[{"hash":"947080066671026725","title":"GTPase-driven cytoskeletal remodeling and neural migration","description":"The top GO terms highlight small GTPase signaling, actin cortical patch assembly, and a marked note on radial glia\u2013guided neuronal migration, suggesting a core theme of cytoskeletal dynamics and motility regulated by GTPases in neural contexts. Transcription-related terms are present but appear less central than the cytoskeletal/motility signals; overall, the cluster seems centered on signaling-driven cytoskeletal remodeling accompanying neural migration. ","confidence":"Medium","size":29,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:2001209","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0090262","count":2},{"id":"GO:0000147","count":2}]},{"hash":"1727511696310764608","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":216,"triangles":729,"max_degree":25,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":17},{"id":"GO:0031047","count":17},{"id":"GO:1901407","count":11},{"id":"GO:0006378","count":11},{"id":"GO:0006369","count":10}]},{"hash":"1089046032572027758","title":"Proteostasis and Ribosome Biogenesis","description":"This cluster is dominated by ubiquitin-related processes (ubiquitination/ERAD) alongside translation and ribosome biogenesis, suggesting a proteostasis module that coordinates protein synthesis, folding, and degradation. Additional signals for mitochondrial complex IV assembly and amino acid starvation response indicate links between protein turnover and energy/metabolism. Overall, the functions cohere around proteostasis with ribosome biogenesis as a central component.","confidence":"Medium","size":29,"edges":8,"triangles":0,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0042254","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0033617","count":3},{"id":"GO:0000122","count":2}]},{"hash":"69513555886243544","title":"Ubiquitin-dependent apoptosis and TNF/JNK signaling","description":"The top GO terms strongly converge on ubiquitin-dependent protein catabolic processes and regulation of apoptotic and TNF/JNK signaling pathways, with additional notes on ubiquitination types and immune-related processes. This suggests a cluster centered on how ubiquitination modulates cell fate decisions and inflammatory signaling, rather than a tight physical interaction network. The single-edge connectivity reinforces a shared functional theme rather than a single complex. ","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:0042981","count":10},{"id":"GO:0046328","count":10},{"id":"GO:0070512","count":10},{"id":"GO:0033151","count":10}]},{"hash":"124658360908948089","title":"Cell Polarity and Cytoskeletal Remodeling","description":"The top GO terms point to establishment and maintenance of epithelial cell polarity, regulation of cell shape, actin filament bundle assembly, cell migration, and Rho signaling, all core to polarity and cytoskeleton-driven morphogenesis and adhesion; a few outliers (heterochromatin formation, synaptic vesicle uncoating) are present but do not override the dominant theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0090263","count":4},{"id":"GO:0060670","count":3},{"id":"GO:0090162","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0016477","count":3}]},{"hash":"1635269959374904476","title":"Embryonic organ morphogenesis and neural development","description":"The top GO terms point to developmental processes shaping organs and tissues, especially heart/arterial morphogenesis and neural development (embryonic heart tube formation, ascending aorta morphogenesis, arterial endothelial differentiation, trochlear nerve development, spinal cord motor neuron fate). Also, transcription by RNA polymerase II and regulation of apoptotic processes align with gene regulation and cell survival during development. Together, these terms suggest a cluster centered on embryonic organ morphogenesis with neural and cardiovascular emphasis.","confidence":"High","size":28,"edges":77,"triangles":55,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":6},{"id":"GO:0042493","count":5},{"id":"GO:0042981","count":5},{"id":"GO:0060842","count":5},{"id":"GO:0045668","count":5}]},{"hash":"1507219398928152585","title":"Unknown","description":"The listed GO terms span diverse areas (metabolic biosynthesis, nucleotide catabolism, cell division, chromosome condensation, apoptosis) with no single unifying function, and the cluster has no edges, indicating a miscellaneous collection rather than a cohesive module.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006212","count":3},{"id":"GO:0007076","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0043547","count":2}]},{"hash":"947632494958473158","title":"Ceramide transport and sterol biosynthesis","description":"The top GO terms point to lipid handling in the secretory pathway, notably ER-to-Golgi ceramide transport and sterol biosynthesis, with supporting signals from membrane trafficking like clathrin-dependent endocytosis. This combination suggests a cohesive theme around lipid transport and lipid biosynthesis within membrane trafficking, rather than a single enzymatic function. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035621","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0016126","count":3},{"id":"GO:0044128","count":3},{"id":"GO:0007281","count":2}]},{"hash":"393631593221846003","title":"Transcription Regulation and Histone Modification","description":"Most terms center on DNA-templated transcription and its regulation, coupled with histone methylation marks (H3K4, H3K27, H3K79) and protein ubiquitination, pointing to chromatin-based control of gene expression. Some terms related to translation initiation and macrophage activation appear but are less indicative of the core theme. Overall, the cluster seems to reflect transcriptional regulation via chromatin modification and associated post-translational processes.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051568","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0034729","count":2},{"id":"GO:1902499","count":2}]},{"hash":"935785570641545070","title":"Golgi-ER trafficking and SNARE complex assembly","description":"This cluster is dominated by GO terms for Golgi organization and ER-to-Golgi vesicle transport, vesicle fusion with the Golgi, and SNARE complex assembly, complemented by terms on exocytic insertion of receptors and synaptic potentiation. This points to a cohesive function in secretory pathway trafficking and SNARE-mediated membrane fusion, including neuronal receptor trafficking at synapses. A vacuole-targeting term is more general vesicle transport and does not contradict the main theme. Overall, the common thread is Golgi-ER vesicle trafficking governed by SNAREs.","confidence":"High","size":27,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0048280","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0098967","count":2}]},{"hash":"270176508415187059","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2}]},{"hash":"2264070112908232688","title":"Diverse substrate transmembrane transporters","description":"Diverse substrate transmembrane transporters: The GO terms cluster around transmembrane transport of a wide range of substrates (ions, sugars, vitamins, xenobiotics, etc.), consistent with a family of transporter proteins rather than metabolic enzymes. The absence of edges does not negate a cohesive transport function across substrates.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0035461","count":2}]},{"hash":"1476584530110521852","title":"Nuclear Gene Expression and Autophagy Metabolism","description":"This cluster shows enrichment for DNA-templated transcription and DNA replication, indicating nuclear gene expression and genome maintenance. It also includes autophagy-related processes (macroautophagy, piecemeal microautophagy of the nucleus) and various biosynthetic steps (thiamine diphosphate, molybdopterin cofactors), suggesting a link between nuclear activity, cellular metabolism, and autophagic turnover.","confidence":"Medium","size":26,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0010763","count":3},{"id":"GO:0045820","count":3},{"id":"GO:0016236","count":3}]},{"hash":"746076209400855952","title":"Epithelial polarity and actin remodeling","description":"The cluster shows strong enrichment for epithelial polarity establishment, actin-driven structures (podosomes, lamellipodia) and Rho signaling regulation, plus vesicle trafficking (COPII) and IGF response, indicating proteins coordinating cell polarity, cytoskeleton dynamics, and membrane transport.","confidence":"High","size":26,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":4},{"id":"GO:0071800","count":4},{"id":"GO:1990314","count":4},{"id":"GO:0048538","count":3},{"id":"GO:0035156","count":3}]},{"hash":"2124796538575475644","title":"Protein synthesis and secretory pathway processing","description":"The cluster is dominated by translation and ribosome biogenesis terms, indicating core protein production, and includes ER-to-Golgi transport, ER-associated degradation, and chaperone-dependent refolding, which together reflect protein maturation and quality control in the secretory pathway. Some DNA-related terms and antibiotic response appear but are less representative of the main theme.","confidence":"High","size":26,"edges":50,"triangles":112,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0006888","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0000002","count":3}]},{"hash":"2207062632436667986","title":"Unknown","description":"The cluster's GO terms are highly heterogeneous, covering DNA-templated transcription, a few metabolic processes (tetrahydrobiopterin and phenylalanine metabolism), protein oligomerization, RNA splicing, plant development, and immune regulation. With edges missing and most terms represented by only one entry, there is no clear shared function unifying the proteins, so a cohesive label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006729","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0043496","count":1},{"id":"GO:0051289","count":1}]},{"hash":"1152228181062267546","title":"Central carbon metabolism and amino acid biosynthesis","description":"The top GO terms point to core energy metabolism (glycolysis, TCA cycle, gluconeogenesis) together with amino acid and cofactor biosynthesis (leucine, biotin, porphyrin). This indicates a cohesive cluster of enzymes involved in central carbon flux and biosynthetic pathways, rather than signaling or transport functions.","confidence":"High","size":25,"edges":269,"triangles":1729,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006099","count":10},{"id":"GO:0019878","count":8},{"id":"GO:0006096","count":7},{"id":"GO:0006103","count":6},{"id":"GO:0033512","count":6}]},{"hash":"1239350062781830720","title":"Translation and ribosome biogenesis","description":"The top GO terms are dominated by translation and ribosome-related processes (translation; ribosomal large subunit biogenesis; ribosome biogenesis; translational initiation; tRNA modification), indicating the cluster centers on protein synthesis machinery. Other terms like macroautophagy and mitochondrial fusion appear as secondary connections, but the primary signal is the ribosome/translation theme. ","confidence":"High","size":25,"edges":130,"triangles":342,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":17},{"id":"GO:0042273","count":4},{"id":"GO:0016236","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0006413","count":3}]},{"hash":"860853583347526239","title":"Developmental Signaling and Apoptosis","description":"The cluster centers on signaling pathways involved in development and cell fate, with terms like apoptotic process, heart development, multicellular organism development, ephrin receptor signaling, and responses related to muscle activity, plus GTPase activity regulation. Although it also includes immune and neural terms (activated T cell proliferation, dendritic spine morphogenesis), the dominant theme ties to developmental signaling and apoptosis, including cardiovascular development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0050798","count":3},{"id":"GO:0060997","count":3},{"id":"GO:0048013","count":3}]},{"hash":"1334956699477379847","title":"Growth and division with ribosome biogenesis","description":"The cluster is dominated by GO terms for cell division, the mitotic cell cycle, and ribosome biogenesis, complemented by TORC1 signaling and mRNA transport, pointing to a coordinated growth and proliferation program. While some terms touch on development and stress responses (ERAD, ER stress\u2013related apoptosis), the core signal centers on growth and division machinery, with ribosome biogenesis as a key component. This suggests a cohesive theme of balancing protein synthesis capacity with cell cycle progression.","confidence":"Medium","size":24,"edges":46,"triangles":27,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0000278","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0070262","count":4}]},{"hash":"30227512318267323","title":"Electron transport and ATP synthesis","description":"The cluster shows a clear emphasis on energy production, with top GO terms for respiratory electron transport chain and ATP synthesis coupled electron transport, suggesting coordinated roles in electron transport and ATP generation. The other terms (ferrodoxin metabolism, xanthine catabolic process, nitrogen fixation) are related to metabolism and electron transfer but appear as weaker or more context-specific signals, while brain development, lactation, and vasculogenesis are less directly connected. Overall, the dominant theme is energy metabolism and electron transport.","confidence":"Medium","size":24,"edges":242,"triangles":1564,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0022904","count":2},{"id":"GO:0007420","count":2},{"id":"GO:2001213","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0006124","count":1}]},{"hash":"1975605299145519680","title":"Neural development and synaptic signaling","description":"The top GO terms cluster around nervous system development and synaptic maturation, including Schwann cell development, dendritic spine morphogenesis, and visual perception, with supporting signaling processes like calcium-mediated signaling and phosphorylation. Some terms also reflect broader developmental processes (angiogenesis, placenta development), but the core theme remains neural development and synaptic function. ","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":4},{"id":"GO:0007601","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0046638","count":3},{"id":"GO:0001525","count":3}]},{"hash":"1181708037987672615","title":"Ribosome Biogenesis and Translation with Fe-S Assembly","description":"Dominant signals are translation and ribosome biogenesis (translation; preribosome large subunit assembly; positive regulation of ribosome biogenesis). Fe-S cluster assembly and iron homeostasis terms accompany these, consistent with Fe-S dependent factors involved in ribosome maturation and related mitochondrial processes. The antibiotic response terms likely reflect translation inhibition stress rather than a distinct function.","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":4},{"id":"GO:0046898","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0006123","count":2}]},{"hash":"1228488031821881841","title":"Membrane nutrient transport and lipid metabolism","description":"The top GO terms cluster around transmembrane transport of xenobiotics, glucose, and vitamins, along with responses to nutrients and regulation of lipid biosynthesis. This points to proteins commonly involved in transporting nutrients across membranes and coordinating membrane lipid metabolism, rather than a single specific pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:1904659","count":2},{"id":"GO:2001247","count":2},{"id":"GO:0042360","count":2},{"id":"GO:0051180","count":2}]},{"hash":"971859249156310803","title":"Immunoglobulin gene diversification","description":"This cluster is driven by clear signals of antibody diversification processes, notably somatic hypermutation (GO:0016446) and isotype switching (GO:0045190), which are central to B cell maturation and antibody diversity. Other terms point to general genome maintenance and cellular remodeling, but the strongest cohesive theme among the top terms is antibody diversification through SHM and class switching. Confidence: High","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000710","count":2},{"id":"GO:0045190","count":2},{"id":"GO:0016446","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1282383900180658776","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0001403","count":2}]},{"hash":"361514062636707621","title":"Cell cycle and transcriptional regulation","description":"The top terms cluster around transcription (DNA-templated transcription, mRNA transport) and cell cycle/mitosis (cell division, mitotic cell cycle), with supporting roles in kinase signaling and protein trafficking (positive regulation of kinase activity, ER-Golgi transport). This suggests a cohesive program coordinating gene expression with cell-cycle progression and related signaling events.","confidence":"High","size":23,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0051301","count":10},{"id":"GO:0006888","count":10},{"id":"GO:0071560","count":9},{"id":"GO:0051402","count":9}]},{"hash":"280010927641895100","title":"Ribosome Biogenesis and Translation Machinery","description":"This cluster is enriched for translation-related terms (cytoplasmic translation, translation, initiation, termination) alongside ribosome biogenesis, rRNA maturation, and subunit assembly, pointing to a cohesive group involved in ribosome production and protein synthesis, with some influence on translational fidelity.","confidence":"High","size":23,"edges":251,"triangles":1730,"max_degree":22,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":19},{"id":"GO:0046677","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0002181","count":4},{"id":"GO:0006450","count":3}]},{"hash":"429699233987393866","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":13,"triangles":1,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0042619","count":8},{"id":"GO:0009103","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0006355","count":5}]},{"hash":"79279267661842199","title":"Cell Cycle and DNA Replication with Transcription","description":"Dominant terms point to cell division and genome maintenance: mitotic cell cycle, DNA replication, DNA-templated transcription, and mRNA processing, with protein localization to kinetochore and telomere capping support genome integrity during division. Additional terms reflect metabolic activity (glucose metabolism) and vascular remodeling (angiogenesis, endothelial cell migration) that can accompany proliferative states, but the core theme is cell-cycle/DNA transcription machinery.","confidence":"Medium","size":22,"edges":9,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0006006","count":7},{"id":"GO:0043536","count":7},{"id":"GO:0034501","count":7},{"id":"GO:0001525","count":7}]},{"hash":"714093118064049795","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034247","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0021983","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0002098","count":2}]},{"hash":"532894415720862609","title":"Unknown","description":"The top terms span cell cycle and mitosis, RNA processing and translation initiation, RNA methylation, plus nutrient/cadmium responses and a developmental term, showing no single cohesive function tying the cluster together. This makes it hard to assign a specific, representative label beyond a broad, Unknown category.