[{"hash":"812414470988436466","title":"Proteasome-Mediated Cell Division Control","description":"The cluster is enriched for ubiquitin-proteasome\u2013dependent degradation pathways (ERAD, SCF, APC) and cell-cycle\u2013related processes like CENP-A\u2013mediated chromatin assembly, microtubule severing, and cell division, indicating a cohesive theme of regulated proteolysis guiding mitosis.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0031146","count":5},{"id":"GO:0031145","count":5},{"id":"GO:0006351","count":5}]},{"hash":"557047000258560729","title":"Genome Maintenance and Cell Cycle Regulators","description":"This cluster is strongly anchored by GO terms for DNA replication, telomere maintenance and capping, base-excision repair, and kinetochore localization, as well as regulation of CDK activity and phosphorylation. These indicate roles in genome stability and cell-cycle control. The presence of additional terms related to Wnt signaling and axonogenesis suggests broader signaling and developmental functions for some members, but the core theme centers on genome maintenance and cell-cycle regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0006288","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0032212","count":2}]},{"hash":"725553672778722503","title":"Ribosome Biogenesis and Protein Synthesis","description":"This cluster is dominated by GO terms tied to translation processes (initiation, elongation, termination), ribosome biogenesis, and related mRNA processing/regulation, pointing to components of the ribosome assembly line and the translation machinery, with additional signals of translational regulation and mRNA decay. The combination suggests a cohesive group of proteins involved in making and operating the ribosome and protein synthesis machinery.","confidence":"High","size":28,"edges":145,"triangles":388,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0051301","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0000288","count":3}]},{"hash":"783677535777795547","title":"Protein Translation and Ribosome Biogenesis","description":"This cluster is dominated by GO terms related to the core translation machinery: translation, cytoplasmic translation, translation initiation/termination, and ribosome biogenesis/disassembly, plus a mitochondrial translation term. The convergence on ribosome function and protein synthesis suggests these proteins work together in assembling and operating ribosomes and translating mRNA. A minor antibiotic response term may reflect stress-related regulation linked to translation.","confidence":"High","size":28,"edges":215,"triangles":1014,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0046677","count":5},{"id":"GO:0006413","count":4},{"id":"GO:0006415","count":4},{"id":"GO:0042254","count":4}]},{"hash":"1823520125143719624","title":"RNA Methylation and Biosynthesis Enzymes","description":"The cluster prominently features RNA modification and mRNA capping terms (tRNA wobble uridine modification; RNA (guanine-N7)-methylation; 7-methylguanosine mRNA capping) along with several biosynthetic processes (sterol, cobalamin, antibiotic biosynthesis) and related metabolism. This points to a set of proteins involved in methylation-related steps across RNA processing and diverse biosynthetic pathways, justifying a name that highlights both RNA methylation and broader biosynthesis functions.","confidence":"Medium","size":28,"edges":10,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0016126","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0006370","count":4}]},{"hash":"755121373925739711","title":"Mitochondrial energy metabolism and membrane dynamics","description":"The top GO terms are strongly mitochondrial-related, covering membrane fission, membrane potential regulation, citrate transport, fatty acid response, and adaptive thermogenesis, which together point to mitochondrial energy production and lipid metabolism as the cluster\u2019s main theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090149","count":3},{"id":"GO:0000002","count":3},{"id":"GO:0032212","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0006843","count":2}]},{"hash":"800719564826337715","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to translation and ribosome assembly (translation, cytoplasmic translation, translational initiation, ribosomal large subunit assembly/biogenesis, and rRNA maturation), indicating a cohesive group of proteins involved in ribosome biogenesis and protein synthesis.","confidence":"High","size":26,"edges":159,"triangles":773,"max_degree":22,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:0042254","count":5},{"id":"GO:0006450","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0000462","count":2}]},{"hash":"2251561621572411506","title":"Unknown","description":"The GO terms are a jumbled mix, including transcription regulation, chromatin organization, unfolded protein response, chaperone-mediated assembly, and mitochondrial protein import, plus outliers like collagen catabolic process and viral release. This lack of a single cohesive theme (and some obsolete terms) makes it hard to assign a concise, representative label.","confidence":"","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035551","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1}]},{"hash":"1436302497212974244","title":"Amino acid catabolism and central carbon metabolism","description":"Based on the top GO terms, there is a clear emphasis on catabolic processes of amino acids (L-alanine, L-lysine, tryptophan, kynurenine, glycine-related) and core central metabolism steps (gluconeogenesis, TCA cycle). A Notch signaling term appears among the top terms, but the dominant pattern is amino acid breakdown feeding energy metabolism. Thus, the label reflects the cluster\u2019s primary functional theme, with minor possible annotation noise.","confidence":"Medium","size":26,"edges":269,"triangles":1808,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0007219","count":7},{"id":"GO:0006094","count":7},{"id":"GO:0017000","count":6}]},{"hash":"1181346084476086328","title":"Cell growth signaling and ribosome biogenesis","description":"The cluster is annotated by GO terms spanning ribosome biogenesis, mRNA transport, and regulation of kinase activity, including mitotic cell cycle and positive regulation of cell proliferation. This pattern points to a cohesive module coordinating protein synthesis machinery with growth and proliferative signaling, via phosphorylation and signaling control. Some terms appear broad or noisy (e.g., obsolete/hypoxia terms), so the connection is plausible but not razor-sharp.