[{"hash":"2261235603400044199","title":"Redox metabolism and mitochondrial energy production","description":"The dominant terms point to oxidation-reduction processes, redox homeostasis, and mitochondrial electron transport (NADH to ubiquinone), with supporting links to energy metabolism (lipoate metabolism) and related catabolic pathways (nitrate assimilation, camphor catabolic process). Although some terms reference developmental processes (sporulation, gastrulation) and apoptosis, the core signal across the cluster is redox biology coupled to energy metabolism, justifying a redox/energy-focused label.","confidence":"Medium","size":29,"edges":12,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042128","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0030435","count":3},{"id":"GO:0006915","count":3}]},{"hash":"1948645987235187127","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":55,"triangles":63,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0000463","count":2}]},{"hash":"763610777436691086","title":"Developmental gene expression and ribosome biogenesis","description":"The cluster includes core gene expression processes (mitotic cell cycle, DNA-templated transcription) and RNA processing (mRNA splicing, rRNA maturation), along with terms tied to ribosome biogenesis (5.8S, LSU/SSU maturation) and developmental processes (multicellular organism and skeletal system development). Additional terms on ER-Golgi transport and ERAD suggest linked protein processing/quality control during protein synthesis. Together these indicate a cohesive theme around gene expression, ribosome assembly, and development, despite some trafficking/export terms. ","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0000463","count":5}]},{"hash":"1393669711514733477","title":"Nuclear import and pore complex assembly","description":"The top GO terms cluster around import of proteins into the nucleus and nuclear pore-associated processes (NLS-bearing protein import into nucleus, nuclear pore complex assembly, ribosomal protein import into nucleus), with related regulatory steps like phosphorylation and desumoylation. A few terms (antibiotic response, lipopolysaccharide biosynthesis) seem less connected and may reflect cross-species annotations, but the core signal points to nuclear transport and ribosome biogenesis processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0016310","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0051292","count":3}]},{"hash":"2081770346672151807","title":"Intracellular trafficking and organelle maintenance","description":"The top GO terms cluster around transport and organization within the cell: Golgi protein retention, intralumenal vesicle formation, mitochondrial import, mRNA export, and microtubule dynamics linked to cell division. This suggests the proteins function together in vesicle trafficking and organelle maintenance rather than a single tissue-specific role; the skin development term is likely incidental.","confidence":"Medium","size":29,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":3},{"id":"GO:0045053","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1452174352098106573","title":"Gram-positive bacterial lipid and siderophore biosynthesis","description":"The proteins in this cluster are strongly tied to lipid-related metabolism (very long-chain and medium-chain fatty acids, lipoteichoic acid biosynthesis) and bacterial-specific biosynthetic pathways (menaquinone biosynthesis, siderophore production). The presence of lipoteichoic acid biosynthesis particularly points to Gram-positive bacteria, while siderophore and menaquinone pathways are hallmark bacterial processes. Some aromatic compound metabolism terms (phenylacetate/phenylpropanoid) may also occur in bacteria, supporting a bacterial metabolic theme. Confidence: High","confidence":"","size":29,"edges":26,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":4},{"id":"GO:0019290","count":4},{"id":"GO:0008206","count":4},{"id":"GO:0000038","count":4},{"id":"GO:0009698","count":4}]},{"hash":"2183605012431571170","title":"Transcription Regulation and RNA Processing","description":"The cluster is dominated by transcription-related processes (negative regulation of transcription by RNA polymerase II, DNA-templated transcription) and RNA processing (mRNA splicing, polyadenylation), suggesting a nucleus-centric gene expression module; other terms such as signaling or viral processes appear less central.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0050849","count":2}]},{"hash":"687412848098067666","title":"Unknown","description":"The top GO terms cover RNA processing, UV-damage DNA repair, lipid transport and phospholipid metabolism, cellular respiration, developmental oocyte differentiation, and cardiac action potential regulation, indicating a broad and non-specific mix rather than a single cohesive function for the cluster.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0070914","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0090201","count":1}]},{"hash":"1685837283156322112","title":"Transcription Regulation and Proteostasis","description":"The GO terms indicate a core emphasis on transcriptional control (DNA-templated transcription, RNAP II\u2013mediated regulation, and negative regulation of transcription) with additional signals for protein quality control, including ER protein folding and ubiquitin-proteasome\u2013dependent degradation, plus links to cell signaling and cycle regulation. This combination suggests a cohesive functional theme around transcription regulation intertwined with proteostasis and related regulatory processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006446","count":2},{"id":"GO:0043161","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0045737","count":2}]},{"hash":"830283906023045188","title":"Stem cell proliferation and development","description":"The cluster is enriched for terms related to cell proliferation, cell division, mitotic cell cycle, and stem cell population maintenance, with supporting signals from gastrulation and development-related processes, suggesting a theme of stem cell-driven growth and early development. Some translation-related terms likely reflect the biosynthetic needs of proliferating cells, but the core pattern centers on proliferation and developmental potential in stem-cell\u2013like contexts.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0019827","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006412","count":2}]},{"hash":"893901713034552739","title":"Mitotic spindle and chromosome segregation machinery","description":"The top terms center on mitosis: mitotic spindle assembly, cell division, microtubule severing, and CENP-A chromatin assembly, indicating a focus on spindle function and chromosome segregation. While ribosome biogenesis and mRNA export appear, the strongest, coherent signal is mitotic apparatus and chromosome dynamics, justifying this label.","confidence":"Medium","size":29,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1210237984131049084","title":"Germ Cell Development and Wnt Signaling","description":"This cluster shows a themes around developmental signaling and movement, with terms for germ cell development and the Wnt signaling pathway, plus cell migration. Although a couple of terms relate to basic metabolism (proton transport and glycogen biosynthesis), the strongest signals point to developmental signaling and cell movement, suggesting a cohesive developmental module. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007281","count":2},{"id":"GO:0044130","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0007205","count":2}]},{"hash":"1184586219510487147","title":"Metabolism-Driven transcription regulation","description":"The top GO terms cluster around transcriptional activity (DNA-templated transcription, RNA Pol II regulation) and regulation driven by metabolic cues (carbon sources, fatty acids, amino acid and nucleotide biosynthesis) and respiration. This suggests proteins that participate in coordinating transcription with cellular metabolism, despite the absence of direct interaction edges in the cluster.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045122","count":1},{"id":"GO:0061414","count":1},{"id":"GO:0035948","count":1},{"id":"GO:1904741","count":1},{"id":"GO:1901714","count":1}]},{"hash":"706528165848150224","title":"Translation Initiation Machinery","description":"The cluster is dominated by GO terms related to translation initiation and its regulation (IRES-dependent initiation, translation reinitiation, preinitiation complex formation, and regulation of translational initiation), including viral translation terms. While some developmental terms appear, they are secondary to the core translation initiation theme, making this label representative of the cluster\u2019s function.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0075522","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0006446","count":5},{"id":"GO:0075525","count":5}]},{"hash":"435258230431792014","title":"Ribosome biogenesis and ER-Golgi trafficking","description":"The set prominently features ribosome biogenesis and cell cycle/mitosis terms, plus multiple vesicle-trafficking GO terms for ER-Golgi transport and COPII budding, suggesting a coordinated role in protein synthesis and secretion during cell proliferation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0034498","count":3},{"id":"GO:0008283","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1481570003521246662","title":"RNA Splicing and Processing","description":"The terms strongly point to nuclear RNA metabolism, especially spliceosome dynamics and mRNA processing (GO:0000388, GO:0000393, GO:0006397), with supporting signals from transcription and DNA replication. Some unrelated or obsolete terms appear, but the core cluster theme is RNA splicing/processing machinery.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2}]},{"hash":"1266681714030679082","title":"Embryonic energy metabolism and organogenesis","description":"The cluster shows enrichment for central carbon metabolism terms (TCA cycle, pyruvate to acetyl-CoA) together with diverse developmental terms (pituitary, forebrain, pancreas, forelimb morphogenesis, inner ear morphogenesis, patterning), suggesting proteins that link metabolic state with embryonic organ development. ","confidence":"Medium","size":28,"edges":241,"triangles":1119,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0021983","count":6},{"id":"GO:0051591","count":6},{"id":"GO:0030900","count":5},{"id":"GO:0009952","count":5}]},{"hash":"1116281395916196604","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":375,"triangles":3198,"max_degree":27,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":19},{"id":"GO:0048026","count":19},{"id":"GO:0000398","count":18},{"id":"GO:0071031","count":16},{"id":"GO:0000464","count":16}]},{"hash":"1076273988617319202","title":"Ubiquitin-regulated chromatin modification and NF-kappaB signaling","description":"Top GO terms indicate a focus on ubiquitin-dependent protein turnover and histone modifications (e.g., H2A K63 ubiquitination, H4-K20 methylation) with links to chromatin turnover, alongside NF-kappaB pathway activation steps. This suggests a cluster where ubiquitin-mediated regulation intersects chromatin dynamics and inflammatory signaling, rather than a single enzyme or pathway, justifying a label that highlights both chromatin modification and NF-kappaB\u2013related regulation.","confidence":"Medium","size":28,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:1901253","count":5},{"id":"GO:0009048","count":5},{"id":"GO:0070535","count":5},{"id":"GO:0036205","count":5}]},{"hash":"1876895094006797440","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070935","count":2},{"id":"GO:2000627","count":2},{"id":"GO:0010738","count":2},{"id":"GO:0006402","count":2},{"id":"GO:0044830","count":2}]},{"hash":"1774644478696679365","title":"Mitotic Cell Cycle and Neural Development Proteins","description":"The cluster shows strong signals for mitotic cell cycle and cell division, plus neural development terms (brain and spinal cord development), suggesting a group of proteins coordinating proliferation with neural differentiation. Chromatin regulation hints (histone acetylation) and ribosome biogenesis align with the needs of dividing, differentiating cells. Together, these terms point to a coherent theme of cell division coupled with neural development.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0007420","count":6},{"id":"GO:0043982","count":5},{"id":"GO:0043547","count":5}]},{"hash":"1668825376874230373","title":"Forebrain development and ER-stress response","description":"GO terms point to neural development (forebrain development, multicellular organism development) alongside stress-induced apoptosis via ER signaling (intrinsic apoptotic signaling pathway in response to ER stress), with supporting signals in DNA repair and RNA processing. This pattern suggests a protein cluster involved in neural development that also engages ER-stress\u2013mediated death and gene-expression regulation rather than a single, uniform function.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0050849","count":2},{"id":"GO:0030900","count":2}]},{"hash":"88747334018883859","title":"Mitochondrial Translation and Respiratory Chain","description":"This cluster centers on mitochondrial processes: translation and mitochondrial ribosome maturation (SSU rRNA), NADH dehydrogenase activity, and assembly of the mitochondrial respiratory chain, indicating a cohesive theme of mitochondrial gene expression and respiration. Some terms are older/obsolete but do not alter the main characterization.","confidence":"High","size":27,"edges":63,"triangles":13,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0070584","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0009939","count":2}]},{"hash":"1620388485752398189","title":"Plant phenylpropanoid metabolism and hormone biosynthesis","description":"The terms cluster around plant-specific metabolism and signaling: stilbene and phenylpropanoid-related catabolic/biosynthetic processes, and strigolactone biosynthesis, together with secondary shoot formation, point to a cohesive theme of plant secondary metabolism and hormone-driven development. Some terms are unusual (antibiotic biosynthesis, polyhydroxybutyrate biosynthesis), but the dominant signals support a plant phenylpropanoid/hormone biosynthesis cluster.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0010223","count":3}]},{"hash":"278541455930478668","title":"Osmolyte biosynthesis and stress response","description":"GO terms emphasize production of osmoprotectants like trehalose and glucosylglycerol, along with cellular responses to heat and desiccation and antibiotic response. While other pathways (lipid metabolism, molybdenum cofactor biosynthesis) are present, the strongest shared theme is osmolyte biosynthesis as part of stress adaptation, justifying the label. ","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006633","count":2},{"id":"GO:1902777","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006777","count":2}]},{"hash":"891638708325735069","title":"Neuronal transcription and RNA processing","description":"The cluster is dominated by GO terms related to transcription and RNA processing (DNA-templated transcription, transcription initiation, mRNA processing/splicing), with additional neuronal-context terms (hippocampus development, regulation of dendritic spine morphogenesis). This suggests a shared theme of neuronal gene expression regulation at transcriptional and RNA-processing levels.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014823","count":2},{"id":"GO:0061001","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0000398","count":2},{"id":"GO:1901998","count":2}]},{"hash":"804344818453122218","title":"Neural development and transcriptional regulators","description":"Most terms point to neural development and transcriptional control: DNA-templated transcription, forebrain development, axon regeneration, and protein localization to synapse, along with multicellular development. Additional terms indicate signaling (Wnt) and ER-stress\u2013related apoptosis, suggesting these proteins are transcriptional regulators coordinating neural development and synaptic maturation with stress-response pathways. Confidence: Medium","confidence":"","size":27,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0048680","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006939","count":3},{"id":"GO:0035418","count":3}]},{"hash":"581177214242308039","title":"Ribosome Biogenesis and rRNA Processing","description":"Dominant GO terms are ribosome biogenesis and rRNA maturation/processing, including LSU rRNA processing, suggesting a nucleolar/biogenesis-focused cluster. Other terms (cell division, Golgi-ER transport) are present but less central to the core function, so the primary theme is ribosome assembly and RNA processing.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0034729","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0010255","count":2}]},{"hash":"244356764640072416","title":"Unknown","description":"The Top Terms span DNA replication/repair (replication fork processing, meiotic recombination resolution) and several phosphatidylinositol metabolism and signaling processes, plus diverse regulatory terms (receptor recycling, locomotion regulation). There is no clear, single functional theme uniting these terms, and there are no network connections to support a cohesive label, so a specific representative name isn\u2019t justifiable.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031297","count":2},{"id":"GO:0000712","count":2},{"id":"GO:0046856","count":1},{"id":"GO:0042518","count":1},{"id":"GO:0031161","count":1}]},{"hash":"2131431802742919610","title":"RNA Pol II Transcription Regulation and Fe-S Cluster Biogenesis","description":"Top terms show DNA-templated transcription and RNA polymerase II promoter regulation, suggesting transcription regulation as the core function of this cluster. In addition, Fe-S cluster assembly and maturation terms imply involvement in Fe-S biogenesis, a feature often associated with transcription factors and DNA-binding proteins. Some terms also indicate responses to bacterial components, which may reflect transcriptional regulation under immune or stress conditions rather than a direct effector function. Together, these hints support a label centered on transcription regulation with Fe-S cluster biogenesis connections.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1903026","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0035264","count":3}]},{"hash":"1478160645091020931","title":"Neurodevelopment and Synaptic Signaling","description":"The top GO terms are dominated by neural development and synaptic activity (e.g., long-term synaptic potentiation, excitatory postsynaptic potential, Bergmann glial differentiation), with additional signals of muscle-related development (myoblast fusion, response to muscle activity) that fit neuromuscular development. A separate T cell receptor signaling term appears but is not central to the main theme; overall, the cluster reflects neurodevelopmental and synaptic signaling programs.","confidence":"High","size":26,"edges":286,"triangles":1862,"max_degree":25,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":19},{"id":"GO:0060291","count":19},{"id":"GO:0050852","count":19},{"id":"GO:0060020","count":19},{"id":"GO:0014850","count":19}]},{"hash":"1420283823682873770","title":"Ubiquitin-Dependent Proteolysis","description":"Most top terms describe ubiquitination-driven protein turnover, including ubiquitin-dependent protein catabolic process, ER-associated degradation (ERAD), and K48-linked ubiquitination, plus autoubiquitination. Some terms touch on chromatin regulation via histone ubiquitination and signaling receptor turnover (Wnt receptor catabolic process), as well as dosage compensation effects on X chromosome. Collectively, the cluster appears enriched for components of the ubiquitin-proteasome system and protein quality control pathways, rather than a single signaling pathway.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0030433","count":9},{"id":"GO:0060816","count":8},{"id":"GO:0016558","count":8},{"id":"GO:0038018","count":8}]},{"hash":"959371918987969208","title":"Nuclear RNA processing and transcription","description":"The top GO terms point to core gene-expression processes: rRNA maturation, mRNA splicing, transcription, transcription-coupled repair, and DNA replication, with additional links to translation initiation and proteasome-related protein turnover. This suggests a cluster centered on nuclear RNA processing and transcription machinery, with related proteostasis and growth signals. ","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1334237814309909732","title":"Lipid and Steroid Biosynthesis","description":"This cluster is dominated by GO terms related to retinoid metabolism (retinol, retinal, retinoic acid) and broad lipid biosynthetic pathways (sphingolipids, very long-chain fatty acids) as well as androgen and testosterone biosynthesis, suggesting a core theme of lipid and steroid/retinoid metabolism. Some outliers (antibiotic response, acetoin catabolic) are less central but do not override the main lipid/steroid signal.","confidence":"High","size":26,"edges":95,"triangles":304,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042572","count":15},{"id":"GO:0009710","count":15},{"id":"GO:0030148","count":15},{"id":"GO:0042574","count":15},{"id":"GO:0002138","count":15}]},{"hash":"1609292690100240238","title":"Ubiquitin-Dependent Proteolysis and NF-\u03baB/TNF Signaling","description":"Most terms point to ubiquitination-driven protein turnover (ubiquitin-dependent proteolysis, autoubiquitination, histone ubiquitination) and downstream signaling in inflammation and immunity (TNF signaling, NF-\u03baB activation, JNK cascade), with an additional link to V(D)J recombination. This suggests a coherent theme around ubiquitin-regulated proteolysis coupled to immune signaling pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0051865","count":10},{"id":"GO:0046328","count":10},{"id":"GO:0070535","count":9},{"id":"GO:1903762","count":9}]},{"hash":"1641358801010132863","title":"Unknown","description":"The top GO terms are highly diverse (heart contraction regulation, mitotic chromosome alignment, osmotic/desiccation stress responses, ascospore formation, transcription by Pol II/III, interferon-beta production, and transepithelial ammonium transport), with no single shared pathway or function tying most proteins together, so there is no coherent theme to label.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098735","count":2},{"id":"GO:0007080","count":2},{"id":"GO:0071474","count":1},{"id":"GO:0071465","count":1},{"id":"GO:1903134","count":1}]},{"hash":"1618456078584132753","title":"Neural xenobiotic response and redox signaling","description":"The top terms point to cellular responses to xenobiotics and ethanol, along with cellular redox homeostasis and regulation of unfolded protein response, all within a neural context (substantia nigra development). This suggests a theme of neural cells mounting detox and redox stress responses, potentially linked to brain region-specific processes. Some terms are peripheral or obsolete, but the core signal is a brain-centered detox/redox stress response.","confidence":"Medium","size":25,"edges":11,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045471","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0070940","count":3}]},{"hash":"1273217450200914259","title":"Unknown","description":"The GO terms are highly diverse, spanning ribosome biogenesis, cell division, retina development, necroptosis regulation, adaptive thermogenesis, and numerous membrane transport processes, with no single unifying function apparent across the cluster.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0060546","count":2},{"id":"GO:1990845","count":2}]},{"hash":"1189205640244400778","title":"Mammary gland development and cell proliferation","description":"The cluster shows strong signals for DNA-templated transcription and core cell cycle processes (G2/M transition and mitosis) plus mammary gland epithelial cell proliferation and angiogenesis, indicating a theme of developmental growth and tissue expansion. A defense-response term is present but does not define the primary function of the group; the dominant pattern aligns with development and proliferative signaling, including mammary tissue context.","confidence":"Medium","size":24,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0050830","count":9},{"id":"GO:0000086","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0000278","count":7}]},{"hash":"1670085317701996578","title":"Mitochondrial translation and respiratory complex assembly","description":"This cluster is enriched for translation, ribosome biogenesis, ribosomal subunit assembly, and mitochondrial matrix import, along with assembly of mitochondrial respiratory chain complexes I and IV, pointing to a cohesive role in mitochondrial protein synthesis and assembly of respiratory machinery. Some other terms (chloroplast chlorophyll biosynthesis, drug responses) appear incidental.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0030150","count":3},{"id":"GO:0033617","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000027","count":2}]},{"hash":"62130435368878631","title":"Ubiquitin-Dependent Proteolysis and Immune Signaling","description":"The enrichment centers on ubiquitin-dependent proteolysis (ERAD, polyubiquitination, autoubiquitination, K63-linked ubiquitination) and links to innate immune signaling (NF-\u03baB, TNF) and transcription, indicating a function in ubiquitin-mediated protein turnover and immune regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0042787","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0060546","count":3}]},{"hash":"8035101146579248","title":"Mitochondrial and Vacuolar Transport and Homeostasis","description":"The terms point to organelle-focused processes: proton and sodium transport, proton motive force-driven ATP synthesis, and vacuolar acidification, along with protein targeting to mitochondrion or vacuole, lipoylation in mitochondria, and copper ion homeostasis. Together they suggest a cohesive theme of energy metabolism and trafficking within mitochondria and vacuoles, with vacuole organization as a connected aspect; translation may be ancillary. ","confidence":"High","size":24,"edges":273,"triangles":1958,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0042777","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0007035","count":3}]},{"hash":"2151450243751334542","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by translation and ribosome-related processes (GO:0006412, GO:0002181, GO:0042254), pointing to a cluster of proteins involved in ribosome assembly and protein synthesis. A few outliers (e.g., antibiotic response, endocytosis) likely reflect incidental or indirect associations, but the core signal is strong for ribosome/translation functions.","confidence":"High","size":24,"edges":215,"triangles":1058,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:0042254","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0007605","count":3},{"id":"GO:0006407","count":3}]},{"hash":"1958681172861036946","title":"Chromatin regulation and transcription in hematopoietic differentiation","description":"The cluster prominently features GO terms tied to DNA-templated transcription, chromatin dynamics (positive regulation of chromatin binding, histone methylation regulation), and RNA processing (alternative splicing), along with differentiation pathways for granulocytes and megakaryocytes, suggesting a coordinated role in chromatin-mediated transcriptional control during blood cell lineage specification. Redox and guanine metabolism appear as supportive processes but are less defining. Overall, the dominant theme is chromatin regulation and transcription during hematopoietic differentiation.","confidence":"High","size":24,"edges":80,"triangles":143,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0035563","count":6},{"id":"GO:0046098","count":6},{"id":"GO:0046886","count":6}]},{"hash":"926202148352343571","title":"Translational Initiation and Reinitiation Regulation","description":"The top GO terms cluster around initiation of translation and assembly of translation preinitiation complexes, including IRES-dependent viral initiation, viral termination-reinitiation, and translation reinitiation, indicating a cohesive function in protein synthesis initiation and its regulation (with a couple of more peripheral terms). ","confidence":"High","size":24,"edges":73,"triangles":113,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2}]},{"hash":"2283879684112078199","title":"RNA Splicing Machinery","description":"Based on the top GO terms, the cluster is dominated by RNA processing and spliceosome-related activities (regulation of alternative mRNA splicing via spliceosome, RNA splicing, spliceosomal complex disassembly, mRNA capping). A few terms touch on unrelated processes like glucose transport or telomere maintenance, but the strongest and most frequent signals point to spliceosome-mediated RNA processing. Therefore, the label \u201cRNA Splicing Machinery\u201d is representative of this cluster.