]},{"hash":"2056273444833929455","title":"Centrosome, spindle, and cilium microtubule dynamics","description":"The top GO terms point to microtubule-based organization: intraciliary transport for cilium assembly, centrosome cycle, and microtubule anchoring at the mitotic spindle pole. These together suggest a cluster centered on microtubule dynamics governing centrosomes, spindles, and cilia. A few other terms (e.g., ubiquitin-dependent proteolysis, erythrocyte development) are less connected, but do not override the dominant microtubule/cytoskeletal theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048822","count":1},{"id":"GO:0043161","count":1},{"id":"GO:0045721","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0033033","count":1}]},{"hash":"2013719861596331981","title":"DNA replication and mitotic cell cycle","description":"This cluster\u2019s top terms are dominated by DNA replication, cell division, and mitotic cell cycle, pointing to genome duplication and progression through cell division as the core theme. Additional terms for transcription-coupled repair and proteostasis indicate broader maintenance of genome integrity and protein quality control, with a few peripheral GO terms related to vesicle formation and degradation pathways. Overall, the label captures the central function while acknowledging related processes.","confidence":"High","size":14,"edges":13,"triangles":0,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1802291009915680172","title":"Unknown","description":"The Top Terms span sporulation, telomerase assembly, chromosome segregation, immune signaling, xenobiotic response, iron transport regulation, and protein phosphorylation, among others. This dispersion suggests no single, coherent biological function characterizes this cluster, and the absence of edges reinforces the lack of functional linkage. Thus, an interpretable short label cannot be assigned; Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901389","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0046777","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0000160","count":1}]},{"hash":"1102860317504510257","title":"Golgi vesicle trafficking and SNARE assembly","description":"Most terms describe vesicle transport involving the Golgi apparatus (ER-to-Golgi, intra-Golgi, Golgi-to-vacuole) and vesicle fusion with the Golgi, plus SNARE complex assembly; a few terms reflect neuronal exocytosis and postsynaptic receptor insertion, which fit within SNARE-mediated membrane fusion. ","confidence":"High","size":14,"edges":11,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":8},{"id":"GO:0090161","count":8},{"id":"GO:0006891","count":8},{"id":"GO:0006888","count":8},{"id":"GO:0006896","count":7}]},{"hash":"1258033348059573940","title":"Vacuolar autophagy and trafficking","description":"Based on the GO terms, the cluster centers on autophagy-related processes and vesicle transport to the vacuole/lysosome, including Cvt pathway targeting, endosome-to-vacuole transport, and autophagy of peroxisomes, as well as lysosome organization. A few terms (spliceosome dynamics, spindle attachment) appear less connected and may reflect broader protein functions, but the autophagy/vesicle-trafficking theme is the most representative signal.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010226","count":1},{"id":"GO:0000388","count":1},{"id":"GO:0032465","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0071275","count":1}]},{"hash":"52024331567674423","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0007420","count":2},{"id":"GO:1901621","count":1},{"id":"GO:1900035","count":1}]},{"hash":"1615474936357143026","title":"Mitochondrial Transport and Membrane Potential","description":"These proteins cluster around mitochondrial function, highlighted by transport of metabolites across mitochondrial membranes (e.g., alpha-ketoglutarate, CoA, TPP), the malate-aspartate shuttle, and regulation of membrane potential, plus links to apoptotic mitochondrial changes. The common theme is mitochondrial transport and membrane potential regulation, so 'Mitochondrial Transport and Membrane Potential' is a representative label.","confidence":"High","size":14,"edges":9,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":7},{"id":"GO:0051881","count":7},{"id":"GO:0015742","count":7},{"id":"GO:0030974","count":7},{"id":"GO:0035349","count":7}]},{"hash":"616641819239957598","title":"Innate Immune Sensing and Antigen Presentation","description":"The terms cluster around classic innate immune recognition pathways (TLR9, NOD2, NLRP3 inflammasome) and their downstream effects on interferon signaling and antigen processing/presentation by dendritic cells, plus MHC class I biosynthesis. The inclusion of positive regulation of cell migration/lamellipodium organization also suggests immune cell trafficking during activation. This combination supports a cohesive label focused on innate sensing leading to antigen presentation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":12},{"id":"GO:0030335","count":12},{"id":"GO:1902745","count":12},{"id":"GO:0070431","count":12},{"id":"GO:0002830","count":12}]},{"hash":"1948069859878444814","title":"Gene regulation and signaling","description":"The top GO terms cluster around regulatory processes: DNA-templated transcription, regulation of nuclear export and protein processing, and Rho-mediated signaling with focal adhesion regulation. While several terms touch on specific tissues or stimuli (cocaine response, NK T cell differentiation, trachea formation), the common thread is broad regulation of gene expression and cell signaling rather than a single pathway. Confidence in this thematic label is Moderate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0042220","count":3},{"id":"GO:1901214","count":2},{"id":"GO:0060440","count":2}]},{"hash":"1378748999125483158","title":"Cardiac muscle signaling and organization","description":"Top terms indicate muscle-specific processes (sarcomere organization; cardiac muscle cell proliferation) and modulation of signaling pathways (small GTPases, adenylate cyclase, guanylyl cyclase). This supports a cohesive theme around cardiac muscle signaling and structural organization, with GPCR-related regulation as a common mechanism. Some outliers (aerotaxis, meiotic regulation) may reflect annotation noise or multifunctionality, but the core appears to be cardiac muscle signaling/assembly.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0007264","count":2}]},{"hash":"1568947436087360479","title":"Stress-Responsive Chromatin Remodeling","description":"The top terms mix environmental stress responses (thermoception, response to heat, pain) with chromatin dynamics (chromatin remodeling, histone modification/exchange), suggesting a cluster where stress signals drive gene expression changes via chromatin regulation; a few outliers (GPI anchor biosynthesis, glucose signaling) are present but not dominant.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048265","count":2},{"id":"GO:0006506","count":2},{"id":"GO:0043044","count":1},{"id":"GO:1900827","count":1},{"id":"GO:0097676","count":1}]},{"hash":"579628743081457629","title":"ER-Golgi vesicle transport and oxidative stress response","description":"This cluster\u2019s GO terms are dominated by regulation of ER-to-Golgi vesicle transport and oxidative stress/detoxification, suggesting proteins involved in the secretory pathway and redox defense. A couple of terms about intestinal epithelial development and platelet maturation appear less connected, but the core theme seems to be vesicle trafficking coupled with oxidative stress management.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060628","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0009246","count":1},{"id":"GO:0036345","count":1},{"id":"GO:0006979","count":1}]},{"hash":"583311637839931751","title":"TLR-NF-kappaB Innate Immune Signaling","description":"These proteins strongly point to innate immune receptor signaling and inflammatory regulation. The top GO terms cover TLR signaling (including MyD88-independent pathways) and LPS response, NF-kappaB pathways (canonical and non-canonical), and regulation of key cytokines (TNF, IL-18, IL-1), along with MHC class I biosynthesis and cell migration. Together they suggest a cohort involved in modulating TLR-driven inflammation and antigen presentation rather than a single metabolic process.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":5},{"id":"GO:0002830","count":5},{"id":"GO:0045345","count":5},{"id":"GO:0032741","count":5},{"id":"GO:0002756","count":5}]},{"hash":"170869194521127261","title":"Mitochondrial redox and ER stress response","description":"Top terms point to redox balance, oxidative/ER stress responses, and mitochondrial protein import, suggesting a module focused on organelle-associated stress management and homeostasis; auxiliary terms like DNA replication and neural signaling regulation appear ancillary. Hence the label captures the primary theme, with moderate confidence given some outlier terms.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0034599","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0055114","count":1}]},{"hash":"171367483093878000","title":"Innate Immune Sensing and Antigen Presentation","description":"The GO terms point to sensing of microbial components (TLR9, NOD2, muramyl dipeptide detection) and inflammasome activity (NLRP3), with downstream signaling including type II interferon responses and enhanced antigen processing/presentation by dendritic cells and MHC class I biosynthesis, indicating a cohesive innate immune and antigen presentation module.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":7},{"id":"GO:0030335","count":7},{"id":"GO:1902745","count":7},{"id":"GO:0070431","count":7},{"id":"GO:0002830","count":7}]},{"hash":"1176183339084700519","title":"Innate Immune Sensing and Antigen Presentation","description":"Top GO terms highlight TLR9 signaling, NOD2 signaling, and NLRP3 inflammasome assembly, plus detection of muramyl dipeptide, all pointing to innate immune sensing of pathogens. They also include positive regulation of dendritic cell antigen processing and MHC class I biosynthesis, suggesting activation of dendritic cells and antigen presentation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034162","count":2},{"id":"GO:0030335","count":2},{"id":"GO:1902745","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0002830","count":2}]},{"hash":"45700599782389814","title":"Innate Immune Signaling and Cytokine Production","description":"The terms converge on innate immune pathways and inflammatory signaling: TLR signaling (MyD88-independent), NF-kappaB regulation, LPS-mediated signaling, and cytokine production/regulation (TNF, IL-18, IL-1), plus MHC class I biosynthesis. This coherent pattern indicates a shared function in initiating and modulating innate immunity and inflammation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030335","count":14},{"id":"GO:0002830","count":14},{"id":"GO:0045345","count":14},{"id":"GO:0032741","count":14},{"id":"GO:0002756","count":14}]},{"hash":"871384447876474392","title":"TLR9/NOD2-Driven DC Activation","description":"The terms point to innate immune sensing via TLR9 and NOD2, detection of muramyl dipeptide, and NLRP3 inflammasome activity, coupled with signaling that promotes dendritic cell antigen processing and MHC class I biosynthesis. This pattern suggests a coordinated pathway from microbial detection to dendritic cell maturation and antigen presentation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034162","count":1},{"id":"GO:0030335","count":1},{"id":"GO:1902745","count":1},{"id":"GO:0070431","count":1},{"id":"GO:0002830","count":1}]},{"hash":"2107278889566743557","title":"Rab-regulated ER-Golgi and endosome trafficking","description":"The top GO terms point to vesicle transport pathways between ER, Golgi, and endosomes (ER-Golgi transport, COPII cargo loading, endosome-to-Golgi routes, and recycling endosome to Golgi). The presence of Rab signal transduction and regulation of GTPase activity supports a Rab-mediated trafficking theme. A retina development term is less aligned but does not override the predominant vesicle trafficking signal.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0060041","count":2},{"id":"GO:1902018","count":1},{"id":"GO:0071955","count":1},{"id":"GO:0032483","count":1}]},{"hash":"697163757335314028","title":"TLR9/NLR Innate Immunity and Antigen Presentation","description":"The proteins are enriched for innate immune sensing and inflammatory signaling: TLR9 signaling, NOD-like receptor pathways (detection of muramyl dipeptide), NLRP3 inflammasome assembly, and downstream antigen processing/presentation (dendritic cell antigen presentation and MHC class I biosynthesis) with interferon signaling, indicating a cohesive role in pathogen recognition, inflammasome activation, and antigen presentation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":4},{"id":"GO:0030335","count":4},{"id":"GO:1902745","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0002830","count":4}]},{"hash":"1113476194232959838","title":"Muscle signaling and sarcomere regulation","description":"This cluster centers on muscle structure and function: sarcomere organization and cardiac muscle cell proliferation are prominent, with supporting GO terms for GTPase signaling, adenylate cyclase/guanylyl cyclase pathways, and ion transport, all of which together point to signaling networks regulating muscle contraction and structural organization.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":3},{"id":"GO:0045762","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0098719","count":2}]},{"hash":"630823740023947177","title":"Unknown","description":"The GO terms span highly diverse processes\u2014from plant-specific chlorophyll biosynthesis and light detection to immune functions (T cell activation, complement activation), extracellular matrix metabolism, and development in cartilage and flowers\u2014indicating no single cohesive biological theme. This mix suggests heterogeneity across species or functions rather than a shared pathway.","confidence":"","size":13,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0015995","count":11},{"id":"GO:0043248","count":11},{"id":"GO:0048455","count":11},{"id":"GO:0006511","count":11},{"id":"GO:0006471","count":9}]},{"hash":"411211527108466109","title":"Neuronal development and synaptic trafficking","description":"The top GO terms emphasize brain and nervous system development, learning, and dendritic spine development, with supporting terms tied to EGFR signaling, tubulin-based cytoskeleton, and ER-Golgi vesicle transport. This points to a cluster enriched for proteins involved in neuronal development and the cellular machinery (microtubules, trafficking, organelle organization) that builds and maintains neuronal processes and synapses.","confidence":"High","size":13,"edges":64,"triangles":164,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0000278","count":3}]},{"hash":"1119591533582971311","title":"ER-Golgi and synaptic vesicle trafficking","description":"The top GO terms cluster around vesicle transport between the ER and Golgi, including retrograde and anterograde trafficking, Golgi to vacuole transport, and synaptic vesicle budding/transport, pointing to a cohesive role in intracellular trafficking and secretion, with some neuronal-specific terms likely reflecting related processes. Pigmentation and Purkinje cell maturation terms are less central but do not override the vesicle trafficking signal.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0016185","count":1}]},{"hash":"862012218095776905","title":"Microtubule Dynamics in Neurons and Mitosis","description":"This cluster centers on microtubule depolymerization and organization (axoneme, plus-end dynamics) together with spindle-related mitotic events and neuron projection maintenance, pointing to proteins that regulate microtubule remodeling in neuronal and cell division contexts.","confidence":"High","size":13,"edges":64,"triangles":181,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0060404","count":13},{"id":"GO:0070462","count":13},{"id":"GO:0048364","count":13},{"id":"GO:0021693","count":13},{"id":"GO:0000022","count":13}]},{"hash":"1543145434900152826","title":"Mitochondrial respiration and redox homeostasis","description":"This cluster is dominated by terms tied to mitochondrial energy production (NADH to ubiquinone), cofactor and TCA-related metabolism (lipoate, 2-oxoglutarate), and redox balance, with additional related processes like membrane potential regulation. Some outliers (camphor catabolic process, stem cell proliferation) likely reflect noise or cross-annotation, but the core signal points to mitochondrial energy metabolism and redox control.","confidence":"High","size":13,"edges":12,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":4},{"id":"GO:0051068","count":4},{"id":"GO:0019383","count":4},{"id":"GO:2000648","count":4},{"id":"GO:0007568","count":4}]},{"hash":"28589046023434484","title":"TGF-beta/BMP Signaling Modulation","description":"The cluster centers on TGF-beta/BMP signaling, including response to TGF-beta stimulus, BMP signaling regulation, and SMAD-related processes, with peptidyl-threonine dephosphorylation as a regulatory mechanism; a few terms (meristem identity, photosystem stoichiometry) appear less directly connected and may reflect broader roles or annotation noise.","confidence":"Medium","size":13,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010074","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0000173","count":1},{"id":"GO:0010991","count":1},{"id":"GO:0042006","count":1}]},{"hash":"1181384609358676195","title":"Unknown","description":"The cluster has no shared GO terms or interaction evidence (no edges, no triangles, and no Top Terms), so a common biological function cannot be inferred. Accordingly, label Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"229252296889785239","title":"Muscle and motor neuron development","description":"These proteins appear linked to skeletal muscle formation and neuronal/motor control, given terms like myoblast differentiation, myotome development, regulation of locomotor rhythm, and negative regulation of motor neuron apoptotic process, plus axonemal dynein complex assembly. Some terms (memory, estrogen receptor signaling, thigmotaxis) are less cohesive with this theme, so confidence is moderate.","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007613","count":2},{"id":"GO:0045661","count":1},{"id":"GO:0030520","count":1},{"id":"GO:0001966","count":1},{"id":"GO:0006355","count":1}]},{"hash":"2303842370045667166","title":"TNF/NF-\u03baB signaling and p53-mediated apoptosis","description":"The cluster is enriched for TNF-mediated signaling, NF-\u03baB pathway regulation (including non-canonical NF-\u03baB), and an intrinsic apoptotic response to DNA damage via p53, pointing to a core theme of immune/stress signaling and programmed cell death. Some related terms about LPS response support an immune-context link, while RNA processing terms appear as ancillary functions that often accompany signaling networks. Overall, a coherent emphasis on TNF/NF-\u03baB\u2013mediated signaling and p53-dependent apoptosis best explains the set.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":2},{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0042347","count":1}]},{"hash":"1062618845402115890","title":"ECM remodeling and adhesion signaling","description":"The cluster is enriched for extracellular matrix\u2013related processes: hyaluronan metabolism, regulation of focal adhesion assembly, integrin-mediated signaling, and metallopeptidase activity, which together point to ECM remodeling and cell adhesion/migration. Developmental cues like chemotaxis and trachea formation support a migratory/adhesive context; a few transcription-related terms may reflect background noise. ","confidence":"Medium","size":13,"edges":43,"triangles":54,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009190","count":3},{"id":"GO:0006935","count":3},{"id":"GO:0030212","count":3},{"id":"GO:0046827","count":3}]},{"hash":"750596202605463952","title":"RNA processing and ribosome biogenesis","description":"This cluster is dominated by RNA-related processes: splicing via the spliceosome, regulatory ncRNA-mediated gene silencing, and mRNA stabilization, plus assembly of the small-subunit processome and the eIF4F complex, indicating a core theme of RNA maturation, splicing, and ribosome/translation biogenesis.","confidence":"High","size":13,"edges":40,"triangles":75,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0006260","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0048255","count":4}]},{"hash":"505374684481716205","title":"Endosomal trafficking and secretion","description":"The dominant GO terms point to vesicle transport involving endosomes (early to Golgi, early to late endosomes) and pathways directing proteins to membranes, plus exosomal secretion and related localization processes. While a few terms like hair follicle morphogenesis and antibiotic response seem less connected, the core signals consistently indicate vesicular trafficking and secretion functions.","confidence":"Medium","size":13,"edges":13,"triangles":1,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0034498","count":3},{"id":"GO:0045022","count":3},{"id":"GO:0032258","count":3},{"id":"GO:1903078","count":3},{"id":"GO:0046677","count":3}]},{"hash":"1880729058707333680","title":"Ion transport and membrane potential regulation","description":"The terms converge on maintaining membrane potential and ion homeostasis, notably potassium and sodium transport, stabilization/regulation of the membrane potential, and cardiac action potential repolarization. While some terms involve broader signaling (cGMP) and sensory inputs (touch, aerotaxis), the dominant signal is ion transport driving cellular excitability. High","confidence":"","size":13,"edges":57,"triangles":107,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030007","count":8},{"id":"GO:0050976","count":7},{"id":"GO:0071805","count":7},{"id":"GO:0098914","count":7},{"id":"GO:0030322","count":7}]},{"hash":"267440045668642748","title":"tRNA methylation","description":"Based on the single observed GO term, tRNA methylation, this cluster's most evident theme is RNA modification via methylation. However, there is almost no network cohesion (no edges/triangles) and only one member carries this annotation, so the signal for a unified function is weak.","confidence":"Low","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1}]},{"hash":"443823690370579524","title":"Unknown","description":"The top GO terms cover a wide range of processes (receptor clustering, Rho signaling, focal adhesion regulation, development of trachea, immune differentiation, and broader cell signaling) with little to no cohesive biological theme across all 13 proteins, and there are no edges or shared core functions to tie them together. This diversity suggests there isn\u2019t a single interpretable function for this cluster, so the safest label is Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043113","count":2},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1}]},{"hash":"1765096346242950222","title":"Autophagy-linked carbohydrate metabolism","description":"The cluster centers on autophagy-related processes (glycophagy; positive regulation of macroautophagy) and carbohydrate catabolism (starch and maltose) with related carbon utilization regulation, suggesting proteins involved in autophagy-driven degradation of carbohydrates, with a minor note of a lipid catabolic term that fits a broader catabolic theme. Habituation appears as a non-core term and may be noise.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061723","count":1},{"id":"GO:0046959","count":1},{"id":"GO:0016239","count":1},{"id":"GO:0005983","count":1},{"id":"GO:0046475","count":1}]},{"hash":"1142723861435491078","title":"Mitochondrial Redox and Iron Homeostasis","description":"This cluster is dominated by GO terms tied to mitochondria, including cellular response to oxidative stress, cell redox homeostasis, and intracellular iron ion homeostasis, as well as protein import into the mitochondrial intermembrane space. Together these suggest a coherent function around mitochondrial redox balance and iron handling, with possible links to quality control via autophagy regulation.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017186","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0016242","count":1}]},{"hash":"1533579788423819752","title":"Glycine Transporters and Glycinergic Signaling","description":"The top terms cluster around glycine transport/import, glycinergic synaptic transmission, and related regulation/secretion, with additional amino acid transport terms (proline, leucine, taurine) and serotonin uptake, suggesting a cohesive group of transporter proteins involved in amino acid neurotransmitter handling at glycinergic synapses, possibly with glial-associated support functions.","confidence":"High","size":13,"edges":13,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0015824","count":2},{"id":"GO:0060012","count":1},{"id":"GO:0015820","count":1},{"id":"GO:1903346","count":1},{"id":"GO:0036233","count":1}]},{"hash":"116194855063129068","title":"Quinone and pigment biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for various quinones (ubiquinone, menaquinone, phylloquinone, plastoquinone) and related pigments (chlorophyll, heme O), pointing to a shared function in producing electron carriers and pigments in photosynthetic or plastid-containing organisms. A few outlier terms exist but do not override the core quinone/pigment biosynthesis signal.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032194","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0042372","count":1},{"id":"GO:0042371","count":1},{"id":"GO:0048034","count":1}]},{"hash":"233925229557892142","title":"Plant Hormone Signaling and Chromatin Regulation","description":"This cluster shows enrichment for plant hormone responses (cytokinin, ABA, gibberellin) alongside chromatin-related processes (chromatin remodeling, subtelomeric heterochromatin formation, shelterin complex assembly), pointing to proteins that integrate hormone signaling with chromatin state to regulate gene expression. Note that an animal term (interleukin-4 response) may be annotation noise, but the predominant pattern is hormone signaling coupled with chromatin regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0009737","count":4},{"id":"GO:0043044","count":4},{"id":"GO:0071353","count":3},{"id":"GO:0035390","count":3}]},{"hash":"15853259692520885","title":"Ribosome assembly and rRNA maturation","description":"The dominant GO terms point to ribosome biogenesis, including large subunit assembly, LSU export, and 5.8S rRNA maturation, indicating a core ribosome biogenesis theme. SRP-dependent cotranslational targeting to membranes also appears, consistent with ribosome-associated protein targeting. A few developmental terms are present at low frequency, likely reflecting multifunctional proteins rather than cluster focus.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":2},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1348055397904658063","title":"Rab-regulated vesicle trafficking","description":"The cluster\u2019s top GO terms cluster around Rab GTPase signaling and vesicle trafficking, notably endocytosis, endocytic recycling, and regulation of Rab-mediated signal transduction, suggesting a shared role in Rab-dependent vesicle cycling. Other terms like histidyl modification, SAM catabolism, and apoptosis appear incidental and do not define the central function of this cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017183","count":1},{"id":"GO:0050843","count":1},{"id":"GO:0048488","count":1},{"id":"GO:0035745","count":1},{"id":"GO:0032483","count":1}]},{"hash":"26955896300842170","title":"TLR9/NOD2 innate immune signaling and inflammasome activation","description":"This cluster centers on innate immune receptors (TLR9 and NOD2) and core inflammatory pathways, including IL-6 production, type II interferon signaling, and NLRP3 inflammasome assembly, along with dendritic cell antigen processing and migration. The GO terms collectively suggest sensing intracellular pathogens (muramyl dipeptide), activating inflammasomes, and promoting antigen presentation, all hallmark steps of innate immune activation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":10},{"id":"GO:0032755","count":10},{"id":"GO:0030335","count":10},{"id":"GO:1902745","count":10},{"id":"GO:0070431","count":10}]},{"hash":"2104479854185174306","title":"Unknown","description":"The GO terms span diverse processes (viral and mitochondrial transcription, transcription initiation, neuron guidance, phagocytosis, and various post-translational and translational regulations) with no clear shared function or pathway. The cluster has no edges or connections, suggesting a heterogeneous or random grouping rather than a coherent biological module.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039695","count":1},{"id":"GO:0006390","count":1},{"id":"GO:0006391","count":1},{"id":"GO:0097374","count":1},{"id":"GO:0006911","count":1}]},{"hash":"1897184567790038153","title":"TLR9/NOD2-driven innate immune activation","description":"This cluster is enriched for TLR9 signaling, NOD2 signaling, muramyl dipeptide detection, NLRP3 inflammasome assembly, IL-6 production, and dendritic cell antigen processing/presentation, plus type II interferon signaling and cell migration\u2014together pointing to innate immune sensing, inflammasome-mediated inflammation, and dendritic cell\u2013mediated antigen presentation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":4},{"id":"GO:0032755","count":4},{"id":"GO:0030335","count":4},{"id":"GO:1902745","count":4},{"id":"GO:0070431","count":4}]},{"hash":"284154470303464824","title":"Innate immune sensing and DC activation","description":"This cluster centers on innate immune sensing pathways (TLR9, NOD2) and inflammasome signaling (NLRP3), coupled with signals for type II interferon responses, antigen processing/presentation by dendritic cells, and MHC class I biosynthesis. The combined topics point to pattern-recognition\u2013driven DC activation and subsequent antigen presentation, with enhanced cell migration supporting immune cell recruitment.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":8},{"id":"GO:0030335","count":8},{"id":"GO:1902745","count":8},{"id":"GO:0070431","count":8},{"id":"GO:0002830","count":8}]},{"hash":"490802649612155588","title":"Innate immune sensing and antigen presentation","description":"The proteins show enrichment for TLR9 and NOD2 signaling, NLRP3 inflammasome assembly, interferon signaling, and dendritic cell antigen processing/presentation with MHC I biosynthesis, indicating roles in pathogen detection and initiation of adaptive immunity. The presence of migration-related terms also aligns with immune cell trafficking to infection sites, supporting a cohesive innate sensing and antigen presentation theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034162","count":1},{"id":"GO:0030335","count":1},{"id":"GO:1902745","count":1},{"id":"GO:0070431","count":1},{"id":"GO:0002830","count":1}]},{"hash":"2222852973481032086","title":"Membrane trafficking and morphogenesis","description":"The top GO terms cluster around membrane remodeling and vesicle traffic, including cleavage furrow formation (cytokinesis), endosome-to-Golgi transport, the Cvt pathway to the vacuole, and prospore membrane formation, plus phosphatidic acid biosynthesis which supports membrane dynamics. Outlier terms like bone development and brood size appear incidental, but the dominant theme is vesicle trafficking coupled to cell morphogenesis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036089","count":1},{"id":"GO:0051044","count":1},{"id":"GO:0031139","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0032258","count":1}]},{"hash":"2275784545036949383","title":"Endomembrane Trafficking Regulation","description":"GO terms across the cluster point to vesicle trafficking and membrane transport within the endomembrane system, including protein localization to endosomes, ER exit regulation, phospholipid translocation, and xenobiotic transmembrane transport. While other terms touch on GTPase activity and cell cycle, the strongest common theme is regulation of intracellular transport between ER, endosomes, and related compartments, with ancillary involvement in vacuole organization and lipid movement.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0060612","count":2},{"id":"GO:0006855","count":1},{"id":"GO:0044088","count":1}]},{"hash":"2275658094876292356","title":"Innate Immune Sensing and Interferon Signaling","description":"GO terms point to innate immune processes: responses to dsRNA, NOD2 signaling, and LPS-mediated signaling, along with positive regulation of interferon-beta production and xenophagy. Together these functions form a cohesive theme of innate immune sensing and antiviral/autophagic defense, with a peripheral note on diadenosine tetraphosphate biosynthesis.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015966","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0043330","count":2},{"id":"GO:0045087","count":2},{"id":"GO:1904417","count":2}]},{"hash":"1910094526878079886","title":"Developmental trafficking and cell polarity signaling","description":"Top GO terms point to EGFR signaling, intracellular transport (COPII vesicle coating regulation, endosome-to-lysosome transport, and vacuole targeting), and developmental processes in brain and epithelial tissues, suggesting a cluster whose proteins coordinate signaling with vesicle trafficking and cell polarity. While some terms (VLDL assembly, hepatocyte apoptotic process) are less directly connected, the dominant theme is developmentally regulated trafficking and polarity.","confidence":"Medium","size":12,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007173","count":3},{"id":"GO:2000171","count":3},{"id":"GO:0034379","count":3},{"id":"GO:0006623","count":3},{"id":"GO:0007420","count":3}]},{"hash":"841649320711255560","title":"Glutamatergic Synapse Signaling","description":"The top GO terms point to neuronal communication at glutamatergic synapses, including synaptic transmission, excitatory postsynaptic potentials, and receptor clustering, plus SNARE-mediated vesicle dynamics and learning-related processes. Energy metabolism and protein quality control terms fit the demands of active synapses, though a DNA replication term seems less connected, suggesting a core synaptic function with some unrelated components. Overall, the cluster centers on glutamatergic synaptic signaling and plasticity.