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007584","count":4},{"id":"GO:2001162","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1493377202705376697","title":"DNA repair and translation machinery","description":"This cluster shows strong enrichment for DNA repair (nucleotide-excision repair, DNA repair) and translation-related processes (translation, tRNA processing, mitochondrial tRNA aminoacylation), suggesting a core of nucleic acid maintenance and protein synthesis. The remaining terms (signaling, transport, chemotaxis, glycogen regulation) are more diverse and less coherent with the main theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006289","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0007229","count":2},{"id":"GO:0010765","count":2}]},{"hash":"1928281254562523411","title":"Epithelial Polarity and Immune Development","description":"The prominent terms indicate roles in establishing epithelial polarity and cell migration, along with immune-related signaling (T cell receptor pathway) and development of thymus, heart, and blood vessels, plus general transcription/RNA processing. This suggests a cluster of proteins coordinating epithelial organization with immune development and signaling pathways, rather than a single narrow function.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0006367","count":2},{"id":"GO:0007613","count":2},{"id":"GO:0006397","count":2}]},{"hash":"1961805006213479442","title":"SNARE-mediated vesicle trafficking","description":"The dominant GO terms point to intracellular transport, especially ER-to-Golgi vesicle trafficking and SNARE complex assembly, indicating a cluster of proteins involved in vesicle fusion and the secretory pathway. A few terms (lens fiber morphogenesis, spindle assembly, apoptotic process) are less central and may reflect incidental annotations rather than core function.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070309","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1602707401579924990","title":"ER protein folding and redox stress response","description":"This cluster is dominated by GO terms for endoplasmic reticulum\u2013related protein handling and redox maintenance, including ER protein folding, protein repair, deglutathionylation, and cellular redox homeostasis/oxidative stress responses. The presence of peptidyl-proline hydroxylation also aligns with oxygen-dependent ER processes. A couple of transcription-related terms appear but are likely ancillary to the core ER folding/redox theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2}]},{"hash":"193996831890265706","title":"Cell Cycle, DNA Repair, and Chromatin Dynamics","description":"This cluster shows enrichment for DNA damage tolerance (error-free translesion synthesis), cell division and mitotic cell cycle terms, and chromatin-related processes near telomeres (subtelomeric heterochromatin formation, heterochromatin maintenance, chromatin silencing at telomeres). While there are also peroxisomal import and NF-kappaB-related terms, the dominant theme ties to replication, DNA repair, and chromatin regulation during the cell cycle.","confidence":"Medium","size":21,"edges":49,"triangles":34,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070987","count":9},{"id":"GO:0016558","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0016562","count":9}]},{"hash":"1489350831432788530","title":"Unknown","description":"The top terms span translation initiation, lipid signaling, proteostasis, differentiation, cell cycle, cytoskeleton, and even a bacterial cytokinesis term, with no single unifying function evident across the cluster. This makes it unclear what concise, representative label to assign. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0032933","count":5},{"id":"GO:1904668","count":5},{"id":"GO:0070306","count":5},{"id":"GO:0030433","count":5}]},{"hash":"1115317187645121222","title":"Developmental signaling and proliferation","description":"This cluster shows a mix of embryonic development processes (mesoderm formation, neuron development, angiogenesis) and signaling (Wnt), alongside general cell-cycle and transcription-related terms (DNA replication, DNA-templated transcription). The recurring theme is coordinated development and growth rather than a single specific pathway, which supports labeling as Developmental signaling and proliferation.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0007064","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0035994","count":2}]},{"hash":"389431563245032013","title":"Translation and ribosome biogenesis","description":"This cluster is dominated by GO terms related to translation and ribosome assembly (cytoplasmic translation, translation, ribosome biogenesis, and ribosomal large subunit assembly), with SRP-dependent cotranslational targeting to membranes also linking to protein synthesis machinery. A few other terms (redox, thiamine biosynthesis) are minor contributes and do not define the main theme. Confidence: High","confidence":"","size":21,"edges":127,"triangles":279,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0042254","count":1}]},{"hash":"1294012657651308733","title":"Chromatin Regulation and Stress Response","description":"The cluster centers on transcriptional control and chromatin state, highlighted by GO terms for DNA-templated transcription and histone H3-K79 methylation, suggesting roles in chromatin regulation. It also includes stress-related and developmental processes, such as ER-stress\u2013induced apoptotic signaling, cadmium response, aging, mitotic cell cycle, and neural tube closure, implying modulation of gene expression in response to stress and developmental cues. Together, these terms point to a coherent theme of transcriptional regulation via chromatin changes intertwined with stress and development signals.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0034729","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0070059","count":2}]},{"hash":"2125046572763222379","title":"Neural development and synaptic signaling","description":"The top GO terms cluster around nervous system development, axon extension, synaptic transmission (glutamatergic), and learning/plasticity, with supporting roles for cholesterol biosynthesis in membrane biology and cell cycle activity during development. This combination points to neural development and synaptic signaling as the core theme of the cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006695","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0008542","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0045773","count":3}]},{"hash":"1557407597864685601","title":"Vesicle trafficking and nuclear regulation","description":"This cluster shows enrichment for intracellular transport processes (ER-Golgi vesicle transport regulation, clathrin-dependent endocytosis, intracellular protein transport, synaptic vesicle coating) together with nuclear/gene-expression related terms (nucleosome assembly, negative regulation of transcription by RNA polymerase III). While some developmental terms are present, the dominant theme appears to be vesicle trafficking coupled with chromatin/gene-expression regulation, suggesting proteins involved in both trafficking pathways and nuclear regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0061101","count":1},{"id":"GO:0060628","count":1},{"id":"GO:0060576","count":1}]},{"hash":"1176936102987589111","title":"Neural development and axonogenesis","description":"The cluster centers on neural development signals: forebrain development, CNS neuron axonogenesis, and axonal fasciculation, supported by cytoskeletal polarization and Rho signaling regulation. While DNA-templated transcription and DNA repair are present, the strongest theme is neuronal development and axon growth/guidance, with actin cytoskeleton dynamics reinforcing this interpretation.","confidence":"High","size":21,"edges":43,"triangles":24,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0021955","count":1}]},{"hash":"1104485531406995472","title":"Developmental transcriptional and signaling regulators","description":"This cluster\u2019s top GO terms center on DNA-templated transcription and various developmental processes (heart development, axon extension regulation, osteoblast differentiation) plus modulation of signaling pathways (PI3K/AKT). Although some terms are obsolete, the common theme appears to be regulatory proteins involved in development and transcriptional control across tissues, suggesting a cohesive role in developmental gene regulation and signaling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000187","count":3},{"id":"GO:0046826","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0030517","count":3}]},{"hash":"307388242406695541","title":"Neuronal migration and axon guidance","description":"This cluster is dominated by neural development themes, notably axon guidance (semaphorin-plexin signaling) and neuron migration (positive regulation of neuron migration, cerebellar granule precursor migration, neuroblast proliferation). While some terms touch broader morphogenesis, the strongest neural-specific signals point to neuronal positioning and axon pathfinding as the cohesive function of the group.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060174","count":1},{"id":"GO:0043087","count":1},{"id":"GO:0021960","count":1},{"id":"GO:0055113","count":1},{"id":"GO:0021935","count":1}]},{"hash":"43678205628741026","title":"Unknown","description":"The top terms span ribosome biogenesis, rRNA maturation, chromatin-related processes, development, and mitotic spindle assembly, plus obsolete annotations and a divergent term. There isn't a single coherent theme binding these proteins; they appear to be a noisy mix of annotations rather than a functionally related cluster, so a confident label cannot be assigned.","confidence":"","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0035948","count":2}]},{"hash":"1772078588945562714","title":"DNA replication and mitotic chromosome maintenance","description":"These proteins cluster around core nuclear processes: DNA replication, cell division, mitotic checkpoint signaling, and centromeric chromatin assembly (CENP-A), plus microtubule severing, which together point to roles in genome duplication and chromosome segregation. Some terms related to vesicle trafficking and peroxisomal import appear as ancillary annotations or background noise, but the dominant theme is replication and chromosome maintenance.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0033314","count":4},{"id":"GO:0061641","count":4}]},{"hash":"2078667845262350664","title":"Mitochondrial Translation and Cristae Biogenesis","description":"The cluster features GO terms centered on mitochondria: positive regulation of mitochondrial translation, protein transport and insertion into the mitochondrial membrane, and cristae formation. These collectively suggest a theme of mitochondrial biogenesis and expression machinery, despite some unrelated terms. Thus the label Mitochondrial Translation and Cristae Biogenesis is representative of the main function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070131","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0051204","count":1},{"id":"GO:0030007","count":1}]},{"hash":"39522200930790724","title":"Unknown","description":"The GO terms indicate multiple, distinct functional axes (apoptosis under ER stress, metal ion response, cell cycle and mitotic spindle dynamics, actin remodeling, and neural development events). There isn't a single cohesive theme tying all proteins together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070059","count":7},{"id":"GO:0071276","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0090307","count":5},{"id":"GO:0030042","count":5}]},{"hash":"1067546882074759591","title":"Cytoskeletal remodeling and morphogenesis","description":"This cluster is dominated by GO terms tied to cytoskeletal dynamics and cell shape changes, including mitotic spindle assembly, regulation of Rho signaling, and stress fiber and podosome assembly, along with various morphogenesis processes (imaginal disc leg, midbrain) and myelination. The common thread appears to be regulation and remodeling of the cytoskeleton to drive cellular architecture and developmental morphogenesis across tissues. ","confidence":"Medium","size":20,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0071802","count":3},{"id":"GO:0035025","count":3},{"id":"GO:0007480","count":3},{"id":"GO:1904424","count":3}]},{"hash":"1265166031052643824","title":"Unknown","description":"The top GO terms are highly diverse, spanning development (ectoderm formation, neuron differentiation, morphogenesis), signaling (NFAT, Hippo), and cytoskeleton remodeling (actin depolymerization), with a few unrelated processes (antibiotic biosynthesis, platelet aggregation, cell wall biosynthesis). There is no single coherent function connecting all proteins, suggesting functional heterogeneity or annotation noise.","confidence":"","size":20,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0090334","count":3},{"id":"GO:0070886","count":3},{"id":"GO:0001705","count":3},{"id":"GO:0030042","count":3}]},{"hash":"2122151505563985832","title":"Cell Growth and Metabolic Regulation","description":"Contains GO terms spanning cell division, osteoblast differentiation, liver regeneration, vesicle transport, and metabolic signaling (insulin/IGF, fatty acids, NAD transport). This pattern suggests a theme of coordinating growth, tissue regeneration, and cellular energy metabolism rather than a single specific function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0070317","count":3},{"id":"GO:0001649","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0097421","count":2}]},{"hash":"2159123165402271897","title":"Xenobiotic stress and vesicle trafficking regulation","description":"The cluster shows strong signals for xenobiotic and chemical-stimulus responses (xenobiotic stimulus and response to cocaine) alongside stress-related responses (UV response and transcription-coupled repair), plus multiple terms related to membrane trafficking (protein transport, endocytosis/pinocytosis regulation, exocytosis). This suggests a coherent theme where cells modulate vesicle trafficking and transport processes in response to chemical and UV-related stress.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0048549","count":2}]},{"hash":"1833667412440360407","title":"Unknown","description":"The top terms span a highly diverse set of processes (immune/stimulus response, proteasomal degradation, nutrient and ion regulation, transcription/replication, mitosis, development, endosome transport, and toxic-substance response) with no clear, single functional theme tying all proteins together, so a cohesive label cannot be assigned. Confidence: None","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071222","count":4},{"id":"GO:0032436","count":4},{"id":"GO:0034198","count":4},{"id":"GO:0010765","count":4},{"id":"GO:0006351","count":4}]},{"hash":"1429955107346742009","title":"Epithelial Polarity and Cytoskeleton Regulation","description":"The cluster is dominated by terms for establishing epithelial cell polarity, tight and adherens junction assembly, and maintaining cell shape, together with actin cytoskeleton remodeling (actin polymerization, podosome assembly) and signaling via small GTPases, EGFR, and Wnt pathways. This pattern points to proteins coordinating polarity, adhesion, and cytoskeletal dynamics in epithelial contexts.","confidence":"High","size":19,"edges":116,"triangles":330,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090162","count":13},{"id":"GO:0071803","count":12},{"id":"GO:0007264","count":12},{"id":"GO:0030838","count":12},{"id":"GO:0070830","count":12}]},{"hash":"2259973089221349116","title":"Antibiotic Stress and RNA Metabolism","description":"Most frequent terms cluster around antibiotic response, SOS response, ribosome biogenesis, mRNA export from nucleus, and tRNA processing, pointing to a theme of cellular responses to antibiotic stress that involve RNA synthesis/processing and ribosome assembly. Some terms (lipopolysaccharide biosynthesis, cell morphogenesis) appear less connected and may reflect annotation noise or species-specific pathways. Overall, the cluster best labeled as antibiotic stress linked to RNA metabolism.","confidence":"Medium","size":19,"edges":32,"triangles":18,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0009103","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0008033","count":3}]},{"hash":"727113612014467770","title":"Translation and Ribosome Biogenesis","description":"Based on the top GO terms, the proteins are enriched for translation processes (translation, initiation, termination, elongation), ribosome export from the nucleus, and rRNA maturation, indicating a cluster centered on ribosome assembly and protein synthesis. Some peripheral terms (glial cell proliferation, antibiotic response) may reflect broader regulatory roles but do not override the dominant translation/ribosome theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006413","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0000462","count":2}]},{"hash":"847553868028305464","title":"Cellular stress responses and development signals","description":"The top GO terms cluster around stress-related responses (ER stress\u2013induced apoptosis, nutrient limitation response, cadmium ion response, defense to bacteria) and development-related processes (forebrain development, neural tube closure), with supporting terms for transcription and cell cycle. This suggests a general theme of how cells react to stress while engaging developmental signaling, rather than a single cohesive pathway. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070059","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0071276","count":3}]},{"hash":"818377240433929748","title":"Mitochondrial Metabolism and Stress Response","description":"The top GO terms cluster around mitochondrial functions: import/transport of metabolites and ions into mitochondria (pyrimidine nucleotides, iron, manganese, NAD), alongside metabolic stress responses (amino acid starvation, fatty acid response) and signaling events (insulin/IGF stimulus), plus mitochondrial-associated apoptosis and liver regeneration, collectively pointing to a mitochondria-centered metabolic regulation and stress response cluster.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":3},{"id":"GO:0097421","count":2},{"id":"GO:1990519","count":2},{"id":"GO:0070542","count":2},{"id":"GO:0061179","count":2}]},{"hash":"43401827288657503","title":"Notch signaling with amino acid metabolism","description":"The top terms mix Notch signaling with several amino acid catabolic and biosynthetic processes, along with the TCA cycle and transcription. This pattern suggests a cluster where regulatory pathways (Notch, transcription) intersect with amino acid metabolism. Therefore, the label emphasizes both Notch signaling and metabolic processes.","confidence":"Medium","size":19,"edges":125,"triangles":411,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0097053","count":7},{"id":"GO:0006099","count":7},{"id":"GO:0019878","count":5}]},{"hash":"630782642269291931","title":"Chromatin modification and cell cycle control","description":"This cluster shows strong hints of chromatin regulation (histone acetylation, ubiquitination) alongside core cell-cycle and transcription processes (DNA-templated transcription, APC/C-dependent catabolic process, cell division, ribosome biogenesis). While there are some broader developmental/cytoskeletal terms (gastrulation, Arp2/3 actin nucleation), the dominant theme relates to chromatin regulation and progression through the cell cycle, making this label representative.