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":3},{"id":"GO:1904659","count":3},{"id":"GO:0008380","count":3},{"id":"GO:0007175","count":2},{"id":"GO:0032211","count":2}]},{"hash":"1035926234768766904","title":"DNA replication and transcription with oxidative stress","description":"The dominant GO terms cluster around DNA-templated transcription, DNA amplification, and cell cycle progression, indicating a transcription/replication\u2013related cluster. Redox and stress-related terms (glutathione metabolism, superoxide generation, cadmium, ethanol) suggest accompanying oxidative stress responses. A photoreceptor axon guidance term may be incidental.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0072499","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0032930","count":2}]},{"hash":"225621458003978315","title":"GPCR-Mediated Sensory Signaling","description":"The cluster\u2019s top GO terms cluster around GPCR signaling and sensory perception, including taste modalities (sweet, umami), vision, and related behavioral responses, suggesting a core theme of GPCR-driven sensory signaling; a few immune/viral terms appear as outliers but do not override the dominant sensory motif.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007626","count":1},{"id":"GO:0001661","count":1},{"id":"GO:0016998","count":1},{"id":"GO:0001582","count":1},{"id":"GO:0007196","count":1}]},{"hash":"410782997947312774","title":"Neural and muscle development signaling with apoptosis regulation","description":"The terms cluster around signaling pathways (Wnt, cAMP, GPCR-related), neural processes (neurotransmitter secretion, dendrite morphogenesis regulation), and muscle development (skeletal muscle fiber development), with additional motifs of ubiquitin-dependent proteolysis and an intrinsic apoptotic response. This suggests a cohesive theme of signaling and developmental regulation in neural and muscular contexts, often coupled with protein turnover and apoptosis, justifying a label focused on neural-muscle signaling and development with apoptosis regulation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0048671","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0042787","count":2}]},{"hash":"186798790202469626","title":"Unknown","description":"The top GO terms are scattered across autophagy regulation, proteolysis, phytochelatin biosynthesis, renal sodium absorption, and sensory perception of sound, with several obsolete terms. There is no clear shared function or coherent biological theme linking the majority of proteins, and the cluster has no edges, suggesting a non-cohesive or mixed set. Therefore a single interpretable label is not supported.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":3},{"id":"GO:0016239","count":2},{"id":"GO:0006508","count":2},{"id":"GO:1904715","count":2},{"id":"GO:0046938","count":2}]},{"hash":"770784347914588833","title":"Ribosome Biogenesis and Subunit Assembly","description":"The top GO terms point to ribosome biogenesis, rRNA maturation, and ribosomal subunit assembly, indicating a core role in ribosome production. Additional terms for transcription and cell cycle suggest broader coordination with gene expression and proliferation, while neural development terms may reflect tissue-specific expression rather than a distinct function. Overall, the cluster centers on ribosome assembly processes.","confidence":"Medium","size":23,"edges":144,"triangles":358,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":9},{"id":"GO:0000463","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0042273","count":6},{"id":"GO:0007275","count":5}]},{"hash":"963970594784499958","title":"Plant secondary metabolite biosynthesis and detoxification","description":"The terms cluster around production and breakdown of plant secondary metabolites (stilbene, strigolactone) and related hormone signaling, shoot formation, and detox/response to toxins, with some primary metabolism (biotin) and xenobiotic catabolism also present. This points to a coherent theme of plant secondary metabolism and toxin response, albeit with some broader metabolism terms mixed in.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0009102","count":4},{"id":"GO:0010223","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0097755","count":3}]},{"hash":"176548960747861078","title":"Ubiquitin-regulated immune signaling","description":"This cluster is dominated by GO terms tied to ubiquitin biology (deubiquitination) and immune signaling pathways such as non-canonical NF-kappaB, TNF-mediated signaling, and Fc-epsilon receptor signaling, pointing to a core function in ubiquitin-controlled immune responses. Supporting terms like RNA stability regulation and cell-cycle-related regulation may reflect broader regulatory layers associated with immune signaling networks.","confidence":"High","size":23,"edges":246,"triangles":1633,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":15},{"id":"GO:0043488","count":10},{"id":"GO:0038061","count":10},{"id":"GO:0038095","count":9},{"id":"GO:0061418","count":9}]},{"hash":"1792699882977455314","title":"Membrane transporters for ions and small molecules","description":"The cluster\u2019s top GO terms are dominated by transmembrane transport activities (potassium ion, 4-hydroxyphenylacetate, vitamin, and antibiotic transport), suggesting a core function in moving ions and small molecules across membranes. Related terms like salt stress response and transporter-related processes support a transporter-centric theme, while the non-transport terms may reflect annotation noise or broader regulatory links. Overall, a transporter-focused label fits best.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0030437","count":2},{"id":"GO:0035562","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0032287","count":2}]},{"hash":"908487306822824298","title":"Unknown","description":"The GO terms are highly diverse, including cytoskeletal assembly, insulin signaling, cell migration, NF-kappaB regulation, amino acid homeostasis and transport, nitrogen-starvation responses, and tissue development/behavior. There isn\u2019t a single cohesive biological process linking these terms, so a singular, intuitive label is not justifiable.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0080144","count":1}]},{"hash":"1835947156341622294","title":"RNA Processing and Nucleocytoplasmic Transport","description":"The top GO terms include mRNA splicing via spliceosome and ribosomal large subunit export from the nucleus, indicating RNA processing and nucleocytoplasmic transport roles. The additional transmembrane transport terms across diverse substrates suggest broader transport-related functions. Together, these points imply a cluster centered on RNA metabolism coupled with cellular transport rather than a single substrate-specific function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0000055","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0032298","count":2},{"id":"GO:1900754","count":2}]},{"hash":"575886250983305377","title":"Mitochondrial fatty acid transport and oxidation","description":"The Top Terms cluster predominantly shows fatty acid transport and beta-oxidation processes (long-chain and medium-chain FA metabolism, carnitine-linked metabolism) together with mitochondrial context (mitochondrial respiratory chain complex III assembly, translation). This combination suggests a module of proteins involved in importing and degrading fatty acids within mitochondria to fuel energy production. Some terms are broader energy-related processes, but the strongest, recurring signals are fatty acid transport/oxidation linked to mitochondrial function.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0034551","count":2},{"id":"GO:0015909","count":2},{"id":"GO:0032000","count":2},{"id":"GO:0019254","count":2}]},{"hash":"259800315865558341","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099132","count":1},{"id":"GO:0042823","count":1},{"id":"GO:0070455","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1900738","count":1}]},{"hash":"881153007742862898","title":"Mitochondrial translation and energy metabolism","description":"The cluster's proteins are enriched for mitochondrial translation, mitochondrial matrix protein import, the TCA cycle, and proton-motive ATP synthesis, plus cytochrome complex assembly. This collectively points to mitochondrial protein synthesis and oxidative phosphorylation machinery driving energy production, with some auxiliary notes on redox and stress-related processes. ","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0015986","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006099","count":2}]},{"hash":"1035351460993861130","title":"Amino acid catabolism and central carbon metabolism","description":"Most terms point to amino acid catabolism (L-kynurenine, L-alanine, L-aspartate, L-threonine, etc.) and oxaloacetate/central carbon metabolism, suggesting a cluster of proteins involved in degrading amino acids to feed the TCA cycle. Some terms (Notch signaling, salicylic acid\u2013mediated defense) appear as outliers or misannotations, so the core theme is metabolic rather than signaling.","confidence":"Medium","size":22,"edges":230,"triangles":1520,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":8},{"id":"GO:0007219","count":8},{"id":"GO:0042853","count":8},{"id":"GO:0019878","count":8},{"id":"GO:0006107","count":6}]},{"hash":"648321664636130351","title":"ER-Golgi trafficking and cell polarity regulation","description":"The top GO terms indicate vesicle transport from the ER to the Golgi, regulation of cell polarity and cell shape, and signaling/modulation through GTPases and phosphorylation, plus a link to Cvt/autophagy pathways. Together, these points suggest a cohesive module centered on intracellular membrane trafficking, polarity establishment, and associated signaling rather than a single isolated function. Therefore, a concise label capturing vesicle trafficking coupled with polarity control is appropriate.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0032005","count":3},{"id":"GO:2000769","count":3},{"id":"GO:0031139","count":3},{"id":"GO:0043547","count":3}]},{"hash":"1911444441199469862","title":"Unknown","description":"The top GO terms span very different biological areas (muscle development, RNA methylation, actin remodeling, spore wall assembly, neural development, viral latency, and renal transport), with little overlap suggesting a single cohesive function. The cluster appears to include proteins involved in diverse processes rather than a shared pathway, so a unified label is not supported.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035914","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0030476","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0050731","count":2}]},{"hash":"2132724605674088401","title":"Mitochondrial respiration and protein complex assembly","description":"The GO terms are dominated by aerobic respiration, mitochondrial electron transport from ubiquinol to cytochrome c, and proton transmembrane transport, pointing to oxidative phosphorylation in mitochondria. The enrichment of protein oligomerization and heterooligomerization terms suggests assembly of respiratory chain complexes. Some outlier terms (viral process, PQQ biosynthesis) likely reflect annotation noise, but the core signal aligns with mitochondrial energy metabolism and complex assembly.","confidence":"High","size":22,"edges":13,"triangles":2,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":4},{"id":"GO:0006122","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0006627","count":2},{"id":"GO:0032461","count":2}]},{"hash":"1802941507996240765","title":"Wnt-regulated skeletal development and vesicle trafficking","description":"The top GO terms point to Wnt signaling modulation and skeletal development (negative regulation of canonical Wnt signaling, cranial skeletal system development, osteoblast fate commitment), suggesting a developmental module governed by Wnt signaling. Additional terms involve vesicle trafficking and cytoskeletal remodeling (endosome-to-Golgi transport, lamellipodium morphogenesis, microvillus assembly, cytokinesis), which are common in signaling during morphogenesis. This combination supports a coherent theme around Wnt-driven bone development with supporting trafficking/cytoskeletal processes.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090090","count":2},{"id":"GO:0030073","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0032534","count":1},{"id":"GO:0000281","count":1}]},{"hash":"450379332110749573","title":"Redox Stress Response and Growth Regulation","description":"Based on the top GO terms, the cluster is centered on oxidative stress response and redox homeostasis (oxidation-reduction, cellular response to oxidative stress, redox balance) with accompanying signals related to growth regulation and transcription (regulation of growth, DNA-templated transcription). A few carbohydrate catabolism terms appear but are likely secondary metabolic links rather than defining features.","confidence":"Medium","size":21,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0040008","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2}]},{"hash":"203304392308455811","title":"RNA splicing and translation regulation","description":"The terms are dominated by splicing (alternative splicing via spliceosome, preinitiation complex formation) and multiple layers of translational control (translation initiation, reinitiation, and miRNA/ncRNA-mediated silencing), plus mRNA stability under stress. This points to a coherent module of post-transcriptional gene regulation at the RNA level, spanning splicing decisions to translational control. ","confidence":"High","size":21,"edges":20,"triangles":5,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":14},{"id":"GO:0048026","count":13},{"id":"GO:0002188","count":11},{"id":"GO:0001731","count":11},{"id":"GO:1901407","count":11}]},{"hash":"1178730606636342512","title":"Regulation of Translation Initiation (IRES)","description":"The prominent GO terms center on regulation and initiation of translation, including preinitiation complex formation, translation reinitiation, and IRES-dependent viral translation. A cohesive theme is translational control and mRNA binding, with some ancillary terms related to transcription and cell cycle.","confidence":"High","size":21,"edges":11,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0001731","count":3},{"id":"GO:1902416","count":3},{"id":"GO:0000122","count":3}]},{"hash":"2200293777764884827","title":"Membrane transporters for sugars and ions","description":"The cluster shows numerous transmembrane transport GO terms for diverse substrates (galactose, sialic acid, nitrite, potassium, etc.), indicating a core theme of membrane transport proteins, with a minor ER stress-related term present but not central to the main function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034976","count":2},{"id":"GO:1903206","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2}]},{"hash":"1944968424788050297","title":"Hormone Processing in Dense Core Granules","description":"This cluster centers on processing of insulin and islet amyloid polypeptide, plus maturation of peptide hormones and regulation of dense core granule transport, indicating a shared function in peptide hormone maturation and secretory granule trafficking. While a few cholesterol transport\u2013related endocytosis terms appear, the dominant signals are secretory peptide processing activities rather than a broad-scope metabolism or development theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905601","count":1},{"id":"GO:0030070","count":1},{"id":"GO:0034231","count":1},{"id":"GO:0007323","count":1},{"id":"GO:1904810","count":1}]},{"hash":"773236488240921054","title":"Vesicle trafficking and signaling","description":"The top GO terms cluster around membrane trafficking and secretory processes (clathrin-dependent endocytosis, catecholamine secretion, acrosome reaction) and link to signaling pathways (tachykinin receptor signaling, Ras pathway regulation, spine development, and muscle contraction). This suggests a cohesive theme of vesicle-mediated transport paired with signal transduction, spanning neuronal, secretory, and reproductive contexts. However, the inclusion of several divergent terms means the label is a best-fit rather than a highly specific function; Confidence: Medium.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0072583","count":2},{"id":"GO:0050432","count":1},{"id":"GO:0007340","count":1},{"id":"GO:0045792","count":1},{"id":"GO:0003374","count":1}]},{"hash":"445229264281610678","title":"Ribosome Biogenesis and Translation Machinery","description":"The cluster is dominated by terms tied to ribosome production and protein synthesis (translation, cytoplasmic translation, ribosome biogenesis, tRNA modification) with accompanying cell-cycle and division terms, indicating a coherent focus on ribosome function and assembly during growth.","confidence":"High","size":21,"edges":20,"triangles":4,"max_degree":16,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0051301","count":4},{"id":"GO:1903833","count":4}]},{"hash":"544169910170277544","title":"Bacterial Biosynthesis and Sporulation","description":"The top GO terms concentrate on microbial biosynthetic pathways (lipopolysaccharide, polyhydroxybutyrate, fatty acids) and sporulation, with additional signals for transcription regulation and antibiotic response. This pattern suggests a cluster of proteins involved in bacterial metabolism tied to sporulation programs, rather than a single specific pathway, though some terms (e.g., retinol and tropane alkaloid biosynthesis) may reflect annotation noise. Therefore, a label emphasizing bacterial biosynthesis with sporulation is appropriate.","confidence":"Medium","size":21,"edges":12,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0006355","count":6},{"id":"GO:0042619","count":6},{"id":"GO:0009103","count":6},{"id":"GO:1902987","count":6}]},{"hash":"1085256751967832082","title":"Developmental Regulation","description":"The top GO terms point strongly to developmental processes (cerebral cortex development, multicellular organism development, beta selection) with supporting roles in transcription, cell growth, and apoptosis. A few terms touch on stress or reproductive contexts, but the core signal is developmental regulation and differentiation.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021987","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0045793","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0009636","count":5}]},{"hash":"1037170699730564038","title":"Translation Machinery and Ribosome Biogenesis","description":"The cluster is dominated by translation-related GO terms (translation, cytoplasmic translation, translational termination, translational elongation, and ribosomal large subunit assembly) plus mitochondrial translation terms, indicating a core theme of protein synthesis and ribosome biogenesis across compartments; a few RNA metabolism terms appear ancillary.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0046677","count":4},{"id":"GO:0006415","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0000027","count":3}]},{"hash":"181754796228298744","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":6,"triangles":0,"max_degree":5,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000463","count":11},{"id":"GO:0042273","count":11},{"id":"GO:0000462","count":11},{"id":"GO:0000398","count":11},{"id":"GO:0000466","count":11}]},{"hash":"1908936334796023384","title":"Ribosome biogenesis and ribosomal assembly","description":"The cluster is enriched for ribosome-related terms: ribosome biogenesis, LSU-rRNA maturation, translation preinitiation complex formation, cytosolic ribosome assembly, and preribosome assembly, indicating a cohesive role in ribosome production and maturation. A few terms touch other processes, but the dominant theme is ribosome formation.","confidence":"High","size":20,"edges":187,"triangles":1088,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0000463","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0000902","count":3}]},{"hash":"1831490547828390615","title":"Mitotic Cell Cycle and Spindle Assembly","description":"The top terms are dominated by mitosis-related processes (cell division, mitotic spindle assembly, mitotic cell cycle, mitotic sister chromatid segregation), indicating the proteins cluster around core mitotic machinery and cell-cycle progression. Additional terms like nuclear pore localization and COPII vesicle budding suggest ancillary roles in nuclear transport and trafficking that can accompany cell division. Overall, the cluster appears to annotate proteins involved in mitosis and cell-cycle control.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0090307","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0090114","count":5},{"id":"GO:0006351","count":4}]},{"hash":"1101329376377695340","title":"Translation initiation and protein trafficking","description":"The top terms show strong representation of translation initiation (preinitiation complex formation, initiation regulation, IRES-dependent initiation) and ER-to-Golgi vesicle transport, with additional RNA processing and ubiquitination terms, suggesting a cluster focused on the early stages of protein synthesis and subsequent handling/secretory pathway steps.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0075522","count":3},{"id":"GO:0007049","count":2}]},{"hash":"1562859561477963163","title":"Chloroplast and mitochondrial biosynthesis and translation","description":"The top GO terms point to chloroplast (light-independent chlorophyll biosynthesis, biosynthesis of lipids like phosphatidylcholine and sterols) and mitochondrial processes (positive regulation and general translation in mitochondria, redox homeostasis, and mitochondrial targeting), plus broader metabolism (tetrahydrofolate). This suggests a cluster of proteins involved in organelle biogenesis and function in plants, specifically plastids and mitochondria, rather than a single cytosolic pathway. Some development-related terms appear but do not dominate the signal, which remains centered on organelle metabolism and protein synthesis.","confidence":"Medium","size":20,"edges":174,"triangles":886,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0006656","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0006412","count":2}]},{"hash":"616810358410299555","title":"Ribosome Biogenesis and RNA Processing","description":"The cluster shows strong representation of rRNA maturation (5.8S, LSU, SSU) and ribosomal subunit biogenesis, plus mRNA splicing, all pointing to nucleolar RNA processing and ribosome assembly. While there are some broader nuclear terms (transcription, cell cycle) present, the ribosome/RNA-processing theme is dominant. ","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0006890","count":5},{"id":"GO:0006888","count":5}]},{"hash":"2049186834977278340","title":"Ribosome Biogenesis and Cell Cycle Regulation","description":"The top GO terms cluster around protein synthesis and cell division: cytoplasmic translation, tRNA modification, and ribosome biogenesis point to ribosomal machinery, while exit from mitosis, cell cycle, cell division, and division septum assembly indicate coordination with division. The presence of protein heterooligomerization reflects assembly of multi-subunit complexes, supporting a role in ribosome assembly and cell-cycle\u2013related processes. Some terms (smoothened signaling, salt-stress response) appear less central, likely background annotations. Overall, the cluster represents proteins involved in ribosome production and the orchestration of cell division.","confidence":"High","size":20,"edges":4,"triangles":0,"max_degree":3,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0010458","count":3},{"id":"GO:0000917","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0051291","count":2}]},{"hash":"1919415730320967455","title":"Transcription Regulation and Histone Modification","description":"The top terms show strong signals for DNA-templated transcription and chromatin state changes via histone acetylation and methylation, indicating a cluster centered on transcriptional control and epigenetic regulation. Other terms touch on cell division and cytoskeletal remodeling (Arp2/3-mediated actin nucleation and GTPase activity), which can relate to gene expression in some contexts, but the dominant pattern is transcriptional regulation with chromatin modifications.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0043982","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0035948","count":5},{"id":"GO:0043981","count":5}]},{"hash":"994908056311499016","title":"ER Proteostasis and Quality Control","description":"Several GO terms point to ER proteostasis: folding and refolding in the ER, handling of misfolded proteins via ERAD-like pathways, and redox homeostasis linked to oxidative folding, all consistent with ER stress\u2013driven translation. A few terms (DNA replication, tRNA import into nucleus) appear unrelated and likely reflect noise, but the dominant signal supports ER protein quality control and stress response.","confidence":"High","size":20,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071374","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0035719","count":2},{"id":"GO:0034975","count":2}]},{"hash":"1264720220442773408","title":"Embryonic Development and Organogenesis","description":"The top GO terms cluster around developmental programs: endocrine system development, cartilage morphogenesis, left/right pattern formation, pancreatic cell development, placental and EMT-related processes, and trophoblast differentiation, all pointing to embryogenesis and organ formation. A couple of broader terms (mitochondrial membrane organization and RNA Pol II preinitiation complex assembly) likely reflect general cellular machinery used during development but do not outweigh the developmental theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048016","count":2},{"id":"GO:0035270","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0003323","count":1}]},{"hash":"2114396324442229908","title":"Unknown","description":"The top GO terms span diverse and largely unrelated functions (SOS response, antibiotic and biotin biosynthesis, DNA damage tolerance, nodulation, transcription regulation, long-term synaptic depression, and various membrane transport processes), with no single shared pathway or biological theme. The network has no edges or connected components (Edges: 0, Triangles: 0, Max Degree: 0), suggesting the proteins are not functionally cohesive, so no meaningful, unified label can be assigned beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0006301","count":2},{"id":"GO:0009877","count":2}]},{"hash":"901818158945721777","title":"RNA processing and translation regulation","description":"The cluster centers on RNA maturation processes (splicing, modification, ncRNA silencing) and control of translation initiation, suggesting a cohesive role in RNA metabolism and translational regulation.","confidence":"High","size":19,"edges":10,"triangles":0,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0035278","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0006446","count":3}]},{"hash":"1893077840236599022","title":"Cofactor and antibiotic biosynthesis","description":"Several top GO terms cluster around biosynthesis of small-molecule cofactors (cobalamin, biotin, menaquinone) and antibiotic biosynthesis, indicating a core theme of metabolite production. Peripheral terms related to protein turnover and stress responses (ubiquitination, cadmium response) are present but seem secondary to the central biosynthetic focus.