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0043113","count":2},{"id":"GO:0035249","count":2}]},{"hash":"1933158685344666765","title":"Signaling and Trafficking Regulators","description":"The GO terms point to regulatory roles in signaling pathways (TGF-\u03b2/BMP, NF-kappaB) and intracellular trafficking processes (nuclear export, vacuole fusion), with additional plant-specific development terms (meristem identity, photosystem adjustments). This suggests a cluster of proteins that modulate signaling and membrane/organelle dynamics rather than performing a single enzymatic function, spanning development and cellular organization across kingdoms. Some terms are obsolete, but the common theme appears to be regulatory functions in signaling and intracellular trafficking.","confidence":"Medium","size":12,"edges":49,"triangles":115,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":9},{"id":"GO:0010074","count":8},{"id":"GO:0071560","count":8},{"id":"GO:0000173","count":8},{"id":"GO:0010991","count":8}]},{"hash":"1305543817484044563","title":"ROS-driven energy metabolism and apoptosis signaling","description":"This cluster centers on hydrogen peroxide metabolism and oxidative stress, with links to mitochondrial electron transport and cytochrome c\u2013heme interactions, as well as apoptosis. It also includes a plant-relevant cue of photosynthesis, suggesting a broader energy/ROS management theme spanning mitochondria and chloroplasts. Together these terms indicate a role in coordinating redox balance with energy production and programmed cell death.","confidence":"Medium","size":12,"edges":55,"triangles":165,"max_degree":10,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0008635","count":3},{"id":"GO:0042743","count":3},{"id":"GO:0010730","count":3},{"id":"GO:0034465","count":3}]},{"hash":"1395174290173090277","title":"Mitochondrial import and membrane regulation","description":"This cluster's top GO terms are centered on mitochondria, notably protein import into the mitochondrial matrix and regulation of mitochondrial membrane permeability, indicating coordinated mitochondrial function and control. Additional terms hint at broader stress-response pathways (lipid metabolism, ubiquitination, histone turnover, TNF signaling, and cell cycle regulation), but the most specific and emphasized signal is mitochondrial import/membrane regulation, justifying the label. ","confidence":"Medium","size":12,"edges":9,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903740","count":4},{"id":"GO:0046902","count":4},{"id":"GO:0070940","count":4},{"id":"GO:0030150","count":4},{"id":"GO:2000134","count":4}]},{"hash":"141000752170496356","title":"Cytoskeleton remodeling and endocytic signaling","description":"This cluster is driven by terms tied to actin dynamics (actin filament branching, focal adhesion assembly), Rho/Cdc42 signaling, EGFR pathway activity, and membrane trafficking (endosome transport, phagocytosis signaling), suggesting a core function in cytoskeleton-driven signaling and endocytosis. Some terms (viral replication, RNA polymerase I transcription) are less directly related and may reflect incidental associations.","confidence":"Medium","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0039694","count":1},{"id":"GO:0010628","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0007173","count":1},{"id":"GO:0051893","count":1}]},{"hash":"2244335975068606576","title":"Lipid Metabolism and Energy Stress Response","description":"The top GO terms point to lipid-related metabolism (ketone body biosynthesis, propionyl-CoA biosynthesis, poly-hydroxybutyrate biosynthesis, lipid hydroperoxide transport) and energy-related processes (response to starvation, adipose and liver development). Sporulation and apoptosis references suggest stress-survival or cell fate decisions that can tie to energy status. Taken together, the cluster seems to reflect metabolic adaptation involving lipids and energy storage/usage, rather than a single, narrow function.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1901029","count":5},{"id":"GO:0030435","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0001889","count":5},{"id":"GO:0042619","count":5}]},{"hash":"1415255373569828478","title":"Unknown","description":"The terms span RNA processing, plant meristem maintenance, TGF-beta/BMP signaling, SMAD/NF-kappaB signaling, photosystem adjustments, and germ-line masculinization, with several entries obsolete, giving no clear shared function for the cluster. With only one edge and no triangles, there is little cohesive biological theme to label the cluster with a specific function.","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0010074","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0000173","count":2},{"id":"GO:0010991","count":2}]},{"hash":"2047484926128046387","title":"ECM Remodeling and Focal Adhesion Signaling","description":"The cluster\u2019s terms cohere around regulation of extracellular matrix disassembly and focal adhesion assembly, with Rho-mediated signaling linking adhesion dynamics to cytoskeletal change. Although immune- and development-related terms appear, the strongest signal is ECM remodeling and adhesion regulation.","confidence":"Medium","size":12,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":12},{"id":"GO:0060440","count":12},{"id":"GO:0051893","count":12},{"id":"GO:0001403","count":12},{"id":"GO:0007266","count":12}]},{"hash":"540194550787376601","title":"DNA replication and cell cycle progression","description":"Based on the dominant enrichment for DNA replication, G1/S transition, and cell division terms (with telomere maintenance via recombination as a related genome maintenance process), the cluster appears focused on genome duplication and mitotic progression. A few terms like angiogenesis and dendritic cell proliferation suggest broader proliferative signaling, but the core theme remains replication and cell-cycle control.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0000722","count":2},{"id":"GO:0001525","count":2}]},{"hash":"1343701514554550916","title":"Neuronal morphogenesis and signaling","description":"This cluster centers on neuronal development, with strong signals for dendrite morphogenesis, hippocampus development, and axon extension, suggesting coordinated neurite outgrowth. It also includes links to cytoskeletal reorganization and focal adhesion regulation, which support neurite navigation and attachment, as well as exocytosis regulation and MAPK signaling (ERK/JNK cascades) related to synaptic activity and growth control.","confidence":"High","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051893","count":12},{"id":"GO:0021766","count":12},{"id":"GO:0045956","count":12},{"id":"GO:0046330","count":12},{"id":"GO:0031532","count":12}]},{"hash":"896967858437923973","title":"Stress Response and Immune Signaling","description":"The GO terms show innate immune and antiviral responses (innate immune response; cellular response to type I interferon; cellular response to dsRNA; defense response to virus) plus heavy metal stress (cadmium and lead ions). There are also hints of plant hormone signaling (negative regulation of gibberellin signaling) and cell cycle processes (cell division; metaphase/anaphase transition), suggesting a broader stress/defense signaling theme rather than a single pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009938","count":8},{"id":"GO:0071276","count":8},{"id":"GO:0045087","count":7},{"id":"GO:0050689","count":7},{"id":"GO:0071357","count":7}]},{"hash":"890167548833667502","title":"Unknown","description":"The top GO terms cover a mix of development (trachea formation), immune differentiation (NK T cell, B cell tolerance), ECM and adhesion remodeling (focal adhesion, ECM disassembly), cytoskeletal signaling (Rho), and even neuron death regulation, with no single cohesive function uniting these proteins. This diversity suggests there isn\u2019t a clear common theme to label the cluster beyond Unknown.","confidence":"","size":12,"edges":15,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":2},{"id":"GO:0060440","count":2},{"id":"GO:0051893","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0007266","count":2}]},{"hash":"1179039268161501028","title":"Methylation Enzymes and Innate Immune Signaling","description":"The cluster centers on various methylation processes (peptidyl-lysine dimethylation/trimethylation, N-terminal methylation, rRNA methylation) and chromatin-related rDNA heterochromatin formation, suggesting a group of methyltransferases involved in gene regulation. It also includes innate immune signaling terms (TLR9 and NOD2 pathways) and immune response modulation, along with cell migration and lamellipodium organization, implying a link to immune cell movement. The common theme appears to be regulatory modification activities that influence chromatin/RNA states and innate immune signaling, hence a combined label.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0018023","count":1},{"id":"GO:0000183","count":1},{"id":"GO:0018013","count":1}]},{"hash":"1164742125397253579","title":"Unknown","description":"The top GO terms span neuronal death, light response, organ development, cell adhesion, nutrient-responsive growth, Rho signaling, immune cell differentiation, protein processing, cardiac hypertrophy regulation, and B cell tolerance\u2014no single shared function or theme emerges. This makes a coherent, high-level label unlikely.","confidence":"","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":1},{"id":"GO:0071486","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1}]},{"hash":"1464986066373523448","title":"Unknown","description":"The GO terms are highly diverse, spanning protein oligomerization, kinase activity regulation, lipid signaling, chromatin modification, cell wall regulation, plant patterning, fungal growth responses, neural development, and ubiquitination. There is no clear, single functional theme connecting these proteins, so a specific cohesive label isn\u2019t evident.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0071902","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0061099","count":1},{"id":"GO:0034729","count":1}]},{"hash":"362743907456809252","title":"Ubiquitin-Proteasome Proteostasis and TOR Regulation","description":"The cluster centers on ubiquitin-dependent protein catabolic processes, including cytoplasmic proteostasis and ribosome-associated degradation, indicating proteostasis via the ubiquitin-proteasome system (N-end rule, histone ubiquitination). Several terms also indicate nutrient sensing and translation regulation, such as cellular response to L-leucine and negative regulation of TOR signaling, suggesting a link between proteostasis and TOR-mediated signaling. Some terms (e.g., suckling behavior, male meiosis) are less connected but do not override the dominant proteostasis/TOR theme.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071629","count":2},{"id":"GO:0001967","count":2},{"id":"GO:0033522","count":2},{"id":"GO:1901718","count":2},{"id":"GO:0070923","count":2}]},{"hash":"2005170391133307768","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0009408","count":1}]},{"hash":"2055296026336372733","title":"Mitochondrial Metabolism and Membrane Transport","description":"This cluster centers on mitochondria: regulation of membrane potential and apoptotic changes, plus transport of key metabolites (alpha-ketoglutarate, thiamine pyrophosphate, coenzyme A) and the malate-aspartate shuttle across mitochondrial membranes. This suggests a cohesive theme of mitochondrial metabolism and membrane transport, with a possible link to growth-factor signaling. Hence the label Mitochondrial Metabolism and Membrane Transport is appropriate.","confidence":"High","size":12,"edges":14,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0030974","count":2},{"id":"GO:0035349","count":2}]},{"hash":"2058037103769766397","title":"RNA processing and ribosome biogenesis","description":"The top terms cluster around RNA biology: ribosome biogenesis, snoRNA- and snRNA-directed pseudouridine synthesis, and telomerase RNA stabilization/assembly, pointing to RNA processing and ribosome/ribonucleoprotein complex assembly. Some other terms (forebrain development, cellular fusion, transcription) are less cohesive with the core RNA-centric theme, but do not outweigh the clear RNA biogenesis signal.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030900","count":2}]},{"hash":"1183358807745582852","title":"Lipid and xenobiotic catabolism with strigolactone biosynthesis","description":"Based on the top GO terms, this cluster centers on catabolic processes for lipids and various xenobiotics (triglyceride, stilbene, prostaglandin, 1,2-dichloroethane catabolism) and includes a plant-development link via strigolactone biosynthesis, which connects to secondary shoot formation. The combination points to a module involved in lipid/xenobiotic breakdown alongside strigolactone production, with a stress/ detox-response component.","confidence":"Medium","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":11},{"id":"GO:0010223","count":9},{"id":"GO:1901601","count":9},{"id":"GO:0046272","count":9},{"id":"GO:0097755","count":9}]},{"hash":"1344611472974454270","title":"Metabolism and Redox Stress Response","description":"This cluster mixes core metabolic processes (tetrahydrofolate and thiamine biosynthesis, dihydrolipoamide metabolism, and mitochondrial NADH to ubiquinone electron transport) with redox-related detoxification (superoxide removal) and stress/defense responses (LPS, alkane and camphor catabolism). The common thread appears to be metabolism integrated with redox balance and stress response mechanisms, rather than a single narrow pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046653","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0019430","count":2}]},{"hash":"538594635018119350","title":"Plant secondary metabolism and detoxification","description":"Most frequent GO terms point to metabolism and breakdown of plant-derived compounds (stilbene and alkaloids, strigolactones) and related catabolic pathways (beta-ketoadipate, cellulose, triglyceride/monoacylglycerol). The inclusion of cellular oxidant detoxification supports a role in processing xenobiotics/plant metabolites. Taken together, these proteins appear to participate in plant secondary metabolism and its detoxification/turnover rather than a single linear pathway. The presence of both biosynthetic (strigolactone) and catabolic terms suggests a broader metabolic role in managing diverse plant compounds.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0019433","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0030245","count":4},{"id":"GO:0042952","count":3}]},{"hash":"1287968250064581495","title":"ER Targeting and Membrane Insertion","description":"The top GO terms point to ER-associated processes, including post-translational targeting to the ER membrane and tail-anchored membrane protein insertion, along with vesicle-mediated transport. A potential link to non-motile cilium assembly may reflect shared involvement of ER-Golgi\u2013dependent trafficking. Several items are marked obsolete or unrelated, suggesting some noise, but the core theme centers on ER targeting and membrane insertion with trafficking.","confidence":"Low","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905515","count":2},{"id":"GO:0051220","count":1},{"id":"GO:1904378","count":1},{"id":"GO:0071816","count":1},{"id":"GO:0048767","count":1}]},{"hash":"1894508161110016430","title":"Ubiquitin-Dependent NF-\u03baB Regulation","description":"The top GO terms show a strong focus on ubiquitination (autoubiquitination, ubiquitin-dependent protein catabolic process, multiple ubiquitin linkages such as K48, K63, and linear) and their impact on signaling, including positive regulation of TNF signaling and canonical NF-\u03baB pathways, plus related processes like histone turnover and necroptosis regulation. This points to a cohesive function centered on ubiquitin-mediated regulation of protein stability and inflammatory signaling, particularly NF-\u03baB. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":9},{"id":"GO:0036205","count":9},{"id":"GO:1903265","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0085020","count":9}]},{"hash":"921700685458094785","title":"Innate antiviral defense regulation","description":"GO terms point to innate immune and antiviral responses, with multiple items describing negative regulation of viral processes (viral transcription, viral release) and modulation of immune pathways (NLRP3 inflammasome, MHC I biosynthesis, LPS signaling). This suggests a cluster of host factors that regulate antiviral defense rather than direct viral components, justifying the label Innate antiviral defense regulation. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0045345","count":4},{"id":"GO:0090086","count":3},{"id":"GO:0071641","count":3}]},{"hash":"1676576810617420353","title":"MVB Sorting and Vacuolar Transport","description":"The dominant GO terms are about multivesicular body (MVB) assembly/sorting and ubiquitin-dependent protein transport to the vacuole via the MVB sorting pathway, pointing to ESCRT-mediated endosomal sorting as the core function of this cluster. Other terms like cell division and apoptotic processes may occur in related cellular contexts, but the strongest signal is MVB-mediated sorting and degradation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0030447","count":1},{"id":"GO:0036438","count":1},{"id":"GO:1901673","count":1},{"id":"GO:0071985","count":1}]},{"hash":"1554606667349033138","title":"Unknown","description":"The GO terms cover diverse processes including gametogenesis (spermatid development, vitellogenesis), organ development (heart morphogenesis), hormone signaling regulation (negative regulation of androgen receptor signaling), general growth and translation machinery (cell growth, arginyl- and glycyl-tRNA aminoacylation), and DNA damage response (negative regulation of mitotic DNA damage checkpoint). There is no clear, single functional theme tying these terms together, so a specific, cohesive label isn\u2019t supported.","confidence":"","size":12,"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:0006420","count":1},{"id":"GO:0006426","count":1},{"id":"GO:1904333","count":1}]},{"hash":"1859026038313135005","title":"Unknown","description":"The GO terms span very different biological areas: development (multicellular organism development; corticospinal tract morphogenesis), calcium signaling and cardiac electrophysiology (detection of calcium ion; regulation of SA node and atrial action potentials; ATPase-coupled calcium transporter activity), and immune/viral interactions (negative regulation of macrophage inflammatory protein 1 alpha production; suppression of viral release; negative regulation of viral transcription). Because there is no single dominant theme or function across the cluster, there isn't a clear, representative label to assign.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090086","count":1},{"id":"GO:0007275","count":1},{"id":"GO:0071641","count":1},{"id":"GO:1902187","count":1},{"id":"GO:0021957","count":1}]},{"hash":"1267151645485822493","title":"Dopamine metabolism and chemical stress responses","description":"The cluster is driven by dopamine-related terms (dopamine catabolic process and positive regulation of dopamine metabolic process) and several offres of chemical stimulus responses (response to ethanol, xenobiotic stimulus, LPS, aluminum ion), pointing to a theme of neurotransmitter turnover coupled with chemical/ xenobiotic stress responses. While there are additional metabolic terms (thiamine biosynthesis, redox) that blur the signal, the dopamine-associated annotations provide the core connection. ","confidence":"Medium","size":11,"edges":52,"triangles":139,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0009228","count":8},{"id":"GO:2000179","count":7},{"id":"GO:0042135","count":7},{"id":"GO:0032496","count":7}]},{"hash":"79645342979327550","title":"Actin-driven endocytosis and adhesion signaling","description":"This cluster centers on actin cytoskeleton dynamics (Cdc42 signaling; actin filament branching), membrane trafficking (plasma membrane to endosome transport), and adhesion-related processes (regulation of focal adhesion assembly), along with related phagocytosis signaling. Melanosome assembly can involve cytoskeletal transport, supporting the theme, while mitochondrial membrane permeabilization and viral replication terms are less central. Overall, the common thread appears to be actin-driven trafficking and adhesion-related signaling. ","confidence":"Medium","size":11,"edges":8,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903232","count":5},{"id":"GO:0039694","count":4},{"id":"GO:0010628","count":4},{"id":"GO:0048227","count":4},{"id":"GO:0051893","count":4}]},{"hash":"335861122094618870","title":"COPII-Mediated Secretory Trafficking","description":"This cluster is dominated by GO terms related to COPII vesicle formation, cargo loading, and ER-to-Golgi transport, plus extracellular matrix component secretion, pointing to a cohesive theme of the secretory pathway and protein trafficking. Other terms like autophagy and apoptotic signaling may reflect related membrane dynamics or stress responses but do not override the central COPII/secretion signal.","confidence":"High","size":11,"edges":25,"triangles":27,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":2},{"id":"GO:0035149","count":1},{"id":"GO:0016236","count":1},{"id":"GO:0061156","count":1},{"id":"GO:0060088","count":1}]},{"hash":"1372547540612554179","title":"Unknown","description":"These GO terms cover a broad mix of developmental processes (trachea formation, myotube differentiation, neural tube patterning), signaling pathways (p38 MAPK cascade, Hedgehog-related pathway regulation), and stress or adhesion-related responses (cold acclimation, cell-matrix adhesion, apoptosis, invasive growth in response to nutrient limitation). There is no single cohesive function or biological process that clearly ties all 11 proteins together, so a specific functional label is not supported.","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0044565","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0035729","count":1},{"id":"GO:0014902","count":1},{"id":"GO:0038066","count":1}]},{"hash":"1794333872670779397","title":"Ribosome Dynamics and Translational Control","description":"The top GO terms point to cytoplasmic translation processes and ribosome-related regulation (ribosome disassembly, translational termination, positive regulation of cytoplasmic translation, selenocysteine incorporation, translational fidelity). This suggests the cluster is cohesive around translation control and ribosome dynamics, with a few outliers related to RNA biology or other processes.","confidence":"Medium","size":11,"edges":10,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032790","count":4},{"id":"GO:1902802","count":4},{"id":"GO:0045903","count":4},{"id":"GO:0019079","count":4},{"id":"GO:0002184","count":4}]},{"hash":"744519450848544512","title":"Microtubule Nucleation and Spindle Assembly","description":"The top GO terms cluster around microtubule nucleation (including gamma-tubulin complex localization) and mitotic spindle assembly, pointing to roles in organizing microtubules during cell division. A few unrelated terms appear (e.g., chlorophyll biosynthesis, trachea formation), but the dominant theme is microtubule organization and spindle formation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051415","count":1},{"id":"GO:0051417","count":1},{"id":"GO:0090307","count":1},{"id":"GO:0033566","count":1},{"id":"GO:0043248","count":1}]},{"hash":"2275675152694732600","title":"Metabolism and stress signaling in tissue homeostasis","description":"These proteins show a mix of vitamin/lipid metabolism (retinol/retinal, prostaglandin, pyridoxal) and sugar biosynthesis, together with signaling and stress-response features (calcium signaling, water deprivation response, anti-apoptotic regulation, tissue homeostasis). The cluster thus appears to couple metabolic biosynthesis with tissue maintenance and stress signaling, rather than a single specific pathway.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":9},{"id":"GO:0042574","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0046370","count":7},{"id":"GO:0071277","count":6}]},{"hash":"118917374641626349","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":51,"triangles":132,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":4},{"id":"GO:0002181","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0042274","count":2}]},{"hash":"1844000005702730953","title":"Nuclear RNA Processing and Chromatin/DNA Repair","description":"These proteins are enriched for mRNA splicing, nuclear mRNA surveillance, regulatory ncRNA-mediated silencing, transcription-coupled NER, chromatin remodeling, and protein import, with some components associating with cytoplasmic stress granules. The common thread appears to be nuclear RNA processing and quality control intertwined with chromatin dynamics and DNA repair, possibly linked to stress responses. ","confidence":"High","size":11,"edges":45,"triangles":120,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":9},{"id":"GO:0031047","count":7},{"id":"GO:0000716","count":7},{"id":"GO:0043044","count":7},{"id":"GO:0071049","count":7}]},{"hash":"977968402631895098","title":"Unknown","description":"The proteins in this cluster show a mix of GO terms spanning development (trachea formation), immune differentiation (NK T cell differentiation, B cell tolerance), and signaling (Rho signaling, focal adhesion regulation), plus general regulatory processes. There isn\u2019t a single clear function or pathway that ties these terms together, so there\u2019s no cohesive theme to assign a specific label beyond Unknown.","confidence":"","size":11,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1}]},{"hash":"1298880857662861184","title":"Diverse Substrate Transporters","description":"Top GO terms are dominated by transmembrane transport activities for a wide range of substrates (sodium ions, phosphate, sugars like arabinose and fucose, sialic acid, 4-hydroxyphenylacetate, xenobiotics, etc.). This suggests a cluster of membrane transport proteins with broad substrate specificity. The presence of a term about neurotransmitter loading into synaptic vesicle hints at vesicle-associated transport roles, but the overall theme remains membrane transport of diverse substrates. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0015751","count":5},{"id":"GO:0006004","count":5},{"id":"GO:0006855","count":5}]},{"hash":"2258349421517821083","title":"Immune vesicle trafficking and antigen presentation","description":"This cluster centers on vesicle trafficking between the ER and Golgi (ER-Golgi and Golgi-ER transport), lysosome targeting, and vesicle movement relevant to immune functions (anterior/posterior synaptic vesicle transport, NK cell degranulation, and antigen processing/presentation via MHC class Ib), suggesting a theme of vesicle-mediated secretion and antigen handling in immune contexts. However, several top terms also point to nuclear processes (DNA-templated transcription, tRNA gene clustering, synaptonemal complex assembly), indicating the cluster is not exclusively immune-related. Thus, the label captures the dominant vesicle- and antigen-processing theme but with moderate certainty.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0043323","count":2},{"id":"GO:0070058","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0007130","count":2}]},{"hash":"1863644391818843020","title":"NF-\u03baB Regulation and Ubiquitin\u2013Proteasome Control","description":"The cluster centers on NF-\u03baB pathway regulation, including positive regulation of NF-\u03baB transcription factor activity and I\u03baB phosphorylation, and on ubiquitin-related proteostasis (ubiquitin/proteasome and ufmylation). While some terms reference broader signaling or older GO terms, the recurring theme is modulation of NF-\u03baB signaling coupled with protein turnover and regulation of proteostasis, suggesting a coherent theme of signaling control and degradation machinery.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":1},{"id":"GO:1990592","count":1},{"id":"GO:0032436","count":1},{"id":"GO:1903721","count":1},{"id":"GO:1905636","count":1}]},{"hash":"2233926205115415776","title":"Ribosome Biogenesis and Cell Division","description":"The Top GO terms cluster around ribosome biogenesis (ribosome biogenesis; ribosomal subunit biogenesis; ribosomal large subunit export from nucleus) and tRNA modification, with accompanying signals for cell cycle and cell division (cell cycle, cell division, cell septum assembly, conjugation with cellular fusion). This suggests a program coordinating ribosome assembly with cell growth and division, rather than a single isolated pathway.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":3},{"id":"GO:0090529","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0042254","count":2}]},{"hash":"844511471692387188","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning calcium signaling, salivary gland\u2013related differentiation, NK cell cytotoxicity, plant hormone response, triglyceride homeostasis, and stress-related transcription, with obsolete annotations as well. There are no edges or connectivity to link these functions, so no single cohesive theme emerges; labeling as Unknown reflects the lack of a unified function for this cluster.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":1},{"id":"GO:0060691","count":1},{"id":"GO:0042267","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0035356","count":1}]},{"hash":"330269044436486012","title":"Ribosome biogenesis and RNA processing","description":"The dominant signals are ribosome biogenesis and associated RNA processing (rRNA maturation, large subunit biogenesis) with a smaller hint of translation initiation regulation. These terms collectively point to proteins involved in ribosome assembly and early translation steps, supporting this label. Some unrelated or obsolete terms appear but do not override the primary theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0030708","count":1}]},{"hash":"1658878798769413994","title":"Broad Metabolite and Nutrient Transport","description":"This cluster is dominated by transport-related GO terms covering a wide range of substrates (cobalt ions, methionine, vitamins, phospholipids, oligosaccharides, very long-chain fatty acids, and even doxorubicin), suggesting a shared role in membrane transport or secretion of diverse metabolites. An outlier term for nucleotide-excision repair appears, but the prevailing signal is transport. ","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":6},{"id":"GO:0015772","count":6},{"id":"GO:0006727","count":6},{"id":"GO:0006824","count":6},{"id":"GO:0042760","count":6}]},{"hash":"1865140664177923135","title":"Calcium-Dependent Cardiac and Platelet Signaling","description":"The top GO terms cluster around calcium export across the plasma membrane, heart morphogenesis, and cardiac muscle contraction, together with kinase-related activities (positive regulation of peptidyl-serine phosphorylation and activation of protein kinase activity) and platelet activation. This suggests a shared theme of calcium-mediated signaling influencing cardiac and platelet functions, with kinase signaling modulating these processes. Some terms (germ cell development, ascospore formation, NHEJ) appear more disparate, likely reflecting broader cellular roles within the cluster. Overall, the label captures the strongest, coherent pattern in the data.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033138","count":2},{"id":"GO:0032973","count":1},{"id":"GO:1990034","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0006303","count":1}]},{"hash":"1260537805182074623","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002635","count":1},{"id":"GO:1902187","count":1},{"id":"GO:1903883","count":1},{"id":"GO:0033280","count":1},{"id":"GO:0000185","count":1}]},{"hash":"97161707049185823","title":"Plant secondary metabolism and hormone biosynthesis","description":"The top GO terms center on plant-specific pathways such as strigolactone and stilbene biosynthesis, along with secondary shoot formation and biotin biosynthesis, pointing to roles in plant growth regulation and secondary metabolite production. Some terms (e.g., prostaglandin catabolic, xenobiotic degradation) are unrelated or noisy, which lowers certainty. Overall, the cluster likely reflects plant hormone and secondary metabolite biosynthetic processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0009636","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0010223","count":4},{"id":"GO:1901601","count":4}]},{"hash":"1189956933632649283","title":"Lipid and retinoid metabolism (adipose-related)","description":"The GO terms cluster around lipid metabolism and retinoid processing (retinol/vitamin A), with links to ether lipids, phosphocholine metabolism, and lipid transport, plus adipose development and lactation, suggesting a cohesive lipid-centric theme tied to fat biology.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070292","count":1},{"id":"GO:0071284","count":1},{"id":"GO:1904177","count":1},{"id":"GO:0006776","count":1},{"id":"GO:0032370","count":1}]},{"hash":"1987006870169783776","title":"Neuronal endosomal trafficking and receptor recycling","description":"The top GO terms point to endosomal processes and synaptic activity, including receptor recycling, endosome size regulation, and glutamatergic synaptic transmission, suggesting a shared role in endocytic trafficking and receptor turnover at synapses; other terms are less cohesive, but the core theme fits neuronal trafficking.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001881","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0060316","count":1},{"id":"GO:0034968","count":1},{"id":"GO:0035023","count":1}]},{"hash":"654050286130701860","title":"Unknown","description":"No GO terms are provided for this cluster (empty Top Terms) and there are no edges or functional signals to tie the proteins together; thus a coherent, representative label cannot be inferred.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1934534946432598966","title":"Wnt/Notch Signaling and Lipid Metabolism","description":"This cluster is dominated by Wnt and Notch signaling terms, plus lipid metabolism and protein turnover terms, suggesting a group of proteins related to developmental signaling that interfaces with lipid metabolism and RNA/protein turnover. The connection is plausible but not tightly specific, so Medium confidence.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034389","count":1},{"id":"GO:0016055","count":1},{"id":"GO:0045581","count":1},{"id":"GO:0007219","count":1},{"id":"GO:0019433","count":1}]},{"hash":"726960281810276923","title":"Unknown","description":"There are no GO terms provided in the Top Terms to guide labeling; without a shared functional theme, there is no clear common function among these proteins beyond network connectivity, so a safe label is Unknown. If GO terms become available, we can assign a more specific label.","confidence":"","size":10,"edges":23,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[]},{"hash":"2079236996145844270","title":"Neural development and axon guidance","description":"The cluster\u2019s top GO terms cluster around neuronal development and axon pathfinding, including dendritic spine development, CNS projection neuron axonogenesis, fasciculation of sensory neuron axon, and ephrin receptor signaling, with supporting involvement of focal adhesion regulation and related signaling. A few terms (iodide transport, nephric duct morphogenesis, and immune-related processes) are less central but may reflect broader expression contexts; overall, neural development is the prevailing theme.