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":3},{"id":"GO:0043982","count":2},{"id":"GO:0043981","count":2},{"id":"GO:0034314","count":2},{"id":"GO:0006351","count":2}]},{"hash":"349035350025316616","title":"Ribosome biogenesis and ER-Golgi trafficking","description":"This cluster is enriched for translation-related processes (translation, tRNA modification, ribosome biogenesis, regulation of translational fidelity) and ER-associated events (protein insertion into the ER membrane, retrograde Golgi\u2013ER transport), suggesting a cohesive theme around ribosome production coupled with secretory pathway protein processing/trafficking. A few terms like cobalamin biosynthesis and cell cycle appear as minor outliers, but the dominant signals support a ribosome/ER-transport-centric function.","confidence":"Medium","size":18,"edges":12,"triangles":4,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0009236","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0099133","count":2},{"id":"GO:0006400","count":2}]},{"hash":"1511716952706325104","title":"Developmental transcription and signaling regulators","description":"The terms point to regulators of gene expression and signaling in development (DNA-templated transcription, mesoderm formation, neuron development) plus associated signaling modulation (negative regulation of smoothened signaling, parathyroid hormone response) and membrane trafficking (caveolin-mediated endocytosis), suggesting a theme of developmental gene regulation and signaling programs rather than a single, tight functional niche.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0071374","count":2},{"id":"GO:1901621","count":2}]},{"hash":"664873044369187288","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0061641","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0006888","count":3}]},{"hash":"417682390024112778","title":"Chromatin Modification by Protein Acetylation","description":"The cluster is dominated by acetylation-related processes, including histone H4 acetylation and various N- and peptidyl acetylations, alongside chromatin organization terms like subtelomeric heterochromatin formation and centromeric cohesion. This points to a coherent theme of chromatin regulation via acetylation. A few outlier terms (angiogenesis, melatonin biosynthesis, mycothiol, acetoin catabolism) may reflect annotation noise or multifunctional proteins, but the acetylation/chromatin signal remains strongest.","confidence":"Medium","size":18,"edges":24,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":9},{"id":"GO:0001525","count":7},{"id":"GO:0045150","count":7},{"id":"GO:0043967","count":7},{"id":"GO:0018003","count":7}]},{"hash":"492710701203540247","title":"Developmental Regulation and Neural Development","description":"The dominant terms point to developmental processes (forebrain, neural tube closure, skeletal system, multicellular development) and transcriptional control (DNA-templated transcription), suggesting a cluster of proteins involved in regulating development, particularly neural development. Some terms reflect stress or immune responses as potential outliers, but the core theme remains developmental regulation and neural formation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0071333","count":5},{"id":"GO:0070059","count":5},{"id":"GO:0030900","count":5}]},{"hash":"699614722864936186","title":"Immune signaling and ubiquitin regulation","description":"The top GO terms cluster around immune signaling pathways (T cell receptor signaling, Fc-epsilon receptor signaling, C-type lectin receptor signaling) and antigen processing/presentation via MHC I, along with viral process. There is also a strong signal for ubiquitin-related regulation (deubiquitination and ubiquitin ligase activity in mitosis) and mRNA stability control, suggesting a cohesive theme of immune signaling coupled with ubiquitin-mediated regulation of protein turnover and gene expression. A minor presence of Wnt planar cell polarity hints at broader regulatory roles but does not override the core immune/ubiquitin theme.","confidence":"Medium","size":18,"edges":62,"triangles":134,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":7},{"id":"GO:0002223","count":6},{"id":"GO:0038095","count":6},{"id":"GO:0060071","count":6},{"id":"GO:0010972","count":6}]},{"hash":"1098384247377523130","title":"Cell cycle and protein complex assembly","description":"The top GO terms point to DNA replication and cell division (e.g., centriole elongation), along with protein complex assembly processes (homooligomerization, chaperone-mediated assembly, inclusion body assembly). Also highlighted are organelle-related assembly events (mitochondrial complex III) and autophagy-related processes, suggesting a cluster of proteins that coordinate cell cycle progression with assembly and maintenance of protein complexes and organelles, with some quality-control/ stress-response connections. Confidence: Medium","confidence":"","size":18,"edges":86,"triangles":188,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":8},{"id":"GO:0051301","count":6},{"id":"GO:0042493","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0090261","count":5}]},{"hash":"1923166745385367519","title":"Vesicle traffic and actin cytoskeleton regulation","description":"The top GO terms cluster around ER-Golgi vesicle transport (anterograde and retrograde), regulation of GTPase activity, and Arp2/3-mediated actin nucleation, plus related signaling like peptidyl-tyrosine phosphorylation. This points to a theme of coordinated vesicle trafficking with cytoskeletal remodeling and signaling, despite some broader terms (mitosis, pigmentation) that are less connected. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0050731","count":5},{"id":"GO:2000601","count":5},{"id":"GO:0000278","count":5}]},{"hash":"182198803494461745","title":"Ribosome biogenesis and mitosis","description":"The cluster is dominated by ribosome-related terms (formation of translation preinitiation complex, translation reinitiation, ribosome biogenesis, ribosomal large subunit biogenesis) and cell cycle/mitosis terms (cell division, cell cycle), with supporting references to centromeric chromatin assembly and microtubule severing. This pattern suggests proteins involved in ribosome production that are linked to mitotic processes, including chromosome maintenance and spindle dynamics, supporting a cohesive theme around ribosome biogenesis intertwined with mitosis.","confidence":"Medium","size":18,"edges":148,"triangles":742,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0042273","count":3}]},{"hash":"1609389812346116745","title":"Chromatin maintenance and DNA repair via ubiquitin signaling","description":"This cluster highlights processes tied to chromatin regulation and genome stability, including telomere maintenance via recombination, subtelomeric heterochromatin formation, and histone H2B ubiquitination, alongside protein quality control by the ubiquitin-proteasome system and spliceosome-mediated mRNA processing. The recurring themes of ubiquitin signaling, chromatin modification, and DNA damage tolerance (translesion synthesis) suggest a cohesive role in maintaining chromatin state and genome integrity, with some broader pleiotropic terms (developmental and hormonal responses) possibly reflecting shared regulatory networks. Overall, the dominant signal points to chromatin maintenance and DNA repair coordinated by ubiquitin pathways.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000722","count":2},{"id":"GO:0010976","count":2},{"id":"GO:0071629","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0016032","count":2}]},{"hash":"1017524050310698720","title":"Bacterial SOS and antibiotic stress response","description":"The terms point to a bacterial stress-response module: SOS response and nucleotide-excision repair indicate DNA-damage coping, while antibiotic response and various transport terms suggest mechanisms to counteract antibiotics and manage stress. The transcription regulation terms align with stress-induced gene regulation. Phosphatidylinositol dephosphorylation is a weaker, less connected term in this cluster. Overall, a cohesive theme is bacterial DNA damage and antibiotic stress response with associated transport and regulation. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0046856","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045892","count":2},{"id":"GO:0000770","count":1}]},{"hash":"2277763629640007053","title":"Unknown","description":"The terms are highly heterogeneous, spanning RNA modification/rRNA maturation and unrelated processes like actin filament formation, plant cell wall biogenesis, and metabolism. There isn\u2019t a single cohesive function that ties the cluster together, so a meaningful label cannot be assigned with confidence.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0000462","count":1}]},{"hash":"853434906055240365","title":"Bacterial sporulation and cell wall biosynthesis","description":"The most frequent GO terms point to sporulation leading to spore formation, peptidoglycan biosynthesis, cell wall organization, and regulation of cell shape, collectively defining processes for spore formation and bacterial cell envelope construction/remodeling. Other terms (embryo sac development, LDL receptor\u2013related processes) appear sparsely and likely reflect annotation noise rather than core function. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":2},{"id":"GO:0042176","count":2},{"id":"GO:0009252","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0008360","count":2}]},{"hash":"2055821081111185530","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000973","count":1},{"id":"GO:0034476","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0071033","count":1},{"id":"GO:1901917","count":1}]},{"hash":"1041741792346869161","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":50,"triangles":21,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0014823","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0006740","count":2}]},{"hash":"1670069206557702821","title":"Amino acid catabolism and xenobiotic detoxification","description":"Cluster shows enrichment in amino acid catabolic processes (tyrosine, phenylalanine), methylglyoxal detox via glutathione, and xenobiotic/antibiotic response, plus oxidative metabolism. While transcriptional regulation and Arp2/3-mediated actin nucleation appear among terms, the dominant signal is metabolic detoxification and amino acid breakdown, suggesting a label focused on catabolic/detox pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":2},{"id":"GO:0006357","count":1},{"id":"GO:0042178","count":1},{"id":"GO:0006572","count":1},{"id":"GO:0019243","count":1}]},{"hash":"817618772747687060","title":"Genome maintenance and stress response","description":"The top GO terms cluster around DNA replication, telomere maintenance and capping, and mRNA processing, all pointing to genome stability and transcriptional regulation under stress. Additional terms like regulation of CDK activity and cell migration suggest cell-cycle control and motility changes, with some metabolic/differentiation terms likely reflecting broader regulatory roles or annotation breadth. Overall, the cluster appears to reflect genome maintenance and cellular stress responses rather than a single, narrow pathway.","confidence":"Medium","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0035994","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0006397","count":4}]},{"hash":"1126597123915957756","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":15},{"id":"GO:0031047","count":14},{"id":"GO:0042273","count":13},{"id":"GO:0035640","count":13},{"id":"GO:0000393","count":13}]},{"hash":"271311466921752217","title":"Ribosome biogenesis and nucleocytoplasmic transport","description":"This cluster centers on ribosome assembly and movement of ribosomal subunits, highlighted by ribosome biogenesis and ribosomal large subunit export from the nucleus, along with general protein transport. The presence of terms related to ER stress response and mitotic processes (spindle assembly, G2/M regulation, cell polarity) suggests a broader link between ribosome production, intracellular trafficking, and cell-cycle events. Confidence is moderate due to the mix of related functions and lack of demonstrated interactions in the Edges/Triangles data.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0015031","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0010971","count":2},{"id":"GO:0045956","count":2}]},{"hash":"2196483507177337160","title":"Mitotic spindle and kinetochore localization; cell cycle control","description":"Most terms point to mitosis\u2014protein localization to the kinetochore and mitotic spindle pole body, and negative regulation of CDK activity and the cell cycle\u2014supported by accompanying MAPK signaling inhibition terms. This suggests a cluster of proteins that operate at the mitotic apparatus while tuning signaling pathways.","confidence":"High","size":17,"edges":121,"triangles":494,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035335","count":7},{"id":"GO:0000200","count":5},{"id":"GO:0050860","count":5},{"id":"GO:0070373","count":5},{"id":"GO:0034501","count":5}]},{"hash":"903163719927373448","title":"Fatty acid catabolism and related metabolism","description":"GO terms show strong representation of fatty acid breakdown (medium- and long-chain) and carnitine metabolism, with supporting aromatic compound catabolic processes. Transcription/translation terms appear but are less dominant, so the primary theme is fatty acid\u2013related catabolic metabolism. ","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0019439","count":2},{"id":"GO:0018896","count":2},{"id":"GO:0019254","count":2}]},{"hash":"1820413488393751489","title":"Metabolic and endocrine signaling","description":"The top GO terms cluster around metabolic regulation and hormonal signaling: cellular response to IGF stimulus, response to vitamin D, fatty acid response, and insulin-related regulation (insulin secretion and IGF signaling). NAD transmembrane transport and mitochondrial nucleotide import point to energy and mitochondrial metabolism, with liver regeneration aligning with metabolic repair and growth. A single neurodevelopment term is present but the prevailing pattern centers on metabolism and endocrine signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":3},{"id":"GO:0097274","count":3},{"id":"GO:0021707","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1663895026839829954","title":"Unknown","description":"The top terms span regulatory processes across apoptosis, chromatin modification/ubiquitin-proteasome pathways, stress signaling (JNK), and even phosphate metabolism. The terms are diverse and not tied to a single cohesive function, and there are no interactions among proteins, making a specific, representative label difficult to justify.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042981","count":1},{"id":"GO:0080040","count":1},{"id":"GO:0009048","count":1},{"id":"GO:2000620","count":1},{"id":"GO:0070535","count":1}]},{"hash":"1300360370220900768","title":"Neural development and synaptic signaling","description":"The cluster is dominated by neural development and synaptic signaling terms, including excitatory postsynaptic potential, hippocampus development, Schwann cell development, and positive regulation of axon extension, which together point to neural development and synaptic activity. A few non-neural terms (such as T cell receptor signaling and meiotic cell cycle) appear, likely reflecting broader signaling roles or noise, but they do not override the neural focus.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060079","count":4},{"id":"GO:0050852","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0045773","count":3},{"id":"GO:0021766","count":3}]},{"hash":"2015303033846965506","title":"DNA Replication and Growth Signaling","description":"This cluster is enriched in DNA replication, mitotic cell cycle, transcription, and key growth-regulating pathways such as Wnt and Hippo, with additional signals related to differentiation (keratinocytes) and cardiac muscle proliferation. The convergence on cell-cycle progression and growth control suggests a module coordinating proliferation with developmental signaling.","confidence":"High","size":16,"edges":85,"triangles":216,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0000278","count":9},{"id":"GO:0007601","count":9},{"id":"GO:0006915","count":9},{"id":"GO:0090263","count":8}]},{"hash":"187610815557953274","title":"Translation machinery under stress","description":"The cluster centers on translation-related processes: translation (GO:0006412), ribosomal large subunit biogenesis (GO:0035640), and regulation of selenocysteine incorporation, indicating a focus on protein synthesis. The presence of SOS response and response to antibiotic terms suggests stress conditions that often influence translation, while other terms like TCA cycle, lysine catabolism, and spliceosomal changes may reflect broader cellular responses or cross-talk, but the core theme remains translation machinery affected by stress.","confidence":"Medium","size":16,"edges":44,"triangles":58,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0006099","count":3},{"id":"GO:0033512","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1736277001889777550","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0031126","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0090084","count":2},{"id":"GO:0071630","count":2}]},{"hash":"982180096905685327","title":"Unknown","description":"The terms cover diverse areas: immune response (TH1), development (neuron maturation, kidney size), signaling (Wnt signalosome), stress responses (manganese ion, mechanical stimulus), and protein regulation (autoubiquitination). The lack of a unifying biological process across most terms makes a specific, representative label unsupported.","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":2},{"id":"GO:0014041","count":2},{"id":"GO:0035751","count":2},{"id":"GO:1903125","count":2},{"id":"GO:0042088","count":2}]},{"hash":"561609577313061085","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0010637","count":1},{"id":"GO:0071432","count":1}]},{"hash":"529425396114364373","title":"Ubiquitin/SUMO modification and innate signaling","description":"The top GO terms cluster around deubiquitination and sumoylation, with ties to proteasomal degradation and regulation of protein turnover, complemented by innate immune signaling pathways (MyD88-dependent TLR signaling, C-type lectin receptor signaling, Fc-epsilon receptor signaling). The presence of cell-cycle related ubiquitin regulation (G2/M transition) further supports a cohesive theme where ubiquitin/SUMO modification controls signaling and turnover, including immune responses. Overall, this label captures the dominant functional theme of the cluster.","confidence":"High","size":16,"edges":113,"triangles":470,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":7},{"id":"GO:0016925","count":6},{"id":"GO:0010950","count":6},{"id":"GO:0034126","count":5},{"id":"GO:0002223","count":5}]},{"hash":"923849423837974207","title":"Ribosome biogenesis and large subunit maturation","description":"The top GO terms cluster around ribosome production and processing\u2014ribosome biogenesis, ribosomal large subunit export from the nucleus, assembly of large-subunit preribosomes, and rRNA processing/maturation\u2014indicating the proteins mainly participate in ribosome assembly and maturation. A few terms (tRNA processing/modification, phosphatidylcholine biosynthesis) are present but do not change the overall ribosome-focused signal.