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0019433","count":4},{"id":"GO:0008285","count":3},{"id":"GO:0031146","count":3}]},{"hash":"2302474597672891881","title":"Unknown","description":"The GO terms are highly diverse, including RNA surveillance (non-stop decay), regulation of Rho signaling, actin-based structures (microspike and filopodium assembly), ubiquitin-like urmylation, and various plant-specific processes (suspensor development, cytokinin biosynthesis, and glycosylation). There isn\u2019t a single cohesive function or pathway that ties the majority of these proteins together, so a concise, representative label cannot be assigned beyond Unknown.","confidence":"","size":19,"edges":10,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070481","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0030035","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0032447","count":1}]},{"hash":"699675146453416074","title":"Developmental transcription and organogenesis (heart and brain)","description":"The top GO terms center on transcriptional regulation (RNA polymerase II transcription, chromatin regulation) and developmental processes across organs, notably heart development (sinus venosus morphogenesis, left ventricle formation, circadian regulation of heart rate) and neural differentiation (GABAergic interneuron differentiation, auditory receptor fate). Additional terms for estradiol response and pancreatic endocrine differentiation point to hormone-responsive transcription controlling organogenesis. This suggests a cluster of proteins coordinating developmental programs via transcriptional control in cardiac and neural tissues.","confidence":"Medium","size":19,"edges":168,"triangles":918,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0071392","count":7},{"id":"GO:0006366","count":7},{"id":"GO:0000183","count":6},{"id":"GO:0003062","count":5},{"id":"GO:0003053","count":5}]},{"hash":"1416618730691520992","title":"Transcriptional Regulation and Chromatin Remodeling","description":"The proteins here are enriched for transcription-related GO terms (DNA-templated transcription, RNA Pol II transcription) and chromatin remodeling, with some development and signaling annotations. This suggests a core function in regulating gene expression during development and differentiation.","confidence":"High","size":19,"edges":68,"triangles":73,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0071353","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0043046","count":4}]},{"hash":"1823730627487571963","title":"Embryonic Development and Neural Signaling","description":"Most GO terms point to embryonic development (in utero) and neural development (neuron projection), with transcriptional regulation and embryonic cell-cycle control. Additional terms indicate broader cellular signaling (cAMP response, membrane potential) and stress responses (DNA damage, oxidative challenge), suggesting a coordinated developmental and neural-differentiation program with regulatory and stress-sensing components. While some metabolic stress terms are present, the core theme revolves around embryogenesis and neural development.","confidence":"Medium","size":19,"edges":9,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001701","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0010976","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0006094","count":2}]},{"hash":"1064174754105013285","title":"Cell Cycle and ER-Golgi Trafficking","description":"This cluster shows strong signals for DNA replication and cell division together with vesicle transport between the ER and Golgi and related membrane fusion processes, suggesting proteins involved in coordinating nuclear replication with intracellular trafficking during cell proliferation rather than a single, isolated function.","confidence":"Medium","size":19,"edges":7,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0034214","count":2},{"id":"GO:2001168","count":2}]},{"hash":"373202738929011610","title":"Hormone Biosynthesis and Organ Development","description":"The top GO terms cluster around biosynthesis of signaling molecules (prostaglandin, bile acid, brassinosteroid, testosterone) and development of hormone-responsive tissues (uterus, digestive tract, prostate). The inclusion of plant-brassinosteroid terms suggests cross-kingdom signals but overall points to hormone biosynthesis linked to organ development.","confidence":"Medium","size":19,"edges":57,"triangles":9,"max_degree":11,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0001516","count":9},{"id":"GO:0033280","count":9},{"id":"GO:0060065","count":9},{"id":"GO:0006699","count":8},{"id":"GO:0090350","count":8}]},{"hash":"1300213735366232762","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":85,"triangles":222,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":9},{"id":"GO:0045292","count":9},{"id":"GO:0001731","count":7},{"id":"GO:0002188","count":7},{"id":"GO:0006406","count":7}]},{"hash":"412258028144543511","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0070535","count":2},{"id":"GO:1903762","count":2},{"id":"GO:0036205","count":2}]},{"hash":"1298064638242993248","title":"Metal ion detox and zinc homeostasis","description":"The top GO terms cluster around metal handling: cadmium ion transmembrane transport, intracellular zinc ion homeostasis, detoxification of zinc ion, and xenobiotic transmembrane transport, suggesting a shared role in metal detoxification and zinc balance. Some unrelated terms (histone modifications and developmental processes) appear, but are less represented, so the core theme is metal transport/detox. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0006882","count":2},{"id":"GO:0010312","count":2}]},{"hash":"1303661999389783975","title":"Diverse transmembrane nutrient and ion transporters","description":"The top GO terms are dominated by transmembrane transport of a range of substrates (nitrate/nitrite, galactose, sialic acid, fucose, vitamins) and inorganic ions (sodium, potassium), indicating a cluster of membrane transport proteins with diverse substrate specificity. While one term mentions metabolism, the common theme is transport across membranes, supporting a transporter-focused cluster label.","confidence":"High","size":19,"edges":61,"triangles":59,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:1900754","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015707","count":2}]},{"hash":"1697130523879726824","title":"Neural tube and forebrain development","description":"The terms are dominated by vertebrate developmental processes, notably neural tube formation/closure and forebrain development, with supporting terms for mesoderm formation and multicellular organism growth, and some cell cycle signals. This suggests a neurodevelopmental program as the core function of the cluster.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071374","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001707","count":2},{"id":"GO:1901621","count":2}]},{"hash":"2274975094983531287","title":"Muscle contraction and calcium signaling proteins","description":"The top terms cluster around skeletal and cardiac muscle function and calcium signaling\u2014muscle attachment, voluntary movement, heart contraction, and calcium detection/transport. This points to a common theme of muscle physiology and calcium handling among the proteins. A few terms (blastocyst formation, translation initiation) are unrelated to muscle biology and may reflect broad annotations rather than core cluster function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016203","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0001825","count":2},{"id":"GO:1901896","count":1},{"id":"GO:0050882","count":1}]},{"hash":"357553822710649734","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000447","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0001731","count":2}]},{"hash":"50402648473639056","title":"Translation initiation and ribosome biogenesis","description":"The top GO terms cluster around translation initiation and overall translation, including preinitiation complex formation, ribosome biogenesis, and reinitiation, with viral translation initiation/termination terms supporting a focus on protein synthesis machinery and its regulation. A few outliers like blastocyst formation are less informative for this cluster\u2019s primary function.","confidence":"High","size":19,"edges":11,"triangles":5,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0001825","count":3}]},{"hash":"2082508556932252000","title":"Developmental signaling and cell cycle regulation","description":"This cluster centers on signals and processes related to development and growth (gastrulation; cellular response to TGF-beta; response to growth hormone) and on control of cell cycle entry (negative regulation of G0 to G1). Additional terms like ER-Golgi transport and proteolysis suggest general cellular maintenance that supports these processes, while a few terms (e.g., rRNA maturation) are more ancillary. Overall, the dominant theme appears to be development-associated signaling intertwined with cell cycle control. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007064","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0034729","count":2}]},{"hash":"1102695138439413870","title":"Amino acid metabolism and nucleotide biosynthesis","description":"This cluster prominently features transsulfuration, L-serine/glycine pathways, and GMP biosynthesis, pointing to amino acid metabolism and nucleotide production as core themes. A few terms related to signaling or development (retina, IL-4 response, mitotic regulation) appear as outliers, suggesting broader cellular regulation beyond metabolism. Overall, the metabolic focus is the strongest signal, hence the label. ","confidence":"Medium","size":18,"edges":150,"triangles":769,"max_degree":17,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0071353","count":6},{"id":"GO:0019346","count":6},{"id":"GO:0060041","count":6},{"id":"GO:0006177","count":6},{"id":"GO:0030071","count":6}]},{"hash":"328968097492860277","title":"Ubiquitin-Proteasome Regulation of Cell Cycle","description":"This cluster is enriched for ubiquitin-dependent proteolysis and proteasome-mediated protein catabolism, including SCF- and APC/C-dependent pathways, K11-linked ubiquitination, and autoubiquitination, along with cell cycle processes (G1/S transition, mitosis) and DNA damage checkpoints. This points to a cohesive theme of ubiquitin-proteasome control of cell division.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0031571","count":3},{"id":"GO:1902916","count":3},{"id":"GO:0000083","count":3}]},{"hash":"1841500025523192993","title":"Nervous system development and dendrite morphogenesis","description":"The cluster shows strong enrichment for nervous system development terms, including nervous system development, central nervous system neuron development, and dendrite morphogenesis, pointing to involvement in neuronal differentiation and dendritic structure. While other terms relate to immune signaling and nuclear processes, these may reflect broader regulatory or housekeeping functions that accompany development. Overall, the dominant neural development theme supports this label, with some context-dependent signals adding nuance.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006281","count":5},{"id":"GO:0046826","count":4},{"id":"GO:0071222","count":4},{"id":"GO:0050852","count":4}]},{"hash":"996885492672356674","title":"DNA maintenance and epithelial development","description":"This cluster combines genome maintenance functions (DNA replication, base-excision repair, transcription regulation) with GO terms tied to epithelial development and cell adhesion/polarity in insect tissues (follicular epithelium, egg chamber, visual primordium), suggesting proteins involved in maintaining genome integrity during epithelial tissue development. Confidence: Medium","confidence":"Medium","size":18,"edges":32,"triangles":21,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0030324","count":2},{"id":"GO:0035753","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0042248","count":2}]},{"hash":"1856861836629620779","title":"Nuclear DNA Maintenance and Gene Expression","description":"The cluster shows a cohesive set of functions centered on nuclear DNA processes\u2014DNA replication, repair, cell cycle, and DNA-templated transcription\u2014as well as mRNA export and related nuclear trafficking, with additional related processes like nuclear autophagy and ER-Golgi transport. These together point to a theme of coordinating genome maintenance with gene expression and RNA processing, despite an outlier term related to lipopolysaccharide biosynthesis. Confidence: Medium","confidence":"","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009103","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1604821198036512687","title":"Transcriptional Regulation and Elongation","description":"The cluster is dominated by GO terms for transcription and transcription elongation (DNA-templated transcription, elongation by RNA polymerase II and I, and regulation of elongation), indicating a cohesive gene-expression control theme. Some translation and immune-response terms appear but are less central.","confidence":"High","size":18,"edges":41,"triangles":0,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006368","count":2},{"id":"GO:0090262","count":2},{"id":"GO:0006412","count":2},{"id":"GO:2001209","count":2}]},{"hash":"1881515753409664682","title":"Bacterial LPS biosynthesis and metal transport","description":"The top GO terms cluster around lipopolysaccharide biosynthesis (a hallmark of Gram-negative bacterial cell envelope formation) and metal ion transport (cadmium and zinc). Additional terms point to broader bacterial metabolism (L-serine biosynthesis, stilbene catabolism) and P450-related oxidation, suggesting a bacterial protein set involved in envelope-related synthesis and metal handling with ancillary metabolic activities. This combination supports a focused label on envelope biosynthesis and metal transport in a bacterial context.","confidence":"Medium","size":18,"edges":14,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0019373","count":1},{"id":"GO:0006874","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0006564","count":1}]},{"hash":"1612473712771129874","title":"Bacterial lipid metabolism and siderophore biosynthesis","description":"This cluster is dominated by biosynthetic and metabolic processes for bacterial lipids and related compounds (lipoteichoic acid, fatty acids, menaquinone), plus siderophore biosynthesis, with supporting metabolic activities such as pyruvate fermentation to acetate. The GO terms point to a cohesive theme of lipid-rich metabolism and iron-chelating secondary metabolite production in bacteria.","confidence":"High","size":18,"edges":128,"triangles":485,"max_degree":17,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0070395","count":12},{"id":"GO:0010124","count":11},{"id":"GO:0019290","count":11},{"id":"GO:0008206","count":11},{"id":"GO:0000038","count":11}]},{"hash":"734421238703438479","title":"Unknown","description":"The top GO terms are highly diverse, spanning cellulose catabolism, transcription regulation, animal development (heart development), protein folding, antibiotic biosynthesis, redox, nitrate assimilation, locomotory behavior, fertilization, and trehalose response. With no edges or shared functional theme among the proteins, there isn\u2019t a coherent common function to bind the cluster. Therefore, Unknown with None confidence. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0017000","count":2}]},{"hash":"2123977774611432033","title":"Gene expression and cell cycle regulation","description":"This cluster is enriched for several gene expression-related processes: mRNA splicing via spliceosome, transcription termination, formation of the translation preinitiation complex, and translation reinitiation, plus a term for negative regulation of G0 to G1 transition. These point to coordinated control of transcription, RNA processing, and translation, with a connecting thread to cell cycle progression. Some peripheral terms (lipid droplet organization, defense response) may reflect broader cellular states but do not define the core theme. ","confidence":"High","size":18,"edges":14,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":4},{"id":"GO:0045292","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4}]},{"hash":"1652808125000423218","title":"Membrane Transporters","description":"The top GO terms show diverse transmembrane transport activities across sugars, ions, vitamins, and even neurotransmitter loading into synaptic vesicles, indicating the proteins mostly function as membrane transporters or vesicular transporters rather than enzymes. This common theme justifies labeling the cluster as Membrane Transporters.","confidence":"High","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042891","count":6},{"id":"GO:0015757","count":6},{"id":"GO:0015739","count":6},{"id":"GO:0035725","count":6},{"id":"GO:0035435","count":6}]},{"hash":"1760920065133012977","title":"Plant meristem development and organ specification","description":"The top GO terms largely point to plant developmental processes\u2014shoot apical meristem regulation, inflorescence meristem growth, fruit development, and abaxial cell fate specification\u2014along with organ position specification and general multicellular development, plus supporting cell division and transcription regulation terms, indicating a cohesive theme of plant organogenesis and patterning.","confidence":"High","size":18,"edges":15,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:1902183","count":2},{"id":"GO:0007275","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0034501","count":2}]},{"hash":"856814774742059654","title":"Embryonic Neural Development and Translation Initiation","description":"The cluster\u2019s strongest signals are translation initiation and formation of the translation preinitiation complex, suggesting a core role in protein synthesis. Added terms point to neural/embryonic development (forebrain development, neural tube closure) and general multicellular development, implying a link between translation regulation and developmental processes. Other terms (hypoxia response, mitotic cell cycle, defense to Gram-positive bacteria) indicate broader stress-related contexts that can accompany development. Overall, the label reflects a plausible fusion of translation machinery with neural/developmental functions.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0001843","count":2}]},{"hash":"2257703985225829343","title":"Chromatin remodeling and histone modification","description":"The terms cluster around chromatin dynamics: histone acetylation (H2A, H4), chromatin remodeling, histone exchange, and transcription regulation (nuclear import of transcription factors, transcription from RNA Pol II), plus DNA repair, suggesting a chromatin-modifying/regulatory module. A couple of outlier terms (antimicrobial peptide production, face morphogenesis) may reflect annotation noise.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042993","count":2},{"id":"GO:0043968","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0043967","count":1},{"id":"GO:0006281","count":1}]},{"hash":"205597703020439067","title":"Ribosome biogenesis and rRNA maturation","description":"Dominant GO terms point to ribosome assembly and RNA processing (ribosomal large subunit biogenesis and maturation of SSU-rRNA), indicating the cluster mainly comprises proteins involved in ribosome biogenesis and rRNA maturation, with some ancillary regulatory terms reflecting broader nucleolar functions. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1966621788088188635","title":"Fungal sporulation and sterigmatocystin biosynthesis","description":"The top GO terms cluster around sporulation and conidium formation (sporulation, conidium formation, prospore remodeling) and steroid- and mycotoxin-related biosynthesis (sterigmatocystin biosynthetic process, its regulation). This pattern points to fungal sporulation together with secondary metabolism, particularly in Aspergillus-like species that produce sterigmatocystin. Some peripheral terms exist, but the dominant signal is spore formation coupled with secondary metabolite biosynthesis.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031322","count":2},{"id":"GO:0045492","count":1},{"id":"GO:0048315","count":1},{"id":"GO:0010914","count":1},{"id":"GO:0043941","count":1}]},{"hash":"787917876258230158","title":"Unknown","description":"The top terms include a mix of amino acid biosynthesis/catabolism (L-lysine, L-alanine, L-glutamate, L-aspartate, L-histidine), a developmental signaling pathway (Notch signaling), and plant immune signaling (systemic acquired resistance, salicylic acid mediated signaling). This combination does not point to a single coherent biological function or pathway underlying the cluster, and several terms are obsolete, suggesting annotation noise. Therefore, no clear representative function emerges.","confidence":"","size":18,"edges":118,"triangles":396,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":11},{"id":"GO:0097053","count":7},{"id":"GO:0007219","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0019551","count":6}]},{"hash":"2188190727538747134","title":"Histone modification and transcription regulation","description":"The cluster is dominated by histone-related GO terms (H3K4/H3K79 methylation and histone deubiquitination) along with transcription (DNA-templated transcription) and protein interactions. This points to chromatin modification coordinating transcription, with supporting roles for protein oligomerization.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034729","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000920","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1361441796111650986","title":"Developmental Growth Regulation","description":"The top GO terms emphasize multicellular organism growth and post-embryonic development, with related signals like cellular response to glucose and transcriptional regulation, suggesting a set of proteins involved in coordinating growth and developmental programs. Some terms refer to metabolic or obsolete pathways, indicating looser, ancillary connections. Overall, the dominant theme is development and growth regulation, though the cluster shows limited cohesion, so the label is provisional.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":3},{"id":"GO:0033153","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0009791","count":2},{"id":"GO:0071333","count":2}]},{"hash":"440275022846133836","title":"RNA processing and ribosome biogenesis","description":"This cluster is enriched for RNA metabolism and ribosome assembly terms: RNA phosphodiester bond hydrolysis (RNA processing), non-stop decay and nonfunctional rRNA decay (RNA quality control), and ribosomal large subunit assembly, with some phosphorylation signals that may regulate these processes. Some metabolic terms (threonine biosynthesis, methionine salvage) and antibiotic response appear as less central signals, suggesting peripheral involvement. Overall, the prominent theme points to RNA processing/decay and ribosome biogenesis functioning together.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0009088","count":3},{"id":"GO:0019509","count":3},{"id":"GO:0046677","count":3}]},{"hash":"459784147570389619","title":"Developmental Growth Signaling and Ribosome Biogenesis","description":"Top GO terms point to development and growth signaling (gastrulation, skeletal system morphogenesis, seminiferous tubule development, response to growth hormone, TGF-beta signaling) along with protein synthesis and RNA maturation (ribosomal large subunit biogenesis, maturation of LSU-rRNA). There is also epigenetic/regulatory activity (histone methylation, peptidyl-serine dephosphorylation). The overall pattern suggests a cluster centered on developmental growth programs that require robust protein synthesis and regulation, though some terms may reflect annotation noise rather than a tight functional link.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034729","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0060416","count":2}]},{"hash":"1280141946707060448","title":"Unknown","description":"The GO terms are highly diverse, spanning apoptotic signaling, GTPase regulation, osmotic and antibiotic stress responses, vitamin and xenobiotic transport, mitotic reassembly, phosphorylation regulation, and ciliary docking, with no connecting edges. This scattered functional profile provides no coherent theme to label the cluster, so it remains Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0035461","count":2}]},{"hash":"422269448820491964","title":"Growth signaling and ribosome biogenesis","description":"The top terms indicate a combination of growth signaling (TGF-beta response, cell division, regulation of GTPase activity) and components of the translation machinery (ribosome biogenesis, tRNA modification), with additional environmental response terms (nutrient, xenobiotic, hydrogen peroxide). This points to a cluster centered on growth regulation that is closely linked to protein synthesis, i.e., growth signaling allied to ribosome biogenesis.","confidence":"Medium","size":17,"edges":18,"triangles":7,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0071560","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0043547","count":3}]},{"hash":"1317155071436711739","title":"Membrane transport and metal ion homeostasis","description":"The top GO terms cluster around proton transmembrane transport and intracellular ion homeostasis (manganese and potassium), with related membrane processes like phospholipid translocation. While a few metabolic terms appear (serine biosynthesis, stilbene degradation), the dominant signal is membrane transport and metal ion regulation, suggesting this label captures the core function of the cluster.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0030026","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0015991","count":3}]},{"hash":"1771618646668380023","title":"Amino acid and vitamin biosynthesis network","description":"The top GO terms are dominated by biosynthesis and catabolism of amino acids (lysine, leucine, alanine, aspartate) and cofactors (biotin, folic acid) plus protoporphyrinogen IX biosynthesis, indicating a metabolic module focused on amino acid and vitamin/cofactor synthesis. Notch signaling appears only as a minor outlier rather than defining the cluster.","confidence":"High","size":17,"edges":23,"triangles":5,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0006782","count":5},{"id":"GO:0097053","count":4},{"id":"GO:0007219","count":4}]},{"hash":"2096830556231652920","title":"Mitochondrial energy production and redox homeostasis","description":"The top GO terms point to mitochondrial ATP synthesis coupled to electron transport and removal of superoxide radicals, indicating a core theme of energy metabolism and redox balance. Other terms (translation, DNA repair) are present but likely reflect broader cellular processes rather than a single cohesive function for the cluster; thus the label emphasizes the dominant mitochondrial energy/redox aspects. ","confidence":"Medium","size":17,"edges":97,"triangles":248,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0042775","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0015774","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042128","count":2}]},{"hash":"1062359793263726581","title":"Mitotic Chromosome Assembly and Microtubule Dynamics","description":"The top GO terms show centromeric chromatin assembly (CENP-A), microtubule severing, and cell division, which together point to mitotic processes and chromosome maintenance. There are additional terms related to multicellular development and vesicle transport, but the strongest signal is mitosis-related chromatin organization and microtubule dynamics, with some peripheral roles in broader cellular functions.","confidence":"Medium","size":17,"edges":13,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0035948","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0006888","count":3}]},{"hash":"595523163861771025","title":"Chromatin remodeling and epigenetic regulation (plant development)","description":"The cluster\u2019s top GO terms revolve around chromatin dynamics (nucleosome disassembly, chromatin organization, DNA replication-dependent chromatin assembly) and epigenetic marks (DNA methylation, histone methylation), plus a note on alternative splicing. Development-related terms like vegetative meristem growth and trichome differentiation suggest this group regulates gene expression through chromatin state during plant development. Together these indicate a cohesive theme of chromatin remodeling and epigenetic control in plants.