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060996","count":2},{"id":"GO:0072178","count":2},{"id":"GO:0097155","count":2},{"id":"GO:2000525","count":2},{"id":"GO:0048013","count":2}]},{"hash":"528732588928496833","title":"Unknown","description":"The top GO terms are very diverse and show no shared functional theme or interactions among the 10 proteins, with no edges linking members. Terms span toxin response, folate and methylation metabolism, dTMP biosynthesis, axon regeneration, cartilage development, redox, and NOS regulation, making a coherent, specific cluster function unlikely.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0019088","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0006231","count":1},{"id":"GO:0031103","count":1}]},{"hash":"1210375877269737490","title":"Nuclear chromatin regulation and cell-cycle control","description":"This cluster centers on nuclear processes: chromatin binding regulation, protein desumoylation/deneddylation, regulation of kinetochore assembly, and controls over DNA endoreduplication and kinase signaling. While a couple terms touch on placental development (tissue-specific roles), the dominant pattern is intracellular regulation of chromatin dynamics and cell cycle progression.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904333","count":1},{"id":"GO:0016926","count":1},{"id":"GO:0010724","count":1},{"id":"GO:0000338","count":1},{"id":"GO:0035562","count":1}]},{"hash":"342727180889354099","title":"Amino acid, porphyrin, and cofactor biosynthesis","description":"The cluster shows multiple GO terms focused on biosynthetic processes for amino acids or their precursors (oxaloacetate, pyruvate, transsulfuration, cysteine, lysine) as well as biosynthesis of cofactors and prosthetic groups (biotin, porphyrinogen IX, coenzyme M). This suggests a cohesive theme of anabolic metabolism building essential metabolites and cofactors. ","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006107","count":4},{"id":"GO:0019551","count":4},{"id":"GO:0019343","count":4},{"id":"GO:0042866","count":4},{"id":"GO:0070814","count":4}]},{"hash":"150945905234788938","title":"Ribosome Biogenesis and SRP-Targeting","description":"The top GO terms cluster around translation and ribosome assembly (translation, maturation of SSU/LSU rRNA, ribosomal large subunit assembly) and SRP-dependent cotranslational protein targeting to the membrane (signal sequence recognition and translocation). This suggests proteins focused on ribosome function and the co-translational targeting of nascent polypeptides to membranes. A bacterial flagellum organization term appears as a secondary annotation and does not override the main theme.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0051301","count":3},{"id":"GO:0006614","count":2},{"id":"GO:0006617","count":2},{"id":"GO:0044781","count":2}]},{"hash":"385285552488081123","title":"Neural development and stress-response signaling","description":"This cluster is enriched for neural development terms (central nervous system neuron development, dendrite morphogenesis) and organ regeneration, alongside stress- and immune-related responses (insulin stimulus, lipopolysaccharide, toxic substances) and basic proliferation processes (DNA replication, cell division, transcription). The combination suggests proteins involved in neural development with associated regenerative and stress-response regulation.","confidence":"Medium","size":10,"edges":13,"triangles":10,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032869","count":6},{"id":"GO:0031100","count":5},{"id":"GO:0009636","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0051301","count":4}]},{"hash":"73023743639075661","title":"Cell signaling and stress response","description":"The set shows enrichment in signaling and regulation under stress and growth cues (Rho signaling, DNA damage checkpoint, osmotic stress response, cadmium response) as well as growth/development references (trachea formation, septation signaling, hypertrophy regulation). This points to a cluster of proteins involved in broader signaling networks that modulate growth, stress adaptation, and regulatory processes.","confidence":"Medium","size":10,"edges":17,"triangles":15,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032436","count":4},{"id":"GO:0060440","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007266","count":3},{"id":"GO:0010614","count":3}]},{"hash":"1589423783030196210","title":"Macrophage cholesterol handling and inflammatory signaling","description":"The terms point to lipid metabolism in macrophages (positive regulation of cholesterol efflux, reverse cholesterol transport, HDL remodeling, triglyceride homeostasis) together with innate immune and inflammatory processes (macrophage activation, TNF production, TLR4 signaling, response to lipoteichoic acid). This suggests a shared theme of lipid handling coupled to inflammatory signaling in macrophages, rather than a single enzymatic function. The lack of network edges doesn\u2019t contradict this theme, as the GO terms collectively imply a cohesive macrophage lipid-immune interface.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010875","count":1},{"id":"GO:0034145","count":1},{"id":"GO:0071223","count":1},{"id":"GO:0043691","count":1},{"id":"GO:0045919","count":1}]},{"hash":"57971869988893676","title":"Unknown","description":"The top GO terms are diverse, spanning meiosis regulation, salt stress response, Ras and small GTPase signaling, sarcomere organization, sodium/mPotassium ion transport, receptor signaling regulation, drug response, and aerotaxis. There is no single dominant function or pathway tying these proteins together, making a clear, representative cluster label unclear.","confidence":"","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051447","count":1},{"id":"GO:0009651","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0045214","count":1},{"id":"GO:0098719","count":1}]},{"hash":"2113227611164631519","title":"RNA splicing and ncRNA-mediated gene silencing","description":"This cluster is characterized by GO terms for mRNA splicing via the spliceosome and regulation of splicing, regulatory ncRNA\u2013mediated gene silencing, and nuclear mRNA surveillance, indicating a core of RNA processing and post-transcriptional regulation. Inner signals of chromatin remodeling and transcription-coupled DNA repair suggest coupling of RNA processing with chromatin state and genome maintenance.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0070584","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2}]},{"hash":"141549075753725834","title":"Ribosome Biogenesis and tRNA Modification","description":"The top terms are dominated by ribosome biogenesis and ribosomal subunit biogenesis, plus a tRNA modification term, pointing to a cluster enriched for ribosome assembly and translation-related RNA processing. Peripheral terms like phosphorylation or cell cycle do not contradict this theme, making the ribosome-focused interpretation the most coherent.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904251","count":1},{"id":"GO:0015937","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0006400","count":1}]},{"hash":"956764846562483120","title":"Cytokinesis and PI signaling in development","description":"The top GO terms cluster around cell division (mitotic cell cycle, cleavage furrow formation) and phosphatidylinositol-mediated signaling, with positive regulation of GTPase activity, suggesting a group of proteins coordinating cytokinesis and PI-driven signaling. Developmental processes (brain and bone development) appear as secondary themes, indicating these proteins may function in growth contexts where division and membrane signaling converge. Additional trafficking-related terms (endosome-to-Golgi transport, Cvt pathway) support a role in membrane trafficking that can accompany cytokinesis and PI signaling. Overall, the cluster points to cytokinesis coupled with PI-mediated signaling during development. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0036089","count":1}]},{"hash":"2056236009869817156","title":"ER-nuclear envelope organization and trafficking","description":"This cluster's GO terms cluster around endoplasmic reticulum organization and nuclear envelope processes (ER inheritance, nuclear pore complex assembly, mitotic nuclear membrane reassembly) and membrane trafficking (protein transport into membranes). A few terms related to ER stress and some plant-specific signals appear as noise, but the core theme is ER/nuclear membrane dynamics and associated trafficking.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032581","count":1},{"id":"GO:0051292","count":1},{"id":"GO:0007084","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0048309","count":1}]},{"hash":"1785592437941811679","title":"Small GTPase Signaling and Muscle Regulation","description":"This cluster is best described by its emphasis on small GTPase\u2013mediated signal transduction and related signaling outputs (Ras signaling, adenylate cyclase regulation, receptor guanylyl cyclase signaling) together with muscle-related processes (sarcomere organization and cardiac muscle cell proliferation). While a few terms like aerotaxis or drug response are less related, the core pattern points to regulation of signaling pathways that influence muscle function.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0007264","count":2}]},{"hash":"781722613749167953","title":"Unknown","description":"The top terms span neural development (neuron differentiation, Schwann cell development), fungal ascospore formation, xenobiotic stress response, glycogen catabolism regulation, and several DNA repair/checkpoint processes. This broad, diverse mix lacks a single coherent theme, so a specific, representative label cannot be reliably assigned.","confidence":"","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030182","count":10},{"id":"GO:2001241","count":10},{"id":"GO:1905213","count":10},{"id":"GO:0035690","count":10},{"id":"GO:0031573","count":10}]},{"hash":"51297195835536270","title":"Lipid catabolism and remodeling","description":"The top GO terms cluster around triglyceride catabolic processes and lipid remodeling, including triglyceride mobilization and catabolism of phospholipids (phosphatidylcholine and phosphatidylethanolamine), suggesting proteins involved in lipid breakdown and turnover. Some entries also touch on regulation of signaling pathways (PKA) and oxidative/detox responses, which often accompany lipid metabolism shifts. ","confidence":"Medium","size":10,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":5},{"id":"GO:0006642","count":3},{"id":"GO:2000480","count":3},{"id":"GO:0046338","count":3},{"id":"GO:0034638","count":3}]},{"hash":"83903109240525555","title":"Calcium signaling in excitable cells","description":"This cluster centers on calcium-dependent signaling and regulation of ion channels and excitability: positive regulation of calcineurin-NFAT signaling, calcium transporter activity, cardiac muscle contraction, regulation of synaptic vesicle exocytosis, and clustering of voltage-gated potassium channels\u2014all tied to Ca2+-mediated muscle and neural function. Some terms (trachea development, xenobiotic response, hydrogen peroxide biosynthesis) are broader or stress-related, but the dominant pattern points to calcium signaling and excitation-contraction/exocytotic control.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0071902","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0045163","count":1}]},{"hash":"1972079074352617792","title":"Cytoskeleton-Driven Membrane Organization","description":"The GO terms cluster around actin/cytoskeleton dynamics and membrane/surface organization (actin filament organization, GTPase regulation, membrane addition during cytokinesis, microvillus/brush border assembly, vesicle transport), with contextual ties to neuronal guidance, balance sensing, and pigment granule transport. This suggests a unifying theme of cytoskeleton remodeling coupled to membrane trafficking shaping cell surfaces and polarity.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0070493","count":1},{"id":"GO:1903480","count":1},{"id":"GO:0016198","count":1},{"id":"GO:0007107","count":1},{"id":"GO:0000011","count":1}]},{"hash":"119742325827056867","title":"Bacterial lipid biosynthesis and transport","description":"The cluster is dominated by GO terms related to lipid metabolism and membrane components, including menaquinone biosynthesis, lipoteichoic acid biosynthesis, various fatty acid metabolic processes, and fatty acid transport/import. These point to a cohesive theme of lipid biosynthesis and lipid-handling in bacteria (with lactose/seed-coat and plant phenylpropanoid terms appearing as outliers, and bioluminescence loosely connected through fatty aldehyde metabolism). Overall, a lipid-focused bacterial membrane/energy metabolism theme fits best.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":8},{"id":"GO:0008218","count":8},{"id":"GO:0019427","count":8},{"id":"GO:0070395","count":8},{"id":"GO:0001579","count":8}]},{"hash":"677339616758937467","title":"Muscle signaling and sarcomere organization","description":"The presence of terms like sarcomere organization and cardiac muscle cell proliferation suggests a muscle-specific theme, complemented by signaling-related terms (small GTPase signaling, regulation of adenylate cyclase, and guanylyl cyclase pathways). Some terms (aerotaxis, meiotic cell cycle regulation) appear unrelated noise, but the core pattern centers on muscle structure and signaling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051447","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0045214","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0007264","count":1}]},{"hash":"674597654879874755","title":"Neuronal mitochondrial quality control and homeostasis","description":"These terms center on mitochondrial quality control (negative regulation of mitophagy, positive regulation of mitochondrial fusion) and neuronal survival/homeostasis (neuron cellular homeostasis, neuron intrinsic apoptotic signaling), suggesting a shared role in maintaining mitochondrial function in neurons; additional terms such as LPS response and cholesterol homeostasis may reflect broader cellular stress responses.","confidence":"Medium","size":10,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903147","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0070782","count":1},{"id":"GO:0001300","count":1},{"id":"GO:0060368","count":1}]},{"hash":"843428570094567006","title":"Ribosome-Associated Ubiquitin-Proteasome Quality Control","description":"The cluster centers on ubiquitin-dependent proteolysis in the cytoplasm, especially ribosome-associated protein degradation and quality control via the ubiquitin-proteasome system. Additional links to the N-end rule pathway and regulation of TOR signaling by ubiquitin suggest a broader theme of proteostasis tied to translation and nutrient sensing. While a few terms (e.g., RISC assembly, some obsolete annotations) are tangential, the dominant signal is proteostasis linked to ribosome function and TOR pathway regulation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071629","count":2},{"id":"GO:0001967","count":2},{"id":"GO:0033522","count":2},{"id":"GO:1901718","count":2},{"id":"GO:0070923","count":2}]},{"hash":"93114097702600484","title":"Embryonic tissue development and transcription regulation","description":"The majority of terms point to developmental processes across tissues (skin, spinal cord, forebrain, cartilage) and overall multicellular development, coupled with DNA-templated transcription. A few stress-related terms are present but less dominant, so the central theme is developmental programing and gene expression.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0001502","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0001403","count":2}]},{"hash":"20265833684065306","title":"Lipid metabolism and immune response","description":"This cluster is enriched for GO terms related to lipid handling (intracellular cholesterol transport, cholesterol efflux, ganglioside catabolic process) and immune/inflammatory signaling (inflammatory response, innate immune response, response to virus, lipopolysaccharide-mediated signaling, necroptotic process), suggesting a common theme of lipid metabolism linked to immune responses and inflammation. Some terms (learning or memory, ecdysteroid biosynthetic process) appear less directly related and may reflect annotation breadth or cross-species annotations.","confidence":"High","size":10,"edges":13,"triangles":1,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":3},{"id":"GO:0032367","count":2},{"id":"GO:0006689","count":2},{"id":"GO:0007611","count":2},{"id":"GO:0033344","count":2}]},{"hash":"2284197205884926574","title":"Plant detoxification and catabolic metabolism","description":"This cluster is dominated by plant-specific detoxification and catabolic processes. GO terms include response to toxic substance and cellular oxidant detoxification, plus catabolic processes for chlorophyll, stilbene, triglycerides, and xenobiotics, and also strigolactone biosynthesis with secondary shoot formation, indicating involvement in plant metabolism and development. Overall, the terms point to a plant-focused metabolism and stress response module.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0009636","count":7},{"id":"GO:0098869","count":6},{"id":"GO:0015996","count":6},{"id":"GO:0019433","count":6}]},{"hash":"1708093405775403140","title":"Plant secondary metabolism and hormone biosynthesis","description":"The top GO terms cluster around biosynthetic and catabolic processes for plant-specific metabolites (antibiotic, biotin, menaquinone, strigolactone, stilbene) and shoot formation, highlighting plant specialized metabolism and hormone-related pathways. Although there are no edges linking the proteins, the recurring theme is plant metabolism and developmental signaling, supporting a label focused on plant secondary metabolism and hormone biosynthesis.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0010223","count":2}]},{"hash":"1723041806440589386","title":"Meiosis-associated chromatin remodeling and transcription","description":"The cluster centers on transcription initiation/clearance by RNA Pol II and chromatin remodeling, with associated histone modifications (acetylation) and regulation of transcriptional activity. The presence of meiotic/mating-type related terms (male meiosis I, mating type switching) suggests this group coordinates chromatin state and transcription during meiosis or mating in yeasts/fungi. Hence a label linking chromatin remodeling with transcription in a meiotic context is appropriate.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001111","count":1},{"id":"GO:2000219","count":1},{"id":"GO:0043044","count":1},{"id":"GO:0031496","count":1},{"id":"GO:0043969","count":1}]},{"hash":"770158007013041745","title":"Innate Immune Sensing and Inflammasome Activation","description":"TopGO terms indicate TLR9 and NOD2 signaling, NLRP3 inflammasome assembly, and interferon pathways, with additional regulation of cell migration and lamellipodium organization, all pointing to a module of innate immune detection and inflammatory response.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046827","count":2},{"id":"GO:0034162","count":1},{"id":"GO:0030335","count":1},{"id":"GO:1902745","count":1}]},{"hash":"1146993678702486506","title":"Zinc ion transport and homeostasis","description":"The top GO terms are dominated by zinc-related processes: zinc ion import across membranes, intracellular zinc ion homeostasis, detoxification of zinc ion, and cellular response to zinc ion starvation, with cadmium ion transmembrane transport hinting at shared metal transport. A limb development term appears incidental. This suggests the cluster centers on zinc transport and metal ion homeostasis.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":3},{"id":"GO:0006882","count":3},{"id":"GO:1903615","count":3},{"id":"GO:0006831","count":3},{"id":"GO:0006830","count":3}]},{"hash":"998712541096583250","title":"Innate Immune Sensing and Dendritic Cell Activation","description":"This cluster is enriched for GO terms linking TLR9 signaling, NOD2 signaling, and NLRP3 inflammasome assembly, along with interferon signaling and enhanced antigen processing/presentation by dendritic cells, including MHC class I biosynthesis. The presence of terms related to positive regulation of cell migration and lamellipodium organization suggests DC maturation and movement. Together these terms point to a cohesive theme of innate immune sensing driving dendritic cell activation and antigen presentation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":9},{"id":"GO:0030335","count":9},{"id":"GO:1902745","count":9},{"id":"GO:0070431","count":9},{"id":"GO:0002830","count":9}]},{"hash":"1869455681631918825","title":"Membrane trafficking and actin remodeling in development","description":"The proteins share signals for membrane shaping and trafficking (clathrin coat assembly, plasma membrane tubulation) and cytoskeletal remodeling (dendritic spine development, actin cable regulation), with adhesion and developmental morphogenesis terms, suggesting a cohesive theme of membrane remodeling and actin dynamics during development.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036119","count":1},{"id":"GO:0030708","count":1},{"id":"GO:0051044","count":1},{"id":"GO:0060996","count":1},{"id":"GO:0044331","count":1}]},{"hash":"439250294744912363","title":"Stress signaling and vesicle trafficking regulation","description":"This cluster centers on GO terms related to regulation of signaling pathways (stress responses such as salt/ABA signaling and apoptotic regulation, TNF regulation, Rho signaling) and vesicle trafficking processes (synaptic vesicle exocytosis and maturation). The mix suggests a group of regulatory proteins that modulate signaling cascades and vesicle dynamics rather than a single, cohesive pathway. Some terms like transcription regulation and SMAD catabolism appear peripheral but do not define a single function for the cluster.","confidence":"Medium","size":9,"edges":31,"triangles":54,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045945","count":2},{"id":"GO:1904468","count":1},{"id":"GO:1902176","count":1},{"id":"GO:2000300","count":1},{"id":"GO:0009738","count":1}]},{"hash":"185018017972841449","title":"Neuronal microtubule dynamics and axon development","description":"The terms cluster around microtubule remodeling, including axonemal and cytoplasmic depolymerization, plus-end dynamics, and spindle-related processes, with neuron projection maintenance and Purkinje cell layer organization pointing to roles in neuronal morphology and axon development rather than mitosis alone. This suggests a cohesive theme of microtubule regulation guiding neurite growth and maintenance in neurons.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060404","count":8},{"id":"GO:0070462","count":8},{"id":"GO:0048364","count":8},{"id":"GO:0021693","count":8},{"id":"GO:0000022","count":8}]},{"hash":"1925246089880060994","title":"Unknown","description":"The GO terms span diverse processes (cell cycle transition, protein processing/modification, cilium assembly, hormone signaling, metal response, ER stress\u2013related translation, ubiquitination, interferon response, and post-translational modifications) with no single cohesive function linking all proteins, so a meaningful cluster label cannot be assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007091","count":1},{"id":"GO:0000413","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0009938","count":1},{"id":"GO:0010288","count":1}]},{"hash":"19840411712585246","title":"Actin dynamics and membrane trafficking signaling","description":"The cluster's GO terms mainly point to actin cytoskeleton dynamics (actin branching, Cdc42 signaling, focal adhesion regulation) and membrane trafficking/endocytosis (plasma membrane to endosome transport, EGFR signaling). Additional terms touch on broader cell signaling and apoptosis (nerve branching morphogenesis regulation, mitochondrial outer membrane permeabilization), but the core theme is cytoskeleton-driven signaling and membrane trafficking.","confidence":"Medium","size":9,"edges":30,"triangles":57,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0039694","count":9},{"id":"GO:0010628","count":9},{"id":"GO:0048227","count":9},{"id":"GO:0007173","count":9},{"id":"GO:0051893","count":9}]},{"hash":"174847044591622137","title":"Bacterial DNA replication and repair (SOS)","description":"The cluster centers on bacterial DNA metabolism: terms point to DNA replication (including rolling circle replication) and homologous recombination repair of double-strand breaks, along with the SOS DNA damage response and even clearance of foreign DNA. These together define a cohesive theme around bacterial DNA replication/repair and stress signaling, justifying a label like this despite some obsolete terms.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006268","count":3},{"id":"GO:0000724","count":3},{"id":"GO:0044787","count":3},{"id":"GO:0070581","count":3},{"id":"GO:2000042","count":3}]},{"hash":"160348198484879239","title":"Ribosome Biogenesis and Cell Division","description":"Based on the GO terms, the cluster centers on ribosome production and maturation (ribosome biogenesis, small/large subunit processes, tRNA modification, nucleus export) together with cell division activities (cell cycle, cell division, septum assembly). This pattern suggests proteins involved in ribosome assembly coupled to cell growth and division, with some stress-response terms appearing but not defining the core theme.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000055","count":5},{"id":"GO:0006400","count":3},{"id":"GO:0090529","count":3},{"id":"GO:1903833","count":3}]},{"hash":"1185267288911840167","title":"Bacterial RNA Methylation and Cofactor Biosynthesis","description":"The cluster prominently features RNA guanine-N7-methylation and rRNA modification, pointing to RNA-modifying enzymes. It also includes biosynthetic processes for cobalamin and menaquinone and antibiotic biosynthesis, suggesting metabolic and secondary metabolism roles in bacteria. Additional terms reference xenobiotic and osmotic stress responses, indicating broader stress adaptation but not core to the main theme. Overall, the data support a RNA modification plus cofactor biosynthesis theme, hence a Medium confidence.","confidence":"Medium","size":9,"edges":10,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0000154","count":3},{"id":"GO:0036265","count":3}]},{"hash":"1246851703006912547","title":"Bacterial cell wall and LPS biosynthesis","description":"This cluster centers on biosynthesis of bacterial cell wall components and envelope polysaccharides, including peptidoglycan, lipopolysaccharide core and O antigen, and related UDP-sugar pathways. The GO terms indicate a cohesive theme of constructing the cell envelope rather than cytosolic processes, supporting a cell-wall\u2013biosynthesis label.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009244","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0045226","count":1},{"id":"GO:0006011","count":1}]},{"hash":"961633945696241043","title":"Angiogenesis and vascular development","description":"The strongest GO signals are angiogenesis, endothelial cell migration, multicellular organism development, and trachea formation, all tying to vascular/organ morphogenesis and the regulation of adhesion and gene expression. A few terms related to nervous system processes appear as outliers, but the core theme centers on vascular development and related transcriptional control.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001525","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0043536","count":3},{"id":"GO:0046827","count":3}]},{"hash":"793414124125065041","title":"Lysosomal trafficking and autophagy","description":"The cluster\u2019s GO terms cluster around lysosome biology and vesicular transport, including lysosome localization, lysosomal lumen acidification, endosome-to-lysosome transport, autophagosome maturation, and secretion of lysosomal enzymes, as well as intracellular protein transport. The presence of retrograde axonal transport and synaptic vesicle fusion to the presynaptic membrane suggests broader vesicle trafficking roles in neurons. A couple of terms related to pigment cell differentiation and NK cell activation appear peripheral but may reflect context-dependent roles of vesicle trafficking in different cell types. Overall, the proteins seem to form a group centered on lysosome-associated trafficking and autophagy.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0033299","count":1},{"id":"GO:0097352","count":1},{"id":"GO:0008333","count":1},{"id":"GO:0031629","count":1},{"id":"GO:0008090","count":1}]},{"hash":"7196802239564854","title":"Unknown","description":"The GO terms span cardiac function, trachea development, immune differentiation, sensory perception, signaling and adhesion, and glucose-responsive growth, with no single cohesive theme. The presence of an obsolete term and the diversity of functions suggest there is no clear unifying function for this cluster.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":1},{"id":"GO:0060048","count":1},{"id":"GO:0060440","count":1},{"id":"GO:1900827","count":1},{"id":"GO:0051893","count":1}]},{"hash":"1026866988629376645","title":"Gram-positive cell wall biosynthesis and lipid metabolism","description":"The top GO terms cluster around Gram-positive cell envelope features (lipoteichoic acid biosynthesis, cell wall organization) and menaquinone biosynthesis, with related lipid transport/metabolism, suggesting a cohesive theme of cell-wall construction and associated energy/lipid pathways in Gram-positive bacteria.","confidence":"High","size":9,"edges":12,"triangles":6,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":3},{"id":"GO:0070395","count":3},{"id":"GO:0071555","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0008218","count":2}]},{"hash":"1697272360011827883","title":"Unknown","description":"The GO terms are highly diverse, with a small set suggesting lipid metabolism (ergosterol biosynthesis, unsaturated fatty acid biosynthesis, and a sphingolipid-related metabolic process) but many unrelated terms (central nervous system myelin maintenance, sebaceous gland differentiation, nitrate assimilation, NO biosynthesis, etc.). There is no coherent, single theme tying all terms together for this cluster, so a specific, representative label cannot be confidently assigned.","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0032286","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0032443","count":1}]},{"hash":"1394820180382653531","title":"Ribosome biogenesis and translation machinery","description":"This cluster is dominated by translation-related terms (translation, initiation, termination) and ribosome biogenesis, with selenocysteine incorporation highlighting specialized translation. Additional RNA-processing terms (mRNA decay) connect to gene expression control, while a few outliers (glial proliferation, antibiotic response) are less central. ","confidence":"High","size":9,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0006353","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006413","count":2}]},{"hash":"2099655021254505356","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0015969","count":2},{"id":"GO:0001680","count":2}]},{"hash":"248346366491214976","title":"DNA replication and cell cycle regulation","description":"Top GO terms such as DNA replication, DNA-templated transcription, and the centrosome cycle point to genome duplication and cell division as core themes. Additional terms related to cell size regulation and development reflect broader growth programs in proliferative cells. Overall, the cluster most plausibly centers on DNA replication and cell cycle control.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0045793","count":5},{"id":"GO:0001890","count":5}]},{"hash":"1196323858037968719","title":"Cilium/Photoreceptor Assembly and Localization","description":"These proteins show a clear signal related to cilia and photoreceptor biology, with non-motile cilium assembly and protein localization to the photoreceptor outer segment pointing to a shared module in ciliary assembly and transport. The other terms (interferon response, ER stress-related translation, cadmium, morphine, photosynthesis) appear more scattered or noisy in such a small cluster, so the core theme is best captured by ciliary/photoreceptor functions. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905515","count":3},{"id":"GO:0009938","count":2},{"id":"GO:0016570","count":2},{"id":"GO:0035457","count":2},{"id":"GO:0071276","count":2}]},{"hash":"2121918572776245793","title":"Regulated adhesion and signaling in development and immunity","description":"The cluster\u2019s top GO terms cluster around regulation of cell adhesion and cytoskeletal signaling (focal adhesion assembly, ECM disassembly, Rho signaling) as well as immune development processes (NK T cell differentiation, B cell tolerance). This suggests a cohesive theme of regulated signaling governing cell\u2013matrix interactions with roles in development and immune modulation, despite some developmental/invasion terms present. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":9},{"id":"GO:0060440","count":9},{"id":"GO:0051893","count":9},{"id":"GO:0001403","count":9},{"id":"GO:0007266","count":9}]},{"hash":"1087604264843267556","title":"Unknown","description":"The top GO terms are highly heterogeneous (cadmium ion response, DNA replication, mitotic cell cycle, trachea formation, focal adhesion regulation, Rho signaling, NK T cell differentiation, etc.), with no single unifying function tying all proteins together. Given this lack of a cohesive biological theme, a simple, specific label is not interpretable. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000278","count":3},{"id":"GO:1901214","count":2},{"id":"GO:0060440","count":2}]},{"hash":"493614602851768674","title":"Transcriptional Regulators, ECM Remodeling, and Immunity Differentiation","description":"The GO terms point to general transcriptional regulation (DNA-templated transcription) together with ECM-related processes (focal adhesion assembly, ECM disassembly) and immune differentiation (NK T cell differentiation, B cell tolerance). This suggests a cluster of proteins that broadly regulate gene expression while influencing cell\u2013matrix interactions and immune cell development, rather than a single, cohesive pathway. Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0046827","count":4},{"id":"GO:1901214","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0001865","count":3}]},{"hash":"1393630093093750679","title":"Bacterial SOS Response and DNA Repair","description":"The top GO terms point to a strong signal for DNA damage response and repair: SOS response, homologous recombination repair, and nucleotide-excision repair dominate the set. While there are additional terms related to RNA processing, export, and transport (and some metabolism/ secretion-related terms), the DNA damage sensing and repair activities are the most representative theme of this cluster, suggesting a bacterial stress-response module centered on genome maintenance.","confidence":"Medium","size":9,"edges":11,"triangles":0,"max_degree":4,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0009432","count":4},{"id":"GO:0006370","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0000056","count":4},{"id":"GO:0000724","count":3}]},{"hash":"1257964418229509508","title":"Unknown","description":"The proteins map to a broad and heterogeneous set of regulatory processes (nuclear protein export, focal adhesion assembly, Rho signaling, immune differentiation, development), with no clear shared function or pathway tying them together. The lack of a cohesive theme and zero edges suggest no meaningful, single-label cluster function can be assigned beyond Unknown. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1}]},{"hash":"2232449523825207633","title":"Unknown","description":"This cluster shows no coherent functional theme: the top GO terms include response to chromate, N-terminal peptidyl-methionine acetylation, and lipid catabolic process, each with only a single annotation and no shared biology. With no connecting edges and no dominant function, there is no clear common theme to name the cluster.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046687","count":1},{"id":"GO:0017196","count":1},{"id":"GO:0016042","count":1}]},{"hash":"257475017163024007","title":"Neuronal microtubule dynamics and projection maintenance","description":"These proteins are enriched for microtubule depolymerization and plus-end dynamics, along with neuron-specific terms like neuron projection maintenance and Purkinje cell layer organization, pointing to a role in dynamic microtubule remodeling that supports neuronal morphology and axon/dendrite stability. Some spindle-related terms may reflect shared microtubule regulatory machinery rather than cell division in neurons.","confidence":"Medium","size":9,"edges":13,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060404","count":8},{"id":"GO:0070462","count":8},{"id":"GO:0048364","count":8},{"id":"GO:0021693","count":8},{"id":"GO:0000022","count":8}]},{"hash":"968988397896119709","title":"Unknown","description":"The GO annotations are highly diverse, including xenobiotic and vitamin D metabolism, lipid signaling (prostaglandin), methylation, potassium ion response, insecticide metabolism, and even sex differentiation, with no clear, shared biological function linking the proteins. Because there is no coherent theme or pathway evident across terms, no specific functional label can be confidently assigned.","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035865","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0001516","count":1},{"id":"GO:0042369","count":1},{"id":"GO:0033280","count":1}]},{"hash":"364171154744504654","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:1901621","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0000740","count":1}]},{"hash":"920896069910644987","title":"ER-mitochondrial stress response","description":"The terms cluster around ER protein folding and unfolded protein response, heat response, and redox homeostasis, plus mitochondrial apoptotic changes and regulation of membrane potential. Additionally, transmembrane transport of key metabolites (alpha-ketoglutarate, thiamine pyrophosphate, CoA) suggests coordinated metabolic and energy-related stress signaling between ER and mitochondria. This supports a cohesive ER-mitochondrial stress and metabolic regulation module.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0006351","count":3}]},{"hash":"393000030895659846","title":"Neuronal development and maturation","description":"The cluster\u2019s GO terms are dominated by neural development signals (positive regulation of neural precursor cell proliferation, neuron maturation, and positive regulation of neuron projection development), suggesting the proteins collectively relate to neuronal differentiation and maturation, despite some metabolism-related terms in the mix.","confidence":"Medium","size":9,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0042551","count":1},{"id":"GO:0006915","count":1}]},{"hash":"2196974443520670955","title":"Regulated signal transduction and cell proliferation","description":"This cluster contains terms mostly about positive regulation of kinase and GTPase activity, mitotic cell cycle, and positive regulation of cell proliferation, suggesting a focus on signaling control of cell growth. Additional terms point to stress responses (hypoxia, hydrogen peroxide biosynthesis) and foundational processes like mRNA transport and ion-channel clustering, implying a broader cellular homeostasis role. Overall, the cluster reflects signaling regulation tied to proliferation, with peripheral stress-related processes.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0008284","count":5},{"id":"GO:0031954","count":5}]},{"hash":"385797842888970608","title":"Metabolic Biosynthesis and Kinase Regulation","description":"The terms point to a mix of catabolic and biosynthetic metabolic processes (phenylacetate and valine catabolism; menaquinone and phylloquinone biosynthesis; fatty acid beta-oxidation; antibiotic biosynthetic process) and GO terms involving kinase activity regulation and lipid signaling (SREBP pathway, regulation of serine/threonine and tyrosine kinases). This suggests a cluster focused on metabolism with connected signaling regulation, rather than a single narrow function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0042372","count":1},{"id":"GO:0006574","count":1},{"id":"GO:0017000","count":1}]},{"hash":"2144150966651027906","title":"Copper Ion Response","description":"The top GO term is a specific copper ion response, suggesting a shared theme among these proteins. However, there are no interactions (edges) and only one protein annotated with this term among the cluster, so the connection is weak and the cluster is not broadly cohesive beyond this single function. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046688","count":1}]},{"hash":"891820590389170586","title":"Cdc42-driven actin remodeling and endocytic trafficking","description":"This cluster is dominated by GO terms tied to the actin cytoskeleton and signaling that governs actin dynamics (actin filament branching; Cdc42 signal transduction) plus processes of membrane trafficking and cell migration (plasma membrane to endosome transport; protein localization to the leading edge; focal adhesion regulation). These together point to a cohesive theme of cytoskeleton-driven remodeling that enables endocytosis, directional movement, and edge localization, with some peripheral terms related to neural morphogenesis and phagocytosis signaling that fit within the broader motility and membrane trafficking context.","confidence":"High","size":8,"edges":10,"triangles":4,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0039694","count":4},{"id":"GO:0010628","count":4},{"id":"GO:0048227","count":4},{"id":"GO:0051893","count":4},{"id":"GO:0090135","count":4}]},{"hash":"1097824168108000911","title":"RNA Processing and Transcription Regulation","description":"This cluster is driven by terms tied to RNA metabolism and transcription control (miRNA processing, maintenance of RNA location, negative regulation of transcription elongation by RNA Pol II, and transcription-related chromatin regulation), suggesting a core theme of gene expression regulation; other terms like vesicle transport and brain structure are present but less central.","confidence":"Medium","size":8,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0072383","count":3},{"id":"GO:0035196","count":2},{"id":"GO:0009190","count":2},{"id":"GO:0051237","count":2},{"id":"GO:0045190","count":2}]},{"hash":"634708579298175492","title":"Unknown","description":"The GO terms span highly disparate processes (photosynthesis, immune and stress responses, hormone metabolism, ubiquitination, chaperone assembly), with no single unifying function or pathway evident. The lack of a cohesive theme makes a specific, representative label inappropriate, so Unknown is the correct choice.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0032496","count":3},{"id":"GO:0031943","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0090035","count":3}]},{"hash":"55269797726981405","title":"Central carbon metabolism and redox detoxification","description":"The cluster is dominated by core metabolic pathways (TCA cycle, glycolysis, 2-oxoglutarate, leucine catabolism) alongside several redox-related terms (redox homeostasis, oxidant detoxification, removal of superoxide radicals), indicating a group of proteins focused on energy production and maintaining redox balance. While there are a couple of outliers (e.g., stem cell proliferation) that are less represented, the prevailing theme is central carbon metabolism coupled with oxidative stress management. This label captures the main functional theme of the cluster.","confidence":"High","size":8,"edges":13,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0006552","count":3},{"id":"GO:0006103","count":3},{"id":"GO:0006096","count":3}]},{"hash":"2259273438012609017","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017001","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0034414","count":2},{"id":"GO:0019243","count":2},{"id":"GO:0034247","count":2}]},{"hash":"1010897227501919169","title":"Sphingolipid and Fatty Acid Metabolism in Adipogenesis","description":"This cluster is driven by lipid metabolism terms: sphingosine and sphinganine metabolic processes, monounsaturated fatty acid biosynthesis, sphingolipid biosynthesis, and white fat cell differentiation, indicating a cohesive role in lipid production and adipocyte development. A few terms like tarsal gland development or obsolete entries appear related only loosely or are species-specific artifacts, but the dominant signal points to lipid biosynthesis and adipogenesis. Overall, the proteins likely participate in fatty acid handling and fat cell differentiation pathways.","confidence":"High","size":8,"edges":16,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046512","count":3},{"id":"GO:0010205","count":3},{"id":"GO:1903966","count":3},{"id":"GO:0050872","count":3},{"id":"GO:0070542","count":3}]},{"hash":"1497939405850092741","title":"Cell Cycle and Developmental Morphogenesis","description":"The majority of terms point to cell division and mitotic regulation (cell division, mitotic cell cycle, meiosis I, regulation of the mitotic cell cycle), along with morphogenesis-related processes (histoblast morphogenesis, neural tube closure). Some terms indicate broader or peripheral responses (dephosphorylation, innate immune response, cellular response to cadmium). Overall, the cluster seems to group proteins involved in controlling cell division during developmental morphogenesis rather than a single focused pathway.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007488","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1348022952939148509","title":"Unknown","description":"The GO terms are broad and scattered (sporulation membrane formation, signaling, cell cycle, proteostasis, lipid droplets, and ubiquitin regulation) with no clear single theme linking the proteins, so a specific, representative label is not justifiable.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0034389","count":1}]},{"hash":"1494981111434594236","title":"Sphingolipid and fatty acid biosynthesis with adipogenesis","description":"Most of the top GO terms describe lipid metabolism: sphingosine and sphinganine biosynthesis/metabolism, monounsaturated fatty acid biosynthesis, and fatty acid response, plus white fat cell differentiation. This points to a cluster centered on lipid biosynthesis and adipocyte-related differentiation. A couple terms (photoinhibition, tarsal gland development) are less central or insect-specific but can tie to lipid-rich tissues or secretions.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046512","count":2},{"id":"GO:0010205","count":2},{"id":"GO:1903966","count":2},{"id":"GO:0050872","count":2},{"id":"GO:0070542","count":2}]},{"hash":"950843285137467623","title":"Antibiotic Response and Nylon Catabolism","description":"This cluster's top GO terms include regulation of beta-lactamase activity, response to antibiotic, and beta-lactam/nylon catabolic processes, pointing to a shared function in antibiotic-related stress response and xenobiotic degradation in bacteria. Other terms appear unrelated or obsolete, but the antibiotic/nylon pattern is dominant.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033252","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0030655","count":1},{"id":"GO:0019876","count":1},{"id":"GO:1901621","count":1}]},{"hash":"328412449644582401","title":"Ribosome biogenesis and translation during cell growth","description":"This cluster centers on fundamental growth and protein-synthesis machinery: ribosome biogenesis, cytoplasmic translation, and tRNA modification, which together support new protein production. Coupled with cell cycle and cell division-related terms (cell cycle, cell division, cell septum assembly) and metabolic cue (glucose catabolic process), the proteins likely participate in growth and proliferation processes. An outlier term about virus-mediated pore formation does not fit the core theme and does not deter the overall interpretation.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903833","count":2},{"id":"GO:0006007","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0039707","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2120577817922342560","title":"Diverse solute transporters","description":"The top GO terms are centered on transmembrane transport of a wide range of substrates (sodium-dependent organic cations, arabinose, nitrite, vitamins, dehydroascorbic acid, neurotransmitter loading into vesicles, etc.), indicating a cluster of membrane transporter proteins with diverse substrates rather than a single specific pathway.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070715","count":4},{"id":"GO:0015751","count":4},{"id":"GO:0035725","count":4},{"id":"GO:1900754","count":4},{"id":"GO:0015707","count":4}]},{"hash":"1034071611587988414","title":"Dendrite morphogenesis and neuronal signaling","description":"The top GO terms point to neuronal development and synaptic organization\u2014dendrite morphogenesis, hippocampus development, excitatory postsynaptic potential, and axonogenesis regulation\u2014coupled with Wnt and JNK signaling pathways that influence neurite growth and synapse formation. While some terms relate to the cell cycle and adhesion, the prevailing theme is neuronal morphogenesis and synaptic signaling, suggesting a cohesive neuronal function for this cluster.","confidence":"High","size":8,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0051893","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0090263","count":5},{"id":"GO:0060079","count":5}]},{"hash":"1654632138089259901","title":"Central carbon metabolism and amino acid biosynthesis","description":"Proteins in this cluster are enriched for core metabolic processes (glycolysis, TCA cycle, oxaloacetate metabolism) and biosynthesis of amino acids (e.g., phenylalanine) and vitamins (thiamine). The presence of glutamate metabolism terms supports a central carbon and amino acid linkage, with xenobiotic response terms playing a minor role. This points to a theme of central metabolism and amino acid/vitamin biosynthesis rather than a specialized function.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0019552","count":3},{"id":"GO:0019551","count":3},{"id":"GO:0006099","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006107","count":2}]},{"hash":"58305979121809044","title":"Ribosome biogenesis and cotranslational targeting","description":"This cluster\u2019s top GO terms cluster around ribosome assembly (ribosome biogenesis; SSU-rRNA maturation) and cotranslational delivery of nascent proteins to membranes (SRP-dependent targeting), which together define translation/assembly processes. While a few terms touch on signaling or chromatin-related processes, the dominant theme is ribosome formation and early translation, supporting this label.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0045900","count":1}]},{"hash":"1470577746115546338","title":"Ribosome Biogenesis and Translation","description":"The dominant terms are ribosome biogenesis, ribosomal small subunit biogenesis, cytoplasmic translation, and tRNA modification, pointing to components of ribosome assembly and mRNA translation. Additional terms for cell cycle and cell division suggest the cluster proteins participate in growth-linked processes that couple ribosome production with cell proliferation. Together these align with a function in ribosome biogenesis and protein synthesis.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:1903833","count":3},{"id":"GO:0006400","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0000747","count":3}]},{"hash":"656139179197638021","title":"Unknown","description":"The GO terms are highly diverse, spanning DNA repair (base-excision repair, DNA recombination), xenobiotic response, aging, cell wall organization, lipoylation, menaquinone biosynthesis, choline catabolism, and tRNA methylation. This broad mix suggests no single cohesive function or theme for the cluster, so a specific label is not confidently defined.","confidence":"","size":8,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0071555","count":2}]},{"hash":"1628915245521407746","title":"RNA Processing and Decay Machinery","description":"This cluster is dominated by RNA metabolism activities: spliceosome and snoRNP assembly, P-body formation, mRNA decapping/deadenylation, tRNA processing, and histone mRNA metabolism, with transcription termination also tied to RNA processing. The ABA/water-stress signals may reflect plant stress-linked regulation of RNA processing, but the core theme is RNA processing and turnover.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":3},{"id":"GO:0000492","count":3},{"id":"GO:0033962","count":2},{"id":"GO:0006369","count":2},{"id":"GO:0009414","count":2}]},{"hash":"1904370086128491540","title":"Neural development and synaptic function","description":"The enriched GO terms cluster around neural signaling and development (excitatory postsynaptic potential, long-term potentiation, visual perception, Schwann cell development, and multicellular organism development), suggesting a developmental program with neural/sensory functions. Additional terms like heart development and apoptotic regulation or cell cycle likely reflect broader regulatory processes that accompany development rather than core function of the cluster.","confidence":"Medium","size":8,"edges":26,"triangles":44,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":5},{"id":"GO:0060291","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0014850","count":5},{"id":"GO:0014044","count":5}]},{"hash":"2079031089051718512","title":"Neural development and synaptic plasticity","description":"The top GO terms cluster around neural development and synaptic function: forebrain development, Schwann cell development, excitatory postsynaptic potential, long-term synaptic potentiation. There are also development-related processes like heart development and angiogenesis, which support a broader developmental theme. Some terms (mitotic cell cycle, response to cadmium) are less specific but may reflect ancillary roles or annotation noise. Overall, the cluster appears to center on neural development and synaptic signaling, hence the label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0001403","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0030900","count":2}]},{"hash":"892629485941381940","title":"Multi-tissue Development and Metabolic Regulation","description":"The top GO terms show development-related processes across organs (heart morphogenesis, ureter maturation, endothelial proliferation, nucleus accumbens development) together with metabolic and signaling processes (retinoic acid signaling, retinal metabolism, GABA/glutamate metabolism, carbon utilization). This pattern suggests a cluster centered on broad developmental programs that are linked to tissue-specific metabolism rather than a single pathway.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":8},{"id":"GO:0015976","count":8},{"id":"GO:0001936","count":8},{"id":"GO:0009450","count":8},{"id":"GO:0006537","count":8}]},{"hash":"114302986859647863","title":"Tryptophan catabolism to kynurenine","description":"Top terms suggest a shared function in tryptophan degradation via the kynurenine pathway (L-tryptophan to kynurenine and downstream anthranilate metabolism), indicating a common metabolic theme despite obsolete GO terms and low connectivity. This supports labeling the cluster as related to tryptophan catabolism to kynurenine.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019441","count":1},{"id":"GO:0043420","count":1}]},{"hash":"117217909146821736","title":"ER-Golgi and endosomal vesicle trafficking","description":"The cluster centers on vesicle trafficking and intracellular transport, with terms covering ER-to-Golgi and Golgi-to-ER transport, anterograde and endosome/lysosome routes, and general intracellular protein transport. The presence of positive regulation of GTPase activity aligns with Rab-mediated vesicle dynamics, supporting a trafficking-focused role. Immune-related terms (NK cell degranulation, MHC class Ib antigen processing) may reflect vesicle secretion in immune contexts but still fit the broader secretory/trafficking theme. Overall, it represents components of the intracellular transport machinery and secretory pathway.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0043323","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0048007","count":1},{"id":"GO:0006890","count":1}]},{"hash":"2283037618203239535","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0009408","count":1}]},{"hash":"1673175783909591430","title":"Unknown","description":"The GO terms are too diverse (eye-related processes, membrane/glycoprotein biosynthesis, autophagy and apoptosis, lipid metabolism, and even fungal cell wall organization) to reveal a single coherent function for this cluster.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045494","count":1},{"id":"GO:0010506","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0042771","count":1},{"id":"GO:0031505","count":1}]},{"hash":"1751288627543755155","title":"Invasive growth and cell wall remodeling","description":"The terms cluster around growth-related morphology (pseudohyphal growth, invasive growth under nutrient limitation, lateral root formation) and extensive cell wall\u2013related catabolic processes (chitin catabolic, cell wall macromolecule, polysaccharide catabolic processes). While defense-related terms and processes like URMylation or tRNA wobble thiolation appear, the shared theme appears to be growth/adaptation that relies on remodeling the cell wall, i.e., invasive growth paired with wall degradation. Confidence: Medium","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010311","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0001403","count":1}]},{"hash":"199583939166760381","title":"Innate mucosal immunity and cell fate regulation","description":"The top GO terms point to antibacterial humoral response and innate immune response in mucosa, indicating a mucosal innate immune focus. At the same time, several terms involve regulation of cell fate processes (necroptosis, apoptosis), cell cycle, transcription, and TLR signaling, suggesting a regulatory cluster where immune signaling intersects with control of cell survival and gene expression. The translation term is supportive of general cellular activity but not defining. Therefore, a label centered on mucosal innate immunity with cell fate regulation is most representative.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0019731","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0000209","count":1}]},{"hash":"2052942186658035698","title":"Diverse specialized metabolite biosynthesis","description":"The terms point to biosynthesis of a broad range of specialized metabolites and lipid-related compounds, including antibiotic and alkaloid biosynthesis, vitamin/phytochemical metabolism, steroids, and fatty acids, suggesting a cohesive theme around production of diverse secondary metabolites and lipids.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0009636","count":4},{"id":"GO:0009710","count":3}]},{"hash":"1712990658334264518","title":"Neural development and synaptic modulation","description":"The top GO terms point to neural development (retina development) and neural processing (prepulse inhibition; negative regulation of glutamatergic transmission), suggesting the core theme is neural development and modulation of synaptic activity. While other terms touch immune signaling and general regulation (GTPase activity, cell proliferation), these appear less central to the cluster\u2019s main function. Confidence reflects a coherent neural/synaptic signal, with some peripheral terms; thus, Medium.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0051967","count":1}]},{"hash":"1451062869348252378","title":"Unknown","description":"The top GO terms span cardiac membrane depolarization, hypoxia and gas-response processes, sensory modalities (aerotaxis, thermoception), calcium and magnesium ion signaling, and smooth muscle/gastric tissue functions. This breadth shows no single cohesive function or pathway linking the proteins, so a specific label isn\u2019t justifiable.","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098912","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0009454","count":1},{"id":"GO:0050955","count":1},{"id":"GO:0051592","count":1}]},{"hash":"1050298677084635717","title":"Meiotic Chromosome Pairing and Chiasma Formation","description":"Based on the top GO terms, the cluster centers on meiosis-specific chromosome pairing and chiasma formation, indicating proteins likely participate in homologous pairing and the formation/maintenance of chiasmata during recombination. Although only a couple of terms are represented, their direct relevance to meiosis supports this cohesive label.","confidence":"Medium","size":8,"edges":9,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051026","count":1},{"id":"GO:0007129","count":1}]},{"hash":"1438274279156450161","title":"Monocyte differentiation and cell adhesion","description":"The top GO terms are dominated by monocyte differentiation and cell adhesion, pointing to immune cell development and cell\u2013cell or matrix interactions. While there are hints of transcriptional regulation, the signals are weak and several terms are obsolete, and there are no edges connecting the proteins, so the association is tentative but the best-supported theme among the available terms.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030224","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0052014","count":1},{"id":"GO:0036523","count":1},{"id":"GO:1902769","count":1}]},{"hash":"154163153889375910","title":"Plant defense metabolites and strigolactone biosynthesis","description":"These proteins cluster around plant-specific metabolic and defense processes, with strong hints from strigolactone biosynthesis, stilbene (phytoalexin) metabolism, antibiotic biosynthesis, and responses to toxic substances. Additional terms touch on plant development and secretion (ER-Golgi transport), while a few terms are non-plant annotations, the dominant theme remains plant secondary metabolism and defense signaling, anchored by strigolactone biosynthesis. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060628","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0010223","count":1},{"id":"GO:1901601","count":1},{"id":"GO:0046272","count":1}]},{"hash":"2191111233117030632","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008612","count":3},{"id":"GO:0034050","count":3},{"id":"GO:0006413","count":3},{"id":"GO:1903272","count":3},{"id":"GO:0006452","count":3}]},{"hash":"33795645502181360","title":"Acrosome formation via Golgi-lysosome trafficking","description":"This cluster is best described by terms tied to intracellular transport and organelle biogenesis related to the acrosome, a lysosome-derived organelle formed through Golgi trafficking (acrosome assembly; Golgi-to-vacuole transport; lysosomal transport; endosome-to-Golgi retrograde transport). The ubiquitin-proteasome\u2013mediated cytoplasmic quality control also fits the broader protein handling context during organelle formation. Some terms like spermatid nucleus elongation and suckling behavior are less directly connected and may reflect broader developmental contexts. Overall, the set centers on acrosome biogenesis linked to Golgi-lysosome trafficking.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007290","count":1},{"id":"GO:0060052","count":1},{"id":"GO:0050881","count":1},{"id":"GO:0048873","count":1},{"id":"GO:0042147","count":1}]},{"hash":"302534989303239600","title":"Unknown","description":"The top GO terms span metabolism (glycogen regulation), autophagy, transcription, development (heart, germ cells, ascospores), DNA repair, kinase signaling, and platelet/cardiac functions, with no single cohesive theme linking all proteins. This indicates the cluster is functionally diverse rather than centered on one biological process.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005979","count":2},{"id":"GO:0016242","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0003007","count":1},{"id":"GO:0006303","count":1}]},{"hash":"984576195275430170","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"This cluster is driven by mitochondrial-focused functions: transport of metabolites across mitochondrial membranes (alpha-ketoglutarate, thiamine pyrophosphate, CoA), the malate-aspartate shuttle, and regulation of mitochondrial membrane potential, with additional notes on apoptotic/necroptotic mitochondrial changes. The common thread is mitochondrial metabolite transport coupled with membrane potential control and related signaling.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060546","count":3},{"id":"GO:0008637","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0030974","count":2}]},{"hash":"832885963951181437","title":"Unknown","description":"This cluster has no edges and no top GO terms, so there is no clear shared function to assign a meaningful label.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1409180069129825846","title":"Unknown","description":"There are 8 proteins but no GO terms or top terms to define a shared function; the Top Terms section is empty, and there are no edges or triangles, so there is no detectable theme to label. Without a common functional signal, I cannot assign a meaningful cluster name.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2179547017091178216","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043124","count":2},{"id":"GO:0030011","count":2},{"id":"GO:1901621","count":2},{"id":"GO:1900035","count":2},{"id":"GO:0036494","count":2}]},{"hash":"2254947414869791756","title":"Microtubule dynamics and spindle organization","description":"Most of the top GO terms describe microtubule depolymerization (axonal, cytoplasmic, plus-end), plus-end directed processes, spindle elongation and midzone assembly, and regulation of microtubule-based processes, with additional terms related to neuron projection maintenance and cerebellar structure. This points to a cluster of proteins that regulate microtubule dynamics across mitosis and neuronal contexts, i.e., regulators of microtubule behavior and spindle architecture.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0060404","count":7},{"id":"GO:0070462","count":7},{"id":"GO:0048364","count":7},{"id":"GO:0021693","count":7},{"id":"GO:0000022","count":7}]},{"hash":"353784978626376528","title":"Golgi Vesicle Trafficking","description":"This cluster has multiple GO terms centered on Golgi localization, Golgi-to-ER and ER-to-Golgi transport, endocytosis, and both anterograde and retrograde vesicle trafficking, indicating proteins involved in Golgi-associated vesicle transport. A couple terms (pigmentation, Purkinje cell maturation) are peripheral noise but do not negate the core trafficking theme.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048313","count":1},{"id":"GO:0043473","count":1},{"id":"GO:0021691","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0051645","count":1}]},{"hash":"1548258018158314727","title":"COPII-Mediated ER-Golgi Transport","description":"Dominant GO terms center on COPII vesicle formation and ER-to-Golgi trafficking, including cargo loading and coat regulation, suggesting a secretory pathway focus. While a few other terms appear, they are less representative; the shared theme is COPII vesicle trafficking and cargo loading.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035149","count":1},{"id":"GO:0016236","count":1},{"id":"GO:0061156","count":1},{"id":"GO:0060088","count":1},{"id":"GO:0070278","count":1}]},{"hash":"417446191260828159","title":"Neuronal signaling and cell cycle proteins","description":"The top terms mix neural-related functions (excitatory postsynaptic potential, Schwann cell development, response to cocaine) with fundamental cell-cycle processes (G1/S transition, meiotic cell cycle, DNA replication, kinetochore localization). This suggests a cluster of proteins involved in both neural signaling/development and cell-cycle machinery, hence the combined label.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0006260","count":2}]},{"hash":"2013576636970033493","title":"Unknown","description":"The listed GO terms are highly diverse (neuron death regulation, plant signaling, trachea formation, focal adhesion regulation, invasive growth under glucose limitation, Rho signaling, NK T cell differentiation, protein processing regulation, histone modification, cardiac hypertrophy) with no clear shared function, indicating the proteins do not form a coherent single-theme cluster.