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000055","count":3},{"id":"GO:0042254","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0006364","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1840085851384471417","title":"Core metabolism and cell growth","description":"The top GO terms cover translation, energy-related processes (mitochondrial complex III assembly), cell cycle/division, glycogen biosynthesis, redox, and cell organization, suggesting a broad set of housekeeping functions rather than a single specialized pathway. While antibiotic response and pheromone export appear, they are less central to the cluster\u2019s core theme. Overall, the cluster seems tied to general metabolism and growth processes, but the diverse terms yield only modest specificity.","confidence":"Low","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0034551","count":2},{"id":"GO:0051301","count":2}]},{"hash":"767840724907035009","title":"ER stress response and ER network organization","description":"GO terms strongly point to ER stress signaling (PERK, IRE1), ER tubular network organization, and ER-to-Golgi transport, suggesting an ER-centered functional theme; a few terms describe broader cellular processes that may be incidental.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903899","count":1},{"id":"GO:1902408","count":1},{"id":"GO:0051292","count":1},{"id":"GO:0071790","count":1},{"id":"GO:1903371","count":1}]},{"hash":"1854014280164074280","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0051259","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1877230182019554896","title":"Mitochondrial translation and tRNA charging","description":"The cluster is dominated by GO terms related to translation and tRNA processing/charging, including mitochondrial serine/threonine/prolyl tRNA aminoacylation and regulation of translational fidelity, suggesting a cohesive role in mitochondrial protein synthesis and tRNA maturation. Some other terms (DNA repair, A-to-I editing) appear less central and may be incidental to the primary theme.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006382","count":2},{"id":"GO:0070158","count":1}]},{"hash":"1609927597092956447","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0090617","count":1},{"id":"GO:0000961","count":1},{"id":"GO:1905639","count":1}]},{"hash":"1463804796841749653","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903830","count":1},{"id":"GO:0006824","count":1},{"id":"GO:0045016","count":1},{"id":"GO:0016042","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1541478504522433111","title":"Epigenetic Regulation of Transcription","description":"This cluster centers on transcriptional control (DNA-templated transcription) reinforced by methylation of histones and arginine residues (histone methylation, PRMT activity), pointing to epigenetic regulation of gene expression; some associated terms reflect stress/response and apoptotic processes, consistent with dynamic transcriptional regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0015966","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0043627","count":3},{"id":"GO:0060374","count":3}]},{"hash":"426952437245010122","title":"Nuclear RNA Processing and Transcriptional Control","description":"The terms cluster around RNA maturation and processing (P-body, spliceosome assembly, rRNA maturation, tRNA processing, histone mRNA metabolism), nuclear import, and transcription termination, with chromatin-related processes (heterochromatin formation) also represented. This points to a cohesive theme of RNA metabolism and nuclear regulation, despite a few peripheral terms.","confidence":"Medium","size":15,"edges":71,"triangles":197,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":6},{"id":"GO:0000245","count":6},{"id":"GO:0030490","count":6},{"id":"GO:0009414","count":6},{"id":"GO:0006369","count":6}]},{"hash":"1460210291528647716","title":"Mitotic division and secretory vesicle transport","description":"This cluster combines mitosis-related processes (mitotic spindle assembly, mitotic cell cycle, cell division) with vesicle trafficking between the ER, Golgi, endosomes, and lysosomes (COPII budding, ER-Golgi transport, retrograde transport, endosome-to-lysosome transfer), suggesting proteins that participate in both cell division and the secretory pathway. The presence of brain development and growth terms may reflect developmental proliferation where these processes are coordinated.","confidence":"Medium","size":15,"edges":22,"triangles":10,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":12},{"id":"GO:0006890","count":12},{"id":"GO:0035264","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0007420","count":12}]},{"hash":"1278787257229101362","title":"Germline Meiosis and Gene Expression Regulation","description":"This cluster centers on germline development, highlighted by meiosis I and male germ-line cyst encapsulation. It also includes elements of transcriptional and translational control (negative regulation of RNAP II, formation of translation preinitiation complex, and regulation of mRNA binding) and protein turnover (ubiquitin-dependent proteolysis), suggesting coordinated regulation of gene expression during gametogenesis. Some terms like photomorphogenesis appear as broader developmental connections, but the core signals point to germline meiosis and associated gene expression control.","confidence":"Medium","size":15,"edges":26,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007127","count":2},{"id":"GO:0001731","count":1},{"id":"GO:0000973","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0070321","count":1}]},{"hash":"1000356904124294323","title":"Redox Homeostasis and Oxidative Stress Response","description":"These proteins cluster around redox biology\u2014detoxifying oxidants, maintaining redox balance, and responding to hydrogen peroxide\u2014indicating an oxidative stress response module. Some terms touch on growth regulation and translation, but the strongest signals are redox-related, so the name reflects the predominant function of the cluster.","confidence":"High","size":15,"edges":94,"triangles":358,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":8},{"id":"GO:0045454","count":6},{"id":"GO:2000255","count":5},{"id":"GO:0030416","count":5},{"id":"GO:0070301","count":3}]},{"hash":"639918691383469801","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0000463","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0007369","count":3},{"id":"GO:0007568","count":3}]},{"hash":"2007392209365106377","title":"Ribosome biogenesis and translation","description":"Based on the prominent GO terms, the cluster is centered on translation and rRNA maturation (LSU/SSU), pointing to ribosome biogenesis and protein synthesis; peripheral terms like DNA repair or chromatin-related processes appear incidental. This combination best captures the core signal of the cluster.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006348","count":2}]},{"hash":"719796310270318769","title":"Membrane trafficking and signaling proteins","description":"The top GO terms point to membrane protein processing and signaling activities (positive regulation of ectodomain proteolysis, integrin signaling, AMPA receptor clustering) along with control of endocytosis and transport of amino acids into/out of the vacuole. This mix suggests a functional theme around coordinating membrane trafficking, receptor signaling, and cargo movement between plasma membrane and intracellular compartments, rather than a single highly specific pathway. Confidence is moderate because some terms (e.g., AMPA receptor clustering) imply context-specific roles, and vacuolar transport hints at species-specific functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051044","count":2},{"id":"GO:0007229","count":2},{"id":"GO:0097113","count":2},{"id":"GO:0045806","count":2},{"id":"GO:0090515","count":1}]},{"hash":"2221737095782269653","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms related to ribosome assembly and rRNA processing (ribosome biogenesis; maturation of SSU/LSU rRNA from tricistronic transcripts; formation of translation preinitiation complex), suggesting a core function in ribosome production and initiation of protein synthesis. The presence of mitotic spindle and microtubule movement terms hints at a broader cell-cycle context, but the strongest signal is ribosome-related, supporting a label focused on ribosome biogenesis and translation initiation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007584","count":4},{"id":"GO:0090307","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0042254","count":3}]},{"hash":"144202237095368871","title":"Rho GTPase\u2013driven cytoskeletal remodeling","description":"The top GO terms cluster around regulation of GTPase activity, especially Rho signaling, and cell migration/extension, which point to roles in actin cytoskeleton dynamics and motility. While developmental terms and a couple of outliers appear, the dominant theme is signaling that controls cytoskeletal remodeling and cell movement. This supports labeling the group as related to Rho GTPase\u2013mediated cytoskeletal dynamics.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021587","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0046786","count":1},{"id":"GO:0060988","count":1},{"id":"GO:0048538","count":1}]},{"hash":"1226441999045558072","title":"Unknown","description":"The terms are highly diverse and only weakly connected, spanning signal transduction regulation, RNA processing (splicing, translation initiation, mRNA tail regulation, ncRNA-mediated silencing), and unrelated processes like glycogen metabolism and blastocyst formation, suggesting no single cohesive function characterizes the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009966","count":1},{"id":"GO:0043666","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0005977","count":1},{"id":"GO:0048026","count":1}]},{"hash":"895090582249607720","title":"Mitotic spindle assembly and cytoskeletal dynamics","description":"The cluster is dominated by mitotic spindle\u2013related terms (mitotic spindle assembly, spindle midzone assembly, kinetochore\u2013microtubule attachment, mitotic metaphase chromosome recapture) and GTPase-related regulation, pointing to microtubule dynamics and spindle organization. Additional terms touch on cytoskeletal roles in neurons and movement, which fits a broader theme of cytoskeletal organization and cell adhesion. Overall, the proteins appear to cluster around microtubule-based division and structural maintenance.","confidence":"Medium","size":14,"edges":84,"triangles":288,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0090307","count":2},{"id":"GO:1990535","count":2},{"id":"GO:0099607","count":2},{"id":"GO:0072092","count":2}]},{"hash":"7918301498494446","title":"Mitosis and Kinase Signaling","description":"Terms center on mitosis and kinase signaling (mitotic cell cycle, spindle assembly, kinase activity, autophosphorylation, GTPase regulation). The cluster appears to represent cell division control and phosphorylation-driven signaling, with a few less-central terms like mRNA transport and ERAD-related processes as potential ancillary functions.","confidence":"High","size":14,"edges":6,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0071902","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0031954","count":6}]},{"hash":"680641412942424107","title":"Gene Expression and Cell Division Regulation","description":"The top GO terms pull in both gene expression processes (translation initiation and preinitiation complex formation, transcription) and cell division/cytoskeletal events (mitotic spindle assembly, actin filament depolymerization, septum digestion after cytokinesis), suggesting a cluster of proteins that coordinate gene expression with cell-cycle and cytoskeletal dynamics. While there is a cohesive core around regulation of expression and division, some terms (e.g., cadmium response, hyaluronan regulation) appear peripheral, so the overall theme is present but not exclusively tight. ","confidence":"Medium","size":14,"edges":72,"triangles":204,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006378","count":2}]},{"hash":"2103054929709667902","title":"Vacuolar Ion Transport and Metabolism","description":"The leading GO terms cluster around vacuolar function and membrane transport: proton transmembrane transport, sodium ion transport, vacuolar acidification, and protein targeting to the vacuole, suggesting a cohesive role in vacuolar ion homeostasis and trafficking. Metabolic terms like nitrate assimilation, tetrahydrofolate metabolism, and copper ion homeostasis fit into broader cellular processes that are often coordinated with vacuolar activity. The translation term appears incidental. Therefore, Vacuolar Ion Transport and Metabolism is a concise, representative label.","confidence":"High","size":14,"edges":75,"triangles":207,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0046653","count":2},{"id":"GO:0009061","count":2}]},{"hash":"772257358528975","title":"Cell cycle regulation and transcription control","description":"The top terms cluster around core cell cycle processes (G1/S transition, cell division) and transcriptional regulation by RNA polymerase II, with supporting signals related to glucocorticoid signaling and liver regeneration. This suggests proteins in this cluster coordinate cell cycle progression with transcriptional control, potentially in proliferative or hepatic contexts, while additional terms reflect stress-related responses (vitamin E, lead) that can modulate these pathways.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033197","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0010288","count":3},{"id":"GO:2000324","count":3}]},{"hash":"728593311371571825","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0097171","count":3},{"id":"GO:0031247","count":2},{"id":"GO:0032361","count":2},{"id":"GO:0009244","count":2}]},{"hash":"358020723744793590","title":"ER-Golgi Trafficking and Golgi Organization","description":"This cluster is dominated by GO terms related to ER-Golgi transport and Golgi apparatus organization: ER-Golgi intermediate compartment organization, Golgi disassembly, ER exit site localization, COPI-coated vesicles, and ARF/GTPase regulation, which together point to vesicle trafficking between the ER and Golgi and Golgi architecture maintenance. One outlier term (hydrotropism) likely represents noise rather than function. Overall, the proteins appear to function in ER-Golgi trafficking and Golgi organization.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090284","count":1},{"id":"GO:0010274","count":1},{"id":"GO:0097111","count":1},{"id":"GO:0010256","count":1},{"id":"GO:0043547","count":1}]},{"hash":"1573189252281322167","title":"DNA replication and transcription regulation","description":"The cluster is enriched for DNA-templated transcription, DNA replication and related unwinding/primer synthesis, plus regulation of transcription by RNA Pol II and mRNA quality control, suggesting a nuclear DNA replication/transcription regulatory module; some annotations appear obsolete or noisy but do not override the core theme.","confidence":"High","size":14,"edges":10,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006268","count":2},{"id":"GO:0006468","count":2},{"id":"GO:0006269","count":2}]},{"hash":"600471934865061265","title":"Transcription and RNA Processing Regulators","description":"The Top Terms cluster around DNA-templated transcription, spliceosomal snRNP assembly, and regulatory ncRNA-mediated gene silencing, pointing to a core theme of transcriptional control and RNA processing. While some terms (e.g., nervous system development, PI3K/AKT signaling) are broader or downstream, the strongest common link is regulation of gene expression at the transcriptional and RNA-processing level. The lack of observed interactions suggests this may reflect shared functional annotations rather than a single physical pathway, but the RNA-centric regulation theme remains clear.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0045956","count":2}]},{"hash":"1381106547949415582","title":"ER-Golgi trafficking and membrane localization","description":"This cluster is dominated by GO terms for ER-Golgi vesicle transport in both directions, ER lumen protein retention, and promotion of protein localization to the plasma membrane, pointing to a shared role in the secretory pathway and membrane trafficking. Transcription/translation terms seem ancillary to this core theme.","confidence":"High","size":13,"edges":13,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0071340","count":1},{"id":"GO:0006621","count":1}]},{"hash":"69450115709940187","title":"mRNA Splicing and Processing","description":"The cluster\u2019s top terms are dominated by mRNA processing and spliceosome-related activities (mRNA splicing via spliceosome, splice site recognition, regulation of splicing and polyadenylation) and include components related to the formation of the translation preinitiation complex, indicating a cohesive role in mRNA maturation and initiation of translation.","confidence":"High","size":13,"edges":44,"triangles":65,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":7},{"id":"GO:0045292","count":6},{"id":"GO:0006378","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6}]},{"hash":"733445320641686864","title":"Neuronal mitochondrial quality control and proteostasis","description":"The top GO terms converge on mitochondrial dynamics and turnover (mitophagy, regulation of mitochondrial fusion) and ubiquitin-dependent protein degradation, with neuron-specific processes (neuron homeostasis, neuron maturation) supporting a neuronal context. Additional terms related to vesicle formation and stress signaling (JNK cascade) fit within cellular quality-control and autophagy pathways. Although one term mentions insulin secretion, the overall pattern points to a cohesive theme of mitochondrial health and proteostasis in neurons.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":2},{"id":"GO:0010636","count":1},{"id":"GO:0046329","count":1},{"id":"GO:1905366","count":1},{"id":"GO:0000423","count":1}]},{"hash":"644473886908735777","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006747","count":1},{"id":"GO:0019350","count":1},{"id":"GO:0015937","count":1},{"id":"GO:1990966","count":1}]},{"hash":"1941085169072603778","title":"Unknown","description":"The GO terms span a broad and disparate set of processes (potassium transport, insulin signaling, brood size regulation, dense core granule transport, ribosome biogenesis/export, tRNA modification, cell cycle, and cellular fusion), with no single unifying function evident. The lack of edges among proteins further suggests this is not a cohesive functional module, so an Unknown label with None confidence is appropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0060378","count":2},{"id":"GO:1904810","count":2},{"id":"GO:0042274","count":1}]},{"hash":"825990434691968712","title":"Mitotic cell cycle and endosomal trafficking","description":"Top GO terms indicate a module combining mitotic progression (exit from mitosis, cell division, mitotic cytokinesis) with endosomal/vesicle trafficking (intralumenal vesicle formation, multivesicular body assembly, endosome transport regulation). This suggests proteins work together to coordinate cytokinesis with membrane remodeling and vesicle sorting; ribosome biogenesis appears less central. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010458","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2248801492599917431","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0030422","count":2},{"id":"GO:0035196","count":2},{"id":"GO:0010087","count":2},{"id":"GO:0051533","count":2}]},{"hash":"1399222952544565892","title":"Fatty acid catabolism","description":"The GO terms point to fatty acid breakdown, including medium-chain and long-chain fatty acid catabolic processes, and involvement of carnitine in FA metabolism. Despite some unrelated or obsolete terms, the strongest shared function is lipid metabolism via fatty acid oxidation, suggesting this cluster centers on fatty acid catabolic activity.