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0071456","count":2}]},{"hash":"95214604489288844","title":"Ubiquitin-Dependent Protein Turnover and Cell Cycle","description":"The cluster is dominated by GO terms related to ubiquitination and protein catabolic processes (protein autoubiquitination; ubiquitin-dependent protein degradation) alongside core cell cycle activities (G1/S transition; DNA replication; meiotic cell cycle). While there are some neural-related terms (excitatory postsynaptic potential; Schwann cell development; response to cocaine), the strongest common theme centers on ubiquitin-mediated regulation of protein turnover affecting cell cycle progression. This makes a cohesive, high-level label appropriate.","confidence":"Medium","size":26,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0000082","count":2},{"id":"GO:2001241","count":2}]},{"hash":"903761285284451058","title":"Protein Synthesis and Quality Control","description":"The GO terms are dominated by translation and ribosome biogenesis, with an ERAD/ubiquitin-dependent degradation pathway term and transcription-related terms, suggesting a cohesive theme around protein production and proteostasis (quality control of proteins). Some metabolic terms are present but do not dominate, leaving translation/quality-control as the core.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0001172","count":2}]},{"hash":"1632632835770311280","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":37,"triangles":21,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006099","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0019878","count":4},{"id":"GO:0098869","count":4}]},{"hash":"1964977708021586610","title":"Nuclear import and RNA processing","description":"Top GO terms center on nuclear import (NLS-bearing proteins, ribosomal protein import into nucleus) and spliceosome/snRNP assembly, with some regulation of desumoylation; these point to nucleocytoplasmic transport and RNA biogenesis as the cluster\u2019s core. A few outlier terms exist but do not override the main theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0042176","count":2},{"id":"GO:0006610","count":2}]},{"hash":"1094427897953531452","title":"Developmental Signaling and Cellular Regulation","description":"The terms point to roles in development (skin and multicellular organism development) and regulation of signaling and protein activities (GTPase regulation, kinase activity, ubiquitin ligase activity), with related processes like mitotic cell cycle and mRNA transport. This pattern suggests a cluster of proteins involved in coordinating growth, differentiation, and signaling during development, even though no single pathway dominates. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0032933","count":3},{"id":"GO:0000278","count":3}]},{"hash":"603794543628031243","title":"Ribosome biogenesis and translation under stress","description":"This cluster is centered on core protein synthesis machinery: translation and ribosome assembly with rRNA maturation, indicating a ribosome biogenesis/translation theme. Additional terms point to proteostasis and stress signaling, such as protein stabilization and negative regulation of ubiquitin ligase activity, plus apoptosis and corticosterone response, suggesting the cluster also integrates cellular stress responses.","confidence":"Medium","size":24,"edges":212,"triangles":1109,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0006915","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0042777","count":3}]},{"hash":"1085287056898373658","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":8,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000466","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000480","count":3}]},{"hash":"621799897259636065","title":"Gene expression and RNA processing","description":"Based on the GO terms, this cluster centers on core gene expression processes: transcription, mRNA processing/export, ribosome biogenesis, translation, and mRNA modification/stabilization. The co-occurrence of transcriptional and post-transcriptional RNA processing terms with translation-related terms suggests a broad RNA metabolism and gene-expression machinery theme. ","confidence":"Medium","size":24,"edges":15,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006353","count":2}]},{"hash":"1789989072729120945","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000447","count":5},{"id":"GO:0000472","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0000747","count":5}]},{"hash":"1939538516148734842","title":"Developmental patterning and signaling regulation","description":"The set includes GO terms tied to embryonic development: mesoderm formation, Wnt and Hedgehog pathway regulation, and neural tube patterning, plus chromatin remodeling and transcription initiation that accompany development. Additional terms on cell migration, DNA replication, and apoptosis/proliferation control suggest integration of growth and differentiation signals during tissue patterning.","confidence":"Medium","size":24,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006468","count":4},{"id":"GO:0048096","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0043065","count":2}]},{"hash":"1059413413436281383","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":23,"triangles":13,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000480","count":8},{"id":"GO:0042273","count":8},{"id":"GO:0000472","count":8},{"id":"GO:0000463","count":8},{"id":"GO:0000462","count":8}]},{"hash":"497992298958095449","title":"Spliceosome-Mediated mRNA Splicing and Processing","description":"The cluster is dominated by spliceosome-mediated mRNA splicing terms (positive and negative regulation) and multiple mRNA processing steps (export, stabilization, modification). Together these terms indicate a coherent role in mRNA maturation and regulation at the level of splicing.","confidence":"High","size":23,"edges":25,"triangles":30,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":9},{"id":"GO:0048026","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0006406","count":6}]},{"hash":"1625578115968288037","title":"ERAD and Membrane Protein Targeting","description":"This cluster is dominated by GO terms for ubiquitin-dependent ERAD, misfolded protein transport, and Sec complex\u2013mediated protein transport, plus general membrane targeting. Together they indicate proteins involved in ER quality control and trafficking to membranes, with a few development terms likely incidental. ","confidence":"Medium","size":23,"edges":21,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0031204","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0032781","count":2}]},{"hash":"1646144766961346613","title":"Spliceosome-Mediated RNA Processing","description":"Top terms are dominated by mRNA