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":1},{"id":"GO:0009938","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1}]},{"hash":"989261452489369288","title":"Unknown","description":"The Top Terms cover immune signaling (T cell activation, complement activation), extracellular matrix and cartilage morphogenesis processes, protein complex assembly, and plant-specific pathways (chlorophyll biosynthesis, light perception). The terms span diverse biological contexts with no single coherent function, so a specific functional label cannot be determined.","confidence":"","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":5},{"id":"GO:0002291","count":4},{"id":"GO:0006471","count":4},{"id":"GO:0006956","count":4},{"id":"GO:0003429","count":4}]},{"hash":"43343848340961541","title":"Negative regulation of endocytosis and autophagy","description":"The cluster\u2019s top GO terms are dominated by negative regulation of membrane trafficking and autophagy-related processes (GPCR/clathrin-mediated endocytosis, autophagosome maturation, store-operated calcium channel activity, TLR3 signaling). This suggests a shared theme of inhibiting endocytic and autophagic pathways, with a few unrelated terms likely reflecting multifunctional proteins or annotation noise. ","confidence":"Medium","size":7,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1904021","count":6},{"id":"GO:1901097","count":6},{"id":"GO:0006289","count":6},{"id":"GO:0006517","count":6},{"id":"GO:1900186","count":6}]},{"hash":"882662096312606519","title":"RNA Processing and Turnover","description":"The cluster shows strong representation of RNA maturation, splicing, and turnover processes\u2014spliceosomal assembly, mRNA splicing, tRNA processing, histone mRNA metabolism, and P-body\u2013related mRNA decapping\u2014indicating a coherent theme of post-transcriptional RNA metabolism and gene expression regulation.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":7},{"id":"GO:0006369","count":7},{"id":"GO:0009414","count":7},{"id":"GO:0070317","count":7},{"id":"GO:0009737","count":7}]},{"hash":"1193479038919712292","title":"Unknown","description":"The GO terms span diverse processes\u2014from kinase signaling regulation and nutrient signaling (TORC1, SREBP) to development, fungal cell wall biogenesis, epigenetic methylation, DNA repair, and stress responses\u2014without a single clear common function linking all members. This makes a cohesive, specific label unreliable.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0061099","count":1},{"id":"GO:0034729","count":1},{"id":"GO:0032995","count":1}]},{"hash":"1059582915791358727","title":"Golgi vesicle transport and cytokinesis","description":"This cluster is driven by Golgi-related processes (Golgi organization, intra-Golgi vesicle transport, protein transport) with a secondary association to cytokinesis and hemocyte proliferation. The common thread is intracellular vesicle trafficking linked to cell division, hence a label around Golgi vesicle transport and cytokinesis.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007030","count":1},{"id":"GO:0033227","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0006891","count":1},{"id":"GO:0035206","count":1}]},{"hash":"981878766944208740","title":"Unknown","description":"The GO terms span very diverse areas (cell cycle transition, protein isomerization, multiple development terms, ciliogenesis, metal ion response, plant hormone signaling, regulation of protein modification, ubiquitination, and interferon response), with no clear common function tying the proteins together. A single coherent label isn\u2019t supported by the data.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007091","count":1},{"id":"GO:0000413","count":1},{"id":"GO:0060613","count":1},{"id":"GO:0021756","count":1},{"id":"GO:1905515","count":1}]},{"hash":"317067877599833759","title":"Secretory vesicle trafficking","description":"The top GO terms point to vesicle- and secretory pathway processes (ER-Golgi transport, intra-Golgi transport, general protein transport, and synaptic vesicle exocytosis), complemented by terms for mucus secretion and eosinophil degranulation, suggesting a theme of secretory vesicle trafficking and secretion rather than a single enzyme or pathway. This combination supports labeling the cluster as Secretory vesicle trafficking.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":3},{"id":"GO:0043308","count":3},{"id":"GO:0043134","count":3},{"id":"GO:0006891","count":3},{"id":"GO:0006888","count":3}]},{"hash":"94878255844332092","title":"Potassium Ion Transport and Membrane Potential Regulation","description":"The top terms cluster around maintaining and regulating membrane potential, especially potassium ion homeostasis and transmembrane transport, with connections to cardiac repolarization and resting potential. A few terms (mechanosensory touch, amyloid-beta metabolism, digestion, and certain endocrine/developmental terms) are less central, but the dominant theme is potassium-mediated control of membrane polarization.","confidence":"Medium","size":7,"edges":10,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0098914","count":2},{"id":"GO:0060075","count":2},{"id":"GO:0030322","count":2},{"id":"GO:0050976","count":2},{"id":"GO:0030007","count":2}]},{"hash":"1765204493206487431","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006620","count":1},{"id":"GO:0051083","count":1},{"id":"GO:0060271","count":1},{"id":"GO:1990182","count":1},{"id":"GO:0048132","count":1}]},{"hash":"113676102418064405","title":"Diverse Transmembrane Transporters","description":"The cluster is enriched for a wide range of transmembrane transport GO terms (nitrite, arabinose, sodium, vitamin, phosphate ions, nitrate assimilation, and fucose transport) plus a vesicular neurotransmitter loading term, indicating a set of transporter proteins handling multiple substrates and vesicle-related transport. This justifies a label centered on membrane transport with diverse substrates.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0015707","count":6},{"id":"GO:0015751","count":5},{"id":"GO:0035725","count":5},{"id":"GO:1900754","count":5},{"id":"GO:0035461","count":5}]},{"hash":"1004913079428821492","title":"Oxidative stress response and detoxification","description":"The cluster is dominated by GO terms tied to redox biology\u2014cellular response to hydrogen peroxide, removal of superoxide radicals, cellular oxidant detoxification, and response to alkyl hydroperoxide\u2014indicating a focus on oxidative stress management. Some terms (DNA replication, NK cell cytotoxicity, lipoprotein biosynthesis, and male gonad development) appear less connected and may reflect background annotations, but the redox-related terms suggest a coherent theme around redox homeostasis.","confidence":"Medium","size":7,"edges":12,"triangles":9,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070301","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0019430","count":3},{"id":"GO:0042267","count":3},{"id":"GO:0042158","count":3}]},{"hash":"2159121988760602267","title":"Osmotic Stress and Carbohydrate/Lipid Biosynthesis","description":"The cluster merges osmotic stress responses (water deprivation, sorbitol, sucrose, mannitol) with biosynthetic processes for lipids and carbohydrates, including lipopolysaccharide and phospholipid biosynthesis. This suggests a theme of adjusting membrane-related metabolism and surface components in response to abiotic/chemical stress.","confidence":"Medium","size":7,"edges":15,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0009414","count":2},{"id":"GO:0072708","count":2},{"id":"GO:0005978","count":2}]},{"hash":"2000827985161431139","title":"Secondary Metabolite Biosynthesis and Transcription Regulation","description":"The cluster centers on several biosynthetic processes (anthocyanin, phenylpropanoid, colanic acid, ubiquinone, galactose, and glutamine metabolism) alongside transcription-related terms (DNA-templated transcription and nitrogen catabolite repression of transcription) and xenobiotic response, suggesting a theme of biosynthesis of secondary metabolites with transcriptional regulation, despite a mix of plant- and bacteria-associated terms.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009410","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0009718","count":2}]},{"hash":"1914038740580720096","title":"Antibiotic and xenobiotic metabolism","description":"The cluster is enriched for antibiotic-related functions (response to antibiotic; antibiotic biosynthetic process) and several xenobiotic-related processes (insecticide metabolic process; xenobiotic catabolic process; vancomycin biosynthetic process), suggesting a cohesive role in detoxification and antimicrobial compound processing. A few terms (vitamin D/prostaglandin biosynthesis, methylation) are peripheral, but the dominant signal supports antibiotic and xenobiotic metabolism. ","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0035865","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0001516","count":1}]},{"hash":"1304459119928173109","title":"Unknown","description":"The GO terms are highly diverse, spanning metal transport, hormone response, cardiovascular regulation, neural development, metabolism, and sensory/anatomical processes, with no common function linking the proteins and no interactions indicated by edges, so a cohesive cluster label cannot be inferred.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":3},{"id":"GO:0033574","count":3},{"id":"GO:1903249","count":3},{"id":"GO:0098736","count":3},{"id":"GO:0061092","count":3}]},{"hash":"1021457883443755089","title":"Transmembrane transporters for vitamins, xenobiotics, and metals","description":"The cluster is enriched for transmembrane transport GO terms across diverse substrates (vitamins, xenobiotics, cobalt ions, oligosaccharides, and even doxorubicin), suggesting a group of membrane transport proteins or exporters. The Type I secretion system term also fits a secretion/export function, reinforcing a transporter/secretion theme. A couple of outlier terms (nucleotide-excision repair, pigment biosynthesis) may be less connected to the core transport function or reflect annotation noise.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":4},{"id":"GO:0042891","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0006289","count":3},{"id":"GO:0015772","count":3}]},{"hash":"2249747942381432172","title":"Metabolism and membrane transport","description":"The cluster centers on metabolism (glucose metabolism, serine biosynthesis) and membrane-associated activities (proton transmembrane transport) plus protein turnover (proteolysis). A few peripheral terms related to signaling or development appear, but the dominant theme points to metabolic and transport functions.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0006508","count":2}]},{"hash":"1599267969486206579","title":"Immune signaling and mitosis regulation","description":"The cluster shows immune-related GO terms (positive regulation of TLR3 signaling, CD8 T cell proliferation, interferon signaling modulation) alongside mitotic spindle regulation terms (chromosome passenger complex localization to the spindle midzone, spindle-microtubule/kinetochore attachment). This suggests proteins involved in both innate/adaptive immune signaling and cell-cycle control, justifying a combined label that highlights both themes. Some vascular/platelet-related terms appear as additional context but are less central. ","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034141","count":2},{"id":"GO:2000587","count":2},{"id":"GO:0030220","count":1},{"id":"GO:2000566","count":1},{"id":"GO:1902212","count":1}]},{"hash":"750148624736206219","title":"Rho-Mediated Adhesion and ECM Remodeling","description":"The top GO terms cluster around cell adhesion and cytoskeletal signaling: Rho protein signal transduction, regulation of focal adhesion assembly, and regulation of extracellular matrix disassembly, plus invasive growth responses, suggesting proteins that modulate adhesion dynamics and ECM remodeling. Some terms related to development or immune differentiation appear but do not dominate; overall the theme points to adhesion/cytoskeletal control with ECM remodeling.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":7},{"id":"GO:0060440","count":7},{"id":"GO:0051893","count":7},{"id":"GO:0001403","count":7},{"id":"GO:0007266","count":7}]},{"hash":"624744691179311028","title":"Unknown","description":"The GO terms are highly diverse (ubiquitination, quinone biosynthesis, multiple carbon metabolism pathways, cell wall organization, vacuole regulation), with no clear shared function or organism context to unify the cluster. Therefore a specific, representative label cannot be determined.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0009234","count":1},{"id":"GO:0034194","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0006094","count":1}]},{"hash":"1923868139899285310","title":"Membrane Ion Transport and Ion Homeostasis","description":"Based on the GO terms, the proteins are enriched for transmembrane transport of metal and monatomic cations (cadmium, potassium, calcium, sodium) and overall ion homeostasis across membranes. While a couple of terms like testosterone response and stilbene catabolic process are less aligned, the dominant pattern is ion transport and homeostasis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":7},{"id":"GO:0033574","count":7},{"id":"GO:0097755","count":7},{"id":"GO:0046272","count":7},{"id":"GO:0030007","count":7}]},{"hash":"99012991092922875","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":1},{"id":"GO:0002635","count":1},{"id":"GO:0090073","count":1},{"id":"GO:2000620","count":1},{"id":"GO:1902187","count":1}]},{"hash":"1351111554514432622","title":"Nuclear transport and mitotic spindle regulation","description":"Many terms point to import into the nucleus (NLS-bearing, snRNP, and hnRNP import) and export of ribosomal subunits, indicating a focus on nuclear trafficking. At the same time, terms for centrosome duplication, astral microtubule organization, and mitotic chromosome movement toward the spindle pole suggest involvement in cell cycle and spindle dynamics. Taken together, the cluster appears to center on nuclear protein transport coupled with mitotic/spindle processes. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010824","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0006608","count":2},{"id":"GO:0006609","count":2},{"id":"GO:0030953","count":2}]},{"hash":"2146895873346583475","title":"Cardiac Muscle Signaling and Sarcomere Organization","description":"The GO terms show a strong muscle-related theme, with sarcomere organization and cardiac muscle cell proliferation pointing to muscle structure and growth. The cluster also includes signaling-related terms (small GTPase signaling, adenylate cyclase activity, receptor guanylyl cyclase regulation), suggesting coordinated signaling control in muscle cells. While a few terms are more general (ion transport, aerotaxis), the dominant pattern supports a muscle signaling/structure theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051447","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0045214","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0007264","count":1}]},{"hash":"2283827728110531715","title":"Mitotic spindle regulation and immune modulation","description":"These proteins show a strong signal for mitotic spindle-related functions, including spindle midzone localization, kinetochore-microtubule attachments, and sister chromatid biorientation. There are also immune and vascular-related terms (CD8+ T cell proliferation, IL-6 regulation, interferon signaling, platelet formation, vascular permeability), suggesting additional regulatory roles beyond mitosis. Overall, the dominant theme is mitotic spindle machinery, with auxiliary immune/vascular signals.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030220","count":1},{"id":"GO:2000566","count":1},{"id":"GO:1902212","count":1},{"id":"GO:0035853","count":1},{"id":"GO:1902425","count":1}]},{"hash":"524542748578285582","title":"Neural development and neuronal stress response","description":"This cluster is anchored by brain-related development terms (initiation of neural tube closure, third ventricle development) and neuronal stress signaling (positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling, regulation of circadian rhythm), with additional but less cohesive terms on ubiquitination and cell cycle. The common thread is neural development coupled with neuronal stress response pathways, though the terms are diverse and not tightly connected, leading to a moderate confidence in a brain-development/stress theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021993","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0071406","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0008285","count":1}]},{"hash":"960977241668788104","title":"Central energy metabolism","description":"The top GO terms point to core metabolic and energy-transducing processes: TCA cycle, pyruvate decarboxylation to acetyl-CoA, fermentation, electron transport chain, and methanogenesis with tetrahydromethanopterin biosynthesis. Additional terms for nucleotide catabolism and photosynthesis suggest broader metabolic activity, but the dominant theme is energy production and central carbon metabolism, justifying a label focused on energy metabolism. The absence of edges implies annotation-driven overlap rather than direct interaction data.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015948","count":1},{"id":"GO:0006113","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0022900","count":1},{"id":"GO:1901285","count":1}]},{"hash":"2135881405280248747","title":"Unknown","description":"The terms are scattered across apoptosis/DNA damage response and skin/neuronal development, with no single cohesive function tying all seven proteins together. While there is an apoptotic/DNA damage signal, several terms concern skin keratinocytes and unrelated developmental processes, making a unified theme unlikely.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008630","count":1},{"id":"GO:0021766","count":1},{"id":"GO:1900740","count":1},{"id":"GO:0043154","count":1},{"id":"GO:0032869","count":1}]},{"hash":"2163760602651181103","title":"Cardiac contraction and conduction regulation","description":"This cluster is dominated by GO terms related to heart function, including cardiac muscle contraction, regulation of heart rate, and regulation of electrical conduction in the heart, with supporting terms like myosin II filament assembly and negative regulation of protein kinase activity that connect to cardiac contractile and signaling machinery. While there are some broader terms (e.g., development and stress response), the strongest signal points to cardiac contraction/conduction processes.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050665","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0072205","count":2}]},{"hash":"1868231386617881548","title":"Symbiont-induced host response","description":"The top GO terms point to interactions where a symbiont affects host processes (e.g., catabolism of host proteins and induction of host cytokine production) along with cell adhesion and other cellular processes. Although several terms are labeled obsolete, the recurring theme is molecular cross-talk between symbiont and host and the resulting host response, rather than a single metabolic pathway. This justifies a label focusing on symbiont-host interaction and the host response.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0052014","count":3},{"id":"GO:0036523","count":3},{"id":"GO:1902769","count":3},{"id":"GO:0007155","count":3},{"id":"GO:0007100","count":3}]},{"hash":"1904017466533822916","title":"Biosynthesis of vitamins and cofactors","description":"The top GO terms cluster around biosynthetic processes for vitamins and cofactors (biotin, menaquinone, cobalamin) and related small-molecule production, suggesting the proteins mainly participate in cofactor/vitamin biosynthesis; a few outliers (xenobiotic response, ribosomal export) are peripheral to the main theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0009234","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0009236","count":3}]},{"hash":"431857280742539393","title":"Nuclear chromatin remodeling and snoRNA processing","description":"The top GO terms cluster around chromatin remodeling and snoRNA/rRNA processing (chromatin remodeling; box C/D snoRNP assembly; snoRNA localization; maturation of SSU-rRNA), indicating a nuclear program that links chromatin state to RNA processing and ribosome biogenesis. Some terms are unrelated or obsolete, but the core theme is chromatin regulation coupled with snoRNP/RNA maturation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0031063","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0000321","count":1}]},{"hash":"2109866888124925359","title":"Neural development and dendrite morphogenesis","description":"The GO terms cluster around neural development (forebrain and hippocampus), dendrite morphogenesis, and regulation of axonogenesis, with MAPK signaling (ERK/JNK) and insulin signaling linked to neuronal differentiation and cytoskeletal dynamics. This supports a cohesive theme of neural development and dendrite/axon morphogenesis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0008286","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0021766","count":3}]},{"hash":"648930611306423380","title":"ER-Golgi vesicle trafficking","description":"The Top Terms cluster strongly center on vesicle transport within the secretory pathway, including ER-to-Golgi and endosome-to-Golgi routes, COPII cargo loading, and Rab-regulated trafficking. This suggests the proteins function together in ER-Golgi vesicle formation, cargo sorting, and endosomal routing.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902018","count":1},{"id":"GO:0071955","count":1},{"id":"GO:0032483","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0034499","count":1}]},{"hash":"9662121658774669","title":"Vacuolar amino acid and ion transport","description":"The GO terms group transmembrane transport into and out of the vacuole for several amino acids (glutamate, arginine, proline, lysine, glutamine) and ions (lithium, potassium), indicating a core theme of vacuolar substrate transport. The single root cap development term is likely incidental noise relative to the dominant transport signal.","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090515","count":1},{"id":"GO:1990818","count":1},{"id":"GO:0015824","count":1},{"id":"GO:0048829","count":1},{"id":"GO:0061402","count":1}]},{"hash":"435751516785130499","title":"NLRP3 Inflammasome and Cytokine Regulation","description":"The top GO terms center on inflammasome biology and cytokine production (IL-1\u03b2, IL-18) with regulatory effects on IL-2, plus processes related to ER/Golgi organization and cytoskeleton-driven trafficking. This combination suggests a cohesive role in inflammasome activation, cytokine processing/secretion, and related intracellular transport\u2014matching a single functional theme for the cluster.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900041","count":2},{"id":"GO:0072616","count":2},{"id":"GO:0007030","count":2},{"id":"GO:1900227","count":2},{"id":"GO:0071158","count":2}]},{"hash":"292814765073525581","title":"Neural Development and Deubiquitination","description":"The terms are dominated by deubiquitination activities across various linkages (K29, K6, linear) and histone deubiquitination, with additional neural development and behavior terms (CNS morphogenesis, adult feeding behavior, righting reflex). This points to a cluster of deubiquitinases potentially involved in neural development and function, even though there are no observed edges in the cluster. Confidence reflects the moderate coherence between deubiquitination function and neural development terms.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035616","count":1},{"id":"GO:0060013","count":1},{"id":"GO:0035523","count":1},{"id":"GO:0044313","count":1},{"id":"GO:0034729","count":1}]},{"hash":"1643925876641992078","title":"Actin cytoskeleton and sarcomere assembly","description":"Most frequent GO terms point to actin-based structure organization and muscle-related assembly: mitotic actomyosin contractile ring assembly, sarcomere organization, postsynaptic actin cytoskeleton organization, and skeletal muscle fiber development. This indicates a cluster centered on actin cytoskeleton dynamics and muscle architecture. Some terms (ascospore wall, inter-male aggression) are outliers or less connected, but the dominant theme is cytoskeletal organization.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030476","count":6},{"id":"GO:0002121","count":6},{"id":"GO:0048741","count":6},{"id":"GO:1903475","count":6},{"id":"GO:0045214","count":6}]},{"hash":"1598809970181369765","title":"Cell division and DNA replication","description":"The proteins cluster around core cell-cycle processes: DNA replication, mitotic spindle assembly, and nuclear fusion-related events (karyogamy), pointing to genome maintenance and cell division. Supporting terms for protein folding and membrane targeting reflect ancillary machinery needed during division, while some apoptotic regulation terms may capture cellular stress responses associated with division. Overall, the dominant theme is cell division and genome maintenance.","confidence":"Medium","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":4},{"id":"GO:0090307","count":3},{"id":"GO:1903382","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0006880","count":3}]},{"hash":"2088210533841477005","title":"Nuclear gene expression and cell cycle control","description":"Top terms point to core nuclear processes: DNA-templated transcription, DNA replication, centrosome cycle, regulation of nuclear DNA replication, and nonsense-mediated decay of nuclear transcripts, with some developmental GO terms. The shared theme is regulation of nuclear gene expression and cell-cycle processes, suggesting this cluster represents proteins involved in coordinating transcription, replication, and RNA quality control during development.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0007098","count":2}]},{"hash":"1094655582556401638","title":"Cdc42-driven actin remodeling and receptor signaling","description":"The terms point mostly to cytoskeletal dynamics and receptor-mediated signaling: actin filament branching, Cdc42 signaling, regulation of focal adhesions, endosome transport, and EGFR signaling. These suggest a theme of coordinated actin remodeling with membrane trafficking and receptor pathways. A few terms (viral replication, mitochondrial permeabilization) are less connected and likely incidental. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039694","count":1},{"id":"GO:0010628","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0007173","count":1},{"id":"GO:0051893","count":1}]},{"hash":"1117706932425044157","title":"Exocyst-Dependent Vesicle Trafficking","description":"Dominant exocyst- and vesicle-trafficking signals: exocyst assembly/localization, exocytosis, and Golgi-to-plasma membrane/vacuole transport, with related ER inheritance and recycling terms. This suggests these proteins function in exocyst-mediated vesicle trafficking and secretion at membranes, possibly including dense-core granule transport.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001927","count":1},{"id":"GO:0006887","count":1},{"id":"GO:0048611","count":1},{"id":"GO:0006893","count":1},{"id":"GO:0006896","count":1}]},{"hash":"1265528751017968426","title":"ER Stress Response and ERAD","description":"This cluster\u2019s top GO terms cluster around endoplasmic reticulum quality control and stress responses: unfolded protein response, ER-to-Golgi vesicle transport, and the ubiquitin-dependent ERAD pathway. These indicate a shared function in managing misfolded proteins and ER homeostasis. Some terms (like DNA replication and checkpoint signaling) are less directly connected, likely reflecting multi-functional proteins, but the dominant theme is ER-associated protein handling and stress response.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1539436033883359922","title":"Retroviral integration and transposition","description":"GO terms point to DNA integration, recombination, replication, and transposition, with RNA-templated DNA synthesis and proviral latency, plus host-entry and apoptosis interaction terms. Together these indicate a cluster of proteins involved in retroviral-like genome integration and transposition, i.e., provirus maintenance and host interactions.","confidence":"High","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0075713","count":1},{"id":"GO:1903704","count":1},{"id":"GO:0046718","count":1}]},{"hash":"1305120744847378385","title":"Unknown","description":"The GO terms are highly diverse, spanning bacterial biosynthesis (menaquinone, lipoteichoic acid, nonribosomal peptide activation), fatty acid metabolism/transport, and plant-specific processes (phenylpropanoid metabolism, seed coat development, bile acid metabolism), plus bioluminescence. This lack of a cohesive functional theme, along with sparse edges, suggests no single module or function ties the proteins together. Therefore, a generic Unknown label with no confident, representative function is appropriate.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":3},{"id":"GO:0008218","count":3},{"id":"GO:0070395","count":3},{"id":"GO:0001579","count":3},{"id":"GO:0009698","count":3}]},{"hash":"544542256237867487","title":"Oxidative Stress Response and Protein Maintenance","description":"This cluster is dominated by GO terms for cellular response to oxidative stress and protein-related maintenance: protein modification and repair activities. The repeated signals for oxidative stress (GO:0006979), protein modification (GO:0006464), and protein repair (GO:0030091) point to a cohesive theme of handling oxidative damage and preserving protein function, including post-translational modifications. A subset of transcription-related terms appears at low frequency, likely representing incidental regulation rather than a core function of the cluster; overall the oxidative stress response and protein maintenance theme best explains the group.","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":2},{"id":"GO:0006464","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0030091","count":2},{"id":"GO:0031564","count":1}]},{"hash":"2195474703105013047","title":"Embryonic morphogenesis and nuclear cell cycle regulation","description":"The top GO terms point to embryonic morphogenesis (cranial skeleton, trachea formation) and nuclear/cell cycle activities (DNA transcription, DNA replication, centrosome cycle, nuclear export). This pattern suggests proteins that coordinate early development with cell-cycle control, rather than a single strict pathway.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048701","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0007098","count":5},{"id":"GO:0046826","count":5}]},{"hash":"1258478915903705071","title":"Mitosis regulation and apoptosis modulators","description":"The GO terms cluster around mitotic control (kinetochore localization, regulation of CDK activity, chromatid biorientation) and checks on proliferation and survival (negative regulation of proliferation, positive regulation of apoptosis), with some associated signaling and migratory functions. This suggests a group of proteins that balance cell division with cell fate decisions, fitting a cohesive label focused on mitosis regulation and apoptosis. ","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0008285","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0016477","count":2}]},{"hash":"432247920021002934","title":"Cell cycle and innate immune signaling","description":"The set contains GO terms for G1/S and G2/M transitions and mitotic processes, transcription, and mammary epithelial proliferation, indicating cell cycle\u2013related functions. It also includes innate immune terms such as response to dsRNA, LPS signaling, and interferon-beta production, suggesting overlap with immune signaling. This points to proteins involved in cell cycle regulation that also interface with immune responses. The connection is present but not tightly specific, so the label aims to capture both themes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0033598","count":2}]},{"hash":"2228351099084413104","title":"Unknown","description":"The top GO terms span diverse biological processes (development, immune differentiation, ECM remodeling, cell adhesion, signaling) with no clear, shared mechanism, and there are no interactions among the proteins (edges 0). This scattered functional mix makes it unlikely to assign a cohesive, specific label, so Unknown with no confidence is appropriate.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0007266","count":1}]},{"hash":"2229445500079024880","title":"Unknown","description":"Top GO terms are not available, and there is no clear shared function among the six proteins based on the data (no triangles, limited connectivity). Therefore, a precise functional label cannot be inferred.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"1615498680269217670","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster centers on ubiquitination-related processes and proteasomal/ERAD-mediated protein catabolism, including ubiquitin-dependent degradation (K48-linked ubiquitination, ERAD) and turnover of receptors like Wnt; a few terms (X-chromosome inactivation, peroxisomal import) are less connected but don't negate the dominant degradation theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":1},{"id":"GO:0060816","count":1},{"id":"GO:0038018","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0016558","count":1}]},{"hash":"952476224730363824","title":"ER\u2013Golgi vesicle trafficking","description":"The top terms are COPII-coated vesicle budding and ER-to-Golgi vesicle transport, pointing to the secretory pathway directing cargo from the ER to the Golgi. Other terms appear at low frequency and are less representative of the core function, suggesting a mainly vesicle-transport cluster with some unrelated annotations. Confidence: High","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0071902","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0061099","count":1}]},{"hash":"1599218548921729341","title":"Genome maintenance and chromatin regulation","description":"This cluster\u2019s top GO terms cluster around nuclear genome maintenance: DNA replication, double-strand break repair, recombination, and heterochromatin formation, with some signals of replication fork protection and meiotic recombination nodules. A few terms (cilium movement, vesicle transport, xenobiotic response) seem less related and may reflect annotation noise or multifunctional proteins. Overall, the dominant theme is genome stability and chromatin dynamics.","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006343","count":1},{"id":"GO:0042140","count":1},{"id":"GO:0030494","count":1},{"id":"GO:0000727","count":1}]},{"hash":"1766368592650774037","title":"Renin-Angiotensin\u2013Mediated Kidney Function","description":"The cluster's top GO terms cluster around kidney-related biology and the renin-angiotensin system, including mesonephros development, regulation of blood volume by renin-angiotensin, aldosterone production, and angiotensin maturation. This suggests a coherent theme related to kidney development and hormonal control of fluid balance, with a few terms (digestion, amyloid-beta metabolism, antibacterial peptide production) that may reflect broader protein functions or annotation noise. Overall, the label captures the dominant theme of renal development and renin-angiotensin signaling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050435","count":1},{"id":"GO:0007586","count":1},{"id":"GO:0002018","count":1},{"id":"GO:0001823","count":1},{"id":"GO:0016540","count":1}]},{"hash":"1131596962396843684","title":"Kinase signaling regulation and growth pathways","description":"This cluster shows recurrent emphasis on regulation of kinase activities (serine/threonine and tyrosine), TORC1 signaling, and ubiquitination, with related growth and regulatory processes (SREBP signaling, pattern formation, invasive growth, dendrite development). The common theme is modulation of signaling and growth via kinase- and ubiquitin-related mechanisms, despite diverse specific processes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0061099","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0032995","count":2}]},{"hash":"806690210854288126","title":"Unknown","description":"Top Terms are empty, so no visible functional theme to group the proteins. Without GO terms or enrichment signals, a meaningful, specific label cannot be assigned.","confidence":"","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"850207368734768112","title":"Unknown","description":"Top GO terms are highly diverse, including immune activation (T cell activation, complement), ECM and cell adhesion/migration, cartilage morphogenesis, and plant-specific processes (chlorophyll biosynthesis, light perception). There is no single coherent function tying these proteins together, suggesting the cluster is not functionally cohesive. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002291","count":1},{"id":"GO:0006471","count":1},{"id":"GO:0006956","count":1},{"id":"GO:0003429","count":1},{"id":"GO:1905050","count":1}]},{"hash":"1183621168236438550","title":"Unknown","description":"This cluster shows no GO terms and consists of isolated proteins (no edges, max degree 0), providing no clear functional theme to tie the proteins together.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"927335391518330730","title":"Unknown","description":"There is no coherent shared function among the terms; they span signaling regulation (TOR, GTPase, MAPKK), development (mushroom body), transport (cadmium ion, intraciliary, phospholipid translocation), metabolism (amino acid response, citrulline biosynthesis), and cardiac regulation, with no edges linking the proteins to a single process. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032008","count":1},{"id":"GO:0016319","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0000186","count":1},{"id":"GO:0071230","count":1}]},{"hash":"728872318689299140","title":"Ribosome biogenesis and LSU maturation","description":"The top GO terms center on maturation and assembly of the large ribosomal subunit (LSU rRNA maturation, large subunit assembly) and export from the nucleus, plus the core translation function, all pointing to ribosome biogenesis and activity. Obsolete or peripheral terms related to mitochondria or histone acetylation do not override the central ribosome theme. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:1902626","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0000055","count":1}]},{"hash":"2284328279303419073","title":"Vertebrate neural development and transcription","description":"The top GO terms center on vertebrate development and gene expression: forebrain development, neural tube closure, multicellular organism development, and DNA-templated transcription, suggesting proteins involved in transcriptional regulation during neural formation. Other terms like rRNA maturation and stress responses appear more general and do not dominate the cluster, but they may reflect background cellular processes. Overall, the core theme is developmental transcriptional control related to neural development. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1287752119847664104","title":"Unknown","description":"No GO terms are provided in the Top Terms, so there is no clear shared function or process to anchor a label. With only network metrics and no functional terms, the cluster cannot be confidently characterized.","confidence":"","size":6,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"839774229122444239","title":"Stress-induced proteostasis and autophagy","description":"The cluster\u2019s terms cluster around oxidative stress response, ER unfolded protein response, autophagosome maturation, and oxidation-dependent protein catabolic processes, pointing to maintenance of protein homeostasis under stress. Some terms appear unrelated (e.g., cilium movement, blastocyst development) likely reflecting annotation noise or multi-function proteins, but the core theme is proteostasis via stress responses and autophagy.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":1},{"id":"GO:0030968","count":1},{"id":"GO:0003341","count":1},{"id":"GO:0032508","count":1},{"id":"GO:1990048","count":1}]},{"hash":"658725251936694966","title":"Unknown","description":"The Top Terms span highly diverse processes including cytokine regulation, synaptic vesicle trafficking, plant ABA signaling and stomatal closure, Rho signaling, salt-stress responses, and apoptotic/necroptotic regulation. With no clear, shared function across all terms and species, there isn\u2019t a cohesive theme to label the cluster beyond Unknown. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904468","count":1},{"id":"GO:2000300","count":1},{"id":"GO:0009738","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0090332","count":1}]},{"hash":"2171467635276716864","title":"RNA processing and transcription regulation","description":"The terms highlight RNA processing steps (mRNA capping, splicing) and regulation of transcription, indicating a cluster centered on RNA maturation linked to transcription control, with some helicase activity hints; despite some obsolete terms, the combined theme is coherent.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031062","count":1},{"id":"GO:0051096","count":1},{"id":"GO:0006370","count":1},{"id":"GO:2000288","count":1},{"id":"GO:0006355","count":1}]},{"hash":"546314209609802380","title":"Unknown","description":"The GO terms associated with these proteins are highly diverse and each appears only once, with a mix of transport-related terms (cobalt, methionine, branched-chain amino acids, glutathione into vacuole, doxorubicin transport) and unrelated processes (nucleotide-excision repair, tRNA clustering, very long-chain fatty acid catabolism). There are no edges or cohesive connectivity to tie them into a single shared function, so a meaningful, specific label cannot be inferred.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":1},{"id":"GO:0006824","count":1},{"id":"GO:0070058","count":1},{"id":"GO:0042760","count":1},{"id":"GO:1900753","count":1}]},{"hash":"1901610680450459801","title":"Endomembrane vesicle trafficking and fusion","description":"The GO terms converge on transport between Golgi, endosomes, lysosomes/vacuoles, tethering/fusion of vesicles, and autophagosome maturation, along with SNARE regulation. This points to a shared role in endomembrane trafficking and organelle fusion, including eye pigment granule organization as a lysosome-related process.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035542","count":1},{"id":"GO:0008333","count":1},{"id":"GO:0097352","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0042144","count":1}]},{"hash":"1655405123426893657","title":"Mitochondrial regulation and sarcomere organization","description":"The top GO terms point to mitochondrial functions, including protein import into the mitochondrial matrix and regulation of mitochondrial membrane permeability, as well as transcription-related processes. There's also a note of cell-cycle regulation and a sarcomere organization term, suggesting a possible muscle-specific context where mitochondrial regulation intersects with cellular growth and muscle structure. Taken together, the cluster seems to center on mitochondrial regulation with a connection to muscle cell organization.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903740","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0070940","count":1}]},{"hash":"366236240601400862","title":"Muscle signaling and sarcomere organization","description":"The cluster includes GO terms tied to muscle cell biology, notably sarcomere organization and cardiac muscle cell proliferation, plus sodium ion import, which together point to muscle structure and electrophysiology. Additional terms reflect intracellular signaling (small GTPase-mediated signaling, Ras pathway regulation, receptor guanylyl cyclase signaling), suggesting signaling pathways active in muscle development or remodeling. Some terms are general or unrelated (DNA-templated transcription, aerotaxis, antipsychotic response), but the dominant pattern centers on muscle function and signaling, supporting this label.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051447","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0098719","count":2}]},{"hash":"364536127438773033","title":"Membrane Transporters for Metals, Nutrients, and Drugs","description":"The top GO terms are dominated by transport across membranes (cobalt ion transport, methionine transport, oligosaccharide transport, vitamin transmembrane transport, doxorubicin transport), suggesting the proteins function primarily as transporters for various substrates, including metals, amino acids, vitamins, and xenobiotics. Other terms (nucleotide-excision repair, ommochrome biosynthesis, very long-chain fatty acid catabolic process, protein secretion by type I secretion system) indicate additional, unrelated roles or annotation breadth. Overall, the strongest signal is transport-related, with diverse substrates, justifying a transporter-centered label. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":6},{"id":"GO:0006289","count":5},{"id":"GO:0015772","count":5},{"id":"GO:0006727","count":5},{"id":"GO:0006824","count":5}]},{"hash":"494442469468887069","title":"Neuromuscular development and lipid metabolism","description":"The top GO terms cluster around lipid droplet organization and adipose tissue development, suggesting lipid metabolism roles; simultaneously there are multiple terms tied to neuromuscular processes, NMJ assembly regulation, and collateral sprouting, indicating involvement in muscle-nerve development and signaling; additional terms about mitochondrial membrane potential and peroxisome inheritance reinforce energy and organelle maintenance aspects in muscle/neuronal cells. Together, these point to a functional module coordinating lipid metabolism with neuromuscular development and energy balance.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034389","count":2},{"id":"GO:0030514","count":2},{"id":"GO:0060612","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0050905","count":2}]},{"hash":"740778646495908198","title":"Unknown","description":"The assigned GO terms are highly heterogeneous, including mitochondrial DNA repair, telomere maintenance regulation, DNA damage response, and various signaling/stress responses (insulin, amyloid-beta, aldosterone), with no single dominant function or pathway emerging. Several terms are obsolete, and there is little connectivity among the terms to justify a coherent label. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043504","count":1},{"id":"GO:0090299","count":1},{"id":"GO:1990166","count":1},{"id":"GO:1904743","count":1},{"id":"GO:1904357","count":1}]},{"hash":"1656962867794623482","title":"Unknown","description":"There are no GO terms or functional connections provided for this cluster (no edges, no terms), so there is no discernible common function to label. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"444438744882403683","title":"Translation initiation and fidelity with spliceosome components","description":"This cluster is enriched for translational processes (initiation, termination, elongation, and translational fidelity) and spliceosome-related assembly/conformational changes, suggesting proteins associated with mRNA processing and translation machinery rather than a single signaling pathway.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:1990416","count":3},{"id":"GO:1990145","count":3},{"id":"GO:0002184","count":3},{"id":"GO:0006413","count":3}]},{"hash":"556886265175275035","title":"Membrane Proteolysis and NFAT Signaling Regulators","description":"A cluster dominated by GO terms on membrane protein proteolysis (ectodomain and intracellular domain proteolysis) and ER-to-cytosol transport, plus positive regulation of the calcineurin-NFAT signaling cascade and immune response. This suggests proteins that process membrane proteins to modulate NFAT-mediated immune signaling, with some auxiliary roles like Ras signaling or DNA repair appearing incidental.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070886","count":1},{"id":"GO:0051533","count":1},{"id":"GO:0006509","count":1},{"id":"GO:0050776","count":1},{"id":"GO:1904211","count":1}]},{"hash":"67162102991572226","title":"Neuronal signaling and vesicle trafficking","description":"Dominant GO terms center on neural signaling (neurotrophin TRK receptor signaling, regulation of synaptic depression, neurofibrillary tangle/tau-related activity) and intracellular transport/secretory pathways (ER to Golgi transport, ER exit, endosome transport). A muscle differentiation term appears but the neural signaling and vesicle trafficking theme best unifies the cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014902","count":1},{"id":"GO:0032460","count":1},{"id":"GO:1900452","count":1},{"id":"GO:1902997","count":1},{"id":"GO:0048227","count":1}]},{"hash":"2204436510374141833","title":"TLR/NLR Mediated Innate Immunity and Antigen Presentation","description":"All top GO terms point to innate immune sensing and signaling (TLR9, NOD2), inflammasome assembly (NLRP3), interferon pathways, and dendritic cell\u2013driven antigen processing and presentation (including MHC class I), indicating a cohesive innate-immune activation module linked to shaping adaptive responses.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":6},{"id":"GO:0030335","count":6},{"id":"GO:1902745","count":6},{"id":"GO:0070431","count":6},{"id":"GO:0002830","count":6}]},{"hash":"2267886236835934396","title":"Innate immune sensing and antigen presentation","description":"This cluster centers on innate immune recognition (TLR9 and NOD2 signaling, NLRP3 inflammasome) and downstream antigen processing/presentation (dendritic cell MHC I biosynthesis), with interferon signaling and migration cues, suggesting a module linking microbial detection to adaptive antigen presentation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":3},{"id":"GO:0030335","count":3},{"id":"GO:1902745","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0002830","count":3}]},{"hash":"1422368156346436357","title":"Vesicle trafficking and signaling regulation","description":"The highest-representation terms are about intracellular transport and vesicle biology, including intracellular protein transport, synaptic vesicle maturation, and regulation of synaptic vesicle exocytosis. While a few other terms (plant hormone signaling, stomatal closure, TNF regulation) appear, they are represented by single instances and do not define the cluster as strongly as vesicle trafficking and related signaling do.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0002023","count":1},{"id":"GO:0009749","count":1},{"id":"GO:1904468","count":1},{"id":"GO:2000300","count":1}]},{"hash":"281218343992358026","title":"Immune Defense and Activation","description":"The top GO terms are dominated by immune-related processes (defense response to virus, innate immune response, complement activation, T cell activation), suggesting the proteins in this cluster are related to immune defense. However, there are outlier terms such as chlorophyll biosynthetic process and cartilage morphogenesis, indicating possible annotation noise or multifunctional proteins. Overall, the cluster appears to represent immune-related functions with some conflicting signals.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015995","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051770","count":2},{"id":"GO:0002291","count":1}]},{"hash":"172079480023456149","title":"Neuronal microtubule dynamics and axoneme maintenance","description":"This cluster centers on microtubule remodeling, with terms for axonemal and plus-end depolymerization, spindle dynamics, and regulation of microtubule-based processes, and it is anchored by neuron-specific functions such as neuron projection maintenance and cerebellar Purkinje cell layer organization, suggesting a neuronal context for microtubule regulation.","confidence":"High","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060404","count":3},{"id":"GO:0070462","count":3},{"id":"GO:0048364","count":3},{"id":"GO:0021693","count":3},{"id":"GO:0000022","count":3}]},{"hash":"71516613331171650","title":"Unknown","description":"The top GO terms span immune signaling (T cell activation, complement), extracellular matrix remodeling (metallopeptidase activity regulation, ECM assembly), adhesion and migration, development (chondrocyte morphogenesis), plus unrelated processes (visual perception, chlorophyll biosynthesis). There is no single cohesive theme linking these functions, suggesting annotation noise or multi-domain proteins with diverse roles. Therefore, I cannot assign a specific, representative label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002291","count":1},{"id":"GO:0006471","count":1},{"id":"GO:0006956","count":1},{"id":"GO:0003429","count":1},{"id":"GO:1905050","count":1}]},{"hash":"1751045971823387321","title":"Unknown","description":"The GO terms include apoptosis regulation (extrinsic apoptotic signaling and general apoptotic regulation), neural development (midbrain dopaminergic neuron differentiation, neural plate development), TORC1 signaling, GTPase activity regulation, and developmental processes from insects and plants (chitin-based larval cuticle pattern formation, microsporogenesis). This mix shows no clear, single biological theme connecting the proteins, so a concise, cohesive label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":1},{"id":"GO:1904948","count":1},{"id":"GO:0035293","count":1},{"id":"GO:0038202","count":1},{"id":"GO:0001840","count":1}]},{"hash":"2077644975926259165","title":"Developmental morphogenesis and vesicle trafficking","description":"The proteins appear to participate in tissue development and morphogenesis (hair follicle, trabecula, cortical neuron migration/differentiation) and in secretory/trafficking pathways (exosomal secretion, endosome-to-Golgi transport, EGFR catabolic processes), with an additional link to cell-survival regulation during ER stress. This combination suggests a cohesive theme around developmental processes coupled with vesicle trafficking.","confidence":"Medium","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":2},{"id":"GO:0031069","count":1},{"id":"GO:1990182","count":1},{"id":"GO:0007174","count":1},{"id":"GO:1904948","count":1}]},{"hash":"1371461870975733794","title":"RNAP II Transcription Regulation","description":"This label fits because the strongest recurring GO terms are about regulation of transcription by RNA polymerase II (both positive and negative regulation), pointing to a core transcription-regulatory function of the cluster. Some terms also touch on related nuclear processes (DNA repair, transcription factor activity) and stress responses, but RNAP II\u2013mediated transcription regulation is the most coherent unifying theme.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010636","count":4},{"id":"GO:1902236","count":4},{"id":"GO:0006289","count":4},{"id":"GO:0043433","count":4},{"id":"GO:0006517","count":4}]},{"hash":"1071930942967762264","title":"Autophagy and vacuolar targeting","description":"The top GO terms cluster around cytoplasm-to-vacuole targeting (Cvt pathway), vacuole localization and autophagy-related protein targeting, as well as ER-Golgi vesicular transport. This suggests a cohesive theme of vesicle trafficking to the vacuole and autophagy-related processes, with a few secondary stress-response terms embedded. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":2},{"id":"GO:0034629","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0010288","count":1},{"id":"GO:0006501","count":1}]},{"hash":"1815380169619222923","title":"Ubiquitin-dependent protein quality control and ER stress response","description":"This cluster is driven by ubiquitination and ER-associated degradation signals (protein autoubiquitination, ubiquitin-dependent ERAD, protein deglycosylation) and includes impacts on ER stress signaling and vesicle formation. While there are hints of DNA repair and mitochondrial dynamics in the set, the strongest cohesive theme is ubiquitin-mediated protein quality control and ER stress response.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0010636","count":4},{"id":"GO:1902236","count":4}]},{"hash":"808114132370965510","title":"DNA replication and chromosome segregation","description":"The top GO terms cluster around sister chromatid segregation, DNA recombination during meiosis, DNA topological changes, replication fork progression, and chromosome separation, collectively pointing to core chromosome maintenance during DNA replication and cell division; the proteins likely function in replication-associated processes and chromosome dynamics rather than a single isolated pathway.","confidence":"High","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000819","count":2},{"id":"GO:0000712","count":2},{"id":"GO:0006265","count":2},{"id":"GO:1902969","count":2},{"id":"GO:0051304","count":2}]},{"hash":"232408563586604448","title":"Amino Acid and Cofactor Biosynthesis","description":"Most terms describe biosynthetic processes for amino acids and cofactors (L-lysine via aminoadipic acid, L-alanine, beta-alanine, biotin, protoporphyrinogen IX, and antibiotic biosynthesis). The dense connections support a cohesive metabolic cluster, though a couple of neuronal terms may reflect multifunctionality or noise rather than core function.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0042853","count":2},{"id":"GO:0019483","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0006782","count":2}]},{"hash":"821214869069780151","title":"Jasmonate signaling and oxylipin biosynthesis in plants","description":"Top GO terms point to plant-specific lipid metabolism and signaling, with fatty acid beta-oxidation, jasmonic acid biosynthesis, and oxylipin biosynthesis as central themes. The inclusion of stamen development and stress responses like ozone and toxic substances further supports a JA/oxylipin\u2013driven pathway linked to plant development and defense. Some terms (animal-related ones) appear as low-representation noise, but do not outweigh the plant-centered signals. Overall, the cluster most plausibly represents jasmonate signaling and oxylipin biosynthesis in plants, reflecting lipid-derived hormonal control of development and stress responses.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033543","count":3},{"id":"GO:0009695","count":3},{"id":"GO:0048443","count":3},{"id":"GO:0010193","count":3},{"id":"GO:0009636","count":3}]},{"hash":"1755934821416748859","title":"Cardiac Electrical Conduction and Contraction","description":"The cluster prominently features GO terms tied to cardiac electrical signaling and contraction, including regulation of electrical coupling involved in cardiac conduction, cardiac muscle contraction, and voltage-gated potassium channel clustering. While other terms point to kinase regulation, xenobiotic response, or developmental processes, these cardiac-related terms provide the most coherent shared function for the group.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0071902","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0045163","count":1},{"id":"GO:0060048","count":1}]},{"hash":"618856191327688893","title":"Prokaryotic central carbon metabolism and energy production","description":"The top GO terms are dominated by core energy-related pathways: glycolysis, the TCA cycle, 2-oxoglutarate metabolism, leucine catabolism, and the respiratory chain, which together point to central carbon metabolism and energy generation in prokaryotes. Additional terms like flagellum-dependent motility, photosynthesis, and methanogenesis suggest metabolic versatility across lineages, but the core signal centers on carbohydrate and amino acid catabolism feeding respiration. This aligns well with a cohesive energy-production/metabolic cluster.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006552","count":2},{"id":"GO:0006103","count":2},{"id":"GO:0006096","count":2}]},{"hash":"403850085530796853","title":"Cardiac and neural electrical signaling","description":"The terms cluster around electrical excitability and signaling in heart and nerve tissues: cardiac muscle contraction, regulation of electrical coupling in cardiac conduction, clustering of voltage-gated potassium channels, and regulation of synaptic vesicle exocytosis, with Schwann cell development supporting nerve conduction. Some outliers (hydrogen peroxide biosynthesis, spindle pole duplication) are less related, but the dominant pattern supports an excitability/signaling theme in excitable tissues.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":5},{"id":"GO:0050665","count":5},{"id":"GO:0045163","count":5},{"id":"GO:0060048","count":5},{"id":"GO:2000300","count":5}]},{"hash":"1544062200015827848","title":"Actin cytoskeleton organization and sarcomere formation","description":"GO terms cluster around actin cytoskeleton organization, sarcomere assembly, skeletal muscle fiber development, and contractile ring formation, indicating a module for organizing actin networks and forming muscle-like contractile structures, with a few outliers (ascospore wall, vacuole inheritance) that may reflect annotation noise.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030476","count":3},{"id":"GO:0002121","count":3},{"id":"GO:0048741","count":3},{"id":"GO:1903475","count":3},{"id":"GO:0045214","count":3}]},{"hash":"2303712234522591618","title":"Interferon-driven antiviral innate immunity","description":"The top GO terms are dominated by innate immune and antiviral responses, including innate immune response, defense response to virus, and cellular response to type I interferon, indicating the cluster centers on interferon-mediated antiviral signaling. Additional terms related to translation regulation under ER stress and ubiquitination may reflect downstream regulation of immune pathways, but the core theme remains antiviral innate immunity. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0007091","count":4},{"id":"GO:1905515","count":4},{"id":"GO:0009938","count":4},{"id":"GO:0008277","count":4}]},{"hash":"1309861397501926725","title":"Mitotic Regulation & Signaling","description":"The terms point to processes governing cell division and the cell cycle (mitotic cell cycle, cell division) with supporting signaling and regulatory pathways (PI3K/AKT, TORC1, NFAT signaling, ubiquitination). Although there are some stress and immune-related terms, the strongest cluster centers on mitotic control linked to broader regulatory signaling networks. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0070979","count":3},{"id":"GO:0051897","count":3},{"id":"GO:0071276","count":3}]},{"hash":"664395313155013416","title":"Calcium-Dependent Kinase Signaling in Cardiac and Neural Function","description":"This cluster centers on calcium-dependent signaling and serine/threonine phosphorylation, including calcineurin-NFAT and PKC pathways, and links to excitation-contraction in heart and neurotransmitter release at synapses, plus regulation of ion channels and calcium transporters. The GO terms converge on kinase activity, calcium signaling, cardiac contraction, potassium channel clustering, and synaptic exocytosis, indicating a cohesive theme of calcium-driven signaling controlling excitability and contraction in muscle and nerve tissues.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010800","count":2},{"id":"GO:0051533","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0071902","count":1},{"id":"GO:0050665","count":1}]},{"hash":"2213524129124226673","title":"Rho signaling and focal adhesion dynamics","description":"This cluster centers on GO terms like GO:0007266 (Rho protein signal transduction) and GO:0051893 (regulation of focal adhesion assembly), pointing to cytoskeletal remodeling and adhesion signaling that drive cell migration and invasion. Some other terms (e.g., response to cocaine, NK T cell differentiation) appear incidental or less representative, but the recurring themes of Rho signaling and focal adhesion regulation support a cohesive function. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":2},{"id":"GO:0014075","count":2},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1}]},{"hash":"1279162617255385871","title":"Rho-driven adhesion and ECM remodeling","description":"This cluster includes GO terms for Rho protein signal transduction, regulation of focal adhesion assembly, and regulation of extracellular matrix disassembly, which together point to regulation of cytoskeletal dynamics and cell-matrix adhesion. While other terms touch on development or immune differentiation, the common theme among the core terms is adhesion and extracellular matrix remodeling driven by Rho signaling.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0007266","count":1}]},{"hash":"2056295047597956351","title":"Bacterial DNA replication and HR repair","description":"The GO terms strongly cluster around DNA replication and double-strand break repair via homologous recombination, including SOS response and regulation of DSB processing, with mentions of bacterial-type and rolling circle replication. This points to a coherent theme of bacterial DNA replication and repair mechanisms, including DNA damage response under stress.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":3},{"id":"GO:0006268","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0044787","count":2},{"id":"GO:0070581","count":2}]},{"hash":"1646519364169251426","title":"Unknown","description":"The listed GO terms span development (trachea formation), nutrient/stress responses (invasive growth under glucose limitation, osmotic stress, cadmium response), multiple signaling pathways (Rho signaling, insulin receptor signaling), cell cycle/checkpoint control, and although some are regulatory, they do not converge on a single clear function or cellular context. There isn\u2019t a cohesive theme to define a specific, concise label for this cluster.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060440","count":5},{"id":"GO:0001403","count":5},{"id":"GO:0007266","count":5},{"id":"GO:0010614","count":5},{"id":"GO:0047484","count":5}]},{"hash":"183022004391061368","title":"Nutrient-starvation\u2013induced fungal morphogenesis and secretion","description":"The top GO terms point to fungal growth responses under nutrient limitation (pseudohyphal/invasive growth) combined with components of the secretory pathway (ER exit, localization to the cell surface, secretion of enzymes). This suggests a theme of growth form changes coupled with secretion during stress in fungi. The immune signaling term is peripheral to the main pattern but does not override it.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070863","count":1},{"id":"GO:2000010","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0033299","count":1},{"id":"GO:0001403","count":1}]},{"hash":"202321647170845738","title":"Sodium and Potassium Ion Transport","description":"This cluster centers on transmembrane movement and homeostasis of monatomic cations, mainly sodium and potassium ions, with related terms for ion import/export and intracellular ion balance. An outlier term for vestibulocochlear nerve formation may be annotation noise, but the dominant signal is ion transport across membranes.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":3},{"id":"GO:0061092","count":3},{"id":"GO:0021650","count":3},{"id":"GO:0030007","count":3},{"id":"GO:0099132","count":3}]},{"hash":"436272009076956174","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0002128","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0000453","count":1},{"id":"GO:0097310","count":1}]},{"hash":"885478581768066409","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0002181","count":1},{"id":"GO:0002128","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0000453","count":1}]},{"hash":"2057139628213782030","title":"Unknown","description":"The only accompanying GO terms are somatic diversification of immunoglobulins and apoptotic process, each tied to a single protein, with no edges connecting proteins. There isn\u2019t a coherent, shared function linking these five proteins, so a meaningful label cannot be inferred.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016445","count":1},{"id":"GO:0006915","count":1}]},{"hash":"1584844962430202976","title":"RNA processing and transcription regulation","description":"The cluster shows strong signals for RNA metabolism: maturation of LSU-rRNA and 5.8S rRNA, mRNA stabilization, and negative regulation of transcription elongation by RNA polymerase II, which together point to RNA processing and transcription control as the core theme. A few terms related to development and Wnt signaling are present but appear incidental given their low counts and lack of a cohesive developmental module.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000470","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0048730","count":1},{"id":"GO:0038031","count":1},{"id":"GO:0021797","count":1}]},{"hash":"1708432091488378881","title":"Unknown","description":"There are no GO terms listed to indicate a shared function, and with zero edges/triangles the cluster has no clear functional signal. Without a recognizable theme, Unknown is the safest label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"293866572747330299","title":"Translation and hypusine biosynthesis","description":"The GO terms cluster primarily around translation processes\u2014initiation, elongation, termination, and frameshifting\u2014plus peptidyl-hypusine biosynthesis, which is linked to translation factor modification. This suggests the proteins function together in the translation machinery, with a few less central terms appearing incidental.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008612","count":1},{"id":"GO:0034050","count":1},{"id":"GO:0006413","count":1},{"id":"GO:1903272","count":1},{"id":"GO:0006452","count":1}]},{"hash":"2242868978547242860","title":"DNA damage response and neural development","description":"The proteins show strong enrichment for DNA damage repair and cell-cycle checkpoint terms (DSB processing via SDSA, intra-S DNA damage checkpoint signaling, maintenance of trinucleotide repeats) alongside neural lineage terms (neuron differentiation, Schwann cell development). While there are also stress-related terms (xenobiotic response), the core themes point to genomic stability processes that may be active in neural development contexts.