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0019439","count":1},{"id":"GO:0018896","count":1},{"id":"GO:0019254","count":1},{"id":"GO:0009409","count":1}]},{"hash":"1429691199720106484","title":"Diverse solute transporters","description":"These proteins carry a mix of substrate-transport GO terms, including fucose, sialic acid, dehydroascorbic acid, organic anions, and xenobiotics, plus osmotic stress response. The common thread is membrane transport of varied solutes, suggesting a cluster of transporters with broad substrate specificity rather than a single pathway. Occasional unrelated terms (senescence regulation, intestinal epithelial maintenance) are likely secondary annotations or noise. Overall, the label reflects the core function of the group.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006004","count":1},{"id":"GO:0015739","count":1},{"id":"GO:0070837","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0042891","count":1}]},{"hash":"625755064127013120","title":"Vacuolar amino acid transporters","description":"Most of the top GO terms point to import into or export from the vacuole for various amino acids (glutamate, serine, histidine, tyrosine, lysine, alanine) and even lithium, suggesting a cohesive function as vacuolar amino acid transporters. The lone plant-related term (root cap development) is less central to the core transporter function, so the dominant theme remains vacuolar amino acid transport.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090515","count":1},{"id":"GO:1901482","count":1},{"id":"GO:0090516","count":1},{"id":"GO:0090513","count":1},{"id":"GO:0089707","count":1}]},{"hash":"1590513268415092666","title":"Secretory Pathway Trafficking","description":"The top GO terms cluster around intracellular transport along the secretory pathway (ER to Golgi to plasma membrane/endosome), including protein localization to the Golgi and ER lumen retention, plus general protein transport. Although some immune and metabolic terms appear, the dominant pattern is ER-Golgi trafficking and Golgi-associated transport, suggesting this cluster represents components of the secretory pathway.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030097","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0043001","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0000042","count":1}]},{"hash":"2230796090610690931","title":"Telomeric and Subtelomeric Heterochromatin Formation","description":"The cluster is dominated by GO terms about chromatin silencing and heterochromatin formation at telomeres, subtelomeric regions, and rDNA, indicating a core role in chromatin organization and transcriptional silencing of repetitive genomic regions. A few terms related to synaptic vesicle regulation and neuronal development appear but are much less represented, so the primary theme remains chromatin-based.","confidence":"High","size":12,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0007286","count":3},{"id":"GO:0031939","count":2},{"id":"GO:0006268","count":2}]},{"hash":"2144852889610116305","title":"Endocytosis and Iron Homeostasis with Vacuolar Proteolysis","description":"This cluster centers on endocytic uptake and iron handling, highlighted by terms for receptor-mediated endocytosis, transferrin transport, and intracellular iron ion homeostasis, complemented by vacuolar protein degradation. While some terms are peripheral (e.g., plant growth regulation, deglutamylation, folic acid metabolism), the strongest signal ties endocytosis to iron trafficking and turnover in the vacuole.","confidence":"Medium","size":12,"edges":10,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0044655","count":1},{"id":"GO:0033572","count":1},{"id":"GO:0006898","count":1},{"id":"GO:0010081","count":1}]},{"hash":"739634333726800273","title":"Mitotic Cycle and Proliferation Signaling","description":"Based on the top GO terms, the proteins cluster around cell cycle progression (mitotic cycle) and positive regulation of cell proliferation, coupled with signaling activity (GTPase regulation, serine/threonine kinase activity, and autophosphorylation). While there are additional terms related to histone modification, mRNA transport, and stress responses (hypoxia, neuron apoptosis), the dominant theme ties to mitotic regulation and proliferative signaling. This makes a cohesive label focusing on growth and division regulation appropriate.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0051402","count":3},{"id":"GO:0043966","count":3},{"id":"GO:0050679","count":3}]},{"hash":"1364373076740193956","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0070059","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0051402","count":2}]},{"hash":"390993592062094352","title":"Bacterial SOS Response and Secretion/Transport","description":"Top GO terms indicate a bacterial SOS/dNA damage response (SOS response, nucleotide-excision repair) and a general response to toxic substances, highlighting the stress-handling aspect. The presence of multiple transport and secretion terms (glycine betaine transport, thiamine transport, doxorubicin transport, peptide pheromone export, Type I secretion) suggests these proteins may function in exporting protective compounds or signaling molecules as part of the stress response. Overall, the cluster appears to join DNA-damage response with associated transport/secretion activities.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0000770","count":1},{"id":"GO:0031460","count":1}]},{"hash":"2179635003307035197","title":"Vertebrate Developmental and Stress Signaling","description":"The terms are dominated by organ/tissue development and vascular-related processes (lung development, hair cycle, adenohypophysis morphogenesis, angiogenesis, blood coagulation), with several items pointing to hormonal and stress responses (glucocorticoid response, cAMP response, hypoxia response, hydrogen peroxide biosynthesis, memory). This suggests a broad theme of vertebrate developmental programs that interface with hormonal and stress signaling, though the mix is quite diverse rather than pointing to a single pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007596","count":2},{"id":"GO:0051384","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0051591","count":2},{"id":"GO:0042633","count":2}]},{"hash":"2135576131081989141","title":"Sterol and fatty acid biosynthesis","description":"The top terms are dominated by lipid and sterol metabolism, including cholesterol biosynthetic processes via lathosterol, ergosterol biosynthesis, fatty acid biosynthesis, ether lipid metabolism, and related sterol oxidation and sphingolipid pathways. A few terms touch neural or immune contexts, but the strongest signal is lipid biosynthesis and membrane lipid remodeling, especially sterol-related pathways.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":1},{"id":"GO:0035754","count":1},{"id":"GO:0033490","count":1},{"id":"GO:0080064","count":1},{"id":"GO:0006675","count":1}]},{"hash":"1310772958974401030","title":"Transcription and Translation Machinery","description":"The cluster's top GO terms center on gene expression: DNA-templated transcription, translation, tRNA processing, and aminoacylation (lysyl-, phenylalanyl-, methionyl-). These align with core transcription/translation processes, suggesting a cohesive functional theme, even though some terms (cytolysis, blood vessel morphogenesis) and the lack of edges indicate noise or broader annotations in this set.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0019835","count":2},{"id":"GO:0006430","count":1},{"id":"GO:0006432","count":1}]},{"hash":"2195267281408834734","title":"Methylation and Chromatin Modification","description":"This cluster centers on methylation-related processes, including peptidyl-lysine dimethylation and trimethylation, N-terminal peptidyl-glycine methylation, and rRNA methylation, along with rDNA heterochromatin formation, suggesting a core theme of epigenetic and RNA modification functions. Some metabolism-related terms (glycolysis, redox homeostasis, mitochondrial electron transport) appear but do not override the dominant methylation/chromatin signal.","confidence":"High","size":12,"edges":63,"triangles":191,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0018027","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0018023","count":3},{"id":"GO:0031167","count":3}]},{"hash":"1414100981264536873","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018937","count":1},{"id":"GO:0072344","count":1},{"id":"GO:0046256","count":1},{"id":"GO:1902167","count":1},{"id":"GO:1990116","count":1}]},{"hash":"820567088958025514","title":"RNA Processing and Mitosis","description":"This cluster highlights RNA processing functions (rRNA maturation and RNA guanine-N7 methylation) alongside mitotic functions (spindle orientation and mitotic cell cycle), suggesting a core theme around RNA biogenesis and cell division, with other terms appearing less cohesively. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0000278","count":2}]},{"hash":"265915945989973415","title":"Mesodermal differentiation and myogenesis","description":"The top GO terms cluster around mesoderm formation, myoblast differentiation involved in skeletal muscle regeneration, and regulation of osteoblast differentiation, indicating a coordinated mesodermal differentiation program affecting muscle and bone lineages. Some terms about DNA replication and cell cycle reflect general proliferation, but the dominant theme is differentiation of mesoderm-derived tissues. ","confidence":"High","size":11,"edges":21,"triangles":10,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:2000657","count":9},{"id":"GO:0045667","count":9},{"id":"GO:0071620","count":9},{"id":"GO:0014835","count":9}]},{"hash":"179115058415636466","title":"RNA processing and ribosome biogenesis","description":"This cluster shows strong representation of spliceosomal activity (disassembly and conformational changes) and ribosomal large subunit biogenesis, pointing to RNA metabolism and ribosome assembly as a core theme; the remaining terms involve telomere maintenance, ubiquitin signaling, and other processes that appear peripheral or context-specific.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000390","count":3},{"id":"GO:0090394","count":3},{"id":"GO:1901582","count":2},{"id":"GO:0031496","count":2},{"id":"GO:0042273","count":2}]},{"hash":"2247003670073365259","title":"Cell Cycle and Mesodermal Myogenic Differentiation","description":"The cluster is dominated by DNA replication and mitotic cell cycle terms, alongside mesoderm formation and myoblast differentiation, suggesting a core role in cell proliferation and mesodermal muscle lineage development. The presence of osteoblast differentiation also hints at broader mesodermal differentiation context.","confidence":"High","size":11,"edges":14,"triangles":7,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0046827","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0032435","count":6},{"id":"GO:2000657","count":5}]},{"hash":"1474338595625169475","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for ribosomal small subunit assembly, translation, and maturation of SSU-rRNA, indicating a core role in ribosome biogenesis and protein synthesis. While there are also terms related to transcription regulation and chromatin  assembly, the strongest and most frequent signals are ribosome-related, suggesting the proteins function together in ribosome production and function, with some ancillary nuclear processes captured by broader GO annotations.","confidence":"High","size":11,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000028","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000462","count":1},{"id":"GO:1902455","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1932550851583548811","title":"RNA processing and translation regulation","description":"This cluster centers on RNA metabolism, including mRNA splicing and spliceosome activity, regulation of translational initiation, and small-subunit ribosome biogenesis (processome assembly). The mix of splicing, poly(A) tail regulation, and translation initiation control suggests proteins tied to RNA processing and how transcripts are prepared for translation, with some developmental context implied by blastocyst formation terms. Overall, a cohesive RNA-centric regulatory theme best fits these terms.","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0060211","count":2},{"id":"GO:1905663","count":2}]},{"hash":"239677399509647029","title":"Developmental Transcription and Stress Response","description":"This cluster centers on embryonic development and transcriptional regulation, evidenced by forebrain development, neural tube closure, multicellular organism development, and DNA-templated transcription terms. It also includes stress-related responses (ER stress-induced apoptosis, cadmium response, defense to Gram-positive bacteria), suggesting a broader developmental program intertwined with cellular stress responses. The isolated edges indicate annotation-driven associations rather than direct interactions, but the dominant themes are developmental transcription and stress-related processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0070059","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0071276","count":4}]},{"hash":"958996807214834766","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0021510","count":3}]},{"hash":"100194142734107918","title":"Chromatin modification and mitotic chromosome segregation","description":"This cluster centers on histone modification processes (acetylation, deacetylation, and methylation of H3/H3K4) and centromeric chromatin assembly (CENP-A), plus mitosis-related functions like sister chromatid cohesion and cell division, suggesting a role in chromatin regulation during chromosome segregation; a few terms are flagged obsolete but do not alter the core theme.","confidence":"High","size":11,"edges":9,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0051013","count":2}]},{"hash":"1159393149989301087","title":"Embryo implantation and trophoblast differentiation","description":"The terms are dominated by embryo implantation and chorionic trophoblast differentiation, pointing to placental development, with supporting signals from transcriptional regulation and membrane signaling (GPCR pathway, receptor clustering) and modulation of BMP signaling. This suggests a cluster centered on embryonic/placental development and differentiation processes. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007566","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0048146","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0051798","count":1}]},{"hash":"2021995926615243059","title":"Sphingolipid and phospholipid biosynthesis","description":"Based on the top GO terms, the proteins cluster around lipid biosynthesis and membrane lipid metabolism, especially sphingolipid and phosphatidylserine pathways. Terms such as sphingolipid metabolic process, phosphatidylserine metabolic process, serine palmitoyltransferase activity regulation, and serine transport point to serine-derived lipid synthesis and membrane homeostasis; myelination and APP-related lipid processes further support a membrane/lipid context. The combination suggests a cohesive theme of lipid biosynthesis rather than disparate functions.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904219","count":1},{"id":"GO:0015825","count":1},{"id":"GO:1902237","count":1},{"id":"GO:0006658","count":1},{"id":"GO:0042552","count":1}]},{"hash":"1345392071091099694","title":"Unknown","description":"The top GO terms span very different biological contexts (mitochondrial translation; proteolysis; plasmid maintenance/recombination; transcription antitermination; plant hormone signaling; steroid receptor assembly; protein folding/ubiquitination). With no edges or coherent functional theme, the proteins do not cluster around a single shared function, so the label Unknown is most appropriate.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0042150","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0006276","count":2}]},{"hash":"2030947652434958514","title":"Transcription Regulation and RNA Processing","description":"Core GO terms point to transcription control (DNA-templated transcription; regulation of transcription elongation by RNA Pol II/I), mRNA capping and rRNA processing, and chromatin-related processes (heterochromatin formation, chromosome segregation). Together these suggest a cohesive theme of transcription regulation intertwined with RNA maturation and chromatin state.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0008298","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0090262","count":1},{"id":"GO:0007059","count":1}]},{"hash":"1167289127594393019","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":15,"triangles":9,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3}]},{"hash":"1608951252056534805","title":"Nuclear Gene Expression & Telomere Regulation","description":"This cluster is driven by GO terms for transcription, translation, and mRNA processing (DNA-templated transcription, translation, and mRNA processing), indicating a core nuclear gene expression program. The presence of telomere maintenance and telomere capping regulation terms suggests a link to chromosome end maintenance. A neural development term and a differentiation term appear less prominently, likely as pleiotropic annotations, but do not define the main theme.","confidence":"Medium","size":10,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0032212","count":2}]},{"hash":"590377803964337924","title":"Apoptosis and JNK Pathway Regulators","description":"The dominant GO terms are apoptotic process and its regulation, plus regulation of the JNK cascade, pointing to involvement in stress-induced cell death pathways. While a few other terms (actin ubiquitination, IL-17 signaling, bud neck localization, blastocyst formation) appear, they are sparse and likely reflect multi-function annotations or noise. Overall, the cluster seems best described as regulators of apoptosis and JNK-mediated stress signaling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042981","count":1},{"id":"GO:0051092","count":1},{"id":"GO:0046328","count":1}]},{"hash":"765634346465929750","title":"Embryonic development and cell-cycle processes","description":"The top GO terms point to developmental programs (heart development, embryonic cranial skeleton morphogenesis) alongside core cellular activities such as DNA replication and apoptotic processes, suggesting a cluster tied to embryonic development with regulation of cell proliferation and cell death. Some endosome transport term appears, but the dominant theme seems development-related with cell-cycle implications.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0048701","count":2},{"id":"GO:2000641","count":2}]},{"hash":"1373929871095149404","title":"Ribosome and Translation Machinery","description":"The top GO terms are dominated by translation- and ribosome-related processes: cytoplasmic and mitochondrial translation, translation in general, ribosomal subunit assembly, translational termination, and ribosome biogenesis, with supporting rRNA processing. A couple of outliers (DNA metabolism and interleukin-4 response) likely reflect multifunctional proteins or annotation noise, but the central theme points to ribosome/protein synthesis machinery.