splicing via the spliceosome, with several entries for regulation of splicing, plus mRNA export and stabilization, and even polyadenylation regulation. This points to a cluster of proteins involved in nuclear RNA processing and spliceosome-mediated mRNA maturation.","confidence":"High","size":22,"edges":73,"triangles":132,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":9},{"id":"GO:0006378","count":7},{"id":"GO:0006406","count":6},{"id":"GO:0048025","count":6},{"id":"GO:1901407","count":6}]},{"hash":"1783249790435184092","title":"Spliceosome-Driven mRNA Splicing Regulation","description":"The top terms are dominated by mRNA splicing via the spliceosome, with both positive and negative regulation of splicing, plus related RNA processing activities such as ncRNA-mediated gene silencing, transcription termination, and mRNA stability. This indicates a cohesive cluster centered on spliceosome-mediated mRNA processing and its regulatory control.","confidence":"High","size":22,"edges":194,"triangles":1052,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":13},{"id":"GO:0048026","count":12},{"id":"GO:0031047","count":12},{"id":"GO:0006369","count":10},{"id":"GO:0006378","count":10}]},{"hash":"2094841850343169108","title":"Fungal cell wall glycoprotein biosynthesis","description":"The top GO terms cluster around fungal cell wall formation and glycoprotein production, including fungal-type cell wall biogenesis, cell wall organization, and cell wall mannoprotein biosynthesis, plus slime layer polysaccharide biosynthesis. These together point to secreted or cell-surface components (mannoproteins and related polysaccharides) being assembled for the fungal cell wall, with ER targeting and translation initiation terms reflecting their synthesis and trafficking. Overall, the dominant theme is fungal cell wall glycoprotein biosynthesis.","confidence":"Medium","size":22,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045047","count":1},{"id":"GO:0006465","count":1}]},{"hash":"2001207062740159105","title":"Vertebrate neural development and craniofacial morphogenesis","description":"This cluster is dominated by GO terms related to development of the nervous system and craniofacial structures (cerebral cortex development, embryonic cranial skeleton morphogenesis, mesoderm formation) and neural patterning (dorsal/ventral neural tube signaling). There are additional terms tied to DNA replication and telomere maintenance, suggesting some cell-cycle context, but the strongest signal is vertebrate neural development and craniofacial morphogenesis.","confidence":"Medium","size":22,"edges":25,"triangles":10,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0021987","count":9},{"id":"GO:0051973","count":8},{"id":"GO:0042220","count":8},{"id":"GO:0032212","count":8}]},{"hash":"1344280648738365172","title":"RNA processing and ribosome biogenesis","description":"The top GO terms indicate roles in ribosome assembly and biogenesis, translation, rRNA maturation, and spliceosome-mediated RNA processing, suggesting the cluster represents proteins involved in RNA metabolism and the production of ribosomes, i.e., core gene expression machinery.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000028","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006417","count":1}]},{"hash":"461405483790555011","title":"Signaling and cytoskeletal remodeling","description":"The GO terms cluster around signal transduction pathways (MAPK, Rho, VEGF) and cytoskeletal dynamics (actin remodeling, myoblast differentiation), spanning neural plasticity, muscle regeneration, and vascular signaling. This points to a cohesive theme of signaling-driven cytoskeletal changes across multiple tissues, with a few outlier cell-cycle terms included. Confidence is Moderate.","confidence":"Medium","size":22,"edges":33,"triangles":14,"max_degree":11,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0060291","count":8},{"id":"GO:0000196","count":7},{"id":"GO:0044565","count":7},{"id":"GO:0033316","count":7},{"id":"GO:0007266","count":7}]},{"hash":"710051447844116353","title":"Neurodevelopment with retinoid and polyamine metabolism","description":"The top GO terms center on brain development (substantia nigra development, angiogenesis in neural contexts) and metabolism (retinol metabolic process, putrescine catabolic process), suggesting a cluster tied to neural differentiation and vitamin A/polyamine pathways. Additional terms (translation, redox homeostasis, kinase activity regulation) reflect broader cellular processes supporting developing neural tissue. While not all terms are brain-specific, the combination of substantia nigra development and retinoid/polyamine metabolism anchors the cluster to neurodevelopment and associated metabolic regulation.","confidence":"Medium","size":22,"edges":11,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":3},{"id":"GO:0009447","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0006469","count":3}]},{"hash":"1655187022193676823","title":"Ubiquitin-Proteasome Degradation & Immune Regulation","description":"The cluster is characterized by strong enrichment for ubiquitin-related processes (ubiquitin-dependent protein catabolic process, protein ubiquitination, autoubiquitination, ERAD pathway), indicating a core link to the ubiquitin-proteasome system. Additionally, terms related to immune signaling (adaptive immune response, negative regulation of RIG-I signaling) suggest these proteins participate in modulating innate immune responses via ubiquitination. A peroxisome matrix import term is present but appears less central to the main theme.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0016558","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0002250","count":6}]},{"hash":"2091882475359853438","title":"Ubiquitin-Dependent Degradation and Peroxisomal Import","description":"The cluster centers on ubiquitin-related protein homeostasis actions (autoubiquitination, ubiquitin-dependent ERAD, ubiquitin-dependent protein catabolic process) and the peroxisomal matrix protein import, suggesting a cohesive theme of ubiquitin-mediated quality control linked to peroxisomal import; immune signaling terms may reflect cross-talk with ubiquitin pathways.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0016558","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0046328","count":6}]},{"hash":"1814445603952680092","title":"Transcription elongation and chromatin regulation","description":"The cluster is dominated by GO terms related to RNA polymerase II transcription elongation and chromatin states (DNA-templated elongation, histone acetylation, heterochromatin formation), implying a nuclear function in transcription regulation and chromatin remodeling. A couple of terms involve Golgi organization and Rho signaling, which may reflect multifunctional proteins in the set, but the core signal centers on transcription and chromatin dynamics.