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006337","count":2},{"id":"GO:0010216","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0043046","count":2}]},{"hash":"730149825129004821","title":"Ribosome Biogenesis and SRP-Dependent Translation","description":"This cluster is anchored by ribosome-related terms: maturation of SSU-rRNA and SRP-dependent cotranslational targeting to the membrane, pointing to roles in ribosome assembly and nascent polypeptide targeting to the ER. Additional entries linking proliferation, apoptosis, and DNA damage response suggest a ribosomal-stress\u2013driven network that connects ribosome function to cell-cycle control and genome integrity. A few outliers (like seminiferous tubule development) exist, but the core theme remains translation/ ribosome biology.","confidence":"Medium","size":17,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0043065","count":1}]},{"hash":"1865455678034730574","title":"Chromatin Modification and Nuclear Regulation","description":"The top terms point to chromatin modification (histone H3 acetylation; H3-K79 methylation) and nuclear processes (protein localization in nucleus; RNA Pol II tethering at the nuclear periphery), with supportive developmental signals. This suggests a coherent theme around chromatin state control and nuclear organization influencing transcription and cell fate, despite some obsolete terms.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0000973","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001833","count":1}]},{"hash":"1607482917963100804","title":"Calcium-dependent exocytosis and developmental signaling in vertebrates","description":"The terms converge on calcium ion-dependent exocytosis, Rho signaling, and neural/cardiovascular development (nervous system, heart, skeletal development, endocardial cushion fusion), plus synaptic potentiation. This points to a cohesive theme of calcium-driven secretion and signaling guiding vertebrate development and neural function, with a few more general stress-related terms that may reflect conserved pathways but do not overshadow the main pattern.","confidence":"Medium","size":16,"edges":56,"triangles":77,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007124","count":7},{"id":"GO:0034198","count":7},{"id":"GO:0045956","count":7},{"id":"GO:0007266","count":7},{"id":"GO:0001501","count":7}]},{"hash":"377525377700665177","title":"RNA processing and ribosome biogenesis","description":"The cluster is enriched for GO terms related to maturation and processing of rRNA (SSU and LSU, including 5.8S) and ribosomal subunit biogenesis, as well as spliceosome assembly and mRNA splicing topics like RNA exon ligation. The inclusion of mitochondrial large ribosomal subunit assembly and cytoplasmic stress granule localization also ties these proteins to RNA metabolism and ribosome maintenance. This combination points to a cohesive theme of RNA processing and ribosome biogenesis.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010165","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000390","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3}]},{"hash":"2131470456703528244","title":"Calcium signaling and myoblast fusion","description":"Enriched terms point to calcium handling (sarcomeric/SR calcium release and calcium-dependent exocytosis), together with myoblast fusion and GTPase-regulated cell migration, suggesting the cluster centers on calcium-regulated muscle cell fusion and movement.","confidence":"Medium","size":16,"edges":12,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0016477","count":4},{"id":"GO:0045956","count":4},{"id":"GO:0042994","count":3},{"id":"GO:0060316","count":3}]},{"hash":"1167238646652109968","title":"Unknown","description":"The GO terms cover a mix of intracellular transport (ER-Golgi, ribosomal export, ceramide translocation, small peptides export), metabolism (very long-chain fatty acid catabolism, glycine betaine transport), and core nuclear/cellular processes (DNA replication, cell division, nucleotide-excision repair). This broad, heterogeneous spread does not point to a single cohesive biological function or pathway for the cluster.","confidence":"","size":16,"edges":16,"triangles":0,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0000056","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0030433","count":3}]},{"hash":"69439359597156935","title":"Amino acid biosynthesis and transsulfuration","description":"The top GO terms cluster around amino acid biosynthesis and related metabolism, notably transsulfuration (cysteine), serine (including D-serine), pyruvate biosynthesis, and other amino acid precursor pathways. This suggests the proteins work together in amino acid biosynthetic and central carbon metabolic processes, despite some outdated GO entries. ","confidence":"High","size":16,"edges":113,"triangles":471,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019346","count":7},{"id":"GO:0019295","count":7},{"id":"GO:0019343","count":7},{"id":"GO:0006535","count":7},{"id":"GO:0009097","count":7}]},{"hash":"580577044636121476","title":"Chromatin remodeling and transcription regulation","description":"Most terms describe chromatin organization and transcription control (rDNA heterochromatin formation; transcription initiation-coupled chromatin remodeling; DNA replication\u2013dependent chromatin assembly; establishment of protein localization to chromatin). The protein heterotetramerization term suggests chromatin-associated complexes. While a few terms pertain to growth, defense, or proteolysis, the dominant signal is nuclear chromatin regulation.","confidence":"High","size":16,"edges":20,"triangles":23,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":8},{"id":"GO:0051290","count":5},{"id":"GO:0000183","count":5},{"id":"GO:0045815","count":5},{"id":"GO:0006335","count":5}]},{"hash":"7988608488717735","title":"DNA Replication and Repair","description":"The majority of GO terms are centered on DNA synthesis and maintenance\u2014DNA replication (leading and lagging strands) and various DNA repair pathways (UV-damage excision repair, homologous recombination, nucleotide-excision repair). A couple of terms (bone ossification, ER unfolded protein response) appear peripheral, but the dominant signal points to DNA replication and repair machinery. Confidence: High","confidence":"","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":2},{"id":"GO:1900101","count":2},{"id":"GO:1903460","count":1},{"id":"GO:1903459","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1884054207248556706","title":"Developmental gene regulation and morphogenesis","description":"These proteins are linked to a broad set of developmental and differentiation processes across several tissues (chromatin remodeling, neural tube formation, cardiogenic morphogenesis, mammary gland development, ureter smooth muscle differentiation, germ-line and T cell receptor\u2013related processes, and TGF-beta\u2013responsive signaling). The common thread is regulation of development and cell fate across multiple lineages, rather than a single pathway, suggesting a general role in developmental gene regulation and morphogenesis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0071864","count":2},{"id":"GO:0003142","count":2},{"id":"GO:0019100","count":2},{"id":"GO:0071560","count":2}]},{"hash":"2147990853716905013","title":"Unknown","description":"The GO terms are highly disparate, spanning post-translational modification (peptidyl-cysteine S-nitrosylation), various small-molecule catabolic and metabolic pathways (glucose, ethanol, retinol/retinoic acid), stress/metal response (copper ion), plant-specific lignin biosynthesis, and even blood pressure regulation. There is no clear, cohesive biological function or pathway tying these proteins together, and network connectivity is absent, so a single interpretable cluster label cannot be confidently assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018119","count":1},{"id":"GO:0019595","count":1},{"id":"GO:0042573","count":1},{"id":"GO:0000947","count":1},{"id":"GO:0046688","count":1}]},{"hash":"1886602782443072669","title":"Unknown","description":"The top GO terms span development (uterus development, angiogenesis, regulation of myelination), metabolism (triglyceride, pyrimidine, thymidine, tryptophan), detoxification, and physiological regulation (chemotaxis, regulation of gastric motility). This broad mix suggests there isn\u2019t a single cohesive function or pathway tying all proteins together, but rather diverse roles across tissues and processes; thus a single informative label is not supported.","confidence":"","size":16,"edges":71,"triangles":214,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":3},{"id":"GO:0006641","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0006206","count":3},{"id":"GO:0000162","count":3}]},{"hash":"1878638603583375141","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":12,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0033615","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0001682","count":1},{"id":"GO:1905267","count":1}]},{"hash":"1894139942948999183","title":"Vesicle trafficking and plant hormone responses","description":"This cluster's GO terms center on ER-Golgi vesicle transport (ER to Golgi and Golgi to ER), suggesting a shared role in intracellular trafficking. The presence of jasmonic acid, gibberellin, and osmotic stress responses points to involvement in plant signaling and stress adaptation, which often intersect with trafficking pathways. Some terms like pigmentation and trichome patterning are peripheral developmental hints, and a few terms (viral process, telomere localization) may be less directly connected.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0009739","count":2},{"id":"GO:1903770","count":2}]},{"hash":"1548829769752438659","title":"Mitochondrial Transport and Membrane Dynamics","description":"The majority of top GO terms describe transmembrane transport of ions and metabolites across mitochondrial membranes (manganese, NAD, phosphate, ATP, ornithine) and mitochondrial membrane fission, plus energy-related processes like adaptive thermogenesis. A couple terms are broader or less directly linked (necroptotic regulation, female pregnancy), but the prevailing theme is mitochondrial transport and membrane dynamics, justifying this label.","confidence":"High","size":16,"edges":25,"triangles":14,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060546","count":8},{"id":"GO:1990845","count":8},{"id":"GO:0036233","count":8},{"id":"GO:0090149","count":8},{"id":"GO:0000066","count":8}]},{"hash":"141509332461392907","title":"Golgi-ER and Synaptic Vesicle Trafficking","description":"The top terms are dominated by vesicle transport, especially retrograde Golgi-to-ER transport and anterograde synaptic vesicle transport, pointing to a core vesicle trafficking theme. Other terms (chromatin organization, rDNA maintenance, mitotic membrane events) appear less cohesive with this main pattern, likely representing background or ancillary functions.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0010815","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0030574","count":1}]},{"hash":"1610529993590836220","title":"Biosynthesis and central metabolism cluster","description":"The proteins are enriched for a range of biosynthetic and energy-related processes, including TCA cycle activity, serine and fatty acid biosynthesis, menaquinone biosynthesis, antibiotic biosynthesis, and iron-sulfur cluster assembly/maturation, plus regulatory response to cAMP. This points to a coherent functional module focused on metabolite and cofactor production rather than a single isolated pathway, with peripheral regulation hints. ","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0006564","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0019700","count":3},{"id":"GO:0051591","count":3}]},{"hash":"1126805968951879764","title":"Mitochondrial Metabolic Regulation and Transport","description":"The GO terms emphasize mitochondrial membrane potential regulation, mitochondrial fission, and transmembrane transport of NAD, manganese, ornithine, and amino acids, alongside cellular responses to amino acid starvation and insulin, and adaptive thermogenesis. Together they indicate a coherent mitochondrial metabolism/energy homeostasis module, rather than a cytosolic pathway cluster, so the name reflects this mitochondria-centered function.","confidence":"High","size":15,"edges":10,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051881","count":5},{"id":"GO:0034198","count":5},{"id":"GO:0032869","count":5},{"id":"GO:0060546","count":4},{"id":"GO:1990845","count":4}]},{"hash":"2179203174939014026","title":"Apoptosis and Neural Development Gene Regulation","description":"This cluster is driven by GO terms for apoptosis (mitotic cell cycle, apoptotic process, positive regulation of apoptotic process) and neural development/synaptic activity (forebrain development, long-term synaptic potentiation, excitatory postsynaptic potential). The presence of mRNA processing and transcription regulation terms suggests broader gene expression control accompanying these processes, indicating a theme where apoptotic decisions intersect with neural development and gene regulation rather than a single cohesive pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0034727","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0060291","count":2}]},{"hash":"2166363647238694477","title":"Transmembrane Transporters and Secretion Systems","description":"The top GO terms indicate a cluster dominated by diverse transmembrane transport activities (vitamins, xenobiotics, taurine, phospholipids, glycerophosphodiesters, fatty acids) and related export/secretion processes, plus a membrane-associated cytochrome complex assembly. This points to a cohesive function around membrane transport and secretion machinery rather than a single substrate, warranting a concise label centered on transmembrane transport and secretion.","confidence":"High","size":15,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":11},{"id":"GO:0006855","count":11},{"id":"GO:0045332","count":9},{"id":"GO:0015734","count":9},{"id":"GO:0001407","count":9}]},{"hash":"998366353371078465","title":"Oxidative Stress Response and Biosynthesis","description":"This cluster is enriched for redox-related terms (oxidation-reduction process and cellular response to hydrogen peroxide) and responses to xenobiotics, suggesting oxidative stress handling. It also includes several biosynthetic processes (tetrahydrofolate, antibiotic, and wybutosine biosynthesis) and metabolic regulation, implying a theme of redox-responsive proteins connected to biosynthetic activities. Some terms are obsolete, so the signal is not perfectly uniform, but the main thread appears to be oxidative stress response coupled with biosynthesis.","confidence":"Medium","size":15,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0070301","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0046654","count":2},{"id":"GO:0007568","count":2}]},{"hash":"311896805060255165","title":"Unknown","description":"The top GO terms are diverse, spanning cell cycle progression (G1/S transition), molybdenum cofactor biosynthesis, and synaptic receptor clustering (glycine and GABA), plus actin dynamics. With no edges connecting proteins and no shared functional theme, there isn't a clear common function linking this cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0006777","count":1},{"id":"GO:0018315","count":1},{"id":"GO:0032324","count":1},{"id":"GO:0072579","count":1}]},{"hash":"186978106894655596","title":"Mitotic Chromatin Assembly and Protein Trafficking","description":"This cluster centers on centromere-associated chromatin assembly (CENP-A) and cell division/microtubule dynamics, complemented by key protein trafficking processes (ER to Golgi transport and peroxisomal matrix import) and protein oligomerization, with oxidative stress response as a secondary context. The combination suggests a theme around mitotic chromatin remodeling alongside broader protein processing and trafficking activities.","confidence":"Medium","size":15,"edges":55,"triangles":99,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0051013","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0016558","count":4}]},{"hash":"1381862143671640438","title":"Translation machinery and ribosome biogenesis","description":"The cluster is dominated by GO terms related to protein synthesis, including general translation, initiation, elongation, termination, and ribosome biogenesis, plus selenocysteine incorporation. This points to components of the translation apparatus and its regulation rather than a single signaling pathway. A few ancillary terms like mRNA decay and glial proliferation appear but do not override the central theme of translation.","confidence":"High","size":15,"edges":103,"triangles":430,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0046677","count":3},{"id":"GO:2000767","count":3},{"id":"GO:0000288","count":3},{"id":"GO:0045901","count":3}]},{"hash":"313723471858090153","title":"Ras/Rac GTPase signaling and actin cytoskeleton remodeling","description":"The terms cluster around regulation of GTPase activities (Ras, Rac) and extensive actin remodeling processes (lamellipodium and actin bundle assembly, membrane tubulation, cell spreading) that coordinate epithelial polarity and cytoskeletal dynamics, suggesting a cohesive theme of signaling-driven cytoskeletal organization. Some peripheral terms (osteoblast fate, IL-7 response) may reflect broader cellular contexts but do not override the core cytoskeletal/polarity focus.","confidence":"High","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0046580","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0097320","count":2},{"id":"GO:0035020","count":2}]},{"hash":"387270439459904660","title":"Ribosome Quality Control and RNA Processing","description":"The top terms point to ribosome-associated ubiquitin-dependent protein catabolic activity and rescue of stalled ribosomes, indicating a focus on ribosome quality control and proteostasis during translation. The presence of mRNA splicing and nuclear localization terms suggests concurrent RNA processing and nuclear functions. Some outlier terms exist, but the dominant theme supports translation surveillance coupled with RNA metabolism.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990116","count":3},{"id":"GO:0018937","count":2},{"id":"GO:0072344","count":2},{"id":"GO:1902167","count":2},{"id":"GO:1903026","count":2}]},{"hash":"1526640565885211122","title":"Ribosome Biogenesis and Translation Initiation","description":"The top GO terms cluster around ribosome assembly and maturation (ribosome biogenesis; maturation of rRNA; large subunit assembly) and initiation/regulation of translation (translation reinitiation; formation of translation preinitiation complex; regulation of translational initiation), with additional viral initiation terms. This suggests proteins involved in assembling ribosomes and initiating protein synthesis, including initiation regulation and viral IRES-associated initiation, making a combined label appropriate.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0008283","count":2}]},{"hash":"1282310816384158560","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0000466","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3}]},{"hash":"1614568238812078111","title":"Ribosome Biogenesis and rRNA Processing","description":"This cluster shows strong representation of rRNA maturation (SSU/LSU and 5.8S) and ribosomal large subunit biogenesis, pointing to a nucleolar role in ribosome assembly. While there are some additional terms related to mRNA splicing and broader cellular processes (e.g., ER-to-Golgi transport and actin regulation) that may reflect annotation noise or shared housekeeping functions, the dominant signal is ribosome biogenesis and rRNA processing.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0000463","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000398","count":3}]},{"hash":"1181290613069936934","title":"Ribosome Biogenesis and Translation","description":"Top terms are dominated by ribosome biogenesis, ribosomal subunit assembly, SSU-rRNA maturation, translation, and translation initiation/reinitiation, pointing to a cluster centered on ribosome production and protein synthesis. A few terms on DNA-templated transcription and mRNA splicing are present but secondary. Overall, the cluster most likely comprises factors involved in ribosome biogenesis and the translation machinery.","confidence":"High","size":15,"edges":29,"triangles":26,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000028","count":2}]},{"hash":"1431447683346876403","title":"Folate cofactor metabolism and manganese homeostasis","description":"The top terms indicate folate-related processes (tetrahydrofolate interconversion and biosynthesis) and a vitamin B2 response, pointing to folate/cofactor metabolism. Additionally, manganese ion homeostasis and transport terms suggest metal ion handling. Although some terms are obsolete and there are no network edges, the shared theme centers on cofactors (folate and manganese) essential for enzymatic activity, justifying a combined label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033274","count":2},{"id":"GO:0070829","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0035999","count":2},{"id":"GO:0055114","count":2}]},{"hash":"806056765780588359","title":"ER-Golgi vesicle trafficking and growth signaling","description":"This cluster aggregates proteins involved in ER-to-Golgi vesicle transport, COPII budding, and retrograde Golgi-ER movement, plus factors regulating GTPase activity and TORC1 signaling, pointing to a coherent role in vesicle trafficking tied to cell growth and proliferation. The brain development and cell division terms suggest broader developmental and proliferative contexts.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0070262","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":4}]},{"hash":"783956082678101294","title":"RNA silencing and translational regulation","description":"Based on the GO terms, this cluster is dominated by ncRNA- and miRNA-mediated gene silencing, regulation of translation initiation, and RNA processing (spliceosome, mRNA stability), plus assembly of the eIF4F complex. Together these point to a cohesive role in post-transcriptional gene regulation, particularly RNA silencing and control of translation, with some associated signals related to differentiation and stress responses. ","confidence":"High","size":15,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":1},{"id":"GO:0060218","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0071356","count":1},{"id":"GO:0031047","count":1}]},{"hash":"1217550378305866581","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":73,"triangles":199,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0044205","count":4},{"id":"GO:0006541","count":4},{"id":"GO:0001889","count":3},{"id":"GO:0071548","count":3},{"id":"GO:0043200","count":3}]},{"hash":"1133163722080704551","title":"Chromatin silencing and heterochromatin maintenance","description":"GO terms point to heterochromatin formation and silencing at repetitive regions (rDNA, subtelomeres, silent mating-type loci), along with nucleosome regulation and histone deacetylation, indicating a chromatin silencing/epigenetic regulation theme. Some terms appear as outliers (aggresome assembly, lignin biosynthesis) but do not shift the primary theme. ","confidence":"High","size":14,"edges":67,"triangles":183,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0070842","count":4},{"id":"GO:0009809","count":3},{"id":"GO:0006344","count":3},{"id":"GO:0000183","count":3}]},{"hash":"1346390078117737746","title":"Neuronal development and dopaminergic signaling","description":"The top GO terms are centered on forebrain development, dendrite morphogenesis, excitatory postsynaptic potentials, and cellular response to dopamine, together with exocytosis-related regulation and calcium-dependent signaling. This points to a cohesive theme of neuronal differentiation and synaptic/dopaminergic signaling, with some cell cycle terms likely reflecting broader cellular contexts. Overall, the cluster seems best described by neuronal development and dopamine-responsive synaptic functions.","confidence":"Medium","size":14,"edges":22,"triangles":7,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0030900","count":9},{"id":"GO:0050852","count":9},{"id":"GO:0048813","count":9},{"id":"GO:0060079","count":9}]},{"hash":"1089473614813102322","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071030","count":1}]},{"hash":"2217889103623059100","title":"Transcription and Protein Acetylation","description":"The top GO terms cluster around DNA-templated transcription and several acetylation processes (N-terminal methionine acetylation, spermine and putrescine acetylation), implying regulation of gene expression through post-translational modification. While other terms touch on metabolism and sporulation, the shared emphasis on transcriptional control and acetylation provides the most coherent theme for this cluster. Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0071962","count":1},{"id":"GO:0032919","count":1},{"id":"GO:0017196","count":1}]},{"hash":"1977603507199028633","title":"Mitochondrial Translation and Respiratory Metabolism","description":"The cluster is anchored by mitochondrial processes: mitochondrial translation, respiration (electron transport) and ATP synthesis, plus mtDNA replication and transcription. It also includes RNA modification activities (pseudouridine synthesis) across RNA types, which ties into mitochondrial gene expression and RNA maturation. A minor term links to energy sensing in glucose-stimulated insulin secretion, reflecting broader cellular energy homeostasis.","confidence":"High","size":14,"edges":70,"triangles":181,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0032543","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0042775","count":1},{"id":"GO:0061179","count":1}]},{"hash":"533943450719447522","title":"Membrane Proteolysis and NFAT Signaling","description":"This cluster is anchored by several GO terms related to membrane protein proteolysis (intracellular and ectodomain) and proteolysis linked to ER-to-cytosol retrograde transport, as well as positive regulation of the calcineurin-NFAT signaling cascade. These overlap to suggest a core theme of regulated membrane proteolysis coupled to calcium-dependent transcriptional signaling pathways, often involved in immune signaling. Other terms present (mRNA export, DNA replication, potassium ion transport, miRNA silencing) are more peripheral to this central theme, indicating some functional diversity, but the membrane proteolysis and NFAT-related functions appear most representative of the cluster. ","confidence":"Medium","size":14,"edges":24,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0050776","count":1},{"id":"GO:0031293","count":1}]},{"hash":"55006738817547186","title":"Cell Cycle and DNA Replication","description":"The cluster is dominated by terms related to DNA replication, G1/S transition, meiotic cell cycle, and kinetochore localization, indicating a shared role in cell division and chromosome maintenance. Some peripheral terms touch on neural development and immune signaling, but the core signal centers on cell cycle processes, justifying the label.","confidence":"High","size":13,"edges":64,"triangles":180,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0060079","count":5},{"id":"GO:0000082","count":5},{"id":"GO:0042220","count":5}]},{"hash":"1970152289838045555","title":"Lipid transport and secretion","description":"The top GO terms converge on membrane-associated transport and export of lipids and related metabolites (phospholipids, glycerophosphodiesters, long-chain fatty acids), plus a secretion pathway (Type I secretion) and xenobiotic export. A few terms (SOS response, obsolete terms) are less informative, but the dominant signal is lipid transport and secretion across membranes, indicating a cohesive membrane transport/secretion cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0009086","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045332","count":2},{"id":"GO:0015734","count":2}]},{"hash":"777409985799775867","title":"Translation machinery and mRNA decay","description":"Most top GO terms converge on protein synthesis via cytoplasmic translation, including initiation, elongation, termination, and translational regulation, as well as deadenylation-dependent mRNA decay and selenocysteine incorporation. This indicates a cluster centered on the translation apparatus and its mRNA turnover controls, with a couple of auxiliary terms (glial cell proliferation, response to antibiotic) likely reflecting secondary roles of some members.