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0000027","count":3},{"id":"GO:0032543","count":1},{"id":"GO:0006415","count":1},{"id":"GO:0090305","count":1}]},{"hash":"1607301222545184114","title":"Bacterial cell envelope biosynthesis and membrane transport","description":"This cluster centers on biosynthetic processes for cell surface components, notably lipopolysaccharide and extracellular polysaccharides, suggesting involvement in envelope assembly. The inclusion of related metabolic (glutamine, cobalamin) and transport-related terms (membrane insertion, vesicle transport) points to proteins functioning in membrane-associated biosynthesis and trafficking, with an additional stress response signal (arsenic). Some terms appear eukaryote-focused (ER/Golgi transport), which may reflect annotation noise, but the core theme appears to be bacterial envelope biosynthesis and related transport. Confidence: Medium","confidence":"","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0045226","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009236","count":1}]},{"hash":"809977325511441179","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000447","count":3},{"id":"GO:0051013","count":3}]},{"hash":"281892973863257602","title":"Plant Developmental Transcription and Chromatin Regulators","description":"The cluster centers on transcriptional control and chromatin-related processes (DNA-templated transcription, ncRNA-mediated silencing, histone exchange, heterochromatin formation) with links to developmental timing and tissue specification (vegetative-to-reproductive transition, segment specification, stomatal development), plus environmental responsiveness (CO2). This combination suggests regulators of plant development via transcriptional and chromatin mechanisms, with some context-dependent signaling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071244","count":2},{"id":"GO:2000122","count":2},{"id":"GO:0015976","count":2},{"id":"GO:2000096","count":1}]},{"hash":"840322851825593935","title":"RNA splicing and translation initiation regulation","description":"This cluster is dominated by GO terms related to RNA processing and splicing (spliceosome activity, splice site recognition, preinitiation complex formation, small-subunit processome assembly) and to initiation of translation (regulation of translational initiation, translation preinitiation complex). These themes point to a cohesive role in RNA maturation and ribosome assembly/translation control, with a few terms (e.g., blastocyst formation) likely unrelated noise. Overall, the label captures the main functional signals of the cluster.","confidence":"High","size":10,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0060211","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1217906681676404389","title":"Mitochondrial Metabolism and Transport","description":"The terms cluster around mitochondria, with transport of NAD, iron, manganese, and thiamine pyrophosphate, plus apoptotic mitochondrial changes and metabolic signaling (fatty acid response, insulin/IGF stimuli), suggesting a mitochondria-centered metabolism and metabolite transport program.","confidence":"High","size":10,"edges":17,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":7},{"id":"GO:1990519","count":7},{"id":"GO:0070542","count":7},{"id":"GO:0061179","count":7},{"id":"GO:1990314","count":7}]},{"hash":"1050832496591861630","title":"Plant secondary metabolism and hormone biosynthesis","description":"The GO terms are dominated by plant-specific secondary metabolism (alkaloid/antibiotic biosynthesis), plus hormone-related pathways (strigolactone biosynthesis) and development (secondary shoot formation), with supporting catabolic processes; together these point to a cluster of proteins involved in plant metabolism and growth regulation.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":2},{"id":"GO:0009820","count":1},{"id":"GO:0010223","count":1},{"id":"GO:0006660","count":1},{"id":"GO:0015996","count":1}]},{"hash":"1217485384908324634","title":"Membrane Growth and Signaling","description":"This cluster centers on membrane-associated processes and growth, indicated by proton transport, vacuolar acidification, lipid metabolism, and cell growth regulation, along with membrane-targeting localization and cell edge dynamics. The GO terms point to membrane biosynthesis and signaling roles that coordinate cellular expansion and intercellular communication, suggesting a cohesive membrane-growth module despite diverse individual terms.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000032","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0046485","count":1}]},{"hash":"21488902732980287","title":"Endomembrane trafficking and actin remodeling","description":"The terms center on vesicle trafficking within the endomembrane system (pinocytosis, endosomal fusion, Golgi-lysosome transport), ER tubular network formation, and filopodium assembly, coupled with PI5P metabolism and Rho signaling that drive actin dynamics. The presence of endosome-associated TLR3 signaling also aligns with membrane trafficking and immune sensing. This combination suggests a cohesive theme of membrane trafficking linked to cytoskeletal remodeling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":2},{"id":"GO:0007183","count":1},{"id":"GO:0010256","count":1},{"id":"GO:1904562","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1245475623521362501","title":"T cell signaling and developmental growth pathways","description":"The top terms include immune signaling (activated T cell proliferation, T cell receptor signaling) along with growth and developmental pathways (Wnt signaling, PDGF receptor signaling, mesoderm formation, neuron development). This suggests a cluster of proteins involved in both T cell\u2013mediated signaling and broader developmental/growth signaling, justifying a label centered on immune signaling with developmental context.","confidence":"Medium","size":9,"edges":12,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050798","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0010863","count":2},{"id":"GO:0048666","count":2},{"id":"GO:0090263","count":2}]},{"hash":"875329850761853679","title":"Diverse Metabolism and Xenobiotic Response","description":"This cluster includes GO terms for antibiotic biosynthesis, quinone biosynthesis (menaquinone and phylloquinone), glycolysis, fatty acid beta-oxidation, amino acid catabolism (valine), oxaloacetate metabolism, and purine biosynthesis, plus a response to xenobiotics. The combination suggests broad metabolic versatility spanning central and secondary metabolism with an ability to respond to xenobiotic stress, rather than a single, cohesive pathway.","confidence":"Medium","size":9,"edges":23,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0006574","count":2}]},{"hash":"721303412826244657","title":"Developmental growth signaling","description":"The cluster shows contributions from developmental processes (axonogenesis, osteoblast differentiation) and cell proliferation (DNA replication, mitotic cell cycle), plus growth-related signaling (PI3K/AKT). Although some terms are metabolic or regulatory, the dominant theme links growth, development, and signaling across tissues, justifying a broad label rather than a specific pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007118","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006695","count":4},{"id":"GO:0007409","count":4}]},{"hash":"233847226113646178","title":"Neuronal synaptic function and protein homeostasis","description":"The top GO terms point to neuronal development and synaptic vesicle cycling (substantia nigra development; regulation of synaptic vesicle endocytosis/exocytosis; excitatory postsynaptic potential) alongside protein turnover processes (protein ubiquitination; microautophagy). Together these suggest a cluster of proteins involved in synaptic transmission and maintaining protein balance at the synapse, even though a few terms touch on other biological processes. Confidence: Medium.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":2},{"id":"GO:1900242","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0035690","count":2},{"id":"GO:2000300","count":2}]},{"hash":"1280557292947500974","title":"Ribosome Biogenesis and Translation Machinery","description":"The top GO terms cluster around ribosome biogenesis and translation (biogenesis, initiation, elongation, cytoplasmic translation), plus subunit export, tRNA modification, and even selenocysteine incorporation, indicating proteins involved in ribosome assembly and overall protein synthesis. Some antibiotic response term appears, but the core theme is ribosome-related processes.","confidence":"High","size":9,"edges":28,"triangles":39,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0000055","count":3}]},{"hash":"1542814951953902829","title":"Integrin-Mediated Adhesion and Immune Signaling","description":"The top GO terms cluster around regulation of integrin-mediated cell adhesion (both positive and general), neutrophil extravasation, TNF response, and complement regulation, with ubiquitination as a common regulatory mechanism. This points to a cohesive theme of immune cell adhesion and inflammatory signaling, with a possible outlier term (myelination in PNS) likely representing noise.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0070245","count":1},{"id":"GO:0033631","count":1},{"id":"GO:0032331","count":1},{"id":"GO:1902203","count":1}]},{"hash":"548137140170793898","title":"P53-mediated intrinsic apoptosis and stress response","description":"This cluster shows strong enrichment for apoptotic signaling and p53-mediated intrinsic pathways (GO:0006915, GO:0072332), with supporting signals from transcriptional regulation and RNA decay that align with stress-induced p53 activity. Oxidative/stress-related terms and calcium signaling further support a theme of apoptosis driven by cellular stress and transcriptional control.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006154","count":1},{"id":"GO:2000757","count":1},{"id":"GO:0036245","count":1}]},{"hash":"1649406661453452521","title":"Regulation of translation initiation","description":"Most frequent terms point to regulation and initiation of translation, including preinitiation complex formation and reinitiation, with some virus-specific IRES-related translation initiation terms. A few RNA processing terms appear but are subsidiary. Thus, the cluster most plausibly represents proteins involved in controlling translation initiation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006446","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0075525","count":4},{"id":"GO:0075522","count":4}]},{"hash":"1261766860216522274","title":"Steroid hormone biosynthesis and lipid metabolism","description":"The top GO terms cluster around steroid hormone production and metabolism (testosterone biosynthetic process, androgen metabolic process, estrogen biosynthetic process, C21-steroid hormone metabolic process) with supporting lipid biosynthesis terms (fatty acid elongation, 3-keto-sphinganine metabolic process). This pattern suggests the proteins collaborate in steroid hormone biosynthesis and broader lipid metabolism, with a few unrelated terms likely due to annotation noise. ","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0061370","count":3},{"id":"GO:0045150","count":3},{"id":"GO:0030497","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0008209","count":3}]},{"hash":"1301647224152988665","title":"Developmental signaling and vesicle trafficking","description":"This cluster shows multiple development-related terms across tissues (skeletal, brain, heart) alongside signaling (Rho/GTPase regulation) and vesicle transport (ER-Golgi), suggesting proteins that coordinate developmental programs with intracellular signaling and trafficking rather than a single specialized function.","confidence":"Medium","size":9,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":4},{"id":"GO:0070208","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0010255","count":3}]},{"hash":"1225627522799717074","title":"Embryonic vertebrate cardiovascular and neural development","description":"The terms cluster around early organogenesis, especially heart tube formation, arterial/endothelial differentiation, and morphogenesis of the aorta, along with neural development such as spinal motor neuron specification and cranial nerve formation, suggesting a developmental program governing cardiovascular and nervous system formation. Some outliers (oleic acid response, humoral immune response) are present but do not dominate the theme.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071400","count":2},{"id":"GO:0042981","count":1},{"id":"GO:0060842","count":1},{"id":"GO:0045668","count":1},{"id":"GO:0021558","count":1}]},{"hash":"2121116156184583914","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000389","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0000350","count":1},{"id":"GO:0000398","count":1},{"id":"GO:1901766","count":1}]},{"hash":"281093313486585871","title":"Wnt-Hippo Signaling in Keratinocyte Differentiation","description":"Top GO terms reveal coordinated signaling (positive regulation of canonical Wnt pathway; hippo signaling) and keratinocyte differentiation, along with processes of cell morphogenesis, apoptosis, DNA replication, and protein turnover. This pattern suggests a module that balances proliferation and differentiation in epidermal cells, integrating Wnt/Hippo cues with ubiquitin-mediated proteolysis and GTPase-driven cytoskeletal dynamics.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0060044","count":3},{"id":"GO:0035329","count":3},{"id":"GO:0006915","count":3}]},{"hash":"1916764435938631586","title":"Neural development and dopaminergic signaling","description":"The top GO terms are dominated by brain development, neuronal maturation, and neuronal migration, including tangential migration to the olfactory bulb and regulation of dopamine receptor signaling, suggesting a cluster centered on neural development and dopaminergic signaling. Some terms refer to general cellular processes or obsolete annotations, but the neural-development theme is prominent enough to warrant this label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903125","count":2},{"id":"GO:1902499","count":2},{"id":"GO:0007420","count":2},{"id":"GO:1903215","count":2},{"id":"GO:1905279","count":2}]},{"hash":"409189725720201299","title":"Mitotic Cell Cycle and Cytoskeleton-ER Trafficking","description":"The cluster centers on cell division and mitotic processes (mitotic cell cycle, cell division) and includes strong signals of cytoskeletal remodeling (ruffle assembly, stress fiber assembly) and mechanical response. It also features vesicle trafficking components (ER to Golgi transport, COPII coating regulation), suggesting coordinated membrane trafficking during division and morphogenesis. Together, these terms point to a functional theme of cell cycle with accompanying cytoskeletal dynamics and ER-Golgi trafficking.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071260","count":2},{"id":"GO:1903215","count":2}]},{"hash":"1548069352571100885","title":"ER\u2013Golgi trafficking and Golgi localization","description":"This cluster is dominated by GO terms related to localization to the Golgi apparatus and ER-to-Golgi transport, including protein-containing complex localization and apical protein localization, plus an ER stress response and small GTPase\u2013mediated signaling, all pointing to vesicle trafficking within the secretory pathway. Some neural development and copper homeostasis terms are present but do not redefine the core trafficking theme.","confidence":"Medium","size":8,"edges":15,"triangles":10,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000042","count":7},{"id":"GO:0034629","count":7},{"id":"GO:0021830","count":7},{"id":"GO:0045176","count":7},{"id":"GO:0034976","count":7}]},{"hash":"279430118782216950","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning animal development (superior colliculus development, hair follicle placode formation, desmosome assembly, renal vesicle formation), plant cell biology (plant-type primary cell wall biogenesis), cellular processes (vacuole fusion, desmosome assembly), and other diverse contexts (host response to symbiont, response to indole-3-methanol). There is no clear, shared function tying the proteins together, so a singular, coherent label cannot be confidently assigned.","confidence":"","size":8,"edges":20,"triangles":22,"max_degree":7,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0080034","count":5},{"id":"GO:0072033","count":5},{"id":"GO:0071681","count":5},{"id":"GO:0060769","count":5},{"id":"GO:0061380","count":5}]},{"hash":"829098888317764228","title":"Developmental Transcription and Cell Cycle Regulation","description":"This cluster is dominated by GO terms for DNA-templated transcription and mitotic processes (DNA-templated transcription, mitotic cell cycle, mitotic sister chromatid segregation), with additional developmental (skeletal system development, neural tube closure) and stress/defense responses (ER-stress\u2013induced apoptosis, cadmium response, defense against Gram-positive bacteria). Together these imply a module of genes coordinating transcriptional regulation and cell division during development while also engaging stress-response pathways. Confidence: Medium.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0001501","count":5},{"id":"GO:0070059","count":4},{"id":"GO:0001403","count":4}]},{"hash":"1105597957178628615","title":"Ribosome Biogenesis and Translation Initiation","description":"GO terms are dominated by ribosome biogenesis, rRNA processing, and 90S preribosome assembly, plus formation of the translation preinitiation complex, pointing to proteins involved in ribosome production and initiation of translation; a few secondary terms are present but less representative.","confidence":"High","size":8,"edges":4,"triangles":1,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0001172","count":3},{"id":"GO:0000463","count":3},{"id":"GO:1905098","count":2},{"id":"GO:0001731","count":2}]},{"hash":"2221642452666513524","title":"Proton Motive Force-Driven Transport","description":"Top GO terms cluster around proton transmembrane transport, proton motive force\u2013driven ATP synthesis, vacuolar acidification, and sodium ion transport, suggesting a shared role in managing membrane potential and ion homeostasis. The presence of a mitochondrial targeting term supports mitochondrial localization for many proteins, while a few terms (angiogenesis, osteoblast differentiation) may reflect broader or less specific annotations. Overall, this cluster appears to reflect membrane energetics and ion transport governed by proton gradients.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0006814","count":2}]},{"hash":"664202704775054900","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0006295","count":1},{"id":"GO:0000734","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0035753","count":1}]},{"hash":"2154086824144991294","title":"Fungal sphingolipid and ergosterol biosynthesis","description":"The cluster\u2019s GO terms center on lipid metabolism, notably sphingolipid biosynthesis (sphingosine, MIPC) and regulation of ergosterol biosynthesis, which are key components of fungal membrane lipid production. A few terms appear obsolete or peripheral, but the core signal points to fungal lipid/sterol biosynthesis pathways.