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0006354","count":2},{"id":"GO:1903358","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0043981","count":1}]},{"hash":"461128910147843515","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms show a strong emphasis on ribosome biogenesis and maturation of ribosomal RNA (LSU and 5.8S), indicating a core role in ribosome assembly and RNA processing. Other terms related to transcription, cell division, and some vesicle trafficking are present but less represented, suggesting these proteins mainly function in ribosome production with auxiliary connections to cellular transport and gene expression processes.","confidence":"High","size":22,"edges":14,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0007420","count":2}]},{"hash":"908387730696915502","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000920","count":2}]},{"hash":"852319621304641792","title":"Muscle development and homeostasis under stress","description":"The cluster is tied to muscle biology, with terms like somitogenesis, muscle attachment, and muscle cell cellular homeostasis pointing to muscle development and maintenance. It is further supported by stress-response terms (response to heat, cellular response to osmotic stress). Some other terms are more peripheral or obsolete, but the dominant signal is a muscle-focused developmental/homeostatic module, occasionally linked to stress adaptation.","confidence":"Medium","size":21,"edges":15,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0098779","count":1},{"id":"GO:0046716","count":1},{"id":"GO:0000183","count":1}]},{"hash":"1219421167677869372","title":"Neural and Vascular Development","description":"The cluster\u2019s top GO terms center on development and neural processes (angiogenesis, axonogenesis, heart development, visual perception, long-term synaptic potentiation), with supporting terms for transcription, cell cycle, apoptosis, and protein export. This mix suggests a cohesive theme of developmental and neural signaling and connectivity, even though an outlier (abscisic acid-activated signaling) might reflect cross-species annotations or broader regulatory roles. ","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0007409","count":2}]},{"hash":"1277208102783668827","title":"Antibiotic stress and membrane transport","description":"The cluster's top GO terms include strong signals for antibiotic response and the SOS response, indicating stress related to drug exposure or DNA damage. In addition, several transport-related terms (branched-chain amino acid, thiamine, taurine, and xenobiotic transport/export) suggest a grouping around membrane transport of nutrients and xenobiotics. Some terms like cytochrome complex assembly and antigen processing appear peripheral, but the dominant theme is stress response coupled with diverse transport functions.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0015803","count":3},{"id":"GO:0015888","count":3},{"id":"GO:0046618","count":3}]},{"hash":"2079080215609566043","title":"Core transcription, replication, and metabolism","description":"This cluster centers on fundamental cellular processes: DNA-templated transcription and DNA replication, along with key metabolic pathways (glycolysis, glucose metabolism, TCA cycle). The presence of a growth-related term (positive regulation of cell size) reinforces a link to cell growth. A few outlier terms related to development (cerebral cortex development, sperm capacitation) suggest some multifunctional or context-specific proteins, but the dominant theme is core gene expression and energy metabolism.","confidence":"Medium","size":21,"edges":55,"triangles":99,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0006096","count":6},{"id":"GO:0006006","count":6},{"id":"GO:0045793","count":6}]},{"hash":"1643572081195561476","title":"Calcium signaling and development","description":"This cluster centers on calcium-dependent signaling, highlighted by the sequestered calcium release and positive regulation of calcineurin-NFAT signaling, with supporting terms for neuronal and skeletal development (axonogenesis, bone development), mechanotransduction, and modulation of signaling pathways (kinase activity, ubiquitination). Together, these suggest a cohesive theme of calcium-driven regulation of development and tissue-specific differentiation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":2},{"id":"GO:0051209","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0019800","count":2}]},{"hash":"174260572730007558","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2151704497907265027","title":"RNA Processing and Genome Maintenance","description":"The GO terms cluster around RNA metabolism (regulatory ncRNA silencing, mRNA splicing, translation initiation/reinitiation, mRNA stabilization, transcription regulation) and genome maintenance (SOS response, nucleotide-excision repair, DNA replication). These together point to a module focused on RNA processing coupled with DNA repair/replication, with some developmental regulation hints (embryonic skull morphogenesis). ","confidence":"Medium","size":20,"edges":21,"triangles":16,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0009432","count":4}]},{"hash":"1112370967242489921","title":"DNA Damage Response with Transcription-Translation Regulation","description":"The cluster is enriched for translation-related terms (GO:0006412) alongside multiple transcription regulation/elongation/termination terms and DNA damage response signals (including p53-mediated pathways and gamma/UV radiation responses). This pattern suggests a cohesive module coordinating gene expression at both transcriptional and translational levels in response to DNA damage. The strong, interconnected GO signals support a high-confidence annotation of a damage-response, expression-regulation cluster.","confidence":"High","size":20,"edges":174,"triangles":901,"max_degree":19,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0032784","count":3},{"id":"GO:0006977","count":3},{"id":"GO:0006354","count":3},{"id":"GO:1902167","count":3}]},{"hash":"927272279555359967","title":"Ribosome biogenesis and nuclear transport during mitosis","description":"The cluster is dominated by GO terms for ribosome biogenesis (including maturation of LSU-rRNA and ribosomal subunit export from the nucleus) and nuclear transport (protein import/export from nucleus), together with mitotic cell cycle and cell division terms. This suggests a cohesive role in coordinating ribosome assembly with nucleocytoplasmic trafficking during cell division. Positive regulation of GTPase activity may relate to regulatory processes in transport and mitosis. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000055","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1757754581650315362","title":"Unknown","description":"The terms span development, chromatin regulation, signaling, transport, metabolism, and sensory processes with no single cohesive function linking all proteins, making a unified label inappropriate.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0043252","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0021510","count":1},{"id":"GO:0000132","count":1}]},{"hash":"1557534697837640972","title":"Aromatic compound metabolism and detoxification","description":"The terms cluster around aromatic/phenylpropanoid metabolism, including catabolic routes (3-phenylpropionate, stilbene, beta-ketoadipate) and alkaloid metabolism, with detoxification and some biosynthetic processes like strigolactone and antibiotic biosynthesis, suggesting a general aromatic secondary-metabolite metabolism theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0019380","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0019433","count":4}]},{"hash":"409630039531697434","title":"Bacterial fatty acid metabolism and lipid biosynthesis","description":"The dominant GO terms are fatty acid metabolic and biosynthetic processes (medium-/long-chain fatty acids) and lipid-related biosynthesis (e.g., lipoteichoic acid), with additional related metabolism terms like retinol and bile acid pathways. The presence of lipoteichoic acid biosynthesis strongly points to a bacterial context, making lipid metabolism the core theme.","confidence":"Medium","size":20,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0036112","count":4},{"id":"GO:0006633","count":4},{"id":"GO:0042572","count":3},{"id":"GO:0019427","count":3}]},{"hash":"1751275373724755224","title":"Prokaryotic translation and transcription core","description":"Top GO terms indicate a strong emphasis on translation and DNA-templated transcription, pointing to bacterial gene expression machinery. The SRP-dependent cotranslational targeting to membrane further supports ribosome-associated protein synthesis. Additional terms such as DNA repair, protein complex assembly, cell division, and flagellum organization suggest broader housekeeping roles, but the core theme remains prokaryotic gene expression and basic cellular processes.","confidence":"Medium","size":19,"edges":35,"triangles":18,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006351","count":2},{"id":"GO:0016032","count":1},{"id":"GO:0006617","count":1},{"id":"GO:0006281","count":1}]},{"hash":"1227858178655189677","title":"Endocytic trafficking and translation","description":"This cluster shows enrichment for endomembrane/vesicle trafficking processes (endocytic recycling, endosome organization, postsynaptic receptor internalization) alongside translation-related functions (translation, ribosomal large subunit export from nucleus). The co-occurrence suggests proteins involved in intracellular trafficking coupled with protein synthesis machinery, though some terms appear peripheral, indicating a moderate level of confidence. ","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0098884","count":1},{"id":"GO:0051262","count":1},{"id":"GO:0048662","count":1}]},{"hash":"18566112103723434","title":"Nucleotide Biosynthesis and DNA Recombination","description":"This cluster is dominated by nucleotide metabolism processes (CDP and ADP biosynthesis, purine ribonucleotide interconversion, and nucleotide phosphorylation/dephosphorylation) with a notable signal for DNA recombination; the brain- and liver-development terms appear secondary, suggesting broader expression patterns beyond metabolism.","confidence":"Medium","size":19,"edges":11,"triangles":3,"max_degree":5,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0046705","count":2},{"id":"GO:0046940","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0046041","count":2}]},{"hash":"1148014699800794165","title":"RNA processing and ribosome biogenesis under stress","description":"The top GO terms cluster around RNA-related processes (rRNA methylation, nuclear mRNA decay, transcription regulation by RNA Pol II, ribosomal small subunit export) and protein methylation, plus stress-related responses (ER stress, xenobiotic, hyperosmotic). This points to a cohesive theme of RNA metabolism and ribosome assembly/modulation, connected to cellular stress responses. Confidence reflects a plausible, though not perfectly singular, common function for the group.","confidence":"Medium","size":19,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006972","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0031167","count":2}]},{"hash":"2227254145551042853","title":"Amino acid biosynthesis and metal ion transport","description":"The cluster\u2019s top GO terms cluster around multiple amino acid biosynthesis pathways (proline, valine, tyrosine, pantothenate) and NADPH regeneration, plus metal ion import (copper and iron). This suggests a metabolic module with emphasis on amino acid/cofactor biosynthesis and metal ion homeostasis, rather than a single linear pathway. The combination is coherent but the diverse terms reduce certainty about a single narrowly defined function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015677","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0055129","count":2},{"id":"GO:0015940","count":2},{"id":"GO:0006740","count":2}]},{"hash":"1779802801875171584","title":"Ribosome biogenesis and translation machinery","description":"The top terms are dominated by translation and translational initiation, plus maturation of SSU-rRNA, indicating enrichment for ribosome biogenesis and protein synthesis components. Secondary terms like PI3K/AKT signaling, starvation response, and apoptosis may reflect broader regulatory roles, but the strongest signal centers on ribosome assembly and translation.","confidence":"High","size":18,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006413","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0015966","count":2},{"id":"GO:0051897","count":2}]},{"hash":"199986131751708132","title":"RNA processing and translation initiation machinery","description":"These proteins are enriched for GO terms tied to RNA biology and gene expression, including DNA-templated transcription, mRNA export, preinitiation complex formation, translation reinitiation, and spliceosome-regulated splicing. The presence of both transcription and translation initiation terms suggests a cluster of factors involved in RNA metabolism and regulation of gene expression; a few cell cycle and cadmium-response