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030182","count":5},{"id":"GO:2001241","count":5},{"id":"GO:1905213","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0031573","count":5}]},{"hash":"1429215805511791973","title":"APC-driven mitotic progression","description":"The top GO terms cluster around mitosis and ubiquitin-mediated proteolysis: mitotic cell cycle, cell division, and especially the anaphase-promoting complex (APC)-dependent catabolic process and K11-linked ubiquitination. This points to proteins functioning in APC-driven regulation of mitosis, facilitating metaphase-to-anaphase transition via targeted degradation. Some histone modification terms appear (obsolete), which may reflect chromatin changes during cell cycle progression. Overall, the dominant theme is ubiquitin-dependent control of mitotic progression.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0000278","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1553513585980006655","title":"Nuclear DNA Repair and RNA Surveillance","description":"The proteins in this cluster are primarily linked to nuclear genome maintenance and RNA quality control, including DNA repair pathways (alternative NHEJ and base-excision repair) and processes governing nuclear RNA surveillance and turnover (nuclear mRNA surveillance and rRNA catabolic processes). An outlier term mentions plastid DNA replication, which may reflect dual localization or annotation noise, but the dominant theme is nuclear DNA repair and RNA processing.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097681","count":1},{"id":"GO:0006287","count":1},{"id":"GO:0033259","count":1},{"id":"GO:0045950","count":1},{"id":"GO:0032066","count":1}]},{"hash":"1401357606069890125","title":"Nuclear processes and ribosome biogenesis","description":"The cluster's top GO terms cluster around nuclear activities (DNA-templated transcription, regulation of protein export from the nucleus, mitotic spindle organization) and ribosome biogenesis/assembly, suggesting a theme of nuclear function linked to ribosome production. A few terms (bone mineralization, leukocyte chemotaxis) are less consistent and do not dominate the set.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007052","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0001833","count":1},{"id":"GO:0042254","count":1}]},{"hash":"344483950224101730","title":"Symbiont-mediated immune suppression","description":"The cluster\u2019s GO terms cluster around host immune modulation by symbionts: suppression of adaptive immune response, antigen processing and MHC II presentation, and perturbation of ubiquitin-like protein modification, plus regulation of tolerance. An outlier term relates to cutin biosynthesis (plant barrier), but the strongest signal is immune suppression/modulation by symbionts.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042795","count":1},{"id":"GO:0042796","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0039648","count":1}]},{"hash":"955373186394257718","title":"Unknown","description":"There are 5 proteins but no edges, no triangles, and no GO terms reported for the cluster, so there is no shared functional signal to define a theme. Without common terms or interactions, we cannot infer a representative function, hence the Unknown label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"621033665171371683","title":"Skeletal Muscle Development and Regeneration Regulators","description":"The terms show a strong emphasis on muscle biology: myoblast fusion, satellite cell activation for skeletal muscle regeneration, and regulation of skeletal muscle differentiation, plus related regeneration processes. Less directly, terms like blastocyst development and mammary gland involution reflect broader developmental roles, but the core theme across the cluster is regulation of muscle formation and repair.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001824","count":4},{"id":"GO:0007520","count":4},{"id":"GO:0051281","count":4},{"id":"GO:0097264","count":4},{"id":"GO:0007586","count":4}]},{"hash":"158523796137548496","title":"Membrane Transport and Nutrient Uptake","description":"Most top GO terms describe transport across membranes (amino acids, vitamins, lipids, metals) and related import/export processes, including branched-chain amino acid transport, vitamin and lipoprotein transport, doxorubicin transport, and glutathione import into vacuoles. While a nucleotide-excision repair term appears, the dominant signal is membrane transport and substrate uptake, suggesting transporters or secretion/uptake facilitators.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":5},{"id":"GO:0006824","count":5},{"id":"GO:0042760","count":5},{"id":"GO:1900753","count":5},{"id":"GO:0071996","count":5}]},{"hash":"1904019201746312089","title":"Embryonic development and transcription","description":"The proteins in this cluster are enriched for DNA-templated transcription and several development-related processes, including forebrain development, neural tube closure, skeletal system development, and multicellular organism development, suggesting a cohesive role in developmental gene regulation. While other terms indicate stress and immune responses, the predominant theme appears to be transcriptional control during embryonic/organismal development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001403","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0001501","count":2}]},{"hash":"1301648033550098186","title":"Neuronal Vesicle Trafficking and Signaling","description":"This cluster centers on intracellular transport processes (ER to Golgi, protein exit from ER, and plasma membrane to endosome transport) with an additional nod to neuronal signaling (neurotrophin TRK receptor signaling and regulation of synaptic depression). The dominant theme is vesicle trafficking relevant to neuronal contexts, suggesting these proteins function together in managing trafficking linked to neural signaling and development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014902","count":1},{"id":"GO:0032460","count":1},{"id":"GO:1900452","count":1},{"id":"GO:1902997","count":1},{"id":"GO:0048227","count":1}]},{"hash":"895707577904764442","title":"Transcription, ribosome biogenesis, and mitosis","description":"Top GO terms show enrichment for DNA-templated transcription, ribosome biogenesis, and mitotic processes (spindle assembly, mitotic cell cycle, cell division), indicating a group focused on gene expression and cell-cycle machinery. While some terms like COPII vesicle budding and brain development are present, the dominant theme across terms is transcription/biogenesis coupled with cell division, suggesting these proteins function in preparing and executing cell proliferation. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007420","count":3}]},{"hash":"1615597731193222661","title":"RNA and protein methylation; ribosome biogenesis","description":"The top GO terms are dominated by methylation-related processes, including rRNA methylation, histone H4-R3 methylation, and peptidyl-lysine dimethylation, with an additional term tied to ribosome biogenesis (ribosomal small subunit export from nucleus). This points to a cluster of proteins involved in RNA/protein modification and ribosome assembly, with some ancillary biosynthetic annotations likely reflecting shared methyltransferase activities. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0043985","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0000056","count":1}]},{"hash":"603780657271806035","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038066","count":2},{"id":"GO:0097011","count":2},{"id":"GO:1904628","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0002635","count":1}]},{"hash":"1107658762386597178","title":"Octopamine-Driven Locomotion","description":"The cluster is best characterized by GO terms concentrated on octopamine signaling and locomotory behavior, suggesting a shared role in invertebrate neurotransmission that governs movement. While some terms (immune response, endothermy) appear unrelated and may reflect annotation noise, the strongest signal ties to neurotransmitter-mediated movement and stimulus responses.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007626","count":1},{"id":"GO:0071927","count":1},{"id":"GO:0002443","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006035","count":1}]},{"hash":"2000937691045144376","title":"Mitochondrial Transport and Membrane Potential","description":"The prominent GO terms cluster around mitochondrial processes: regulation and changes of mitochondrial membrane potential, apoptotic mitochondrial changes, and transport of key metabolites (alpha-ketoglutarate, thiamine pyrophosphate, CoA) across membranes, plus the malate-aspartate shuttle. These point to a cohesive theme of mitochondrial metabolism and membrane transport/dynamics, with a few obsolete terms incidental to the broader mitochondrial function signal. ","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0030974","count":1},{"id":"GO:0035349","count":1}]},{"hash":"1049228187510987152","title":"Mitochondrial Membrane Potential and Metabolite Transport","description":"This cluster centers on mitochondrial function, with terms about regulating membrane potential, apoptotic mitochondrial changes, and transmembrane transport of key metabolites (alpha-ketoglutarate, thiamine pyrophosphate, coenzyme A), plus the malate-aspartate shuttle. The included obsolete terms still point to mitochondrial genome maintenance and localization to the mitochondrial membrane, reinforcing a mitochondrial context. Overall, the proteins appear linked to mitochondrial energy metabolism and metabolite exchange across membranes.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0030974","count":1},{"id":"GO:0035349","count":1}]},{"hash":"533734539078519938","title":"Macrophage inflammatory signaling and lipid regulation","description":"Top terms indicate macrophage-driven innate immune activation (positive regulation of macrophage activation, TNF production, cytolysis) and TLR4 signaling with responses to lipoteichoic acid, suggesting a macrophage inflammatory role. Concurrent lipid-related terms (cholesterol efflux, reverse cholesterol transport, triglyceride homeostasis) imply coupling between immune signaling and lipid metabolism in these proteins. A single obsolete term (signal peptide processing) appears minor relative to the main theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1},{"id":"GO:0010875","count":1},{"id":"GO:0034145","count":1},{"id":"GO:0071223","count":1}]},{"hash":"2272939465577060799","title":"RNA Splicing and Ciliary Components","description":"The cluster shows strong enrichment for RNA processing terms (RNA splicing, snoRNA splicing, nuclear mRNA surveillance, and spliceosome-related activity), with additional but weaker signals for ciliary processes (cilium assembly and intraflagellar transport). The RNA processing theme is the most coherent throughline across the members, though a subset may relate to ciliary functions as well.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":1},{"id":"GO:0035721","count":1},{"id":"GO:0000350","count":1},{"id":"GO:0009560","count":1},{"id":"GO:0008380","count":1}]},{"hash":"1100910368172271704","title":"Unknown","description":"The top GO terms span apoptosis (p53-mediated), innate immune signaling (TNF and LPS response), RNA processing (miRNA and siRNA processing), and other unrelated processes (plant immune regulation, dosage compensation, courtship behavior). With only a single edge and no cohesive functional theme, there is no clear unifying function for this cluster. ","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0042347","count":1},{"id":"GO:0033209","count":1}]},{"hash":"1360701131491766777","title":"Immune signaling and cell fate regulators","description":"This cluster is enriched for GO terms that describe regulatory roles across innate immune signaling (regulation of toll-like receptor signaling), programmed cell death (regulation of necroptotic and apoptotic processes), and general regulatory processes like ubiquitination, transcription, and cell cycle. The common thread is modulation and control rather than direct execution, suggesting these proteins act as regulators of immune signaling and cell fate decisions via ubiquitin-mediated mechanisms. Confidence: Medium","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034121","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0060544","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0071157","count":1}]},{"hash":"1909291581961013257","title":"Unknown","description":"The GO terms are very diverse (melatonin biosynthesis, ectoine biosynthesis, various acetylations, putrescine and glucosamine metabolism, and mitotic chromatid cohesion), with no clear shared pathway or function across the proteins. The network has no edges, further supporting the lack of a cohesive cluster theme. Therefore Unknown with None confidence.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":4},{"id":"GO:0019491","count":4},{"id":"GO:0018002","count":4},{"id":"GO:0046208","count":4},{"id":"GO:0018003","count":4}]},{"hash":"1024854036962471560","title":"Endothelial signaling and morphogenesis","description":"This cluster centers on signaling pathways linked to vascular development and morphogenesis, including Wnt and activin/TGF-beta\u2013related signaling, adiponectin signaling, and hormone response (testosterone). The presence of endothelial tube morphogenesis alongside transcription regulation terms suggests these proteins coordinate signaling cascades that drive endothelial development and gene expression, making the endothelial development theme the most coherent label. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033574","count":1},{"id":"GO:0032927","count":1},{"id":"GO:0018105","count":1},{"id":"GO:0016055","count":1},{"id":"GO:0006356","count":1}]},{"hash":"1801802261975837237","title":"Cytoskeleton remodeling and EGFR signaling","description":"The top terms converge on actin cytoskeleton dynamics and receptor-driven signaling: actin filament branching; regulation of focal adhesion assembly; Cdc42 signal transduction; EGFR signaling; and plasma membrane to endosome transport. This points to a cohesive role in coordinating cytoskeletal remodeling with receptor trafficking and downstream signaling, relevant to cell movement, membrane trafficking, and neurite branching. The viral RNA genome replication term seems incidental to the core theme. ","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0039694","count":4},{"id":"GO:0010628","count":4},{"id":"GO:0048227","count":4},{"id":"GO:0007173","count":4},{"id":"GO:0051893","count":4}]},{"hash":"1453403806871902116","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002635","count":1},{"id":"GO:1902187","count":1},{"id":"GO:0033280","count":1},{"id":"GO:0000185","count":1},{"id":"GO:0061158","count":1}]},{"hash":"841983771760504607","title":"Unknown","description":"The terms are highly diverse and do not point to a single cohesive function or pathway (ranging from karyogamy and DNA replication to iron-sulfur cluster assembly and various regulatory processes). Several terms are obsolete or broad, making it difficult to assign a specific, representative label to the cluster.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":2},{"id":"GO:1903382","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0006880","count":1},{"id":"GO:1902037","count":1}]},{"hash":"657362364143674393","title":"Unknown","description":"The top terms span both nutrient/metal transport (cobalt ion, methionine, branched-chain amino acids, vitamins, doxorubicin transport) and unrelated processes (ribosome biogenesis, nucleotide-excision repair, fatty acid catabolism, secretion, fertilization), with no single cohesive function tying all proteins together. This lack of a consistent theme across the cluster leads to an Unknown labeled cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007338","count":2},{"id":"GO:0006289","count":1},{"id":"GO:0006824","count":1},{"id":"GO:0042760","count":1}]},{"hash":"102271651203188555","title":"Cdc42-driven actin remodeling and vesicle trafficking","description":"This cluster centers on cytoskeleton dynamics and membrane trafficking, as shown by Cdc42 signaling and actin filament branching, along with ER-to-Golgi and endosome transport, and EGFR signaling. Focal adhesion regulation and morphogenesis terms further tie cytoskeletal remodeling to cell adhesion and shape changes. A viral replication term appears peripheral, but the core theme links actin remodeling with vesicle trafficking and signaling.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0039694","count":3},{"id":"GO:0010628","count":3},{"id":"GO:0048227","count":3},{"id":"GO:0007173","count":3}]},{"hash":"608506200068812554","title":"Ubiquitin-Proteasome Regulation of Cell Cycle","description":"The GO terms center on ubiquitination events (autoubiquitination, K11-linked), SCF-dependent tagging, and proteasomal degradation, alongside cell-cycle stages (G2/M, mitotic cycle) and DNA repair. This points to a cohesive theme where the ubiquitin-proteasome system controls cell-cycle progression and genome maintenance, with related protein turnover in ER-associated degradation contributing to quality control.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0070911","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1679815757155910966","title":"Unknown","description":"The four proteins are associated with a broad and diverse set of GO terms, spanning neural development, extracellular matrix remodeling, neuropeptide processing, thyroid hormone response, immune cytotoxicity, ossification, Wnt signaling, toxin response, mitochondrial autophagy, and surfactant homeostasis. There isn\u2019t a single cohesive biological theme that clearly ties these functions together, so a precise, representative label cannot be confidently assigned.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":1},{"id":"GO:0034769","count":1},{"id":"GO:0010813","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0001913","count":1}]},{"hash":"856312044137411680","title":"Ribosome Biogenesis and Translation","description":"Most terms are about translation and ribosome assembly/biogenesis (translation, translational elongation, ribosomal large/small subunit assembly, ribosome biogenesis). The presence of mitochondrial translational termination and rRNA processing terms further supports a core function in ribosome-mediated protein synthesis, including mitochondrial context. This suggests the proteins participate in ribosome construction and function rather than unrelated processes.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006414","count":1},{"id":"GO:0070126","count":1},{"id":"GO:0006415","count":1},{"id":"GO:0000027","count":1}]},{"hash":"290697254879422107","title":"Dendritic spine and synaptic vesicle regulation","description":"The GO terms are dominated by neuronal functions: positive/negative regulation of dendritic spine and dendrite development, synaptic vesicle budding, and calcium-dependent exocytosis, suggesting a theme around synapse formation and neurotransmitter release. Other terms (lipoprotein assembly, epithelial polarity, ubiquitination, myeloid apoptosis) are less directly related and may reflect broader multifunctionality or noise. Overall, the cluster most coherently maps to synaptic/dendritic processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060999","count":2},{"id":"GO:0055108","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0034379","count":2},{"id":"GO:0070142","count":2}]},{"hash":"850996421724487858","title":"Hippocampal neuron development and synaptic signaling","description":"The top GO terms point to hippocampus development, dendrite morphogenesis, excitatory synaptic activity, and calcium-dependent exocytosis, all consistent with neuronal development and synaptic regulation in the hippocampus. Additional terms for Wnt signaling, JNK cascade, and actin remodeling support neurite outgrowth and synapse formation processes, reinforcing a coherent theme of hippocampal neuron development and synaptic function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051893","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0021766","count":4},{"id":"GO:0045956","count":4}]},{"hash":"2264274602833164752","title":"Unknown","description":"The top GO terms span cell cycle (metaphase/anaphase transition), protein isomerization, various developmental tissues (fat pad, striatum), metabolism, ciliogenesis, transcription by RNA polymerase III, GPCR signaling regulation, and lead ion response. This wide, non-cohesive mix provides no clear unifying function for the cluster, so a single representative label is not supported.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007091","count":3},{"id":"GO:0000413","count":3},{"id":"GO:0060613","count":3},{"id":"GO:0021756","count":3},{"id":"GO:0008653","count":3}]},{"hash":"1367177946497286425","title":"DNA Damage Response & Cell Cycle Regulation","description":"This cluster is dominated by terms related to DNA repair (both nonhomologous end joining and homologous recombination), chromosome dynamics during meiosis (synaptonemal complex organization) and mitosis (mitotic spindle elongation), and ubiquitin-mediated regulation (protein autoubiquitination, K11-linked ubiquitination). Together, these indicate a cohesive theme of DNA damage sensing/repair and control of cell-cycle progression, with some ubiquitin-signaling regulation, while a few immunity-related terms may reflect cross-talk or multifunctionality of the involved proteins.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006303","count":4},{"id":"GO:0070193","count":4},{"id":"GO:1901487","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0070979","count":4}]},{"hash":"200364518939749954","title":"Neuronal development and synaptic signaling","description":"The top terms cluster around hippocampal neuron development, dendrite morphogenesis, and regulation of synaptic activity (excitatory postsynaptic potential, calcium-dependent exocytosis) with supporting roles for Wnt signaling, JNK cascade, and actin cytoskeleton remodeling, pointing to a neuronal development/synaptic function theme.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051893","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0045956","count":2}]},{"hash":"188904596672290621","title":"ER Stress Proteostasis and Secretory Trafficking","description":"The cluster centers on responses to misfolded proteins, the ER unfolded protein response, SNARE-mediated vesicle trafficking between the ER and Golgi, and related proteostasis/secretory pathway activities (with a peroxisomal import element). While a couple of terms are less related (e.g., mitotic checkpoint signaling), the dominant signal points to ER stress\u2013driven proteostasis and trafficking.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1903862","count":4},{"id":"GO:0071218","count":4},{"id":"GO:0035494","count":4},{"id":"GO:0016562","count":4},{"id":"GO:0034599","count":4}]},{"hash":"985817023901792381","title":"Rho-regulated focal adhesion and cytoskeleton signaling","description":"The top GO terms center on Rho protein signal transduction and regulation of focal adhesion assembly, pointing to signaling pathways that control cytoskeletal dynamics and cell adhesion, which are core to cell movement and morphogenesis (supported by related terms like trachea formation and invasive growth). Some terms (e.g., NK T cell differentiation, plant-specific signaling) appear peripheral, likely noise, but the dominant theme ties to cytoskeletal regulation and adhesion signaling.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":4},{"id":"GO:0009938","count":4},{"id":"GO:0060440","count":4},{"id":"GO:0051893","count":4},{"id":"GO:0001403","count":4}]},{"hash":"1837754622695310070","title":"Ubiquitin-Proteasome Regulation of Immune Response and Mitosis","description":"The set of terms centers on defense against viruses and innate immunity, alongside mitotic cell cycle processes and ubiquitin-dependent proteolysis (SCF and APC pathways). This suggests proteins that link immune signaling with cell-cycle control through targeted protein degradation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0000278","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0045087","count":2}]},{"hash":"47416490160475475","title":"Neural and Schwann Cell Development","description":"The GO terms show a clear emphasis on neural lineage, with neuron differentiation and Schwann cell development being the strongest signals, indicating the proteins may function in neural and glial development. The other terms relate to stress responses and DNA damage repair, which are less cohesive with the neural-development theme, suggesting some broader or secondary roles. Overall, the central theme is neural and Schwann cell development with accompanying stress-related processes.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030182","count":3},{"id":"GO:2001241","count":3},{"id":"GO:1905213","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0031573","count":3}]},{"hash":"2229948645462467965","title":"Unknown","description":"The top GO terms span calcium signaling, tissue maintenance, stress responses, and several distinct biosynthetic/metabolic pathways, with no single cohesive function tying all four proteins together. There are no edges among proteins, suggesting little apparent functional coupling. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":2},{"id":"GO:0001894","count":1},{"id":"GO:0009414","count":1},{"id":"GO:0042821","count":1},{"id":"GO:0001516","count":1}]},{"hash":"761118221916698284","title":"Mitochondrial translation machinery","description":"The top GO terms cluster around mitochondrial translation and ribosome assembly, including mitochondrial translation, translational termination, and ribosomal large subunit assembly, suggesting the proteins participate in mitochondrial protein synthesis and ribosome biogenesis. The other terms appear more divergent and may reflect annotation noise or multifunctionality, but the core signal points to mitochondrial translation machinery.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006415","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0000027","count":1},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1}]},{"hash":"511047248734642687","title":"Unknown","description":"The Top Terms include lipid metabolism (ergosterol biosynthesis regulation, unsaturated fatty acid biosynthesis, MIPC metabolism) and other disparate processes (nitric oxide biosynthesis, nitrate assimilation, CNS myelin maintenance). With only scattered related terms and no clear, cohesive function linking all four proteins, there isn't a confident, specific label to assign.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0006636","count":1}]},{"hash":"1338134904391308505","title":"Bacterial DNA replication and SOS repair","description":"GO terms indicate DNA unwinding and replication, rolling circle replication, homologous recombination repair, SOS response, and clearance of foreign DNA, all pointing to bacterial DNA metabolism and damage response. The cluster likely represents proteins involved in bacterial DNA replication, repair, and stress signaling.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":3},{"id":"GO:0006268","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0044787","count":2},{"id":"GO:0070581","count":2}]},{"hash":"458801896940000099","title":"Rho signaling and ECM remodeling","description":"This cluster centers on cytoskeletal signaling and cell-matrix interactions, highlighted by Rho protein signal transduction, regulation of focal adhesion assembly, and regulation of extracellular matrix disassembly. While some terms relate to development or immune differentiation, the strongest and most consistent signals point to pathways that coordinate actin dynamics, adhesion, and ECM remodeling, supporting a cohesive theme of cytoskeletal-adhesion regulation.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":3},{"id":"GO:0060440","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007266","count":3}]},{"hash":"890912139320222554","title":"ERK and p38 MAPK Signaling Cluster","description":"The top GO terms center on ERK1/ERK2 and p38 MAPK cascades and PMA- and cytokine-driven signaling, with supplementary cues from Rho signaling and focal adhesion regulation, suggesting a shared role in MAPK-mediated stimulus responses. Despite no network connections, the functional theme is clear: MAPK signaling pathways activated by external cues.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1904628","count":4},{"id":"GO:0038066","count":4},{"id":"GO:0097011","count":4},{"id":"GO:0070371","count":4},{"id":"GO:1901214","count":3}]},{"hash":"345415998679424013","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning embryonic development (cranial skeleton, trachea formation), DNA replication and mitotic checkpoints, various signaling and adhesion processes, invasive growth, and immune differentiation, with no clear, single function tying the proteins together. Hence no cohesive label beyond Unknown is justified.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":2},{"id":"GO:0007095","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1}]},{"hash":"1901210868173467378","title":"Unknown","description":"The GO terms span development, immune differentiation, cytoskeletal signaling, and extracellular matrix remodeling, with no coherent central function and no edges connecting proteins. This makes it unclear to assign a single representative function, so Unknown is appropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":3},{"id":"GO:0060440","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007266","count":3}]},{"hash":"1061732009388923153","title":"Unknown","description":"The terms mix innate immune defense and proteasome regulation with cell cycle and developmental morphogenesis, showing no single cohesive function to bind the cluster; proteins may be multifunctional or annotations are broad, making a specific label inappropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045842","count":2},{"id":"GO:0000278","count":2}]},{"hash":"339537881675746922","title":"Innate immune response proteins","description":"This cluster centers on innate immune response as the top GO term (GO:0045087) with two proteins, suggesting an immune-related theme, and includes related signaling terms (Rho signaling, NK T cell differentiation). However, the presence of diverse terms (placenta development, trachea formation) and no connecting edges imply an imperfect, broad annotation rather than a cohesive functional module, so the label is cautious.","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0001893","count":2},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1}]},{"hash":"1310941690759873323","title":"Hippocampal Neuron Development and Synaptic Signaling","description":"The GO terms cluster around neural development and synaptic activity, including hippocampus development, dendrite morphogenesis, excitatory postsynaptic potentials, and calcium-dependent exocytosis. Additional signals like Wnt and JNK cascades point to pathways regulating neurite outgrowth and synapse formation, with some adhesion-related terms tying to cytoskeletal changes. Overall, the set suggests a function in hippocampal neuron development and synaptic signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051893","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0045956","count":2}]},{"hash":"1580569310905890963","title":"Unknown","description":"There are no GO terms provided to ground a functional theme for these four proteins, so a shared function cannot be inferred from the available data. Unknown is the appropriate label in this case.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"2155147230290637988","title":"Unknown","description":"This cluster shows a mix of terms spanning apoptosis signaling, TORC1 signaling, GTPase regulation, meiosis, cilium transport, nuclear pore assembly, and protein desumoylation, with no obvious unifying function. The presence of both reproductive processes and general cellular signaling/structure terms suggests heterogeneous roles rather than a single coherent functional theme.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0009556","count":2},{"id":"GO:0060188","count":2}]},{"hash":"1131078757033162145","title":"RNA processing and post-transcriptional regulation","description":"The Top Terms cluster around RNA-level regulation, including RNA silencing (regulatory ncRNA- and miRNA-mediated) and various post-transcriptional processing steps (spliceosome-mediated splicing, mRNA stabilization/modification), plus components involved in translation initiation and ribonucleoprotein assembly. This suggests a cohesive theme of RNA metabolism and regulation rather than a single signaling pathway.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0048255","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0045292","count":1}]},{"hash":"1481760247282192153","title":"Plant defense signaling and protein quality control","description":"The top GO terms emphasize plant defense (jasmonic acid/ethylene-dependent systemic resistance) and stress responses (positive regulation of ROS-mediated programmed cell death) alongside protein homeostasis (polyubiquitinated misfolded protein transport; regulation of protein stability). Together, these indicate a cluster focused on how plants sense stress and coordinate protein quality control to defend against damage. A few terms are unrelated or archaic, but the dominant signal fits plant stress response with proteostasis.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070845","count":4},{"id":"GO:0031647","count":4},{"id":"GO:0061186","count":4},{"id":"GO:1901300","count":4},{"id":"GO:0051038","count":4}]},{"hash":"1218489438568933914","title":"Unknown","description":"There are no GO terms or interactions to link the four proteins, so there is no clear shared function to anchor a label. Without a common theme, a specific, representative name cannot be justified.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1236280087898748953","title":"Ion and small molecule transporters","description":"The GO terms collectively point to transmembrane transport activities for a range of substrates, including ions (potassium, sodium, nitrite), organic cations, sugars/arabinose, vitamins, and neurotransmitter-related vesicular loading. This coherence suggests a cluster of membrane transporter proteins handling diverse small molecules and ions, rather than a single specific substrate. High confidence that this label captures the cluster\u2019s function.