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0051301","count":3},{"id":"GO:0000288","count":3},{"id":"GO:0045901","count":3},{"id":"GO:0006415","count":3}]},{"hash":"1269266386956298460","title":"Nervous System Development and Metabolism","description":"The presence of brain development and spinal cord development terms suggests a neural-development focus, while epithelial differentiation and mitotic processes indicate broader cell differentiation. Nearby metabolic terms (molybdenum cofactor biosynthesis, transsulfuration, glycerol metabolism, redox homeostasis) imply metabolic support for development. Together, the cluster appears to couple neural development with cellular metabolism rather than a single narrow pathway.","confidence":"Low","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006777","count":2},{"id":"GO:0019346","count":2},{"id":"GO:0070329","count":2},{"id":"GO:0021510","count":2}]},{"hash":"663120822255659505","title":"Virus-host interaction and immune modulation","description":"These terms cluster around viral life-cycle steps (virion assembly, translocation of proteins into host cytoplasm, pore complex assembly) and host immune responses (TNF production, IgG isotype switching). Some terms are more general stress responses, but the overall theme points to proteins involved in virus-host interactions and immune signaling.","confidence":"Medium","size":13,"edges":25,"triangles":23,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0033198","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0046931","count":4},{"id":"GO:0051131","count":4},{"id":"GO:1904469","count":4}]},{"hash":"1700384524767466281","title":"Metabolic Stress Response","description":"These proteins show enrichment for core metabolic processes (one-carbon metabolism, shikimate pathway, adenine biosynthesis) alongside diverse stress-response terms (response to hypoxia, response to xenobiotic stimulus, response to glucocorticoid). The shared theme appears to be metabolic adjustment under various stress conditions, rather than a single specific pathway. Some GO terms are marked obsolete, likely reflecting historical annotations rather than new biology; the lack of observed interactions (Edges 0) suggests a broad, high-level grouping rather than a tightly connected module.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006730","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0019510","count":2}]},{"hash":"2230759667098254857","title":"Plant secondary metabolism and hormone biosynthesis","description":"The terms cluster around plant-related processes such as stilbene catabolism, strigolactone biosynthesis, and secondary shoot formation, with supporting catabolic and toxin-response terms that together point to a broad plant metabolism/hormone-related cluster rather than a single narrow function.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":1},{"id":"GO:0010223","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0097755","count":1},{"id":"GO:1901601","count":1}]},{"hash":"970172382145722490","title":"ER Protein Quality Control","description":"The terms cluster around endoplasmic reticulum proteostasis\u2014ERAD, chaperone-assisted folding, misfolded protein transport, and redox-related folding. These point to a coherent function in ER quality control and protein folding. A couple terms (DNA replication, tRNA import) are outliers but do not negate the dominant ER proteostasis theme.","confidence":"High","size":13,"edges":12,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0071374","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0035719","count":2}]},{"hash":"947096394580310475","title":"UV-induced DNA damage response and translesion synthesis","description":"This cluster is dominated by GO terms linking DNA replication (DNA-templated replication) with translesion synthesis (both error-free and error-prone) and a cellular response to UV-C, all pointing to a DNA damage tolerance and replication-stress program activated by UV lesions. Some translation initiation terms and a couple of archaic salvage terms appear as noise, but the core theme centers on coping with UV-induced DNA damage via replication and TLS pathways.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":2},{"id":"GO:0070987","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0071494","count":1},{"id":"GO:0006446","count":1}]},{"hash":"979927474283949751","title":"Actin-driven cytoskeleton remodeling and cell polarity","description":"This cluster shows enrichment in terms related to actin cytoskeleton dynamics (pseudopodium assembly, dendrite development, and actin reorganization) and cell polarity (epithelial apical/basal polarity), plus vesicle trafficking and differentiation processes, suggesting proteins that coordinate cytoskeletal remodeling, polarity establishment, and related signaling.","confidence":"Medium","size":13,"edges":35,"triangles":35,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":4},{"id":"GO:0045859","count":4},{"id":"GO:0030225","count":4},{"id":"GO:0006623","count":3},{"id":"GO:0045197","count":3}]},{"hash":"1653715907563095699","title":"Acetylation-Driven Polyamine and Amino-Metabolic Pathways","description":"Many top terms point to acetylation (N-terminal acetylation; spermine, spermidine, putrescine acetylation) and polyamine metabolism (putrescine, spermidine, spermine), with MELatonin biosynthesis and glucosamine/arginine metabolism suggesting broader amine- and amino-sugar metabolic connections. The presence of a chromatin-related term (centromeric cohesion) hints at acetylation\u2019s role in chromatin regulation. Together, these indicate an acetylation-centric network linking protein modification and amine metabolism. ","confidence":"Medium","size":13,"edges":73,"triangles":238,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071962","count":10},{"id":"GO:0032919","count":10},{"id":"GO:0017196","count":10},{"id":"GO:0032920","count":10},{"id":"GO:0006041","count":10}]},{"hash":"858823178473309443","title":"Plant chloroplast gene expression and metabolism","description":"This cluster prominently features chloroplast-specific processes such as chloroplast mRNA processing, alongside broader plant metabolism themes (redox homeostasis, cofactor biosynthesis like ubiquinone and molybdenum cofactor) and a developmental note (meristem development). The combination suggests a plant-centric module tying chloroplast gene expression to cellular metabolism and development, though the mix of terms also spans general metabolism, so the link is plausible but not exclusive.","confidence":"Medium","size":13,"edges":23,"triangles":18,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0019432","count":2},{"id":"GO:0031426","count":1},{"id":"GO:0006744","count":1},{"id":"GO:0080163","count":1}]},{"hash":"162158309163430692","title":"Mitotic spindle and microtubule organization","description":"The dominant GO terms cluster around mitosis and cytoskeletal microtubule dynamics (microtubule nucleation, spindle pole body duplication, spindle midzone assembly, cytoplasmic microtubule organization, cell cycle, and cell division). Some terms like neuron differentiation and interleukin-4 response are present but less representative, so the overall theme is mitotic spindle formation and microtubule organization.","confidence":"High","size":12,"edges":16,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0007020","count":3},{"id":"GO:1903087","count":3},{"id":"GO:0051258","count":2}]},{"hash":"1285356724023586573","title":"Mitosis and DNA replication","description":"The cluster is dominated byGO terms related to DNA replication (GO:0006260) and mitotic processes such as centrosome separation (GO:0007100), metaphase chromosome alignment (GO:0007080), and cytokinesis (GO:0000281). There are also chromatin-related activities (DNA unwinding and nucleosome mobilization) and cell polarity/cell shape regulation, all of which point to coordinated cell cycle progression, chromosome dynamics, and cytoskeletal remodeling. Despite some obsolete terms, the prevailing theme connects DNA replication with mitotic chromosome segregation and division.","confidence":"High","size":12,"edges":46,"triangles":86,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":4},{"id":"GO:0032508","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0007100","count":3},{"id":"GO:0007080","count":3}]},{"hash":"2161684167302119282","title":"Heat Stress, Transcriptional Regulation, and Mitophagy","description":"The cluster contains GO terms tied to heat/stress responses, both general transcription and its negative regulation, and autophagy-related processes like mitophagy and nucleophagy, plus cytoskeletal remodeling (actin filament bundle assembly). This combination points to a coordinated stress-adaptation program where transcriptional changes accompany organelle turnover and cytoskeletal dynamics. Some terms (defense, lipidation) may reflect broader stress signaling, but the core theme is stress-induced transcriptional control with autophagy.","confidence":"Medium","size":12,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0045892","count":2}]},{"hash":"1082339827317563241","title":"Neural development and synaptic signaling","description":"The cluster is dominated by neural-related terms: nervous system development, hippocampus development, dendrite morphogenesis, axon extension, excitatory postsynaptic potential, and calcium-dependent exocytosis, plus dopamine response, pointing to roles in neuronal growth and synaptic communication. A single immune signaling term (T cell receptor signaling) appears among the top terms, which may reflect annotation overlap or multifunctional proteins, but the overall theme centers on neural development and synaptic function.","confidence":"Medium","size":12,"edges":20,"triangles":13,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050852","count":8},{"id":"GO:0048813","count":8},{"id":"GO:0060079","count":8},{"id":"GO:0033138","count":8},{"id":"GO:0000278","count":8}]},{"hash":"1804582817879088616","title":"Translation initiation machinery","description":"The top GO terms are dominated by translation initiation-related processes, including regulation of translational initiation, formation of the translation preinitiation complex, and cytoplasmic translational initiation, with several terms pointing to initiation steps. A few other terms (ethylene response, NO signaling) are less representative and do not define the cluster, so the core theme remains protein synthesis initiation. This suggests the proteins function together in the initiation phase of translation.","confidence":"High","size":12,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0071369","count":1},{"id":"GO:0043547","count":1}]},{"hash":"1678554023203769073","title":"Vesicle trafficking and ER-Golgi transport","description":"Most terms point to intracellular transport between the endoplasmic reticulum and Golgi, including regulation of COPII vesicle coating, ER-to-Golgi vesicle transport, and Golgi organization, plus localization to the phagophore assembly site and the Cvt pathway, which relate to autophagy-related vesicle trafficking. These recurring themes indicate a coherent cluster centered on vesicle trafficking and Golgi/ER dynamics. A few other terms (splicing, apoptosis, development) are broader cellular processes that may reflect broader roles of the proteins or incidental connections.","confidence":"High","size":12,"edges":36,"triangles":46,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0034497","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0003400","count":2}]},{"hash":"342659127680432927","title":"Myogenesis and Growth Factor Signaling","description":"The strongest terms point to muscle differentiation and regeneration (positive regulation of satellite cell activation, myoblast fusion) together with various growth factor\u2013related pathways (VEGF receptor signaling, thrombopoietin signaling, cellular response to growth factor stimulus). While some terms cover general cellular processes (spliceosomal assembly, sumoylation regulation), the muscle development and growth factor signaling themes predominate, suggesting a myogenesis-related cluster with growth factor responsiveness.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0014718","count":2},{"id":"GO:0033234","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0000245","count":1},{"id":"GO:0007520","count":1}]},{"hash":"200528153910029344","title":"Growth Factor Signaling and Actin Remodeling","description":"The cluster\u2019s GO terms center on cellular responses to growth factors (PDGF, TGF-beta) and signaling pathways (Ras, angiotensin, endothelin), combined with direct roles in actin nucleation, polymerization, and actin-dependent cell motility. This suggests a theme of growth factor\u2013driven remodeling of the actin cytoskeleton to promote cell movement, despite a couple unrelated terms that may be incidental. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043007","count":1},{"id":"GO:0036120","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0046580","count":1},{"id":"GO:0051127","count":1}]},{"hash":"110401518201949078","title":"ESCRT-driven endosomal sorting and trafficking","description":"The top GO terms cluster around ESCRT function, endosome maturation (early to late endosome transport), multivesicular body (MVB) sorting, ubiquitin-dependent degradation, and even viral budding via the ESCRT machinery, all pointing to a core role in ESCRT-mediated endosomal trafficking and protein turnover. Some terms related to cell cycle and spindle regulation may reflect mitotic roles of ESCRT components, but the dominant theme is ESCRT/MVB\u2013dependent sorting and degradation. ","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:2000641","count":3},{"id":"GO:0039702","count":3},{"id":"GO:0043162","count":3},{"id":"GO:0071454","count":3}]},{"hash":"1411407693871838259","title":"Neural development and actin remodeling","description":"The cluster prominently features neural development terms (forebrain development, neural tube closure, multicellular organism development) together with actin cytoskeleton regulation (Arp2/3-mediated actin nucleation) and signaling (peptidyl-tyrosine phosphorylation) and transcriptional control, suggesting proteins involved in neural development with cytoskeletal dynamics and signaling. Some terms like ER stress-induced apoptosis and immune defense are present but less central to the main theme.","confidence":"Medium","size":12,"edges":9,"triangles":0,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050731","count":4},{"id":"GO:2000601","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0070059","count":4}]},{"hash":"1189746754977233800","title":"Dopaminergic Synapse Signaling and Cytoskeletal Remodeling","description":"This cluster is dominated by neuronal-related terms: dendrite morphogenesis, excitatory postsynaptic potential, calcium-dependent exocytosis, and cellular response to dopamine, plus actin cytoskeleton remodeling and dopaminergic signaling. These collectively point to synaptic function and structural remodeling in neurons. Some immune-related terms (T cell receptor signaling, beta selection) and cell cycle reference may reflect annotation noise or broader regulatory roles, but the core theme remains neuronal synaptic signaling and cytoskeletal dynamics.","confidence":"Medium","size":12,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":2},{"id":"GO:0043366","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0048813","count":2}]},{"hash":"192848583883003826","title":"Broad-substrate membrane transporters","description":"The top GO terms point to transmembrane transport of a wide range of substrates (galactose, sialic acid, sodium, phosphate, nitrite, siderophores, arabinose, fucose) and even neurotransmitter loading into synaptic vesicles, suggesting a cohesive group of membrane transporter proteins with broad substrate specificities. The absence of network edges does not contradict this shared functional theme. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042891","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0035435","count":2}]},{"hash":"398731915699114165","title":"Mitochondrial Fe-S Cluster Biogenesis and Respiration","description":"The cluster shows strong signals for mitochondrial metabolism, including iron homeostasis and Fe-S cluster biogenesis (intracellular iron, response to iron(II), iron incorporation into metallo-sulfur clusters) and respiratory processes (mitochondrial electron transport, succinate to ubiquinone, and positive regulation of succinate dehydrogenase). A chromatin remodeling term and an unusual proprioception term appear, likely as noise or misannotation, but the dominant theme is mitochondrial function and iron\u2013sulfur chemistry.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0006879","count":1},{"id":"GO:0090201","count":1},{"id":"GO:0018283","count":1},{"id":"GO:0010040","count":1}]},{"hash":"1052916493316444543","title":"Membrane transport and secretion","description":"Most GO terms center on movement of molecules across membranes or through secretion/translocation pathways, including phospholipid translocation, glycerophosphodiester and fatty acid transport, xenobiotic export, and Type I secretion. Additional terms touch on membrane-associated complex assembly (cytochrome) and peroxisomal import, with an outlier related to antigen processing (MHC I). This suggests a cohesive theme around membrane transport/secretion, though the presence of some immune-related and prokaryotic-specific terms indicates functional diversity within the cluster.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0045332","count":1},{"id":"GO:0015734","count":1},{"id":"GO:0001407","count":1},{"id":"GO:0017004","count":1}]},{"hash":"955507598810682322","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":11,"triangles":1,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0016311","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0006189","count":2}]},{"hash":"1468595346359917066","title":"Amino acid and nucleotide biosynthesis with translation","description":"Top terms show strong signals for amino acid and nucleotide biosynthesis (glutamine, histidine, GMP, NAD+) together with translation, indicating a core theme of metabolic biosynthesis linked to protein synthesis. Hormonal response terms and liver development suggest a liver-associated regulatory context, but the central link remains biosynthetic metabolism coupled to translation.","confidence":"Medium","size":11,"edges":13,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0009435","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0071548","count":1}]},{"hash":"618353600651631567","title":"Diverse biosynthetic pathways","description":"Top GO terms point to multiple biosynthetic processes across varied metabolites (antibiotics, biotin, purines, ubiquinone, chlorophyll) and to RNA/arginine methylation activities, suggesting a cluster centered on broad biosynthetic and modification functions rather than a single pathway. The presence of a few outlier terms (e.g., response to cocaine, obsolete processes) likely reflects annotation noise, but the overarching theme is biosynthesis and related modifications.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0009102","count":2},{"id":"GO:0009113","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009086","count":2}]},{"hash":"1687205939924680193","title":"Xenobiotic/Antibiotic Response and RNA Modification","description":"The cluster is enriched for cellular response to xenobiotic stimulus and antibiotic-related processes, alongside RNA (guanine-N7)-methylation and rRNA modification, suggesting proteins involved in both xenobiotic/antibiotic defense and RNA-processing/modification pathways. Some terms like hormone signaling and differentiation appear ancillary, but the dominant theme centers on xenobiotic/antibiotic response with RNA modification activity.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0046677","count":2}]},{"hash":"958624380596596520","title":"Heterochromatin Formation and Chromatin Regulation","description":"This cluster is dominated by GO terms related to heterochromatin formation (pericentric and subtelomeric), indicating a core function in chromatin organization and epigenetic regulation. While there are additional terms touching on transcription regulation, cell-cycle-related processes, and signaling responses, the strongest signals are about establishing and maintaining heterochromatin, suggesting proteins here are tied to chromatin structure rather than discrete signaling pathways.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030702","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0000083","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0036120","count":2}]},{"hash":"1203737054100410770","title":"ER Protein Folding & Stress Response","description":"The cluster is dominated by GO terms for endoplasmic reticulum protein folding, ER stress response, and redox homeostasis, with supporting protein repair signals, suggesting a cohesive module of ER quality control and stress signaling rather than general transcription or viral processes.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0034976","count":1},{"id":"GO:0046826","count":1},{"id":"GO:0006662","count":1}]},{"hash":"1434794740706389595","title":"Amino-sugar and carbohydrate metabolism","description":"The top GO terms point to amino-sugar (glucosamine, N-acetylglucosamine, UDP-N-acetylglucosamine, N-acetylneuraminate) metabolism alongside broader carbohydrate metabolic processes and pentose phosphate pathway activity, indicating a cohesive theme around carbohydrate flux and amino-sugar turnover, with both catabolic and biosynthetic aspects.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0042594","count":2},{"id":"GO:0006043","count":1},{"id":"GO:0019262","count":1},{"id":"GO:0006048","count":1}]},{"hash":"2158451889450289002","title":"GTPase-Mediated Signaling and Cell Adhesion","description":"This cluster centers on small GTPase signaling (GO:0042997) and multiple receptor-initiated pathways (TCR, ephrin, PDGF receptor, and Wnt signaling), plus cell adhesion and epithelial polarity. The shared GO terms imply a cohesive module linking intracellular GTPase-driven signaling with adhesion dynamics and epithelial organization.","confidence":"High","size":11,"edges":8,"triangles":0,"max_degree":4,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0042997","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0048013","count":4}]},{"hash":"1122483427550128503","title":"Embryonic organ morphogenesis","description":"The terms cluster around morphogenesis and organ development, notably embryonic digestive tract morphogenesis, neural crest cell migration, endocrine pancreas development, and ureteric bud branching morphogenesis. A few terms (detoxification, transcription regulation) are present but do not dominate the cluster\u2019s theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0048557","count":2},{"id":"GO:0001755","count":2}]},{"hash":"208855679079811614","title":"RNA processing and translational regulation","description":"The top GO terms cluster around RNA metabolism and translation control\u2014alternative splicing, mRNA stability under stress, regulation of translational initiation, and assembly of the eIF4F complex, alongside miRNA- and ncRNA-mediated silencing. A few outliers (chemotaxis, cilium localization, estrogen receptor signaling) are present but not dominant, so the core signal points to RNA processing and translational regulation.","confidence":"Medium","size":11,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":1},{"id":"GO:0097499","count":1},{"id":"GO:0033146","count":1},{"id":"GO:0035278","count":1},{"id":"GO:0031047","count":1}]},{"hash":"1674473683263020709","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006362","count":1},{"id":"GO:0031442","count":1},{"id":"GO:0031648","count":1},{"id":"GO:0090262","count":1}]},{"hash":"88821871585833818","title":"Ribosome Biogenesis and Cotranslational Membrane Targeting","description":"The cluster shows a cohesive signal around translation and ribosome biogenesis, plus SRP-dependent cotranslational targeting to membranes (signal recognition, translocation), which points to ribosome-associated protein synthesis and delivery to membranes. The actin-related terms suggest accompanying cytoskeletal rearrangements that can support trafficking or membrane organization, while the membrane energy terms align with membrane-associated processes. Overall, a membrane-targeted translation/biogenesis theme best fits these terms.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042254","count":1}]},{"hash":"266403959969802763","title":"Muscle Development and Transcription","description":"This cluster is characterized by GO terms related to DNA-templated transcription and muscle development: DNA-templated transcription; skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration; myotube cell development. While other terms are broader (e.g., cerebellar cortex development, hepatocyte homeostasis, IL-6 production), the strongest signals tie transcriptional activity to muscle differentiation, suggesting a group of proteins involved in muscle formation and regulation at the transcriptional level.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0014834","count":1},{"id":"GO:0097676","count":1},{"id":"GO:0014904","count":1},{"id":"GO:1903699","count":1}]},{"hash":"1997773408988087372","title":"Retinoid and lipid biosynthesis","description":"The top GO terms show a clear emphasis on retinoid metabolism (retinol, retinal, retinoic acid biosynthesis) along with several lipid biosynthetic processes (sphingolipid, methyl-branched fatty acids). While there is a broader transcription regulation term, the dominant signal is metabolic pathways for vitamin A derivatives and lipids, suggesting a cohesive cluster of enzymes involved in retinoid and general lipid biosynthesis. Some terms (like tropane alkaloid and testosterone biosynthesis) may reflect broader plant metabolic capabilities, but they do not override the retinoid/lipid theme.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042572","count":3},{"id":"GO:0009710","count":3},{"id":"GO:1902321","count":3}]},{"hash":"929402740549773802","title":"Chromatin Remodeling and DNA Replication Control","description":"The cluster centers on chromatin dynamics and cell cycle processes: histone modification (peptidyl-lysine N6-acetylation), subtelomeric heterochromatin formation, DNA replication\u2013dependent chromatin assembly, and mitotic chromosome condensation, with links to regulation of DNA replication and cell division. Some peripheral terms (response to morphine/cold, tRNA gene clustering) are less central but do not overwhelm the core chromatin/replication theme.","confidence":"High","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0006275","count":2},{"id":"GO:0070058","count":2},{"id":"GO:0007076","count":2}]},{"hash":"1760891030666130349","title":"Mitochondrial tRNA aminoacylation and translation","description":"This cluster is dominated by GO terms related to charging mitochondrial tRNAs and mitochondrial protein synthesis (lysyl-, asparaginyl-, and aspartyl-tRNA aminoacylation; overall translation; tRNA processing). The presence of tRNA wobble modification and processing supports a role in mitochondrial translation machinery. A few unrelated terms like DNA replication/recombination appear but are not central to the cluster's core function.","confidence":"High","size":11,"edges":10,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070154","count":5},{"id":"GO:0071915","count":5},{"id":"GO:0072581","count":5},{"id":"GO:0070145","count":5},{"id":"GO:0006412","count":5}]},{"hash":"1114811411980630807","title":"Membrane transporters for xenobiotics and nutrients","description":"The top GO terms are dominated by transmembrane transport activities for xenobiotics, vitamins, taurine, and glycerophosphodiesters, along with phospholipid translocation, pointing to a cluster of transporter proteins handling diverse substrates across membranes. Some terms such as translation and cytochrome complex assembly are less central and may reflect multifunctional annotations or noise, but the core theme is membrane transport. Therefore, the label captures the main function of the cluster without overreaching.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0051301","count":2}]},{"hash":"467273797192839136","title":"Plant secondary metabolite biosynthesis and lipid catabolism","description":"The top GO terms point to biosynthesis of plant secondary metabolites (strigolactones, stilbenes, biotin, and antibiotic-related pathways) and related P450 epoxygenase activity, together with catabolic processes for lipids (triglycerides, phosphatidylserine) and related aromatic compound breakdown. This suggests a metabolic cluster centered on production and breakdown of small molecules in plants, with some developmental context implied by secondary shoot formation. The connection is present but somewhat broad, so the label reflects a general metabolic theme with moderate confidence.