terms appear as secondary processes but do not override the main theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0048026","count":4}]},{"hash":"1508808446536800625","title":"Neural development and epigenetic regulation","description":"This cluster combines developmental processes (multicellular organism development, blastocyst development, CNS formation, efferent axon development) with transcriptional and epigenetic control (DNA-templated transcription, protein methylation, histone H2A acetylation), suggesting coordinated gene expression regulation during neural differentiation. While some terms reflect general cellular processes (mitotic cell cycle, cytoplasmic translation), the presence of neural development terms centers the theme on neural formation and its epigenetic regulation.","confidence":"Medium","size":18,"edges":21,"triangles":10,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006479","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0001824","count":2}]},{"hash":"2056807940258504754","title":"Angiogenesis and Muscle Growth Signaling","description":"The terms cluster around vascular growth and muscle development (angiogenesis, VEGF signaling, myoblast differentiation, cardiac muscle proliferation) with supportive growth signaling (insulin receptor pathway, MAPK, Rho) suggesting a shared theme of growth-and-proliferation signaling across tissues; a few outliers (dendritic cell proliferation, meiotic checkpoint) are less representative.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0060358","count":2},{"id":"GO:0000196","count":1},{"id":"GO:0044565","count":1}]},{"hash":"504787801032844783","title":"Unknown","description":"GO terms span diverse processes including metabolism (TCA, glyoxylate, acetate/propionate pathways), cobalamin biosynthesis, RNA capping, ubiquitin-dependent degradation via MVB sorting, and cytoskeletal organization, with no clear unifying function.","confidence":"","size":18,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0075141","count":1},{"id":"GO:0032923","count":1},{"id":"GO:0006099","count":1}]},{"hash":"908194332123127958","title":"Mitochondrial Lipid Metabolism and Brain Development","description":"The top GO terms cluster around lipid metabolism and mitochondrial lipid handling (SREBP signaling, cardiolipin metabolism, stress-induced mitochondrial fusion), along with signals of neural development (forebrain and brain development). This suggests a set of proteins involved in mitochondrial lipid homeostasis with links to neuronal development. Some other terms (ERAD, histone deacetylation) are less central but may reflect broader cellular regulation.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0016575","count":2}]},{"hash":"877773731699604758","title":"Transcriptional and chromatin regulation with RNA silencing","description":"The cluster shows enrichment for DNA-templated transcription, chromatin remodeling and histone modification regulation, along with post-transcriptional control via ncRNA- and miRNA-mediated silencing and splicing regulation. This points to a cohesive module governing gene expression at both transcriptional and post-transcriptional levels, including chromatin dynamics and RNA-based silencing.","confidence":"High","size":17,"edges":12,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0035278","count":2},{"id":"GO:2000617","count":2}]},{"hash":"1098190559159451148","title":"ER-Golgi transport and ER stress response","description":"The set of GO terms centers on endoplasmic reticulum stress response and vesicle trafficking between the ER and Golgi, including COPII coating, Golgi organization, and retrograde transport. This points to a cohesive role in the secretory pathway and ER quality control. A couple of terms touch on ribosome biogenesis and translation, which may reflect peripheral associations with protein synthesis, but the dominant signal is ER-Golgi trafficking and stress response.","confidence":"Medium","size":17,"edges":13,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0034976","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0003400","count":2},{"id":"GO:0097284","count":2}]},{"hash":"1201690773280541764","title":"Vesicle trafficking and cytoskeleton dynamics","description":"The top GO terms are dominated by ER-to-Golgi vesicle transport and COPII-coated vesicle budding, together with actin filament depolymerization and regulation of GTPase activity, indicating a cluster centered on the secretory pathway and cytoskeletal remodeling. Some terms relate to broader transport or cell-cycle processes, but the core theme ties vesicle trafficking to cytoskeletal regulation, justifying this label over others.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0090344","count":2}]},{"hash":"935152589014649441","title":"Bacterial DNA metabolism and translation","description":"Top GO terms show DNA replication, repair, and recombination, along with translation and SSU-rRNA maturation, suggesting a core function in nucleic acid metabolism and protein synthesis in bacteria. Contextual terms like teichoic acid biosynthesis and redox homeostasis appear but do not define the cluster\u2019s main theme.","confidence":"Medium","size":17,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0015937","count":2},{"id":"GO:0006310","count":2}]},{"hash":"1002050977593796023","title":"Nuclear RNA Processing and Spliceosome Assembly","description":"This cluster is dominated by GO terms linked to nuclear RNA processing and spliceosome assembly (spliceosomal and snRNP assembly), with additional RNA maturation activities (tRNA processing, SSU-rRNA maturation) and mRNA decapping/decay in the nucleus, suggesting a cohesive role in nuclear RNA metabolism and RNA processing.","confidence":"High","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0006369","count":1}]},{"hash":"1372155177824369071","title":"Mitosis and ER-Golgi trafficking","description":"Predominant GO terms include cell division, mitotic cell cycle, and DNA replication, alongside ER-to-Golgi vesicle transport and SNARE disassembly, indicating a cluster of proteins tied to cell-division machinery and secretory pathway dynamics.","confidence":"Medium","size":17,"edges":7,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0006888","count":4},{"id":"GO:0001824","count":4},{"id":"GO:0043547","count":4}]},{"hash":"721597561634192167","title":"DNA Repair and RNA Processing","description":"The cluster is dominated by nucleic acid\u2013related terms: nucleotide-excision repair, transcription, mRNA splicing via spliceosome, and mRNA decay, plus chromatin formation. These point to genome maintenance and RNA biology as the core theme. Vesicle transport and cytochrome complex assembly appear as additional, less central connections, possibly reflecting multifunctional proteins or broader cellular roles, but do not override the nucleic acid\u2013focused signal. Therefore, labeling as DNA Repair and RNA Processing captures the primary shared function of the cluster.