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0070715","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0035725","count":2},{"id":"GO:1900754","count":2}]},{"hash":"391699581297555188","title":"Synaptic vesicle trafficking and receptor recycling","description":"Label reflects the strong representation of receptor recycling and glutamatergic synaptic transmission, with supporting hints from endosome size regulation and vacuole fusion, all pointing to membrane trafficking dynamics in neurons. Some terms are unrelated or obsolete, but the core theme is neuronal vesicle trafficking and receptor recycling.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001881","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0060316","count":1},{"id":"GO:0034968","count":1},{"id":"GO:0035023","count":1}]},{"hash":"220547318117231148","title":"Unknown","description":"The terms include toll-like receptor signaling, Wnt signalosome assembly, and diverse morphogenesis processes across different organs, with no single shared pathway or function evident for all proteins. Therefore a generic Unknown label with no clear theme is appropriate.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034154","count":1},{"id":"GO:0060658","count":1},{"id":"GO:0034123","count":1},{"id":"GO:0014068","count":1},{"id":"GO:1904887","count":1}]},{"hash":"1799504028010355044","title":"Unknown","description":"These terms span diverse processes from immune signaling (TLR, IL-18, MHC I biosynthesis) to developmental morphogenesis (Wnt signalosome, nerve branching, imaginal disc polarity) and organ size, with no single dominant shared function. Therefore no cohesive theme can be assigned to this cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030335","count":1},{"id":"GO:1904887","count":1},{"id":"GO:0002830","count":1},{"id":"GO:2000172","count":1},{"id":"GO:0035564","count":1}]},{"hash":"270822888289682005","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0009408","count":1}]},{"hash":"1471605725463946058","title":"Antiviral Innate Immune Response","description":"These proteins are enriched for GO terms related to antiviral defense and innate immunity (suppression of viral release by host; defense response to virus; innate immune response). Although a few unrelated terms appear, the dominant theme is host antiviral innate defense.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1903762","count":1}]},{"hash":"824501867333319355","title":"Unknown","description":"This cluster has four proteins but no reported GO terms or interactions, so there is no shared functional signal to define a label. Without functional annotation or network connections, a meaningful label cannot be determined.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"463445767811314893","title":"DNA Damage Response and Chromosome Maintenance","description":"The cluster\u2019s top terms center on double-strand break repair (NHEJ and HR), synaptonemal complex organization, and mitotic spindle elongation, which together point to chromosome maintenance during DNA repair and cell cycle. Ubiquitination terms further support regulation of repair proteins, while a few immune signaling terms are present but secondary to the core theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006303","count":4},{"id":"GO:0070193","count":4},{"id":"GO:1901487","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0070979","count":4}]},{"hash":"1024377666016622747","title":"Unknown","description":"The GO terms are a mix of neural development/metabolism (e.g., nucleus accumbens development, GABA catabolic process, retinal metabolic process, retinoic acid receptor signaling) and non-neural organ development (heart morphogenesis, ureter maturation). There is no single dominant functional theme tying all terms together.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":1},{"id":"GO:0015976","count":1},{"id":"GO:0001936","count":1},{"id":"GO:0009450","count":1},{"id":"GO:0006537","count":1}]},{"hash":"1412537185910542386","title":"Unknown","description":"The GO terms are highly heterogeneous across domains and processes (bacterial LPS biosynthesis, plant stress responses, autophagy-related vacuolar processes). With no evident shared function or interaction among the four proteins (no edges/triangles), there isn\u2019t a unifying theme to label the cluster beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0034496","count":1},{"id":"GO:0010618","count":1},{"id":"GO:0045490","count":1},{"id":"GO:0080151","count":1}]},{"hash":"1216911424023642569","title":"Unknown","description":"No top GO terms are provided and there are no edges or shared functions among the four proteins, so there is no clear common theme to define a label. Without a detectable function, the prudent designation is Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1406920922133113444","title":"Unknown","description":"The top GO terms are diverse and do not point to a single cohesive function or process. They touch on kinase activity regulation, TORC1 signaling, SREBP signaling, ubiquitination, fungal cell wall biogenesis, plant tissue patterning, glucose-responsive invasive growth, and neuronal dendrite development, among others. This heterogeneity makes it hard to assign a common, interpretable function to the cluster beyond a general \u201cregulatory/signaling\u201d theme, so Unknown with no confidence is appropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0061099","count":1},{"id":"GO:0034729","count":1},{"id":"GO:0032995","count":1}]},{"hash":"1899490909845334642","title":"Unknown","description":"The terms include thymine and uridine transport but also cerebellar development and various apoptosis/ER stress-related regulations, with no single cohesive function linking all four proteins. The mix prevents a confident, specific label. ","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035364","count":1},{"id":"GO:0015862","count":1},{"id":"GO:0009405","count":1},{"id":"GO:1904721","count":1},{"id":"GO:1902236","count":1}]},{"hash":"1799277005695001458","title":"Unknown","description":"There are no GO top terms nor network connections in this cluster (edges/triangles = 0), so there is no clear functional theme to name; it remains Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1665437378175073281","title":"Lipid Metabolism and Sphingolipid Synthesis","description":"The terms point mainly to lipid pathways: fatty acid biosynthesis, sphingolipid metabolism (sphinganine, sphingosine, sphingolipid-related processes), and sterol regulation, with myelin maintenance reflecting lipid-rich CNS membranes. This common lipid theme, plus fat response and cholesterol esterification signals, supports a cohesive cluster centered on lipid metabolism and sphingolipid signaling.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050872","count":1},{"id":"GO:0006667","count":1},{"id":"GO:0010873","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0006636","count":1}]},{"hash":"475044041931016052","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006293","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0006295","count":1},{"id":"GO:0006362","count":1},{"id":"GO:0000717","count":1}]},{"hash":"1789568692473806740","title":"Innate immune sensing and antigen presentation","description":"The GO terms converge on innate immune sensing via TLR9, NOD2, and NLRP3, detection of muramyl dipeptide, and downstream antigen processing/presentation by dendritic cells (MHC I), plus interferon signaling. This suggests a function around pathogen recognition and initiating antigen presentation, justifying the label.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034162","count":3},{"id":"GO:0030335","count":3},{"id":"GO:1902745","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0002830","count":3}]},{"hash":"160068474610259570","title":"Mitochondrial respiration and energy metabolism","description":"The top GO terms are dominated by mitochondrial energy production processes (mitochondrial electron transport, aerobic respiration, proton transmembrane transport), suggesting the cluster centers on mitochondrial energy metabolism. Peripheral terms like symbiont entry into host cell and viral process may reflect context or regulatory interactions but do not outweigh the core energy-related signals.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0051291","count":2}]},{"hash":"2160962646725286069","title":"Polyamine metabolism and hypusine biosynthesis","description":"The two most represented terms are peptidyl-hypusine biosynthetic process and spermidine catabolic process, pointing to polyamine metabolism and hypusine formation; other GO terms appear as noise, but this shared theme is the best unifying explanation for the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008612","count":1},{"id":"GO:0042102","count":1},{"id":"GO:0051289","count":1},{"id":"GO:0042593","count":1},{"id":"GO:0046203","count":1}]},{"hash":"426849905991590254","title":"Endosomal trafficking and exosome secretion","description":"This cluster features GO terms tied to vesicle biology: regulation of multivesicular body size, endosome-to-Golgi transport, and exosomal secretion, suggesting endosomal trafficking is the core theme. The other terms related to morphogenesis and neural development may reflect attachments of these processes to developing tissues, but the strongest signal is vesicle trafficking and exosome biology.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010796","count":2},{"id":"GO:0031384","count":2},{"id":"GO:0031069","count":1},{"id":"GO:1990182","count":1},{"id":"GO:0007174","count":1}]},{"hash":"1513830565442031922","title":"Nuclear envelope and chromosome organization","description":"Most top GO terms point to nuclear envelope processes and chromosome dynamics (centromere clustering at the mitotic interphase nuclear envelope; telomere tethering at nuclear periphery; nuclear envelope organization; centrosome localization; homologous chromosome pairing at meiosis; nuclear migration along microfilament). This coherent theme suggests the proteins function in nuclear architecture and chromosomal behavior rather than general signaling. A few terms about osteoblast differentiation or collagen biosynthesis are less central but don\u2019t override the dominant nuclear-centric pattern.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072766","count":1},{"id":"GO:0034398","count":1},{"id":"GO:0045669","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0032967","count":1}]},{"hash":"1306260361280497152","title":"Neuronal vesicle trafficking and actin remodeling","description":"This cluster centers on neural development and synaptic function, with GO terms for brain development, regulation of synaptic vesicle exocytosis, endosome transport, and actin filament branching, plus related signaling. While a few terms are unrelated noise, the core theme ties vesicle trafficking to cytoskeletal dynamics in neurons.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0039694","count":2}]},{"hash":"2164246604263107619","title":"Developmental processes and stress responses","description":"This cluster contains GO terms tied to organismal development (skeletal system development, multicellular organism development, neural tube closure) alongside stress- and transcription-related processes (ER stress-induced apoptosis, cellular response to cadmium, DNA-templated transcription, response to glucose limitation, mitotic cell cycle). The combination suggests proteins involved in developmental regulation that are also engaged in cellular stress responses and transcriptional control, rather than a single narrow function. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0001501","count":2}]},{"hash":"691851813501161072","title":"Sumoylation and transcription regulation cluster","description":"Sumoylation is a central function (protein sumoylation) and is connected to transcription control by RNA polymerase II, with additional signals pointing to broader stress response and DNA repair processes. This pattern suggests a cohesive module where post-translational modification (sumoylation) influences gene expression and cellular stress signaling, rather than unrelated separate processes.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0010636","count":1},{"id":"GO:1902236","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0043433","count":1}]},{"hash":"2286057075089239989","title":"Unknown","description":"The top GO terms are highly diverse, covering cardiac membrane depolarization, thermoception and heat/cold responses, spindle assembly, various differentiation and maturation processes, and neuronal regulation; there is no clear, common function tying these proteins together, and with no edges among them and scattered annotations, a coherent cluster label cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900827","count":1},{"id":"GO:0050955","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0051225","count":1},{"id":"GO:0006530","count":1}]},{"hash":"2300120432880795637","title":"Developmental signaling and ECM remodeling","description":"The enriched GO terms point to developmental processes (neural precursor proliferation, ossification, Wnt signaling) and extracellular matrix remodeling (basement membrane disassembly), suggesting a theme of developmental signaling coupled with tissue remodeling. Some terms are broader or tangential (thyroid response, autophagy, immune activity), but the central pattern appears to be development-related signaling and ECM dynamics.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":2},{"id":"GO:0034769","count":2},{"id":"GO:0010813","count":2},{"id":"GO:0097067","count":2},{"id":"GO:0001913","count":2}]},{"hash":"1272555620530994839","title":"Unknown","description":"The top GO terms span a highly diverse set of biological processes, from lipid/sterol biosynthesis (ergosterol, cholesterol, unsaturated fatty acids) to mitochondrial inheritance and even immune-related processes, with no clear shared function across the cluster. With only three proteins and a single-edge connection, there isn\u2019t a cohesive theme to name a specific function, so Unknown is most appropriate.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0032443","count":3},{"id":"GO:0006636","count":3}]},{"hash":"459845176605872028","title":"Neural development and cell-cycle signaling","description":"The GO terms cluster around neural development signals (cerebellar cortex formation, Bergmann glial differentiation, regulation of axon regeneration) and core cell-cycle control (G1/S transition, CDK activity regulation, kinetochore localization). Additional signaling pathways (insulin receptor signaling, T cell receptor signaling) suggest broader signal transduction context but still align with development and proliferation regulation. Overall, the group seems to reflect coordination between neural differentiation programs and cell-cycle control rather than a single metabolic or immune function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0021697","count":2},{"id":"GO:0000082","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0008285","count":2}]},{"hash":"1621749161037657268","title":"Unknown","description":"The GO terms cover unrelated areas (neural death regulation, development, ECM/focal adhesion regulation, Rho signaling, and immune differentiation) with no clear common function linking all proteins, and the cluster has no edges, so a cohesive label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1},{"id":"GO:0051893","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0007266","count":1}]},{"hash":"1010527935272867326","title":"Unknown","description":"The top GO terms span cell cycle transitions, protein folding/modification, cilium assembly, metal response, hormone signaling, GPCR signaling, ER-stress translation, ubiquitination, and antiviral defense, with no single unifying function evident across the three proteins. This makes a coherent cluster label difficult; I therefore designate Unknown.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007091","count":2},{"id":"GO:0000413","count":2},{"id":"GO:1905515","count":2},{"id":"GO:0010288","count":2},{"id":"GO:0009938","count":2}]},{"hash":"1334758351258373571","title":"Translation and RNA processing factors","description":"The top GO terms are dominated by translation-related processes (initiation, termination, and overall translation) and tRNA aminoacylation/modification, with a smaller signal for spliceosomal tri-snRNP assembly, suggesting a cluster of RNA processing and protein synthesis components. An occasional brain-related term appears but does not define the core function. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":1},{"id":"GO:0006424","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0006433","count":1}]},{"hash":"2123364403495971472","title":"Unknown","description":"The GO terms are highly diverse (ion response, methylation, prostaglandin and vitamin D metabolism, xenobiotic/antibiotic metabolism, sex differentiation), with no prevailing biological process or molecular function tying the proteins together. Because no coherent theme emerges, 'Unknown' is the appropriate label.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035865","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0001516","count":1},{"id":"GO:0042369","count":1},{"id":"GO:0033280","count":1}]},{"hash":"618676249200007125","title":"Unknown","description":"The top GO terms span immune differentiation (NK T cell differentiation, B cell tolerance induction), developmental processes (trachea formation, neuron death regulation), and cytoskeleton/tissue remodeling (Rho signaling, focal adhesion, ECM disassembly), with no single unifying function or pathway linking them. There are no edges to suggest a cohesive functional module, so a specific label isn\u2019t justifiable. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901214","count":3},{"id":"GO:0060440","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007266","count":3}]},{"hash":"960672401356402773","title":"Adhesion and ECM remodeling signaling","description":"The top GO terms cluster around regulation of focal adhesions, extracellular matrix disassembly, and Rho-mediated cytoskeletal signaling, all pointing to cell adhesion, migration, and ECM remodeling processes. Additional terms touch on related developmental and immune contexts, which can involve adhesion and remodeling as well, but there isn't a single tightly connected pathway, making the theme plausible but not definitive.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901214","count":2},{"id":"GO:0060440","count":2},{"id":"GO:0051893","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0007266","count":2}]},{"hash":"1882253611671204789","title":"DNA-Templated Transcription Regulation","description":"The strongest signals are GO terms for DNA-templated transcription and its regulation, suggesting the cluster centers on transcriptional control. The other terms point to related signaling and developmental processes, but transcription regulation appears to be the core theme among these proteins.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0097011","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006355","count":2},{"id":"GO:1901214","count":1}]},{"hash":"2262333979395160108","title":"Unknown","description":"The GO terms are highly diverse and do not point to a single coherent function or pathway across the three proteins (metal ion transport and homeostasis, calcium signaling, lipid translocation, hormonal response, cardiovascular and neural development, and even plant-specific catabolic processes). This lack of a unifying theme suggests there is no confident, interpretable cluster label beyond Unknown. ","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":1},{"id":"GO:0033574","count":1},{"id":"GO:1903249","count":1},{"id":"GO:0098736","count":1},{"id":"GO:0006882","count":1}]},{"hash":"1272693350956115199","title":"ER Stress and Protein Folding","description":"This cluster is biased toward proteostasis and endoplasmic reticulum (ER) stress responses, with terms like negative regulation of ER stress-induced apoptotic signaling and chaperone/cofactor-dependent protein refolding, plus post-translational protein targeting to membranes. While other terms (e.g., DNA replication, iron-sulfur cluster assembly) appear, the strongest signal centers on protein quality control and stress signaling in the secretory pathway, supporting a proteostasis-related cluster label.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903382","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0006880","count":1},{"id":"GO:1902037","count":1}]},{"hash":"1274980648661371095","title":"Unknown","description":"This cluster has no GO terms in the Top Terms, so there is no clear shared function to name; without functional annotations a cohesive theme cannot be inferred from the proteins alone.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"1765489580259173091","title":"Nuclear periphery chromatin tethering and transport","description":"Top GO terms cluster around localization to the nuclear envelope, telomere tethering to the nuclear periphery, and tethering of RNA Pol II DNA to the periphery, plus import of proteins into the nucleus and chromatin silencing/dynamics. Together these suggest a function in nuclear periphery chromatin organization and nuclear transport regulation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035080","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0035392","count":2},{"id":"GO:0036228","count":2},{"id":"GO:0034398","count":1}]},{"hash":"1679217341419422645","title":"ER stress and vesicle trafficking","description":"This cluster\u2019s strongest signals center on ER quality control and the secretory pathway: unfolded protein response in the endoplasmic reticulum, cellular response to misfolded protein, and ER-to-Golgi vesicle transport, along with SNARE complex disassembly indicating vesicle fusion dynamics. While there are a few outlier terms (metal ion homeostasis and peroxisomal protein import), the shared theme appears to be ER stress management and trafficking through the secretory pathway, with subsidiary links to oxidative stress.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010960","count":1},{"id":"GO:0030026","count":1},{"id":"GO:1903862","count":1},{"id":"GO:0071218","count":1},{"id":"GO:0035494","count":1}]},{"hash":"1613083182847468508","title":"Unknown","description":"GO terms are highly diverse with no shared biological process or pathway evident (potassium ion response, methylation, prostaglandin and vitamin D metabolism, xenobiotic/insecticide processing, sex differentiation), and there are no edges linking the proteins. There is no cohesive theme to assign a specific label, so Unknown with confidence None.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035865","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0001516","count":1},{"id":"GO:0042369","count":1},{"id":"GO:0033280","count":1}]},{"hash":"1661157379806687295","title":"Unknown","description":"The top GO terms are a mix of nervous system development (neuron apoptotic process, neuron differentiation, Schwann cell development) and unrelated processes (GPI anchor attachment, xenobiotic response, DNA repair, glycogen regulation). With zero edges and no clear clustering of a single cohesive function, there isn\u2019t a reliable, shared theme tying these proteins together.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":1},{"id":"GO:0016255","count":1},{"id":"GO:0030182","count":1},{"id":"GO:2001241","count":1},{"id":"GO:1905213","count":1}]},{"hash":"1734308896225562164","title":"Unknown","description":"The GO terms are highly heterogeneous (lipid metabolism, cholesterol transport, lipid transport, ubiquinone/menaquinone biosynthesis, aerobic respiration) and include tissue/hormone terms and even antibiotic biosynthesis, yielding no single coherent function to define the cluster with confidence.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060009","count":1},{"id":"GO:0036111","count":1},{"id":"GO:0032385","count":1},{"id":"GO:1901373","count":1},{"id":"GO:0032150","count":1}]},{"hash":"1129292922073174314","title":"Developmental signaling and differentiation","description":"The top GO terms point to various developmental and differentiation processes (dendritic cell proliferation, myotube differentiation, trachea formation, dorsal/ventral neural tube patterning) along with associated signaling and remodeling activities (p38MAPK cascade, cell-matrix adhesion). There are also stress- and metabolism-related responses (cold acclimation, apoptosis execution, response to HGF stimulus, invasive growth with glucose limitation). Taken together, the cluster appears centered on development/differentiation with broader signaling and remodeling context, 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:0044565","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0035729","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0038066","count":2}]},{"hash":"217617508820104026","title":"Histone Modification and Immune Signaling","description":"The top terms point to chromatin regulation via histone modification (ubiquitination of H2A, acetylation of H4-K16, autoubiquitination) as the core theme, with additional signals related to immune pathways (IL-17 signaling) and vitamin D response, suggesting an epigenetic control center linked to immune/metabolic signaling.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070535","count":2},{"id":"GO:1903762","count":1},{"id":"GO:0002635","count":1},{"id":"GO:0090073","count":1},{"id":"GO:2000620","count":1}]},{"hash":"529973083202718738","title":"Mitochondrial Translation and Mitophagy","description":"The top GO terms cluster around translation, autophagy of mitochondrion (mitophagy), and regulation of cellular respiration, all pointing to mitochondrial function and energy metabolism. The combination suggests proteins involved in mitochondrial protein synthesis and mitochondrial quality control. The aging term is obsolete and likely noise. Overall, a mitochondria-centered function label fits well.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000422","count":1},{"id":"GO:0043457","count":1},{"id":"GO:0010259","count":1}]},{"hash":"991686321596677009","title":"Unknown","description":"The terms span diverse processes (antibiotic and cycloheximide response, translation, NK T cell differentiation, Rho signaling, focal adhesion regulation, trachea formation, and other development-related terms). With no network connections (edges/triangles) and only scattered, heterogeneous GO terms, there is no clear, cohesive function tying these proteins together. Therefore Unknown with confidence None.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0006412","count":1},{"id":"GO:1901214","count":1},{"id":"GO:0060440","count":1}]},{"hash":"582165499306055775","title":"Unknown","description":"The listed GO terms cover ribosome biogenesis, immune signaling (T cell activation, complement), developmental processes (imaginal disc morphogenesis, cartilage morphogenesis), extracellular matrix and adhesion, metallopeptidase regulation, and even chlorophyll biosynthesis, which span distant biological contexts with no clear single theme linking the proteins; thus no cohesive function emerges for the cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007475","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0010835","count":1},{"id":"GO:0002291","count":1},{"id":"GO:0006956","count":1}]},{"hash":"1006607476766502698","title":"DNA repair and meiosis","description":"The terms strongly indicate DNA damage response pathways (NHEJ and HR repair) and meiotic chromosome organization (synaptonemal complex), with ubiquitination processes and mitotic spindle dynamics suggesting cell-cycle regulation. Immune signaling terms appear peripheral in this small cluster. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006303","count":3},{"id":"GO:0070193","count":3},{"id":"GO:1901487","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0070979","count":3}]},{"hash":"1067621147120402839","title":"DNA Repair and Meiosis Coordination","description":"This cluster is dominated by GO terms for double-strand break repair (NHEJ and HR) and synaptonemal complex organization, pointing to DNA damage response and meiotic chromosome maintenance. A related term about mitotic spindle elongation suggests a broader link to cell division, though ubiquitination and some immune signaling terms appear less central. Overall, the core theme centers on DNA repair and meiosis/cell division.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006303","count":3},{"id":"GO:0070193","count":3},{"id":"GO:1901487","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0070979","count":3}]},{"hash":"1363048559977894786","title":"CENP-A Centromeric Chromatin Assembly","description":"This cluster\u2019s top GO term points to CENP-A containing chromatin assembly, i.e., centromeric/kinetochore chromatin formation. While other terms are sparse or obsolete, the centromere-associated assembly signal provides a coherent theme for the group. Confidence: Medium","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034080","count":1},{"id":"GO:0090073","count":1},{"id":"GO:2000774","count":1},{"id":"GO:0044030","count":1},{"id":"GO:0032463","count":1}]},{"hash":"1988240597767271236","title":"DNA Damage Repair and Ubiquitination","description":"The cluster\u2019s top GO terms cluster around double-strand break repair via NHEJ and HR, synaptonemal complex organization (meiotic/recombination context), and ubiquitination processes (autoubiquitination and K11-linked ubiquitination), with accompanying cell-cycle related activity like mitotic spindle elongation. This suggests a coherent module focused on DNA damage response, chromatin remodeling, and protein turnover through ubiquitin signaling, even though a few immune signaling terms appear in the mix. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006303","count":3},{"id":"GO:0070193","count":3},{"id":"GO:1901487","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0070979","count":3}]},{"hash":"1314491164045392053","title":"Bacterial sugar nucleotide biosynthesis and O-antigen pathways","description":"The top GO terms cluster around sugar-nucleotide biosynthesis (UDP-/GDP- derivatives, galactose metabolism) and O-antigen biosynthesis, pointing to bacterial cell-surface polysaccharide assembly. While a few terms are unrelated outliers, the dominant signal is polysaccharide/sugar nucleotide\u2013driven biosynthesis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010253","count":1},{"id":"GO:1902135","count":1},{"id":"GO:0009243","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006012","count":1}]},{"hash":"656494000375074531","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903740","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0030150","count":1},{"id":"GO:2000134","count":1}]},{"hash":"844802586944346939","title":"Organ and Tissue Development","description":"The top GO terms point to development across multiple organs (genitalia, placenta vasculature, kidney, neural tube, liver, skin) and include a JAK-STAT signaling connection, suggesting the proteins are involved in broad organogenesis and tissue differentiation rather than a single specific function. This makes \"Organ and Tissue Development\" a coherent, concise label that captures the shared theme of developmental processes across various tissues.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031659","count":1},{"id":"GO:0048806","count":1},{"id":"GO:0060674","count":1},{"id":"GO:0007259","count":1},{"id":"GO:0001822","count":1}]},{"hash":"2280435159251908054","title":"Embryonic Eye Morphogenesis","description":"This cluster is dominated by GO terms tied to embryonic development and eye formation, including in utero embryonic development, neuroepithelial differentiation, embryonic digit morphogenesis, and camera-type eye development. The presence of cilium assembly and Hedgehog signaling (Smoothened) terms supports a role in developmental patterning and ocular morphogenesis, suggesting these proteins participate in early developmental processes with an emphasis on eye formation.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":1},{"id":"GO:0001944","count":1},{"id":"GO:0001701","count":1},{"id":"GO:0043010","count":1},{"id":"GO:0007224","count":1}]},{"hash":"941070974102647237","title":"T Cell Differentiation and Leukocyte Migration Regulation","description":"This cluster is dominated by GO terms related to T cell development and differentiation (thymus and alpha-beta T cell differentiation, germinal center formation) and immunity-related regulation (negative regulation of leukocyte migration, histamine secretion, integrin-mediated adhesion). While a couple of terms like xanthine biosynthetic process and lung alveolus development are less coherent with the core theme, the strongest signal is adaptive immune development and leukocyte trafficking.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0046111","count":3},{"id":"GO:0070244","count":3},{"id":"GO:0002686","count":3},{"id":"GO:0048286","count":3},{"id":"GO:0033632","count":3}]},{"hash":"1093342296178608409","title":"Unknown","description":"No GO terms shown to link the three proteins; with only two edges and no enriched terms, there is no clear shared function to name this cluster.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"335178539651266963","title":"Actin Cytoskeleton and Membrane Remodeling","description":"The terms cluster around actin filament organization, mitotic contractile ring dynamics, membrane addition at cytokinesis, and microvilli/brush border assembly, all pointing to cytoskeletal-driven structural changes and membrane remodeling. Other terms touch on related signaling (GTPase regulation) or trafficking (pigment granule transport, vacuole inheritance) that can interface with these processes, suggesting a cohesive theme despite some peripheral items. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070493","count":1},{"id":"GO:1903480","count":1},{"id":"GO:0016198","count":1},{"id":"GO:0007107","count":1},{"id":"GO:0000011","count":1}]},{"hash":"1109086800179172580","title":"Isoprenoid biosynthesis","description":"The top terms cluster around isoprenoid/terpenoid biosynthesis (geranyl, farnesyl, and geranylgeranyl diphosphate biosynthetic processes) and related products like cholesterol and monoterpenes, suggesting a shared role in isoprenoid lipid synthesis. A few terms reference protein transport and exocytosis, which are less central to this theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901663","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0033384","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0033386","count":1}]},{"hash":"335916838978687374","title":"Unknown","description":"There are no edges or GO terms linking these proteins, and the Top Terms are empty, so no single function emerges. The ReCIPE additions do not provide a cohesive functional signal, leaving the cluster without a clear theme.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"382254668835968983","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":1},{"id":"GO:0002635","count":1},{"id":"GO:0090073","count":1},{"id":"GO:2000620","count":1},{"id":"GO:1902187","count":1}]}]