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0009102","count":3},{"id":"GO:0010223","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0097755","count":3}]},{"hash":"652523032105039843","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":18,"triangles":14,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1902177","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000453","count":1},{"id":"GO:0002938","count":1}]},{"hash":"789902158618202087","title":"Neural development and transcription","description":"Dominant signals are neural development terms (forebrain development, neural tube closure, multicellular organism development) and transcriptional activity (DNA-templated transcription). Other terms reflect cell cycle and stress or immune responses that can occur during development or under cellular stress, but the core theme remains neural development with associated gene expression.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0001843","count":4}]},{"hash":"109983001049537894","title":"DNA Repair and Genome Maintenance","description":"The cluster is heavily enriched for nucleotide-excision repair and DNA repair terms (NER), pointing to a core function in genome integrity. Related signals include regulation of homologous recombination and telomere loop dynamics, suggesting a broader role in chromatin-associated genome maintenance, with some peripheral terms that may reflect annotation noise or broader cellular contexts.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033683","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0048016","count":2},{"id":"GO:0042144","count":2}]},{"hash":"154401506097971756","title":"Mitochondrial protein assembly and turnover","description":"The strong presence of mitochondrial electron transport (ubiquinol to cytochrome c) plus GO terms for protein oligomerization and ubiquitin recycling points to processes governing mitochondrial protein complex assembly and proteostasis. Some outlier terms (viral/hormone catabolism) appear incidental, but the core pattern centers on mitochondrial metabolism coupled with protein assembly and turnover.","confidence":"High","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":3},{"id":"GO:0006627","count":2},{"id":"GO:0032461","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0016032","count":2}]},{"hash":"1127756172105049724","title":"Chromatin assembly and histone modification","description":"Proteins in this cluster are cohesively linked to establishing and maintaining chromatin states, including subtelomeric and silent heterochromatin formation, DNA replication-dependent chromatin assembly, and various histone modifications that regulate transcription and chromatin structure. The presence of chromatin organization and transcription elongation regulation terms supports a theme of chromatin-based control of gene expression, with some association to cell cycle\u2013related chromatin dynamics.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":2},{"id":"GO:0031567","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0033523","count":1},{"id":"GO:0032968","count":1}]},{"hash":"1059620634446811613","title":"RNA Processing and rRNA Maturation","description":"The top GO terms are dominated by RNA metabolism, including maturation of SSU-rRNA, rRNA processing, and snoRNA splicing, with additional RNA-processing terms like pre-mRNA cleavage. This points to a cluster centered on RNA processing and ribosome biogenesis, even though a few non-RNA-related terms (antibiotic response, various catabolic processes) appear as noise. Confidence: Medium","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0019243","count":1},{"id":"GO:0010197","count":1},{"id":"GO:0017001","count":1}]},{"hash":"1850838537399405977","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0044205","count":2},{"id":"GO:0006207","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0007626","count":1},{"id":"GO:0032263","count":1}]},{"hash":"77720975209177022","title":"Ubiquitin-Dependent Proteolysis and Histone Modification","description":"The top GO terms cluster around ubiquitin-dependent protein catabolic processes and multiple histone modifications (ubiquitination, acetylation, methylation) as well as histone catabolic activity, suggesting a core theme of protein turnover linked to chromatin regulation. Additional terms related to immune signaling (TNF-mediated signaling) and V(D)J recombination point to broader chromatin- and ubiquitin-mediated control of gene expression in immune contexts, while other items hint at related regulatory processes. Overall, the proteins appear connected by a shared role in ubiquitin-driven regulation of chromatin state and transcription, with ancillary links to immune-related remodeling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0070535","count":4},{"id":"GO:1903762","count":4},{"id":"GO:2000620","count":4},{"id":"GO:0033209","count":4}]},{"hash":"713138188677044270","title":"Innate immune signaling and apoptosis","description":"The top GO terms point to innate immune responses (response to LPS, defense against Gram-positive bacteria, NF-kappaB/TNF signaling) and an apoptotic pathway (p53-mediated signaling in response to DNA damage). These collectively suggest a cluster of proteins involved in stress- and immune-related signaling leading to cell fate decisions, with an additional note of general transcriptional regulation under stress. ","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0061408","count":2},{"id":"GO:0042347","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0033209","count":1}]},{"hash":"1565759799511580781","title":"Mitochondrial Transport and Energy Metabolism","description":"These proteins appear linked to membrane transport, especially across mitochondria, including mitochondrial membrane fission and transport of ATP, NAD, ornithine, phosphate, and manganese ions. While a few terms touch on broader processes (adaptive thermogenesis, pregnancy, necroptosis), the dominant theme is mitochondrial transport and energy-related function.","confidence":"Medium","size":10,"edges":14,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060546","count":4},{"id":"GO:1990845","count":4},{"id":"GO:0036233","count":4},{"id":"GO:0090149","count":4},{"id":"GO:0000066","count":4}]},{"hash":"1978067043127456226","title":"Unknown","description":"The terms span immune signaling (cellular response to interleukin-4), metabolism (transsulfuration, GMP biosynthesis, cysteine biosynthesis), cell cycle regulation, transport, and development, with no single cohesive function tying the proteins together. Consequently, there isn\u2019t a concise, representative label beyond Unknown.","confidence":"","size":10,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":2},{"id":"GO:0019346","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0006177","count":2},{"id":"GO:0045794","count":2}]},{"hash":"924012648277124772","title":"Interferon signaling and RNA granule assembly","description":"The cluster is enriched for innate immune signals (RIG-I pathway, type I interferon response, defense against bacteria) alongside RNA metabolism and translational control (stress granule and P-body assembly, mRNA decapping, inhibition of translation). These themes often co-occur during antiviral responses, where RNA granules regulate mRNA fate while interferon pathways are activated. Some transcription/chromatin-related terms may reflect broader regulatory changes during immune signaling, but the core connection is antiviral signaling with RNA granule dynamics.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0031087","count":1},{"id":"GO:0060340","count":1},{"id":"GO:0034063","count":1},{"id":"GO:0033962","count":1}]},{"hash":"702105524773318087","title":"Innate Immune and ER Stress Response","description":"The cluster shows terms tied to innate immune signaling (innate immune response-activating signaling, non-canonical NF-kB signaling, phagocytosis) and ER stress/quality control (ER unfolded protein response, protein folding), with transcriptional regulation (DNA-templated transcription) likely coordinating these responses. A sperm-egg binding term appears unrelated and may reflect a shared domain rather than core function. Overall, the data point to immune and ER-stress related roles.","confidence":"Medium","size":10,"edges":13,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0033144","count":1},{"id":"GO:0010204","count":1},{"id":"GO:1901224","count":1},{"id":"GO:0007339","count":1}]},{"hash":"2050948379662662132","title":"Chemical and metal stress response","description":"The proteins show multiple GO terms related to responses to various chemical stimuli (fatty acids, zinc and cadmium ions, xenobiotics, ethanol) plus a metabolic (heme biosynthesis) and regulatory (transcription elongation) aspect, suggesting a broad cluster centered on chemical/metabolic stress responses rather than a single specific pathway.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":3},{"id":"GO:0010043","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0001666","count":2}]},{"hash":"1645859454583700352","title":"Golgi- and synaptic vesicle trafficking","description":"Top GO terms reveal coordination of Golgi apparatus\u2013related transport (Golgi ribbon formation, intra-Golgi and ER-to-Golgi trafficking, vesicle fusion with Golgi, endosome-to-Golgi transport) and SNARE complex assembly, plus neuronal exocytosis and synaptic plasticity (neurotransmitter release, receptor insertion, and long-term potentiation). This pattern supports a cohesive role for SNARE-mediated vesicle trafficking functioning at the Golgi and at synapses. ","confidence":"High","size":10,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":3},{"id":"GO:0006891","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0098967","count":3},{"id":"GO:0048280","count":3}]},{"hash":"1720150835428130803","title":"Multisubstrate Transmembrane Transport","description":"Based on the GO terms, these proteins are annotated with transport activities across membranes for a variety of substrates (sugars, ions, nitrite, vitamins, aromatic compounds). The unifying theme is transmembrane solute transport rather than a single substrate or process, suggesting a broad transporter-type cluster.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0015707","count":3},{"id":"GO:0071805","count":3}]},{"hash":"783216370944421960","title":"Unknown","description":"The top terms span xenobiotic response, apoptotic regulation, phosphatase activity, DNA replication, lipid and glycogen metabolism, and developmental processes in vascular and nervous systems. The terms are too diverse to define a single cohesive function for this cluster, so Unknown.","confidence":"","size":9,"edges":16,"triangles":14,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035690","count":5},{"id":"GO:2001241","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006685","count":4}]},{"hash":"1710904247084787653","title":"Steroid Hormone Biosynthesis and Gland Development","description":"This cluster is dominated by GO terms for steroid biosynthesis (testosterone biosynthetic process, androgen metabolic process, prostaglandin biosynthetic process) and gland/tissue development (prostate gland growth, mammary gland development, digestive tract development). The convergence on steroid production and its impact on gland development supports a cohesive theme of steroid hormone pathways influencing glandular formation and maintenance, despite one plant-specific term (brassinosteroid biosynthetic process) appearing. Confidence: High.","confidence":"","size":9,"edges":6,"triangles":4,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0061370","count":8},{"id":"GO:0008209","count":8},{"id":"GO:0006699","count":4},{"id":"GO:0090350","count":4},{"id":"GO:0016132","count":4}]},{"hash":"1474711208161335460","title":"Ribosome Biogenesis and Translation","description":"The cluster\u2019s top GO terms are dominated by translation (GO:0006412) and rRNA processing (the ITS1 cleavage term), with several terms touching protein complex formation and transport, which together point to ribosome assembly and protein synthesis as the core function. A few terpenoid biosynthesis terms appear but seem incidental to the main signal. ","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006695","count":1},{"id":"GO:1901663","count":1},{"id":"GO:0043693","count":1},{"id":"GO:0033386","count":1}]},{"hash":"1874648451442345707","title":"Cell stress response and cell cycle checkpoints","description":"This cluster centers on processes tying DNA replication and mitotic checkpoint signaling to stress-induced responses, including ER stress\u2013triggered apoptosis and ER-associated degradation pathways, suggesting a coherent theme of cell cycle surveillance under stress. Some terms appear obsolete or unrelated (e.g., ABA biosynthesis), likely reflecting annotation noise rather than a core function.","confidence":"Medium","size":9,"edges":14,"triangles":8,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0030433","count":3},{"id":"GO:1905150","count":2},{"id":"GO:0090419","count":2}]},{"hash":"1381773482184702655","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006417","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0043248","count":2},{"id":"GO:0032436","count":2},{"id":"GO:0000472","count":1}]},{"hash":"2230249258692767400","title":"Skeletal muscle actin remodeling and contraction","description":"The dominant GO terms point to actin cytoskeleton dynamics (actin filament bundle assembly, regulation of ruffle formation, membrane tubulation) and muscle function (skeletal muscle contraction, actomyosin ring activity, subsynaptic reticulum organization), suggesting a cluster centered on cytoskeletal remodeling in muscle and NMJ architecture. Some terms appear unrelated noise (e.g., translation initiation, cocaine response), but the core theme is actin-driven muscle structure and contraction.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:1990414","count":2},{"id":"GO:1903526","count":1},{"id":"GO:0032233","count":1},{"id":"GO:1900028","count":1}]},{"hash":"1447397151296134057","title":"Erythroid/Megakaryocytic Differentiation Regulation","description":"This cluster is dominated by terms about promoting differentiation of erythrocytes and megakaryocytes and regulating transcription, along with epigenetic regulation of transcription. These motifs point to hematopoietic lineage control, especially erythroid and megakaryocyte pathways, governed at the transcriptional/epigenetic level.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045654","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0034720","count":3},{"id":"GO:0010725","count":3}]},{"hash":"171050043305838820","title":"Fungal glycoprotein biosynthesis and ER-Golgi trafficking","description":"Dominant GO terms center on N- and O-linked glycosylation, cell wall mannoprotein biosynthesis, and ER-to-Golgi vesicle trafficking, indicating maturation of secreted glycoproteins in the fungal secretory pathway. Some other terms appear as minor signals, but the core theme is secretory pathway\u2013mediated glycoprotein processing.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":1},{"id":"GO:0030097","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0006491","count":1},{"id":"GO:0006493","count":1}]},{"hash":"428334683784457908","title":"Unknown","description":"The GO terms span diverse developmental and cellular processes (haltere morphogenesis, forebrain regionalization, Hippo signaling, actin regulation, thyroid hormone response, transcription), with no common function or pathway binding the cluster, and no edges connecting proteins. Therefore there is no coherent functional theme to name the cluster beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900103","count":1},{"id":"GO:0048735","count":1},{"id":"GO:1904425","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0030835","count":1}]},{"hash":"396272630367196302","title":"Epigenetic Chromatin Modification","description":"Based on the top GO terms, the cluster is dominated by chromatin-related processes: histone modifications (H3-K4 trimethylation, H3-K23 acetylation), nucleosome assembly, and DNA methylation/heterochromatin regulation. While there are a few immune tolerance terms present, the strongest signal centers on epigenetic regulation of chromatin state, justifying this label as representative of the cluster\u2019s function.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0080182","count":3},{"id":"GO:2000791","count":2},{"id":"GO:0043972","count":2},{"id":"GO:0002509","count":2},{"id":"GO:0032602","count":2}]},{"hash":"356387671589880012","title":"Unknown","description":"The top GO terms span metal ion homeostasis, immune signaling, sulfur amino acid metabolism, retina development, nucleotide biosynthesis, cell cycle regulation, and metabolic stress, with several obsolete terms present. There is no single unifying function or pathway that ties these terms together for this cluster, so a coherent, specific label isn\u2019t supported.","confidence":"","size":9,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030026","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0019346","count":1},{"id":"GO:0060041","count":1},{"id":"GO:0006177","count":1}]},{"hash":"1615904061827312184","title":"Vitamin A and xenobiotic small-molecule metabolism","description":"Top GO terms center on retinol/retinal metabolism and several small-molecule catabolic pathways (ethanol, D-xylose, naphthalene, norepinephrine) along with related metabolic response processes. This pattern suggests a cluster of proteins involved in broad processing of diverse small molecules, particularly vitamin A derivatives, sugars, alcohols, and other xenobiotic-like substrates, rather than a single specific pathway.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":6},{"id":"GO:0046370","count":5},{"id":"GO:0042574","count":4},{"id":"GO:0006068","count":3},{"id":"GO:0006069","count":3}]},{"hash":"2091099397663672559","title":"Plant metabolism and metal stress responses","description":"The cluster's top GO terms reflect diverse metabolic activities, with a standout plant-specific lignin biosynthesis term and copper ion response, along with various catabolic and retinoid-related processes. This pattern points to proteins involved in plant metabolism and stress signaling rather than a single, cohesive function, hence the label.","confidence":"Medium","size":9,"edges":29,"triangles":47,"max_degree":8,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0018119","count":4},{"id":"GO:0042573","count":4},{"id":"GO:0000947","count":4},{"id":"GO:0046688","count":4},{"id":"GO:0019518","count":4}]},{"hash":"336212203406750067","title":"Developmental morphogenesis signaling","description":"This cluster is enriched for GO terms tied to tissue morphogenesis and developmental signaling, including lung morphogenesis, cartilage condensation, endocardial cushion fusion, and retinal axon guidance, as well as the ERK1/ERK2 cascade that mediates developmental signaling. While some terms (e.g., responses to ionizing radiation and LPS signaling) are broader stress responses, the strongest common theme is developmental tissue formation and communication between signaling pathways.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071479","count":2},{"id":"GO:0003274","count":1},{"id":"GO:0010825","count":1},{"id":"GO:1900436","count":1},{"id":"GO:0031663","count":1}]},{"hash":"1685676438446440981","title":"Neural and heart development","description":"The GO terms point to developmental differentiation across neural lineages (astrocyte and interneuron fate, auditory receptor cells) and cardiac development (sinus venosus morphogenesis, heart rate regulation), with stem cell proliferation as a related theme.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048712","count":5},{"id":"GO:2001038","count":5},{"id":"GO:0006366","count":4},{"id":"GO:2000774","count":3},{"id":"GO:2000648","count":3}]},{"hash":"397563288058584143","title":"Transcription, RNA processing, and TORC1 signaling","description":"This cluster\u2019s top GO terms cluster around DNA-templated transcription, mRNA transport, and rRNA maturation, with TORC1 signaling linking to ribosome biogenesis and gene expression control. Additional terms about phosphatase activity and GTPase regulation suggest broader regulation of signaling and trafficking that supports gene expression programs. The combination points to a cohesive theme of nuclear gene expression regulation and ribosome biogenesis, with TORC1 as a central regulator.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0051028","count":3}]},{"hash":"1745098445669250385","title":"Unknown","description":"The terms span highly diverse processes (sperm capacitation, LPS biosynthesis, ABA signaling, MHC I antigen presentation, vesicle docking/exocytosis, and various phosphorylation-related activities), showing no clear, single theme to tie the proteins together; thus a specific functional label cannot be justified.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":3},{"id":"GO:0016311","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0045332","count":2}]},{"hash":"1191250479617717945","title":"Methylation and diverse biosynthetic processes","description":"This cluster\u2019s prominent GO terms center on methylation (peptidyl-arginine asymmetrical dimethylation, tRNA methylation, tRNA wobble modification, histone methylation) and a variety of biosynthetic pathways (cobalamin, ubiquinone, tagatose-6-phosphate lactose catabolism, ADP-L-glycero-manno-heptose). The strongest recurring signal is methylation-related functions, with several distinct biosynthetic processes also represented, suggesting a theme around modified biomolecules and metabolism. Confidence: Medium","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0090398","count":2}]},{"hash":"512601136618198736","title":"Arginine and RNA methylation enzymes","description":"This cluster is dominated by GO terms for RNA methylation (rRNA guanine-N7 methylation) and peptidyl-arginine methylation, plus arginine-containing post-translational modification (peptidyl-arginine hydroxylation). These point to enzymes involved in arginine-focused protein modifications and RNA methylation, suggesting a unifying theme around methylation/modification rather than a single metabolic pathway. Some peripheral terms about biosynthesis and stress responses may reflect broader metabolic roles of these proteins.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":1},{"id":"GO:0019919","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0017000","count":1}]},{"hash":"1355764173574566898","title":"Unknown","description":"The top GO terms span several distinct themes (ER\u2013Golgi transport, ribosome biogenesis, rRNA maturation, and various developmental/signaling responses) with no single cohesive function linking all members, so a specific, confident label cannot be assigned.","confidence":"","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0034729","count":2},{"id":"GO:0010697","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0071560","count":2}]},{"hash":"1537972911831909557","title":"RNA Processing and Ribosome Biogenesis","description":"The strongest signals are about maturation of rRNA (LSU and 5.8S) and related RNA processing steps, which point to ribosome biogenesis. Other terms (mRNA splicing, DNA replication, methylation) are supportive of nucleic acid metabolism and general cellular processes, but the dominant theme centers on RNA maturation and ribosome assembly.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0036068","count":1}]},{"hash":"1961299976955219632","title":"ER protein folding and ERAD quality control","description":"This cluster centers on endoplasmic reticulum protein handling: folding in the ER, ER-associated degradation (ERAD), chaperone-assisted refolding, and misfolded protein transport, all tied to ER stress responses and redox balance. The combination of folding-related and quality-control GO terms suggests a cohesive ER quality-control machinery theme, with some noise from other processes.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0071374","count":6},{"id":"GO:0036494","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0035719","count":6}]},{"hash":"914382036941657176","title":"RNA modification and ribosome biogenesis","description":"The cluster\u2019s strongest signals are ribosome biogenesis and RNA modification via pseudouridine synthesis of rRNA and snRNA, indicating a core theme of RNA processing and ribosome assembly. Some outlier terms related to unfolded protein response and telomere maintenance appear but are less central to the main RNA-processing theme, suggesting possible annotation noise or broader nuclear RNA biology.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0031120","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0031118","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1235080296396107675","title":"Cell Cycle and Transcription Regulation","description":"The dominant signals are positive regulation of cyclin-dependent kinase activity (cell cycle control) and regulation of transcription from RNA polymerase II promoters, along with meiosis-related processes (homologous chromosome pairing) and proliferation signals. Although some terms touch on stress responses and tissue-specific processes (ER unfolded protein response, stomatal opening, mammary gland proliferation), the core theme centers on controlling cell division and gene expression, making this label a concise reflection of the cluster\u2019s main function. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":3},{"id":"GO:1990069","count":2},{"id":"GO:2000775","count":2},{"id":"GO:0010673","count":2},{"id":"GO:0030968","count":2}]},{"hash":"1546143211745094581","title":"Ubiquitin-Mediated DNA Damage Repair","description":"The top GO terms cluster around ubiquitination processes (autoubiquitination, ubiquitin-dependent ERAD, ubiquitin linkage types) and DNA repair activities (nucleotide-excision repair, DNA repair regulation, meiotic DSB formation). This pattern indicates a functional group centered on ubiquitin signaling that modulates DNA repair and related stress responses.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0070911","count":7},{"id":"GO:0071455","count":6},{"id":"GO:0043524","count":6}]},{"hash":"1093047338845092127","title":"Unknown","description":"The Top Terms span very diverse processes\u2014stress responses (hyperoxia, abscisic acid), DNA repair and ubiquitination, meiosis, and neuronal development\u2014without a single cohesive function linking them. This lack of a clear shared theme makes it inappropriate to assign a specific, representative label to the cluster. Confidence: None","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071455","count":7},{"id":"GO:0043524","count":7},{"id":"GO:0045739","count":7},{"id":"GO:0033182","count":7},{"id":"GO:0044314","count":7}]},{"hash":"1651196670408720310","title":"Dendritic Spine Morphogenesis and Actin Remodeling","description":"The top GO terms point to neuronal morphogenesis (dendrite development, dendritic spine morphogenesis) and cytoskeletal regulation (actin remodeling, pseudopodium assembly, vesicle size), along with a note on inhibitory regulation of excitatory synaptic signaling. While a few terms touch on non-neuronal processes like vacuole targeting and epithelial polarity, the strongest signal is neuronal dendrite/spine formation and synaptic regulation via actin dynamics.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0006623","count":1},{"id":"GO:0045197","count":1},{"id":"GO:0016358","count":1},{"id":"GO:0097494","count":1}]},{"hash":"1226968783948441140","title":"DNA Replication and Fork Elongation Factors","description":"The Top Terms show several DNA replication\u2013related functions (DNA replication, leading strand elongation, mitotic DNA replication checkpoint signaling) indicating a cluster centered on replication machinery and fork progression. While other terms touch on protein folding/assembly and trafficking, the dominant signal is replication-related, justifying a replication/fork-related label.","confidence":"Medium","size":7,"edges":8,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0034214","count":4},{"id":"GO:0018279","count":4},{"id":"GO:0033314","count":4},{"id":"GO:0006272","count":4}]},{"hash":"1142649333525454706","title":"Ubiquitin-Proteasome Mediated Degradation","description":"The cluster is dominated by ubiquitination and proteasomal degradation processes: K11/K48-linked ubiquitination, ERAD, SCF- and APC-dependent proteolysis, and ubiquitin chain formation, pointing to ubiquitin-driven protein turnover and cell-cycle\u2013related proteolysis, with a few related peroxisomal import and developmental terms as secondary associations.","confidence":"High","size":7,"edges":7,"triangles":4,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0010994","count":3},{"id":"GO:0000278","count":3}]},{"hash":"207689874711234215","title":"Cell Cycle and Transcription Regulation","description":"Based on the top GO terms, the proteins are enriched for negative regulation of transcription by RNA polymerase II and regulation of the cell cycle (each appearing twice), with additional signals related to DNA recombination, mRNA stability, and redox/homeostasis. This suggests a cluster of factors that collectively modulate transcriptional activity and cell-cycle progression, with ancillary roles in DNA processing and stress responses.