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":3},{"id":"GO:0017004","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0030466","count":2},{"id":"GO:0006891","count":2}]},{"hash":"2225255500694296514","title":"Genome maintenance and proteostasis","description":"Top GO terms cluster around DNA repair, DNA replication, piecemeal microautophagy of the nucleus, and ubiquitin-dependent ERAD pathways, all pointing to genome maintenance and protein quality control. While other terms touch on immune signaling and development, the core theme is coordination of genome integrity with proteostasis, justifying this label.","confidence":"Medium","size":17,"edges":51,"triangles":101,"max_degree":10,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0034727","count":4},{"id":"GO:0006281","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0051436","count":3}]},{"hash":"1347215710380519611","title":"Cell Cycle and Ribosome Biogenesis under ER Stress","description":"This cluster shows strong signals for cell division and cell cycle, plus ribosome biogenesis and export, and includes ER stress\u2013related responses. Together they point to a theme where proliferative growth is coordinated with protein synthesis capacity and stress adaptation, with a few ancillary terms related to multicellular processes.","confidence":"Medium","size":17,"edges":17,"triangles":0,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0007049","count":5},{"id":"GO:0034976","count":4},{"id":"GO:0034198","count":4},{"id":"GO:1903206","count":4}]},{"hash":"1099854561647231478","title":"Chromatin modification and transcriptional regulation","description":"This cluster is characterized by GO terms centered on DNA-templated transcription and histone modification (methylation and acetylation), pointing to regulation of gene expression through chromatin state. The presence of mRNA processing and translation terms fits the broader theme of gene expression control, while a few terms related to signaling and mitosis suggest additional regulatory roles. Overall, the dominant signal is chromatin-based transcriptional regulation, with some noise from related processes.","confidence":"Medium","size":17,"edges":15,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0006412","count":1}]},{"hash":"1363050256510774938","title":"Fungal beta-glucan synthesis and cell growth","description":"The cluster includes a strong fungal-specific term: fungal-type cell wall beta-glucan biosynthetic process, along with karyogamy, pointing to fungal reproduction. Other terms reflect core cellular machinery (DNA replication, iron-sulfur cluster assembly, protein targeting), which are common to many organisms. The combination suggests a fungal-context cluster centered on cell wall biosynthesis and general growth/replication processes, though some terms are more universal. ","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:1902037","count":1},{"id":"GO:0070880","count":1},{"id":"GO:1903382","count":1},{"id":"GO:0006880","count":1}]},{"hash":"1389676396867628162","title":"Mitotic spindle assembly and centrosome dynamics","description":"The cluster is dominated by GO terms related to mitosis: mitotic spindle assembly, spindle orientation, and centrosome separation, plus kinase activity regulation. While there are a few terms tied to development or fungal growth, the strongest signal centers on mitotic spindle formation and its regulation, justifying this label.","confidence":"Medium","size":17,"edges":34,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0000132","count":3},{"id":"GO:0007118","count":3}]},{"hash":"1439408563111758270","title":"Mitotic cell cycle and translation initiation","description":"The top GO terms cluster strongly around mitosis and cell division (mitotic cell cycle, anaphase-promoting complex-dependent catabolic process, establishment of mitotic spindle orientation, and general cell division), indicating a primary role in coordinating cell cycle progression. In addition, multiple terms relate to translation initiation and reinitiation (translation reinitiation, formation of translation preinitiation complex), suggesting a linked function between cell-cycle control and the regulation of protein synthesis. Some chromatin modification terms appear but are less represented. Overall, the cluster seems to reflect proteins involved in mitosis with concurrent regulation of translation initiation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0002188","count":4},{"id":"GO:2001162","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0001731","count":4}]},{"hash":"1277970051343148584","title":"Nuclear mRNA processing and splicing regulation","description":"The cluster is dominated by GO terms tied to mRNA processing in the nucleus\u2014stabilization, export, polyadenylation regulation, tail shortening, and both positive and negative regulation of spliceosome-mediated splicing\u2014as well as general mRNA modification. This cohesive set points to a group of proteins functioning in mRNA maturation and splicing control within the nucleus.","confidence":"High","size":17,"edges":10,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:1900363","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0006406","count":2}]},{"hash":"83637471654082049","title":"RNA processing and apoptotic regulation","description":"The top terms cluster around apoptotic processes alongside multiple RNA processing steps (mRNA stabilization, export, modification, splicing regulation, and polyadenylation). This suggests a group of proteins linked to RNA metabolism that can influence cell fate decisions, i.e., apoptosis. Some terms are obsolete, and there are no interactions shown, but the GO signal points to a coherent theme of RNA processing linked to apoptotic regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0048255","count":2},{"id":"GO:1900363","count":2},{"id":"GO:1905663","count":2}]},{"hash":"1867705991847575832","title":"Proteostasis and Stress Response","description":"This cluster is enriched for ubiquitin-proteasome system components (protein ubiquitination; proteasome regulatory particle assembly) and stress-related GO terms (response to cold, cellular response to mechanical stimulus) and apoptotic processes in various cell types, suggesting a coherent theme around protein quality control under stress and stress-induced remodeling, with some involvement in cell cycle and polarity as downstream or parallel