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006627","count":1},{"id":"GO:0000746","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0070542","count":1},{"id":"GO:0006675","count":1}]},{"hash":"1760639370342355933","title":"Terpenoid/isoprenoid Biosynthesis","description":"Top GO terms point to multiple steps in terpenoid/isoprenoid production, including geranyl/farnesyl/geranylgeranyl diphosphate and monoterpene biosynthesis, as well as cholesterol biosynthesis. This suggests the cluster comprises proteins involved in lipid isoprenoid biosynthesis; a couple of terms (peptidyl-tyrosine dephosphorylation, protein heterotetramerization) are less directly related but do not override the main theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0035335","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0009102","count":2}]},{"hash":"2188583789039969486","title":"DNA replication and repair proteins","description":"This cluster is driven by core GO terms for DNA repair (GO:0006281) and DNA replication (GO:0006260), suggesting a group of proteins involved in genome maintenance and DNA synthesis. A few other terms (developmental differentiation, signaling) appear but are less representative and may reflect multifunctional annotations or noise. Overall, the dominant theme is genome integrity maintenance.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":4},{"id":"GO:0006260","count":3},{"id":"GO:2000657","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0045667","count":2}]},{"hash":"609498970957489273","title":"Proteostasis and cell cycle regulation","description":"This cluster centers on protein homeostasis and cell-cycle control, with terms for regulating the cell cycle, negative regulation of proteasomal degradation, and chaperone-mediated assembly, plus energy/cytoskeleton\u2013related processes that support protein quality control and trafficking.","confidence":"Medium","size":7,"edges":7,"triangles":3,"max_degree":4,"top_function":"protein folding","top_go_terms":[{"id":"GO:0071157","count":4},{"id":"GO:0032435","count":3},{"id":"GO:1901856","count":3},{"id":"GO:0051131","count":3},{"id":"GO:0071318","count":3}]},{"hash":"85872394102747379","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":8,"triangles":2,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0006265","count":2},{"id":"GO:0042273","count":2}]},{"hash":"121597978720136453","title":"Lipid metabolism and small-molecule catabolism","description":"This cluster is characterized by multiple GO terms tied to the breakdown and processing of lipids and related small molecules (lipid hydroperoxide transport, cholesterol metabolism, ketone body and polyhydroxybutyrate biosynthesis) as well as some amino-acid and aromatic compound catabolic processes. While there is one term about protein homooligomerization (a structural feature) and a hormone-response term, the dominant pattern points to lipid and small-molecule metabolic pathways, suggesting a function centered on lipid metabolism and catabolic activities.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0009725","count":4},{"id":"GO:1901373","count":4},{"id":"GO:0014070","count":4},{"id":"GO:0006550","count":4}]},{"hash":"1030343049532953887","title":"Skeletal muscle development and sarcomere assembly","description":"The cluster shows strong signals for skeletal muscle fiber development, skeletal muscle fiber adaptation, and skeletal muscle thin filament assembly, suggesting a core role in muscle development and sarcomere organization. Other terms like regulation of endocytosis and cell polarity are present but less defining, so the dominant muscle-related terms guide the label. ","confidence":"Medium","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0021762","count":6},{"id":"GO:0048741","count":6},{"id":"GO:0030100","count":3},{"id":"GO:0000281","count":3},{"id":"GO:0070527","count":3}]},{"hash":"1367256465729043309","title":"Developmental Signaling and Morphogenesis","description":"The terms cluster around signaling pathway regulation (NFAT, Hippo), developmental processes (ectoderm formation, neuron differentiation, morphogenesis of kidney structures), and cytoskeletal remodeling (actin depolymerization), suggesting a broad theme of signaling-driven development and morphogenesis rather than a single, narrow function.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0090334","count":2},{"id":"GO:0070886","count":2},{"id":"GO:0001705","count":2},{"id":"GO:0030042","count":2}]},{"hash":"1891950442890339363","title":"P53-linked Translation and Ubiquitin Regulation","description":"Proteins in this cluster converge on translation (GO:0006412) and regulation of ubiquitin-dependent proteolysis, alongside cell cycle control and p53 pathway signals (GO:0071158/7, GO:1901798). The inclusion of stress-response to actinomycin D and protein stabilization terms suggests a role at the intersection of ribosome function, cell-cycle regulation, and ubiquitin-mediated proteostasis, consistent with a p53-connected translation-ubiquitin regulatory axis.","confidence":"High","size":7,"edges":11,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:2000059","count":2},{"id":"GO:0072717","count":2},{"id":"GO:0071158","count":2},{"id":"GO:0032986","count":2}]},{"hash":"666490596042706239","title":"Chaperone-assisted organelle assembly and stress response","description":"This cluster's top GO terms center on protein complex assembly and quality control across organelles and cytoskeleton: chaperone-mediated protein complex assembly, mitochondrial respiratory chain complex III assembly, centriole elongation, and cilium movement. The presence of stress granule disassembly also points to cellular protein homeostasis under stress. A few terms like DNA replication appear less connected or are legacy annotations, but the dominant theme ties to assembly of multi-protein complexes and organelle/cytoskeletal structures guided by chaperones. Therefore, the label reflects a coherent functional theme rather than a single pathway.","confidence":"Medium","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0090261","count":2},{"id":"GO:0051131","count":2},{"id":"GO:1903724","count":2},{"id":"GO:0000733","count":2}]},{"hash":"1204360930749404739","title":"Mitochondrial translation and tRNA charging","description":"The cluster\u2019s top terms cluster around protein synthesis: translation and mitochondrial tRNA aminoacylation (for tryptophan, tyrosine, and valine), pointing to a common theme of mitochondrial protein synthesis. While there are also notes on ER-Golgi transport and morphogenesis, these appear peripheral to the core translation-related signals. This suggests a translation-centric function for the cluster, with some multifunctional annotations.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0001525","count":1},{"id":"GO:0070183","count":1},{"id":"GO:0001570","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1828709932878290249","title":"Mitochondrial Translation and tRNA Charging","description":"The dominant GO terms are about mitochondrial protein synthesis, with multiple entries for mitochondrial tRNA aminoacylation (asparaginyl-, lysyl-, and aspartyl-) and translation overall, indicating a cluster of proteins involved in mitochondrial translation machinery. A few unrelated terms (NK cell activation regulation, wing cell fate specification, ER-to-cytosol protein transport proteolysis, spermatid differentiation) may reflect noise or broader roles, but the core theme is mitochondrial translation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072581","count":1},{"id":"GO:0070145","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0070154","count":1},{"id":"GO:0071915","count":1}]},{"hash":"1625069116208755970","title":"Yeast Ras/cAMP signaling and transcription","description":"This cluster is dominated by terms tied to yeast-specific signaling and transcription regulation (negative regulation of Ras signal transduction, positive regulation of adenylate cyclase activity, carbon catabolite repression of transcription, DNA-templated transcription, and protein localization to bud neck). Together these point to Ras/cAMP signaling and transcription control in yeast. A couple entries like sensory perception of smell and response to clozapine appear incidental or cross-species annotations but do not define the overall theme. The label Yeast Ras/cAMP signaling and transcription captures the central function.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007608","count":1},{"id":"GO:0034638","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0045762","count":1},{"id":"GO:0046827","count":1}]},{"hash":"880337229664792263","title":"Spindle Assembly and Cytokinesis","description":"The GO terms are dominated by microtubule dynamics and spindle-related processes (mitotic spindle assembly, establishment of meiotic spindle orientation, plus- and minus-end microtubule activities) and cytokinesis (actomyosin ring assembly, cell plate formation). A couple of terms related to neuron projection maintenance and stress granule disassembly appear, but they do not override the central emphasis on spindle assembly and microtubule-driven cell division.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0010938","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0000915","count":2},{"id":"GO:1990535","count":2}]},{"hash":"837515724728304017","title":"Growth and Differentiation Signaling","description":"This cluster centers on multiple developmental and growth-related signaling pathways (Wnt, Hippo, PI3K/Akt, insulin and growth hormone signaling) and differentiation processes (keratinocytes, osteoblasts), plus apoptosis regulation, indicating a cohesive theme of growth, proliferation control, and cell fate decisions across tissues.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":5},{"id":"GO:0035329","count":5},{"id":"GO:0060044","count":5},{"id":"GO:0030216","count":5},{"id":"GO:0006915","count":5}]},{"hash":"155086153457494938","title":"Mitochondrial DNA replication and lipid metabolism","description":"The cluster is dominated by mitochondrial-related terms: positive regulation of mitochondrial DNA replication, stress-induced mitochondrial fusion, and mitochondrial inheritance, plus cardiolipin metabolism and the SREBP signaling pathway, all pointing to mitochondrial genome maintenance and lipid homeostasis. A few terms (cell adhesion and IL-2 production) seem incidental, so the core theme is mitochondria-driven genome dynamics and membrane lipid regulation.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000049","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0060355","count":2},{"id":"GO:0090297","count":2},{"id":"GO:0032623","count":2}]},{"hash":"779658237366507363","title":"Unknown","description":"The cluster's terms span viral life cycle steps (entry, virion assembly, ESCRT-mediated budding), host-symbiont interactions, and unrelated cellular processes (mRNA splicing, nuclear body organization, Leydig cell differentiation, steroid biosynthesis regulation). The mix lacks a single cohesive function or pathway, so a specific label cannot be assigned with confidence.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0030260","count":1},{"id":"GO:0030238","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0030575","count":1}]},{"hash":"1476157664609411018","title":"Ubiquitin-Dependent DNA Damage Response","description":"Proteins in this cluster are dominated by ubiquitination-related processes (autoubiquitination, polyubiquitination, ERAD) and DNA damage response pathways (NHEJ, postreplication repair, G1 checkpoint). The presence of JNK and NF-kappaB signaling terms alongside telomere maintenance and chromatin-related repair suggests a module where ubiquitin signaling interfaces with genome stability and stress-response pathways. This makes a cohesive label: ubiquitin-mediated genome stability and damage signaling.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:1902916","count":5},{"id":"GO:0042275","count":5},{"id":"GO:0031571","count":5}]},{"hash":"336262675760519750","title":"Embryonic organogenesis and retinoic acid signaling","description":"These proteins are enriched for developmental processes across multiple organs (ureter, midgut, pancreas, olfactory pit, Harderian gland) and pattern formation, with retinoic acid biosynthesis highlighted by GO:0042904. The combination suggests a theme of embryonic organ development and RA-mediated morphogenesis rather than a single tissue-specific function.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035799","count":4},{"id":"GO:0060166","count":4},{"id":"GO:0001936","count":4},{"id":"GO:0006069","count":4},{"id":"GO:0007494","count":4}]},{"hash":"1705579142267998176","title":"Cell Cycle Progression and Mitotic Control","description":"This cluster is best characterized by terms tied to cell-cycle progression and mitosis: G1/S transition of the mitotic cell cycle, G0 to G1 transition regulation, mitotic spindle assembly, and overall cell division. DNA-templated transcription and transcription-related terms suggest coordinated gene expression with cell-cycle events, while peptidyl-serine dephosphorylation and actin filament depolymerization point to regulatory signaling and cytoskeletal changes during division. ER-to-Golgi vesicle transport hints at broader growth-related processes accompanying the cycle, with hypoxia response and tRNA-linked regulation appearing as secondary associations. ","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2}]},{"hash":"661064037197746836","title":"Mitochondrial carrier proteins and metabolism","description":"The GO terms point to transport of cofactors and ions across the mitochondrial membrane (NAD, thiamine pyrophosphate, iron, manganese), a hallmark of mitochondrial carrier proteins (e.g., SLC25 family). The inclusion of apoptosis-related mitochondrial changes and metabolic signaling (fatty acid response, insulin/IGF stimuli, liver regeneration) suggests a cohesive role in mitochondrial transport linked to metabolic regulation, supporting this label as representative. ","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":3},{"id":"GO:0097421","count":2},{"id":"GO:1990519","count":2},{"id":"GO:0070542","count":2},{"id":"GO:0061179","count":2}]},{"hash":"2002681154968556912","title":"Nucleolar ribosome biogenesis and rRNA transcription","description":"Based on the top GO terms, the proteins are enriched for ribosome biogenesis, SSU rRNA maturation, translation, and nucleolar transcription by RNA polymerases I and III, along with nucleologenesis. This points to a cohesive nucleolar program coordinating ribosome assembly with nucleolar transcription, with a minor hint of ncRNA-mediated chromatin regulation.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0000028","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006468","count":1}]},{"hash":"472057315884113196","title":"Translation machinery and RNA processing","description":"The top GO terms are dominated by translation-related processes (general translation, translation initiation, mitochondrial translation, cytoplasmic translation regulation, translational elongation) and RNA processing (spliceosomal tri-snRNP complex assembly, selenocysteine incorporation), suggesting a cluster centered on the ribosome/translation apparatus and RNA metabolism, with a minor influence from chromatin regulation terms and signaling responses. ","confidence":"High","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006413","count":3},{"id":"GO:1902802","count":2},{"id":"GO:0032543","count":2}]},{"hash":"12209372365220365","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0042273","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0000393","count":1},{"id":"GO:1904570","count":1}]},{"hash":"1331703308739805660","title":"RNA processing and transcriptional regulation","description":"The cluster's top GO terms are dominated by RNA-related processes: rRNA methylation/modification, 7-methylguanosine mRNA capping, and negative regulation of transcription by RNA polymerase II, indicating involvement in RNA maturation and transcription control, with other terms likely reflecting broader metabolic or stress responses.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0046690","count":3},{"id":"GO:0031167","count":3}]},{"hash":"286929154888961238","title":"Unknown","description":"The top GO terms cover a mix of mitotic cell cycle, cell division, photosynthesis, snoRNP assembly, and various chromatin/protein quality-control processes, with several entries labeled obsolete. There is no clear, single functional theme linking these terms, and the cluster has no internal edges, making it difficult to assign a cohesive biological role. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0000492","count":2},{"id":"GO:0039544","count":1}]},{"hash":"1605639605209853486","title":"Neuronal spine morphogenesis and Rac signaling","description":"The terms cluster around dendritic spine development and actin-driven remodeling in neurons, with Rac-mediated signaling, lamellipodium/ruffle assembly, and hippocampus development indicating synaptic maturation and cytoskeletal dynamics. Golgi-to-plasma membrane transport may support membrane trafficking needed for spine formation. This combination supports a cohesive role in Rac-dependent dendritic spine morphogenesis.","confidence":"High","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":5},{"id":"GO:0060999","count":5},{"id":"GO:0061001","count":5},{"id":"GO:0016601","count":4},{"id":"GO:0010592","count":4}]},{"hash":"1468956722316463920","title":"Unknown","description":"GO terms in this cluster are scattered across diverse metabolic and organismal processes (lipid, alkaloid, glucuronoside, phosphatidylserine catabolism; neuromuscular and musculoskeletal movement) plus plant-specific terms like secondary shoot formation and an odd buoyancy regulation, yielding no single cohesive function for all proteins.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031413","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0019216","count":1},{"id":"GO:0050905","count":1},{"id":"GO:0050881","count":1}]},{"hash":"1776468446373984436","title":"Neuronal endocytosis and dendrite dynamics","description":"This cluster highlights membrane trafficking and signaling in neurons: clathrin-dependent endocytosis, endocytic recycling, and transport between endosomes and the Golgi, along with Rho-regulated cytoskeleton dynamics and dendrite extension. The presence of GABAergic synaptic transmission supports a neuronal vesicle trafficking theme. Some terms like mitochondrial inheritance, apoptosis, and ribosomal export may reflect general cellular housekeeping shared across cell types and not the core driver of the cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0072583","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0034498","count":2}]},{"hash":"1397677512154221328","title":"Fatty acid and vitamin biosynthesis","description":"These proteins show strong representation of fatty acid biosynthesis and related lipid metabolism (including beta-oxidation and long-chain fatty acid synthesis) and of quinone biosynthesis (menaquinone and phylloquinone), pointing to lipid and vitamin biosynthetic roles. Additional terms cover catabolism of amino acids like valine and aromatic compounds (phenylacetate), and even antibiotic biosynthesis, suggesting broader small-molecule metabolism. The common thread is metabolism centered on lipid and cofactor (vitamin) biosynthesis, with related catabolic processes.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0010124","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0006574","count":2},{"id":"GO:0006635","count":2}]},{"hash":"886793359389016405","title":"RNA processing and nuclear transport","description":"This cluster is dominated by RNA-related and nuclear processes: P-body assembly, spliceosomal complex assembly, maturation of SSU-rRNA, tRNA processing, histone mRNA metabolism, and import into nucleus, plus transcription termination by RNA polymerase II. These point to a coherent theme of RNA maturation and nuclear transport/processing, with some secondary terms (stress response, chromatin organization) that may reflect broader regulatory links. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":4},{"id":"GO:0000245","count":4},{"id":"GO:0030490","count":4},{"id":"GO:0009414","count":4},{"id":"GO:0006369","count":4}]},{"hash":"574926367808582396","title":"PNS myelination and Schwann cell development","description":"The top GO terms emphasize neural development and peripheral nervous system myelination, including Schwann cell development and PNS myelination, with supporting neural patterning terms. Some immune regulation and cell division terms are present but appear ancillary to the main neural/theme, so the label reflects the core function of this cluster.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0021762","count":5},{"id":"GO:0050774","count":5},{"id":"GO:0022011","count":5},{"id":"GO:0051315","count":5},{"id":"GO:0001915","count":5}]},{"hash":"1922457164597113343","title":"Unknown","description":"The top GO terms cover a mix of nitrogen and amino acid metabolism, peptide/protein catabolism, and metal ion/homeostasis processes with no single cohesive function tying the cluster together, making a specific, representative label difficult.","confidence":"","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009442","count":1},{"id":"GO:0035609","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0043171","count":1},{"id":"GO:0006879","count":1}]},{"hash":"719250866160306450","title":"Auditory perception and receptor clustering","description":"The top GO terms include sensory perception of sound and vocalization behavior, pointing to neural processing in auditory pathways. Additional terms about receptor clustering and protein localization to cellular structures suggest synaptic organization and neuronal signaling. While some terms (e.g., NOD2 signaling, morphine response) are less directly linked, the strongest signal centers on neural/sensory signaling and receptor organization. Confidence: Medium.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032416","count":1},{"id":"GO:0071625","count":1},{"id":"GO:0071896","count":1},{"id":"GO:0070433","count":1},{"id":"GO:1904781","count":1}]},{"hash":"1209960235558066756","title":"Membrane trafficking and signaling regulation","description":"The proteins are tied to endomembrane system organization and trafficking (endomembrane system, ER-to-Golgi ceramide transport, clathrin-dependent endocytosis) and also connect to signaling and cytoskeletal processes (Rho signaling, filopodium assembly, GPCR desensitization), suggesting a shared role in surface receptor trafficking and downstream regulation.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010256","count":1},{"id":"GO:0007281","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0072583","count":1}]},{"hash":"1108746601648387211","title":"Bacterial transporters and SOS response","description":"This cluster is enriched for transporter and secretion-related GO terms (peptide pheromone export; glycine betaine, thiamine, taurine, molybdate, and doxorubicin transport; type I secretion), with a smaller subset pointing to DNA damage response (nucleotide-excision repair; SOS response). The dominant transport/secretion theme with a secondary repair signal suggests proteins involved in membrane transport and stress response, hence this label.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000770","count":3},{"id":"GO:0031460","count":3},{"id":"GO:1900753","count":3},{"id":"GO:0015888","count":3},{"id":"GO:0006289","count":3}]},{"hash":"1506101106924315869","title":"Proteostasis: nuclear and ER protein quality control","description":"This cluster centers on protein quality control and folding across compartments: nuclear ubiquitin-proteasome\u2013mediated quality control, regulation of nuclear export related to protein handling, ER protein folding, and associated stress responses (redox homeostasis, heat response). The common thread is maintenance of protein integrity and turnover (proteostasis) rather than a single linear pathway, supporting a concise label around nuclear/ER proteostasis mechanisms.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0071630","count":1},{"id":"GO:0046825","count":1},{"id":"GO:0006626","count":1}]},{"hash":"2164488928162843611","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0034475","count":2},{"id":"GO:0071042","count":2},{"id":"GO:0071035","count":2},{"id":"GO:0071051","count":2}]},{"hash":"131169076171930049","title":"Intracellular vesicle trafficking and antigen processing","description":"Most terms point to intracellular transport via vesicles: retrograde Golgi-ER, anterograde synaptic vesicle transport, and endosome-to-melanosome trafficking, plus antigen processing via MHC class Ib, which involves vesicular pathways. Although there are some cell-cycle and chromatin assembly terms that are less connected, the dominant theme is vesicle trafficking and related processing.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0099590","count":1},{"id":"GO:1900126","count":1},{"id":"GO:0048007","count":1},{"id":"GO:2001241","count":1}]},{"hash":"111688409205586222","title":"Mitochondrial Energy Metabolism and Protein Turnover","description":"This cluster is driven by terms related to energy production and mitochondrial function, notably proton transmembrane transport and aerobic respiration, suggesting mitochondrial respiration. Additional terms about protein catabolic processes and ubiquitin recycling imply ongoing protein turnover and quality control, which often accompany mitochondrial maintenance. The insulin receptor signaling term adds a metabolic regulation context, aligning with energy metabolism. Some terms appear unrelated (symbiont entry into host cell, obsolete mating pheromone maturation), likely reflecting annotation noise, but the dominant theme centers on mitochondrial energy production and protein turnover.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:1902600","count":4},{"id":"GO:0009060","count":3},{"id":"GO:0010815","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0071432","count":3}]},{"hash":"1617576783438326683","title":"Heterochromatin maintenance and chromatin remodeling","description":"The cluster\u2019s top GO terms consistently point to chromatin regulation: heterochromatin formation/maintenance (rDNA, silent mating-type cassette), regulation of nucleosome density, and peptidyl-lysine deacetylation (histone deacetylation). DNA-templated transcription also fits within chromatin state control, supporting a role in epigenetic regulation rather than metabolism or signaling. ","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045820","count":2},{"id":"GO:0006344","count":2},{"id":"GO:0034983","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060303","count":2}]},{"hash":"1631621814855924313","title":"DNA replication and viral genome replication","description":"The top GO terms are dominated by DNA replication and viral genome replication, suggesting the proteins cluster around genome replication activities. While there are some ancillary or obsolete terms (e.g., ribosomal biogenesis, telomere-related processes), the replication signals are strongest, supporting a label centered on replication functions.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1901582","count":1},{"id":"GO:0051092","count":1}]},{"hash":"1526438395980064215","title":"Epithelial polarity and actin dynamics","description":"This cluster centers on establishment and maintenance of epithelial cell polarity and concurrent remodeling of the actin cytoskeleton and cell adhesion. Dominant GO terms include epithelial polarity, cell shape regulation, actin filament polymerization, podosome assembly, and adhesion-dependent spreading, with supportive signaling inputs from small GTPases, EGFR, and Wnt pathways. A cohesive label that captures polarity establishment with actin-driven remodeling fits best, whereas the few outliers (e.g., engulfment of apoptotic cells) appear less central. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0030838","count":2},{"id":"GO:0071803","count":2}]},{"hash":"313088842127161719","title":"Fungal cell wall synthesis and mating","description":"This cluster\u2019s top terms include fungal-type beta-glucan biosynthetic process and karyogamy in conjugation, which strongly point to fungal cell-wall biosynthesis and reproductive/mating processes. Other terms are generic cellular processes (DNA replication, SRP targeting) and do not contradict this theme, but they dilute specificity. Overall, the label captures the most distinctive signals from the set, though it may not encompass all proteins in the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006880","count":1},{"id":"GO:0000902","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0000742","count":1}]},{"hash":"1219530900926056567","title":"DNA replication and repair","description":"The top GO terms cluster around DNA replication, nucleotide-excision repair, and SOS response, with additional links to cell-cycle regulation and centrosome dynamics, suggesting a core role in genome maintenance and replication control. A few development-related terms appear but are less represented, likely reflecting incidental annotations. Overall, the cluster seems best characterized by genome integrity and replication processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0010571","count":2},{"id":"GO:0007098","count":2}]},{"hash":"432907325281678193","title":"Translational Regulation and Cell Cycle Control","description":"The top terms center on translation, including general translation (GO:0006412) and regulation of translation initiation, plus mitochondrial translation termination, with additional terms tied to cell cycle regulation, p53 signaling, and ubiquitin-related proteolysis\u2014together suggesting a module that links protein synthesis control with cell cycle checkpoints and stress responses (e.g., actinomycin D). This points to a coherent function around coordinating translation and cell cycle in stress conditions.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:1901194","count":1},{"id":"GO:0070126","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0072717","count":1}]},{"hash":"1524289749351570688","title":"Unknown","description":"The GO terms are highly diverse, covering signaling, development, apoptosis/phagosome maturation, DNA repair, cytoskeleton organization, social/behavioral processes, heart morphogenesis, and metabolism, with no clear shared pathway or function. Edges are zero, offering no evidence of a cohesive interaction network. Because there is no single, interpretable theme tying these terms together, a specific functional label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051897","count":1},{"id":"GO:0007281","count":1},{"id":"GO:0043276","count":1},{"id":"GO:0006303","count":1},{"id":"GO:0031529","count":1}]},{"hash":"1647179743028190842","title":"Mitochondrial nutrient and metal transport","description":"This cluster is dominated by GO terms describing mitochondrial transport of nutrients and cofactors (pyrimidine nucleotide import, thiamine pyrophosphate transport, NAD transmembrane transport) and metal ions (iron, manganese) into mitochondria, along with mitochondrial apoptotic changes. The liver regeneration hint and fatty acid response reflect metabolic regulation linked to mitochondrial function in energy homeostasis. Taken together, these proteins likely act at the mitochondrion to import essential cofactors and metals, supporting metabolic activity and apoptosis-ready states.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":3},{"id":"GO:1990519","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0061179","count":3},{"id":"GO:1990314","count":3}]},{"hash":"1717367428502966028","title":"Unknown","description":"The GO terms span chromatin-related processes, sporulation, steroid/sterol biosynthesis, hair follicle development, and bacterial biosynthesis, with obsolete terms as well, showing no single coherent function linking all members.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010847","count":1},{"id":"GO:0043486","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0016126","count":1}]},{"hash":"2259009556474297080","title":"Unknown","description":"The Top Terms show a mix of mitochondrial function (complex IV assembly, cytochrome-c oxidase activity), post-translational modification (farnesylation), and various developmental terms, with no single coherent theme across the four proteins. Therefore, there is no clear functional cluster to label.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904960","count":1},{"id":"GO:0018343","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0007420","count":1}]},{"hash":"438401498362882323","title":"Ribosome biogenesis and translation","description":"These proteins are enriched for ribosome-related terms, notably ribosome biogenesis, ribosomal subunit export from the nucleus, and tRNA modification, pointing to roles in ribosome assembly and protein synthesis. The presence of cell cycle and division terms aligns with growth coordination, while iron transport and stress-response terms appear peripheral noise rather than core functions.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0015684","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000055","count":1}]},{"hash":"2125808149208202758","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0072321","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0021762","count":1},{"id":"GO:0015986","count":1}]},{"hash":"270959645420021455","title":"Unknown","description":"The terms are highly heterogeneous; only a couple relate to protein folding and autophagosome assembly, while others cover lipid, sugar, and specialized biosynthesis across diverse organisms, giving no clear shared function for the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000045","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0030097","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0019388","count":1}]},{"hash":"1801991215104206803","title":"RNA processing and translation initiation regulation","description":"Most terms point to RNA maturation and processing (mRNA splicing via spliceosome, splice-site recognition) and control of translation initiation (formation of the translation preinitiation complex, regulation of translational initiation, small-subunit processome assembly, and regulatory ncRNA-mediated gene silencing). Together they suggest proteins involved in RNA processing and the regulation of translation initiation, with a few peripheral or obsolete terms present. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0060211","count":1},{"id":"GO:1905663","count":1}]},{"hash":"2170974688276086214","title":"Chromatin regulation and transcription control","description":"The GO terms are dominated by DNA-templated transcription and chromatin-related processes (histone deacetylation, heterochromatin maintenance, telomere silencing, cohesin loading regulation). While there are a few muscle-related terms, the core signal is epigenetic regulation of transcription through chromatin state, justifying a label focused on chromatin-mediated transcription control.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0031939","count":2},{"id":"GO:0045820","count":2},{"id":"GO:0006344","count":2},{"id":"GO:0045668","count":2}]},{"hash":"1231879941275100436","title":"Nuclear RNA Processing and Ribosome Biogenesis","description":"Proteins here are enriched for RNA maturation and processing in the nucleus\u2014P-body and spliceosomal complex assembly, maturation of SSU-rRNA, tRNA processing, histone mRNA metabolism, and nuclear import\u2014collectively pointing to roles in RNA processing and ribosome biogenesis rather than other pathways. The presence of nuclear import together with RNA processing terms supports a nuclear RNA maturation theme.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0030490","count":3},{"id":"GO:0009414","count":3},{"id":"GO:0006369","count":3}]},{"hash":"468663595295644705","title":"Protein Complex Assembly and Disassembly","description":"The top GO terms cluster around assembly/disassembly of protein complexes and related structures, including SNARE complex disassembly, chaperone-mediated assembly, stress granule disassembly, and mitochondrial complex III assembly, as well as centriole elongation and inclusion body assembly. This suggests a theme of dynamic protein complex organization with links to cell-cycle processes such as cell division and DNA replication.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0035494","count":2},{"id":"GO:0006260","count":1},{"id":"GO:0090261","count":1},{"id":"GO:0051131","count":1}]},{"hash":"839898917636110553","title":"Unknown","description":"The top GO terms mix core cellular processes (translation, ribosome biogenesis, rRNA processing) with plant-specific cell wall and glycan biosynthesis terms, and with only three proteins there is no clear, coherent function bridging these terms. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0009834","count":1},{"id":"GO:0016266","count":1}]},{"hash":"38401722217919293","title":"Embryonic and Neural Organogenesis","description":"This cluster\u2019s GO terms are dominated by embryonic development across multiple tissues (eye/visual system, forebrain, cerebellum, heart, skeletal muscle, placenta, thyroid) and neural patterning (axon guidance, visual perception). The common theme is developmental processes in early life, especially neural development, suggesting the proteins act in embryogenesis and tissue morphogenesis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031290","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0030878","count":2}]},{"hash":"1617027842818416589","title":"Semaphorin-Rho Axon Guidance","description":"The terms point to semaphorin-plexin signaling and regulation of Rho GTPase activity, with both positive and negative regulation of axonogenesis, indicating a theme of axon guidance and cytoskeletal remodeling during neuronal development. Other terms about cellular mechanics and protein localization support a broader context but do not define the core function as strongly. Overall, the cluster appears to group proteins involved in semaphorin-driven signaling that modulates actin dynamics to steer axon growth.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:1901164","count":1},{"id":"GO:0071526","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0050771","count":1}]},{"hash":"1734701724721530492","title":"Musculoskeletal and nervous system development","description":"The GO terms point to differentiation and morphogenesis in muscle (myoblast differentiation), bone (osteoblast differentiation, cranial skeleton morphogenesis), and neural elements (neuron adhesion, axon fasciculation), with supporting growth signaling (PI3K/AKT). This suggests a coordinated developmental program spanning muscle, bone, and nerve tissues, rather than a single, narrow function. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000657","count":1},{"id":"GO:0051897","count":1},{"id":"GO:0045667","count":1},{"id":"GO:0007158","count":1},{"id":"GO:0071620","count":1}]},{"hash":"1316831799859814211","title":"Triglyceride and phospholipid catabolism and remodeling","description":"The top GO terms cluster around triglyceride catabolic processes, triglyceride mobilization, and phospholipid catabolic processes (phosphatidylcholine and phosphatidylethanolamine), indicating lipid breakdown and remodeling as the shared function. Some endocytic trafficking terms are present but lipid metabolism dominates the signal.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":1},{"id":"GO:0034638","count":1},{"id":"GO:2000480","count":1},{"id":"GO:0006642","count":1},{"id":"GO:0036153","count":1}]}]