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0007050","count":2},{"id":"GO:0042493","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0043488","count":1}]},{"hash":"983258439600998873","title":"mRNA decay and translation","description":"This cluster is dominated by RNA metabolism signals, with translation (GO:0006412) and several mRNA decay processes (deadenylation- and decapping-dependent decay) plus nuclear-transcribed mRNA catabolic processes, suggesting a group of proteins involved in post-transcriptional regulation and RNA turnover; some terms like steroid biosynthetic process and transcription may reflect peripheral roles or noise. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1901919","count":1},{"id":"GO:0006154","count":1},{"id":"GO:0015967","count":1},{"id":"GO:0006694","count":1}]},{"hash":"1354415628959759054","title":"Ubiquitin-Proteasome Regulation and Immune Signaling","description":"This cluster is centered on ubiquitin-mediated protein turnover, featuring deubiquitination and proteasomal protein catabolic processes, with accompanying immune signaling pathways (TNF-mediated and Fc-epsilon receptor pathways) and viral-process involvement. The presence of cell-cycle regulation and mRNA stability terms adds context to broader post-transcriptional and cell-cycle regulation, but the strongest signal is ubiquitin-proteasome\u2013related functions linked to immune signaling.","confidence":"Medium","size":7,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":4},{"id":"GO:0038095","count":3},{"id":"GO:0061418","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0010972","count":3}]},{"hash":"76607241048912509","title":"Epigenetic transcription and DNA repair regulation","description":"Proteins in this cluster are linked to DNA-templated transcription and chromatin state regulation (heterochromatin maintenance, histone modifications), as well as regulation of double-strand break repair via homologous recombination. Although a few terms touch on immune signaling, the dominant signals point to epigenetic control of transcription and genome maintenance, suggesting involvement in coordinating gene expression with DNA damage responses.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0046325","count":1},{"id":"GO:0010569","count":1},{"id":"GO:1900226","count":1},{"id":"GO:0006344","count":1}]},{"hash":"982844982248381422","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by translation-related GO terms, with translation (GO:0006412) appearing three times, plus ribosomal large subunit assembly and maturation of SSU-rRNA, indicating a primary function in protein synthesis machinery and ribosome biogenesis. Other terms such as fatty acid oxidation, transcription antitermination, and stress/virus responses appear only once and are likely incidental or context-specific, making the core theme clearly centered on ribosome function. ","confidence":"High","size":7,"edges":10,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0009437","count":1},{"id":"GO:0033539","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0006415","count":1}]},{"hash":"610227766362319754","title":"Unknown","description":"The top GO terms span immune signaling, drug responsiveness, hypoxia/HIF-1 signaling, neuronal apoptosis regulation, plant secondary growth, chaperone-mediated assembly, and nitric oxide biosynthesis, with only single terms each; there is no clear unifying function tying these proteins together.","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033160","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0042220","count":1},{"id":"GO:0097411","count":1},{"id":"GO:0043524","count":1}]},{"hash":"1363529200873034065","title":"Unknown","description":"The listed GO terms are very diverse, spanning lipid biosynthesis (unsaturated fatty acids, ergosterol, MIPC), nitrogen metabolism (nitric oxide biosynthesis, nitrate assimilation), mitochondrial inheritance, and even mammalian development (myelin maintenance, sebaceous gland differentiation). There is no cohesive shared function linking these terms, so a single interpretable label cannot be assigned.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006636","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0006809","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0006675","count":1}]},{"hash":"1667465486417001197","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060743","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0003208","count":1},{"id":"GO:0071455","count":1},{"id":"GO:0060841","count":1}]},{"hash":"157846487341187929","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006189","count":1},{"id":"GO:0006730","count":1},{"id":"GO:0033320","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0071951","count":1}]},{"hash":"1758943762457796311","title":"Unknown","description":"The top GO terms span plant development (sepal formation), environmental response (UV-A), several viral processes (virion assembly, viral release, uncoating), plus protein folding, lipid droplets, and leukocyte migration. This mix suggests no single cohesive function ties the proteins together, and with only a couple of edges and no triangles, assigning a specific biological theme is not supported.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048453","count":2},{"id":"GO:0071492","count":2},{"id":"GO:0050714","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2}]},{"hash":"353282977445285901","title":"Ribosome biogenesis and translation machinery","description":"The cluster is dominated by GO terms related to ribosome assembly and function\u2014translation, ribosome biogenesis, rRNA processing, and ribosomal large subunit biogenesis\u2014along with rRNA modification (pseudouridine synthesis) and tRNA aminoacylation, plus translational fidelity maintenance. This points to proteins involved in ribosome maturation, rRNA/tRNA processing, and translation accuracy. A few ancillary terms (transcription, heat response) are less central. Overall, the group reflects core ribosome/translation processes.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006364","count":2},{"id":"GO:0042273","count":2},{"id":"GO:1990145","count":1}]},{"hash":"987168047120962370","title":"Nuclear DNA maintenance and RNA processing","description":"The top GO terms cluster around nuclear genome maintenance (nucleotide-excision repair, DNA recombination, DNA replication) and RNA processing/biogenesis (rRNA maturation, spliceosomal disassembly, ribosomal large subunit biogenesis, mRNP complex assembly, transcription start site regulation). This suggests a functional group of nuclear factors involved in both genome integrity and maturation of RNA for gene expression. Some terms are obsolete or peripheral (e.g., selenite response), but the core signal supports a dual role in DNA maintenance and RNA processing.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006260","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1086755586842329473","title":"Inflammation and ECM remodeling","description":"The GO terms for this cluster predominantly point to host defense responses (defense against Gram-positive bacteria, defense against fungi/yeast, complement activation) together with proteolytic remodeling processes (plasminogen activation and elastin catabolic process, plus positive regulation of plasminogen activation). These together suggest an inflammatory response coupled with extracellular matrix remodeling. Some terms like mRNA splicing and exocrine pancreas development are less connected, but the strongest signal centers on immune defense and tissue remodeling.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:1900738","count":1},{"id":"GO:0050830","count":1},{"id":"GO:0001878","count":1},{"id":"GO:0050832","count":1}]},{"hash":"2028883587208416685","title":"P-body mediated translation regulation","description":"The top GO terms cluster around cytoplasmic translation and translation processes, with specific emphasis on P-body assembly and mRNA turnover (deadenylation-dependent decapping) and negative regulation of translational initiation. This points to a role in cytoplasmic mRNA processing bodies and translational control, with secondary, less-specific links to nucleotide metabolism. So the cluster seems best labeled as P-body\u2013related translation regulation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0019674","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0006741","count":1}]},{"hash":"1708295401217246683","title":"Multisubstrate Transmembrane Transporters","description":"These proteins appear to be membrane transporters handling a variety of substrates, as shown by the top GO terms for transmembrane transport of diverse solutes: sugars (galactose, arabinose), ions (sodium, potassium, nitrite), sialic acid, and 4-hydroxyphenylacetate, along with a note on related metabolic processes like fucose metabolism and vitamin transport. The common theme is broad substrate translocation across membranes, consistent with a cluster of diverse solute transporters rather than a single substrate-specific enzyme.","confidence":"High","size":7,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0071805","count":2}]},{"hash":"764356388611778669","title":"Lipid biosynthesis and metabolism","description":"This cluster is dominated by GO terms for lipid synthesis and related pathways (CDP-diacylglycerol, triglyceride, ether lipids, phosphatidylcholine regulation, cutin biosynthesis), with supporting links to mitochondrial energy metabolism; a few terms touch on development or immune functions, but lipid production/metabolism is the central theme.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010143","count":2},{"id":"GO:0021587","count":2},{"id":"GO:0006663","count":2},{"id":"GO:0070970","count":2},{"id":"GO:0016024","count":2}]},{"hash":"2101258688086072468","title":"Ribosome Biogenesis and Translation Regulation","description":"This cluster centers on ribosome assembly, cytoplasmic translation, and SRP-dependent membrane targeting, highlighting protein synthesis machinery. It also includes RNA-level regulation\u2014alternative splicing, ncRNA-mediated silencing, and mRNA stability control\u2014suggesting coordinated post-transcriptional regulation alongside translation. A few terms (interleukin-4 response and kinase activation) seem less central, likely ancillary. ","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0032147","count":1}]},{"hash":"330550559875321387","title":"Membrane Trafficking and Lipid Transport","description":"Based on the frequent GO terms, the cluster centers on membrane-associated processes: vesicle docking in exocytosis, phospholipid translocation, and transmembrane transport of taurine and glycerophosphodiesters, plus xenobiotic export and cytochrome complex assembly tied to membrane function. While a couple of terms relate to transcription regulation and ubiquitination, the dominant signal is membrane trafficking and lipid/solute transport, suggesting a cohesive functional theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006904","count":2},{"id":"GO:0043124","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0006363","count":2},{"id":"GO:0045332","count":1}]},{"hash":"453991555083345969","title":"Golgi Vesicle Trafficking","description":"The dominant GO terms center on vesicle transport involving the Golgi (intra-Golgi, ER-to-Golgi, Golgi-to-vacuole) and Golgi ribbon formation, indicating proteins involved in Golgi-associated trafficking and organization. A few non-Golgi terms are present but do not override the main theme.","confidence":"High","size":7,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006891","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0090161","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0006888","count":2}]},{"hash":"737160354806355547","title":"Neuronal development and vesicle trafficking regulation","description":"I labeled it Neuronal development and vesicle trafficking regulation because the top terms strongly point to nervous system development (GO:0007399) and positive regulation of neuron projection development (GO:0010976). There are also signals of membrane trafficking control, such as negative regulation of exocytosis (GO:0045920) and negative regulation of pinocytosis (GO:0048550), which aligns with vesicle turnover in neural contexts. While some terms are obsolete and less specific, the core theme ties neuron growth with regulation of vesicle trafficking, supporting this as the cluster function.","confidence":"High","size":7,"edges":12,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0071398","count":1},{"id":"GO:0061508","count":1},{"id":"GO:0006186","count":1},{"id":"GO:0030819","count":1}]},{"hash":"1078811102107963435","title":"Unknown","description":"The seven proteins show a mix of GO terms spanning fungal cell wall biosynthesis, immune signaling, ER stress response, neuromuscular junction assembly, and developmental patterning, with no shared functional thread linking them. This lack of a coherent theme makes a single representative label inappropriate.","confidence":"","size":7,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006078","count":1},{"id":"GO:0042546","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0045064","count":1},{"id":"GO:1903694","count":1}]},{"hash":"982132247045360048","title":"Mitochondrial dynamics and autophagy regulation","description":"The terms cluster around mitochondria-related processes: outer membrane permeabilization, transport along microtubules, microautophagy, mitochondrion-ER tethering, and phospholipid homeostasis. Added GTPase signaling indicates coordinated control of movement and membrane remodeling, while xenobiotic response suggests stress-associated remodeling. Together, these imply a module governing mitochondrial dynamics, lipid balance, and autophagic turnover, with links to vesicle trafficking.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097345","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0047497","count":2}]},{"hash":"2166691677074248430","title":"DNA metabolism and protein homeostasis","description":"The top GO terms show strong signals for nuclear DNA replication and DNA-templated transcription, while several other terms point to proteostasis-related processes (protein unfolding/hexamerization, SCF complex/disassembly under stress) and Golgi/vesicle trafficking. This suggests a cluster that touches both nuclear DNA metabolism and cytosolic protein processing/trafficking, perhaps reflecting multifunctional components or co-occurring modules. Given the mixed signal, the label aims to capture both aspects without over-committing to a single function.","confidence":"Medium","size":7,"edges":12,"triangles":11,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0034214","count":4},{"id":"GO:0048219","count":4},{"id":"GO:0090261","count":4}]},{"hash":"964361270768762032","title":"Mitochondrial Transport and Membrane Dynamics","description":"The top terms are dominated by transport across membranes (NAD, phosphate, manganese, glycine, ornithine) and mitochondrial-specific processes (mitochondrial membrane fission, mitochondrial ATP transport) with supporting ideas like adaptive thermogenesis and links to cell survival; together they point to proteins involved in mitochondrial membrane transport and dynamics rather than a single cytosolic pathway. A noise term like female pregnancy appears incidental. Confidence reflects a coherent mitochondrial transport/dynamics theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060546","count":4},{"id":"GO:1990845","count":4},{"id":"GO:0036233","count":4},{"id":"GO:0090149","count":4},{"id":"GO:0000066","count":4}]},{"hash":"493451313303145643","title":"Unknown","description":"The GO terms are highly diverse (membrane transport, ATP synthesis, splicing, transcription termination, differentiation, and endosomal acidification) with no single dominant function, so there isn\u2019t a clear common theme to label this cluster.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":1},{"id":"GO:0030908","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0006933","count":1}]},{"hash":"699716249649061472","title":"Glycan biosynthesis and cell wall assembly","description":"The cluster\u2019s top GO terms cluster around polysaccharide and cell envelope construction (UDP-D-galactose metabolism, capsule biosynthesis, chitin and mycolate cell wall assembly, cell wall organization). This points to a shared function in glycan production and cell wall formation across species; a few terms appear peripheral (e.g., actomyosin contractile ring, CNS myelin maintenance) and may represent noise. ","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0052573","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0071769","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0000916","count":1}]},{"hash":"57036463347545973","title":"Cell Polarity and Vesicle Trafficking","description":"The cluster shows GO terms centered on epithelial cell polarity and protein trafficking/localization to the Golgi and vacuole (e.g., establishment/maintenance of epithelial polarity, protein localization to Golgi, protein targeting to vacuole), suggesting a shared role in organizing cell architecture and the secretory pathway. Some terms are unrelated or fringe annotations (e.g., neural development or nuclear envelope organization) and do not strongly redefine the theme. Best-fit label is \"Cell Polarity and Vesicle Trafficking\" with moderate confidence.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009231","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0031584","count":1},{"id":"GO:0045197","count":1}]},{"hash":"1851709936189973028","title":"Male gonad development and ECM organization","description":"Dominated by male gonad development and extracellular matrix organization terms, suggesting a link between reproductive development and ECM components. However, many terms are obsolete or peripheral, and there are no edges, so overall functional coherence is weak.","confidence":"Low","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:1901536","count":2},{"id":"GO:0030198","count":1},{"id":"GO:0033195","count":1},{"id":"GO:0017004","count":1}]},{"hash":"1228162985236876453","title":"Amino acid and vitamin biosynthesis","description":"The top GO terms cluster around biosynthetic processes for several amino acids (proline, tyrosine, valine) and pantothenate (vitamin B5), with a few other metabolic terms (galactarate catabolic process, metal ion import). The common thread is metabolic biosynthesis rather than a single pathway or complex, so a concise label capturing this biosynthetic focus fits best. While the edges are absent and some terms are heterogeneous, the recurring theme of amino acid and vitamin biosynthesis supports this naming.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015677","count":1},{"id":"GO:0055129","count":1},{"id":"GO:0015940","count":1},{"id":"GO:0098706","count":1},{"id":"GO:1903206","count":1}]},{"hash":"1700350476019041871","title":"Nucleotide salvage and catabolism","description":"The cluster is dominated by GO terms related to nucleotide metabolism, especially salvage pathways (AMP salvage, UMP salvage, nicotinate nucleotide salvage) and catabolic steps (inosine, deoxyguanosine catabolic processes, urate biosynthesis). While a couple terms touch on cell-cycle regulation and metabolic stress (glucose starvation), the overall theme centers on the processing and recycling of nucleotides, suggesting a coherent functional module in nucleotide metabolism.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051726","count":2},{"id":"GO:0009166","count":1},{"id":"GO:0044209","count":1},{"id":"GO:0019358","count":1},{"id":"GO:0046638","count":1}]},{"hash":"836746113747932535","title":"RNA splicing and processing","description":"The cluster highly emphasizes RNA maturation activities\u2014tRNA processing, mRNA splicing via the spliceosome, and spliceosomal assembly\u2014along with RNA decay processes (P-body assembly, deadenylation-dependent decapping) and transcription termination, suggesting a coherent role in RNA processing and turnover.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":5},{"id":"GO:0070317","count":4},{"id":"GO:1990141","count":4},{"id":"GO:0000290","count":4},{"id":"GO:0009414","count":4}]},{"hash":"511413353743234982","title":"Cardiac and neural development","description":"The top GO terms cluster around developmental processes in heart structures (sinus venosus morphogenesis, left ventricle formation, regulation of heart rate) and neural/ sensory differentiation (cerebral cortex interneuron differentiation, auditory receptor fate). A couple of terms refer to general cellular processes (RNA modification) but the strongest signal is organ-specific development, suggesting the cluster represents cardiac and neural development themes.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007117","count":1},{"id":"GO:0017183","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0003062","count":1},{"id":"GO:0003053","count":1}]},{"hash":"771699178091627123","title":"GPI Anchor Biosynthesis and ER-Golgi Trafficking","description":"The top GO terms center on GPI anchor biosynthesis and ER-to-Golgi trafficking, implying a role in glycosylated protein maturation and transport; the adjacent sugar-nucleotide metabolism terms likely supply precursors for glycosylation.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046109","count":1},{"id":"GO:0006098","count":1},{"id":"GO:0009052","count":1},{"id":"GO:0006014","count":1},{"id":"GO:0070863","count":1}]},{"hash":"1594157250926169016","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0032147","count":1},{"id":"GO:0070935","count":1},{"id":"GO:2000627","count":1}]},{"hash":"1518050262050333044","title":"Autophagy and Protein Modification in Stress Response","description":"This cluster centers on autophagy-related processes (macroautophagy, mitophagy, nucleophagy) and transcriptional regulation, with supporting protein modification pathways (neddylation, lipidation) and stress/defense signaling. The strongest common theme appears to be stress-induced protein turnover coupled with transcriptional control, rather than a single specialized function.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0045892","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0044805","count":2}]},{"hash":"1104185543234835931","title":"Nuclear gene expression and genome maintenance","description":"This cluster centers on nuclear processes: transcription (DNA-templated transcription), RNA processing/splicing, DNA replication and repair, chromatin organization (pericentric heterochromatin formation), and cell-cycle regulation. The convergence of transcription, splicing, replication/repair, and chromatin-related GO terms points to a cohesive theme of coordinating gene expression with genome integrity, with a few peripheral stress-response terms (e.g., response to antibiotic, water deprivation) that do not redefine the core function.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1893489716408938814","title":"Unknown","description":"This set includes terms spanning neural development (striatum), various developmental processes (cartilage), immune signaling (NF-kappaB activation, IL-8 and IL-1 responses), apoptosis, and insect-specific processes (chitin catabolic, ecdysis). The terms are diverse and do not point to a single cohesive biological function or pathway, suggesting a heterogeneous cluster rather than a unified theme.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021756","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0072606","count":2},{"id":"GO:0000272","count":2},{"id":"GO:0007250","count":2}]},{"hash":"20975501897196085","title":"Ribosome biogenesis and proteostasis under stress","description":"The cluster is enriched for translation and ribosomal small subunit assembly, indicating ribosome production, alongside proteasome-related protein catabolic regulation and mitophagy, which point to protein quality control and organelle turnover. Additional terms like cellular response to toxic substances and transcription regulation fit a broader stress-survival and growth program, with spindle pole body duplication and cell morphogenesis providing cell-cycle context. Together, they suggest a cohesive theme around ribosome biogenesis, translation, and proteostasis under stress.","confidence":"Medium","size":6,"edges":9,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:1901799","count":3},{"id":"GO:0030474","count":3},{"id":"GO:1903071","count":3},{"id":"GO:0006357","count":3}]},{"hash":"2027328792888408521","title":"Cardiac membrane potential regulation","description":"This cluster includes GO terms about membrane repolarization and hyperpolarization in atrial cardiac muscle cells, suggesting a focus on electrophysiological regulation of membrane potential. Several other terms (pain, mechanosensation, vulval location, T cell signaling) appear unrelated and may reflect annotation noise, but the dominant theme is cardiac membrane potential dynamics.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098914","count":1},{"id":"GO:0019233","count":1},{"id":"GO:0060372","count":1},{"id":"GO:0050982","count":1},{"id":"GO:0034608","count":1}]},{"hash":"554652967701662677","title":"RNA processing and transcriptional regulation","description":"The terms cluster around regulation of gene expression at multiple levels\u2014chromatin remodeling and transcription, ncRNA-mediated silencing, RNA splicing, and translation initiation\u2014suggesting a broad regulatory role rather than a single enzymatic function.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0006446","count":2}]},{"hash":"1263887154587800964","title":"Stress-Responsive Cytoskeleton and Vesicle Trafficking","description":"The cluster shows enrichment for stress-related GO terms (cellular response to xenobiotic stimulus; hyperosmotic response) alongside cytoskeleton and vesicle trafficking processes (pseudopodium assembly, actin remodeling, ribosomal export, vacuole targeting). This suggests proteins involved in adapting to stress via cytoskeletal dynamics and vesicular transport, rather than a single, narrow function.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0006972","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0006623","count":1},{"id":"GO:0045197","count":1}]},{"hash":"683796871816105414","title":"Cell Division & ER-Golgi Trafficking","description":"The terms point to core roles in cell proliferation, mitotic progression, and general cell division, with supporting signals of secretory pathway activity (ER-Golgi transport and COPII vesicle budding). This suggests a cluster of proteins coordinating division with membrane trafficking rather than a single isolated function.","confidence":"Medium","size":6,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0090114","count":2}]},{"hash":"935557237031274892","title":"ER protein folding and ER stress response","description":"This cluster\u2019s GO terms are dominated by endoplasmic reticulum\u2013related processes: protein folding in ER, misfolded protein transport, and translation initiation regulation in response to ER stress, all pointing to ER quality control and the unfolded protein response. Other terms (e.g., cristae formation, DNA replication) are less central, possibly reflecting broader multifunctional proteins or annotation noise, but the strongest signal is ER protein folding and stress response.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048279","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0035786","count":1},{"id":"GO:0071374","count":1}]},{"hash":"2277039050703073251","title":"Unknown","description":"These terms cover divergent developmental processes (microgametogenesis, somatic embryogenesis, cell differentiation) and assorted signaling and protein homeostasis activities (TGF-beta signaling, GTPase regulation, phosphatidylinositol dephosphorylation, autophagosome and proteasome regulation). There is no clear common function tying all six proteins together, so a single interpretable label cannot be confidently assigned.","confidence":"","size":6,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055046","count":1},{"id":"GO:0010262","count":1},{"id":"GO:0045466","count":1},{"id":"GO:0046856","count":1},{"id":"GO:0048633","count":1}]},{"hash":"543382157547161220","title":"Ribosome biogenesis and translation","description":"This cluster is characterized by GO terms about maturation of rRNA subunits (SSU/LSU and 5.8S), translation, translational initiation/termination, and no-go decay, indicating a cohesive group of ribosome assembly and translation-related proteins. While a few other terms appear, the translation-centric signals dominate, supporting this interpretation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090398","count":2},{"id":"GO:0070072","count":1},{"id":"GO:0035167","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1507882344215541131","title":"Motor neuron development and axon guidance","description":"This cluster's top GO terms center on neuronal development, especially motor neuron differentiation, axon guidance, and associated cytoskeletal dynamics (lamellipodium assembly and actin regulation), as well as neuron migration and cell fate specification. Although a couple of terms are insect-specific (eclosion, haltere morphogenesis), the overarching theme is neuronal development and wiring. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045805","count":2},{"id":"GO:0048735","count":2},{"id":"GO:0010735","count":2},{"id":"GO:0021527","count":2},{"id":"GO:0021937","count":2}]},{"hash":"2155871728876307027","title":"Germline development and meiotic RNA processing","description":"The GO terms point to germline-specific processes (germarium-derived germ-line cyst encapsulation, stem cell maintenance) and meiotic cell cycle, with supporting RNA processing activities (primary miRNA processing, RNA editing, mRNA destabilization, cap-independent translation initiation), suggesting a cluster centered on germline development with meiotic and RNA-regulatory features.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046020","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0019827","count":1},{"id":"GO:0061157","count":1},{"id":"GO:0030708","count":1}]},{"hash":"1636984708437152265","title":"Cytoskeleton Remodeling and Cell Polarity","description":"This cluster centers on dynamic cytoskeletal changes (actin remodeling, pseudopodium and dendritic spine morphogenesis) and polarity establishment (epithelial polarity, EMT), with supporting vesicle trafficking signals (targeting to vacuole, vesicle size regulation). The shared theme appears to be cytoskeleton-driven morphogenesis across cell types, linking shape change with polarity cues.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006623","count":3},{"id":"GO:0045197","count":3},{"id":"GO:0016358","count":3},{"id":"GO:0097494","count":3},{"id":"GO:0031274","count":3}]},{"hash":"942306722253791330","title":"Unknown","description":"No GO terms are provided for this cluster, and the network is small (6 proteins, 3 edges, max degree 2, 0 triangles), giving no coherent functional theme. Without enrichment signals, a meaningful label cannot be assigned, so Unknown is the best choice.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"1099162817106374396","title":"Organogenesis and Development Signaling","description":"These proteins cluster around developmental organogenesis and signaling. Endocardial cushion fusion, lung morphogenesis, cartilage condensation, and multicellular organism development point to tissue formation, while ERK cascade and retinal ganglion cell axon guidance reflect underlying signaling guiding neural and organ development. A few terms appear unrelated, but the dominant theme is developmental processes coordinated by signaling pathways.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0003274","count":4},{"id":"GO:0010825","count":4},{"id":"GO:1900436","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0031290","count":4}]},{"hash":"2203912216303159050","title":"Cytoskeleton Dynamics and Transport","description":"The top GO terms cluster around cytoskeletal organization and movement (actomyosin ring assembly, spindle pole dynamics, axonemal microtubule changes) and intracellular transport (anterograde dendritic transport, chloroplast movement). Additional terms reference structural development and tissue organization, which often rely on cytoskeletal scaffolding. Overall, the shared theme is proteins involved in cytoskeletal dynamics and cargo transport across diverse organisms, justifying this label with a moderate level of confidence.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000915","count":3},{"id":"GO:0098971","count":3},{"id":"GO:0000742","count":3},{"id":"GO:0021685","count":3},{"id":"GO:0000073","count":3}]},{"hash":"655532046922919111","title":"Aromatic compound metabolism and PPP/NAD pathways","description":"These proteins show enrichment across several metabolic routes: aromatic compound processing (phenylacetate catabolism and chorismate biosynthesis), central carbon metabolism (pentose phosphate shunt and fructose metabolism), and NAD/NADP cofactor turnover, with menaquinone biosynthesis adding to energy metabolism. One GO term refers to mRNA decapping, which appears unrelated and may be annotation noise. Overall, the cluster is best described by metabolism-centric themes, especially aromatic compound processing and PPP/NAD metabolism.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0046496","count":1},{"id":"GO:0031087","count":1},{"id":"GO:0006000","count":1}]},{"hash":"1405328777447818793","title":"Ribosome assembly and translation","description":"The top GO terms are dominated by translation (including mitochondrial translation) and ribosome assembly, suggesting the proteins function together in ribosome biogenesis and protein synthesis. A few other terms (DNA metabolic process, transcription) appear but are not central to the cluster's theme, so the label reflects the main shared function.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0090305","count":1},{"id":"GO:0006259","count":1}]},{"hash":"1120979929220437373","title":"Ribosome biogenesis and translation regulation","description":"The top GO terms cluster around ribosome production and function: ribosome biogenesis, cytoplasmic translation, ribosomal subunit export, tRNA modification, and mRNA decay, all pointing to assembly and control of the protein-synthesis machinery. Additional terms about cell cycle/division suggest a link between ribosome biogenesis and proliferation. The single antibiotic response term may reflect ribosome-targeted effects, reinforcing the core link to translation machinery. Overall, this cluster is best described as ribosome biogenesis and translation regulation.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0006400","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0042254","count":1},{"id":"GO:2000767","count":1}]},{"hash":"2236818032307734099","title":"Germline development and RNA regulation","description":"The cluster shows strong links to germline development, including germarium-derived oocyte fate determination and germ-line cyst formation, combined with RNA-based regulation such as regulatory ncRNA-mediated gene silencing and miRNA processing, plus RNA editing and chromatin-related hints. This points to proteins coordinating germline specification with post-transcriptional control and chromatin state. ","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007294","count":2},{"id":"GO:0016573","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0030727","count":1}]},{"hash":"1111295930429110492","title":"Developmental differentiation across tissues","description":"The GO terms cluster around tissue-specific differentiation and transcriptional regulation across multiple organ systems (nephron, urogenital system, pancreatic beta cells, heart, nerve branching, inner ear), suggesting a theme of developmental differentiation rather than a single pathway. This makes a label like \"Developmental differentiation across tissues\" appropriate and representative.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":1},{"id":"GO:0048096","count":1},{"id":"GO:0045599","count":1},{"id":"GO:0051891","count":1},{"id":"GO:0072182","count":1}]},{"hash":"1365070307429596192","title":"DNA replication and chromatin maintenance","description":"The top GO terms cluster around core DNA replication activities (DNA replication, replication initiation, and related unwinding) and chromatin organization (subtelomeric heterochromatin formation), suggesting a shared role in genome replication and chromatin maintenance. Several other terms (apoptosis, splicing, development, immune response) appear sporadically and may be incidental annotations, not central to the cluster\u2019s function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006268","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0000398","count":2}]},{"hash":"57374519841909041","title":"RNA Splicing and Processing","description":"This cluster is dominated by GO terms tied to RNA metabolism: spliceosomal assembly and mRNA splicing, transcription termination, mRNA decay pathways, and tRNA processing, plus P-body assembly. The recurring signal is RNA processing and spliceosome\u2013related functions, with some peripheral hints at chromatin or stress-related processes that are less central.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:1990141","count":2},{"id":"GO:0000290","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0000387","count":2}]},{"hash":"484268296809847024","title":"Mitochondrial transport and energy metabolism","description":"The top GO terms cluster around mitochondria and membrane transport: mitochondrial membrane fission; transmembrane transport of NAD, ATP, phosphate, manganese, L-ornithine, and glycine; plus energy-related processes like adaptive thermogenesis. Negative regulation of necroptotic process also aligns with mitochondrial signaling roles. Overall, the pattern points to a mitochondria-centered set of transport and energy metabolism functions, with one outlier term (female pregnancy) not altering the main theme.","confidence":"High","size":5,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060546","count":3},{"id":"GO:1990845","count":3},{"id":"GO:0036233","count":3},{"id":"GO:0090149","count":3},{"id":"GO:0000066","count":3}]},{"hash":"2057783611699438443","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning cellulose and peptide catabolism, amino-acid biosynthesis, deglutamylation, transport, and plant development. There is no clear, dominant shared function across all proteins to justify a concise, specific label.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1},{"id":"GO:0009442","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0035609","count":1},{"id":"GO:0043171","count":1}]},{"hash":"940276718719014395","title":"Mitochondrial matrix protein import","description":"Top GO term GO:0030150 (protein import into mitochondrial matrix) suggests a shared role in delivering proteins to the mitochondrial matrix. With only one protein annotated for this function and the rest unannotated, the connection is present but modest, so the label is a best-effort representation of the cluster\u2019s theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":1}]},{"hash":"709950653220675016","title":"RNA Splicing and Decay Machinery","description":"The proteins cluster around RNA processing and metabolism: spliceosome assembly and mRNA splicing, transcription termination, tRNA processing, and P-body assembly, plus a deadenylation-dependent decapping pathway. The convergence on RNA maturation and turnover suggests this group functions in RNA processing and regulation of gene expression, with chromatin-related terms possibly reflecting broader transcriptional control links. Overall, a coherent RNA processing/turnover theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:1990141","count":2},{"id":"GO:0000290","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0000387","count":2}]},{"hash":"1755001291377928166","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around ribosome assembly and the machinery of protein synthesis: ribosome biogenesis, translation and translational initiation, plus tRNA modification and even ribosome disassembly, indicating a focus on ribosome production and execution of translation. A few terms touch mRNA decay and stress/antibiotic response, but the dominant theme remains ribosome formation and cytoplasmic translation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001172","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006400","count":1}]},{"hash":"2250300794049378885","title":"Virus assembly and host immune response","description":"The cluster includes virion assembly and host-cell entry/trafficking terms (virion assembly, translocation into host cell cytoplasm, pore and chaperone-mediated complex assembly) alongside immune-related terms (TNF production, isotype switching to IgG). This combination suggests a theme around virus-host interactions, encompassing viral assembly and host immune signaling, despite some noisy or unrelated terms in the mix.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033198","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0046931","count":2},{"id":"GO:0051131","count":2},{"id":"GO:1904469","count":2}]},{"hash":"334462067848729874","title":"Cytoskeletal remodeling and cell movement","description":"The GO terms center on actin cytoskeleton organization, polarity establishment, contractile ring activity, and motility processes such as mesenchyme migration, phagocytosis, and endocytosis. Together these indicate a cohesive module of cytoskeletal dynamics that drive cell shape changes, division, and movement.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":2},{"id":"GO:0030240","count":2},{"id":"GO:0000281","count":2},{"id":"GO:0032508","count":2},{"id":"GO:0006909","count":2}]},{"hash":"68335318340230810","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060528","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0003208","count":1},{"id":"GO:0071455","count":1},{"id":"GO:0060841","count":1}]},{"hash":"1121535911868593580","title":"Unknown","description":"The four proteins show diverse annotations: mitochondrial intermembrane-space protein import, a single obsolete term related to transcription factor catabolic regulation, cellular response to iron ion starvation, and protein ubiquitination. There is no clear, shared biological process or molecular function linking all members, and with such sparse, conflicting terms, a coherent label cannot be assigned.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:1901485","count":1},{"id":"GO:0010106","count":1},{"id":"GO:0016567","count":1}]},{"hash":"2236041452057421478","title":"Cannabinoid biosynthesis","description":"The top GO terms are dominated by cannabinoid-related processes, specifically olivetolic acid biosynthetic process (GO:1901697) and cannabinoid biosynthetic process (GO:1901696), which strongly indicate a function in cannabinoid production. The other terms largely reflect general cellular processes (vascule targeting, polarity, cytoskeleton dynamics) that are less cohesive with cannabinoid biosynthesis, suggesting the core theme of this cluster centers on cannabinoid biosynthesis with auxiliary cellular functions. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901697","count":1},{"id":"GO:1901696","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0045197","count":1},{"id":"GO:0016358","count":1}]},{"hash":"1047796515460226353","title":"Signaling and Morphogenesis","description":"This small cluster centers on GO terms tied to signal transduction (phosphorylation, cytokinin-activated signaling, osmosensory signaling) and some developmental processes (face morphogenesis, retina development). While terms span different organisms, the shared theme appears to be regulation of signaling pathways that influence development.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0080038","count":1},{"id":"GO:0007234","count":1},{"id":"GO:0009736","count":1}]},{"hash":"884015495250139312","title":"Photorespiration and plant carbon metabolism","description":"The top GO terms predominantly point to photorespiration (GO:0009853), glycolate catabolic and oxidative photosynthetic carbon pathway processes, plus amino acid biosynthesis (glutamate) and other core metabolic pathways like isoprenoid biosynthesis. Together these terms suggest a cluster of proteins involved in plant primary metabolism with a focus on carbon flow and photorespiratory metabolism.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018924","count":1},{"id":"GO:0080114","count":1},{"id":"GO:0019516","count":1},{"id":"GO:0009854","count":1},{"id":"GO:0097054","count":1}]},{"hash":"772850161936103640","title":"Ribosome Assembly and Translation","description":"Most top terms point to ribosome biology\u2014translation, maturation of SSU-rRNA, and large subunit assembly\u2014along with SRP-dependent cotranslational targeting to membranes, all indicating a cluster centered on ribosome biogenesis and translation. Some outliers like IRE1-mediated UPR or flagellum organization are likely incidental noise rather than core functions.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0044781","count":1},{"id":"GO:0006614","count":1}]},{"hash":"1325847640351013564","title":"Ribosome Biogenesis and Translation Modifications","description":"This cluster centers on ribosome-related processes and translation machinery, including ribosome biogenesis and disassembly, regulation of translational termination, and various protein and tRNA/histidine modifications (e.g., diphthamide) that tie directly to translation. The presence of protein repair and oxidative stress response terms suggests maintenance of proteostasis under stress, aligning with a broader ribosome/translation-focused proteome. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0030091","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0006464","count":1},{"id":"GO:0006400","count":1}]},{"hash":"473499187712030499","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0034476","count":1},{"id":"GO:0071039","count":1},{"id":"GO:0071035","count":1},{"id":"GO:1901917","count":1}]},{"hash":"1288082480765765712","title":"Nuclear transport and ribophagy","description":"Top GO terms center on nucleocytoplasmic transport (protein import into nucleus, mRNA export from nucleus) and vesicle trafficking, with a notable inclusion of ribophagy. This points to a core function in nuclear import/export and selective ribosome turnover, with some peripheral terms that are less connected. Overall, the dominant theme is nuclear transport and ribophagy.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":1},{"id":"GO:2000156","count":1},{"id":"GO:0045571","count":1},{"id":"GO:0042307","count":1},{"id":"GO:0034517","count":1}]},{"hash":"267022153821592410","title":"Unknown","description":"This cluster\u2019s terms span diverse metabolic pathways (carbohydrate and hydrocarbon catabolism; retinoid and retinal metabolism; norepinephrine and testosterone biosynthesis; stress/metabolic responses). There is no single cohesive function tying all terms together, so an Unknown label with None confidence is appropriate.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042843","count":1},{"id":"GO:0035229","count":1},{"id":"GO:0018931","count":1},{"id":"GO:0042572","count":1}]},{"hash":"750942228510960597","title":"Immune Defense and Proteolysis","description":"The top GO terms point to host defense (defense responses to Gram-positive bacteria and fungi/yeast, complement activation) and proteolytic remodeling (plasminogen activation and elastin catabolic process). Together they suggest a cluster of proteins involved in immune defense linked to extracellular matrix remodeling, with some other developmental terms likely incidental. Confidence: Medium","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1900738","count":1},{"id":"GO:0050830","count":1},{"id":"GO:0001878","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0031639","count":1}]},{"hash":"1051289401387468707","title":"Gram-positive cell wall and lipid biosynthesis","description":"This cluster centers on teichoic acid and lipoteichoic acid biosynthesis, together with cell wall organization and fatty/lipid biosynthetic processes, pointing to bacterial envelope biogenesis typical of Gram-positive organisms. While a few terms touch broader lipid pathways (lipid A, antibiotic biosynthesis), the dominant pattern is synthesis of cell wall\u2013associated lipids and envelope components.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0043041","count":1},{"id":"GO:0070400","count":1}]},{"hash":"1594163335895128066","title":"Unknown","description":"The listed GO terms are inconsistent: some indicate mitochondrial targeting/insertion, while others point to nucleotide biosynthesis and RNA processing/editing. There is no clear, single function tying the three proteins together, so a specific label is not warranted.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0046656","count":1},{"id":"GO:1901909","count":1}]},{"hash":"2154547596861175962","title":"Fungal mating and cell wall biosynthesis","description":"The cluster features fungal-specific processes such as karyogamy in conjugation and beta-glucan biosynthesis, plus shared cellular functions like SRP-dependent translocation and DNA replication. These terms together point to a fungal cell biology module tied to mating-related development and cell wall construction, with membrane targeting as a core process.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0070389","count":1}]},{"hash":"164978461329477959","title":"Fatty Acid Metabolism and Lipid Biosynthesis","description":"This cluster is dominated by GO terms for fatty acid biosynthesis (short- and medium-chain), saturated fatty acid elongation, and fatty acid beta-oxidation, along with cholesterol metabolism. These recurrent annotations point to a coherent function in lipid metabolism and energy-related pathways, with some hormone response context and a liver-associated term likely reflecting tissue expression. The antibiotic biosynthetic process appears as an outlier but does not negate the lipid-focused theme.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0051790","count":3},{"id":"GO:0019367","count":3},{"id":"GO:0051792","count":3},{"id":"GO:0001889","count":2}]},{"hash":"238646100361302357","title":"Cell Polarity and Neuronal Morphogenesis","description":"The top GO terms cluster around cytoskeleton remodeling (actin dynamics, pseudopodium assembly, vesicle size regulation) and cell polarity (apical/basal polarity, epithelial\u2013mesenchymal signaling), with strong emphasis on neuronal development (dendrite development and dendritic spine morphogenesis) and associated membrane trafficking. Together these suggest a theme of coordinated polarity establishment and actin-driven morphogenesis in neural and migratory contexts.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0045197","count":1},{"id":"GO:0016358","count":1},{"id":"GO:0097494","count":1},{"id":"GO:0031274","count":1}]},{"hash":"1914042736820430392","title":"Nutrient-responsive RNA Pol II transcription","description":"The terms show regulation of transcription from RNA polymerase II promoter in response to various nutrient signals (nonfermentable carbon source, oleic acid) and metabolic states, plus general DNA-templated transcription and regulation of cellular respiration. There is an outlier aflatoxin biosynthesis term, likely a misannotation, but the shared theme is transcriptional control tied to metabolism rather than a single metabolic product. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045122","count":2},{"id":"GO:0061414","count":2},{"id":"GO:0035948","count":2},{"id":"GO:1904741","count":2},{"id":"GO:0061429","count":2}]},{"hash":"1240736040403229548","title":"Ubiquitin-mediated proteolysis and chromatin modification","description":"The top GO terms cluster around ubiquitin pathways: SCF complex assembly, ubiquitin-dependent protein catabolic processes via multivesicular body sorting, and histone H2A K63-linked ubiquitination, plus a histone H4-K16 acetylation term. This points to a shared theme of ubiquitin signaling regulating protein turnover and chromatin state. Other terms (viral process, TNF signaling, V(D)J recombination) are less representative and appear as isolated annotations. Overall, the main signal is ubiquitin-dependent regulation. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010265","count":1},{"id":"GO:0043162","count":1},{"id":"GO:0070535","count":1},{"id":"GO:1903762","count":1},{"id":"GO:0016032","count":1}]},{"hash":"944144486276315113","title":"Chromatin silencing and heterochromatin maintenance","description":"The cluster is dominated by GO terms related to chromatin state and transcriptional regulation, including DNA-templated transcription, heterochromatin formation/maintenance, nucleosome density regulation, and histone deacetylation. Together these indicate epigenetic control of gene expression through chromatin remodeling and silencing. A couple of terms on metabolism or apoptosis seem incidental to the core theme. Confidence reflects the strong link to chromatin-based transcriptional repression.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006344","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0034983","count":2}]},{"hash":"24552322208104596","title":"Developmental Morphogenesis and Signaling","description":"The top GO terms cluster around embryonic development and tissue morphogenesis, including endocardial cushion fusion, cartilage condensation, and lung morphogenesis, plus signaling involvement via the ERK cascade and retinal axon guidance. Some terms like lysosome localization or centrosome duplication are more general cellular processes, but collectively they point to development-associated signaling and morphogenesis as a coherent theme.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032418","count":1},{"id":"GO:0003274","count":1},{"id":"GO:0010825","count":1},{"id":"GO:1900436","count":1},{"id":"GO:0031663","count":1}]},{"hash":"309354862969731328","title":"Proton/Sodium Transport and PMF-Driven ATP Synthesis","description":"The top GO terms cluster around proton transmembrane transport, sodium ion transport, and ATP synthesis driven by proton motive force, indicating a core membrane energetics/ion-transport function. Several other terms appear unrelated or broad (angiogenesis, osteoblast differentiation, transcription termination, flagellum assembly), suggesting some noise, but the energy metabolism signal is clear and cohesive.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0006933","count":1},{"id":"GO:0001649","count":1}]},{"hash":"223023713485841555","title":"Unknown","description":"There is no common GO term signal or network connectivity among the proteins (no edges, no triangles, zero max degree) and no terms listed to guide a functional label. The mention of ReCIPE re-added proteins does not provide a clear shared function for naming.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1441893064070729576","title":"Nucleotide and Cofactor Biosynthesis","description":"The top GO terms cluster around biosynthetic and metabolic steps for nucleotides and cofactors (NAD+ biosynthesis, coenzyme A biosynthesis, AMP/CDP/ADP salvage and phosphorylation, purine ribonucleotide interconversion, etc.). This points to a shared role in nucleotide metabolism and cofactor production, with one outlier term (liver development) likely incidental. Therefore, this label captures the main functional theme of the cluster.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009435","count":1},{"id":"GO:0044209","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0015937","count":1},{"id":"GO:0046940","count":1}]},{"hash":"339060755680542519","title":"Fungal sterol and sphingolipid biosynthesis","description":"The top GO terms are dominated by sterol and lipid metabolism, including ergosterol biosynthesis and related sterol oxidation, as well as sphingolipid metabolism (mannosyl-inositol phosphorylceramide). This points to fungal lipid biosynthesis pathways as the core function of this cluster, despite some outlier terms present in the list. Thus the label emphasizes the strongest, most coherent signal among the terms.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0006809","count":2},{"id":"GO:0000001","count":2}]}]