processes.","confidence":"High","size":17,"edges":13,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0071260","count":3}]},{"hash":"325993024396094552","title":"Neural development","description":"The top GO terms show strong emphasis on neural structure formation: neuron projection development, retina development, spinal cord development, and neural tube closure, indicating a neurodevelopmental cluster. Supporting terms like chromatin organization and spindle orientation reflect cellular processes involved in neural progenitor proliferation and differentiation, while glucose signaling and GTPase regulation are general modifiers often linked to developmental signaling. Overall, the proteins seem tied to nervous system development and formation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0031175","count":5},{"id":"GO:0060041","count":5},{"id":"GO:0021510","count":4},{"id":"GO:0000132","count":4},{"id":"GO:0043982","count":4}]},{"hash":"415246166811933740","title":"Immune signaling and antiviral defense","description":"The cluster\u2019s top GO terms cluster around immune processes: innate immune response, defense response to virus, T cell homeostasis, and positive regulation of NF-kappaB signaling, suggesting the proteins function in immune signaling and antiviral defense, potentially linked via ubiquitin-dependent protein turnover that modulates signaling pathways. Some peripheral terms (ascus formation, cell budding, EMT, meiotic repair) may reflect annotation noise or multi-functionality rather than a core theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0043029","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051607","count":3}]},{"hash":"1574926118629929305","title":"Ribosome Biogenesis and Translation Initiation","description":"The key GO terms point to ribosome-related processes: maturation of SSU-rRNA, formation of the translation preinitiation complex, and translation reinitiation, which together indicate ribosome biogenesis and initiation of translation. A related term about GTPase activity supports involvement of translation GTPases. The developmental terms seem ancillary noise, so the strongest coherent theme is ribosome and translation, leading to a translation-centered cluster label.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3}]},{"hash":"2269450411888310746","title":"Heterochromatin formation and transcription regulation","description":"This cluster is dominated by chromatin-related terms, including heterochromatin assembly and silencing at subtelomeric and mating-type loci, as well as nucleosome-related processes and DNA-templated transcription. These themes point to regulation of chromatin state and transcription; auxiliary terms like deubiquitination and aggresome assembly may reflect broader proteostasis cross-talk with chromatin regulation, but the core signal is chromatin silencing and transcription control.","confidence":"High","size":16,"edges":8,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070842","count":4},{"id":"GO:0060303","count":3},{"id":"GO:0030466","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0031939","count":3}]},{"hash":"1184456374499776476","title":"Developmental gene expression and growth","description":"The cluster shows strong representation of development-related GO terms (multicellular organism development, forebrain development, neural tube closure, skeletal system development) along with DNA-templated transcription and mitotic cell cycle, suggesting a group focused on developmental gene regulation and proliferation. Some stress/defense terms are present as outliers, but the core signal supports a developmental-expression-and-growth theme. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0050830","count":4}]},{"hash":"700092662829827214","title":"DNA Damage Response and Repair","description":"The top GO terms show a clear emphasis on genome maintenance: DNA replication, the SOS response, and nucleotide-excision repair, suggesting a core focus on DNA damage sensing and repair. Additional terms related to meiotic DSB formation and ascospore formation indicate links to recombination and cell division, while several developmental terms (lung/mesoderm development, EMT) may reflect broader roles in differentiation or pleiotropy. Overall, the cluster appears centered on DNA damage response and repair with some divergent developmental connections.","confidence":"Medium","size":16,"edges":8,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0009432","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0030324","count":2}]},{"hash":"1261084407716278173","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000350","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0007127","count":2},{"id":"GO:0006357","count":2},{"id":"GO:0033077","count":1}]},{"hash":"1026473456113862471","title":"Neurodevelopment and axonogenesis","description":"Based on the top GO terms, the majority point to neural development and neuronal patterning, including substantia nigra development, axonogenesis, neural tube patterning, and interneuron migration. While some terms touch on vesicle trafficking and signaling regulation, the dominant theme is neurodevelopmental processes governing neuron growth and connectivity, which best captures the cluster\u2019s shared function.","confidence":"Medium","size":16,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0072221","count":2}]},{"hash":"1663712802250676265","title":"Mitotic cell cycle and chromatin regulation","description":"This cluster\u2019s top GO terms are strongly enriched for mitotic processes (establishment of mitotic spindle orientation, mitotic cell cycle) and chromatin dynamics (chromatin organization, histone acetylation), suggesting a core connection to cell division and chromatin remodeling. While several development- or sensory-related terms appear (spinal cord development, neural tube closure, taste perception), the dominant signal centers on mitosis and chromatin regulation, indicating these proteins may function together in cell-cycle control or chromatin modification during division. Overall, the cluster is best described by a cell-cycle/chromatin theme with some pleiotropic developmental annotations.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000132","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0021510","count":2},{"id":"GO:0043982","count":2}]},{"hash":"1598682926331187371","title":"Ribosome Biogenesis and Cell Division","description":"The GO terms cluster around rRNA maturation (5.8S and LSU), transcription, and cell cycle/division processes, suggesting proteins involved in ribosome assembly linked to cell proliferation. Some terms like phosphate transport and neuron differentiation are less connected, but the core signal is ribosome maturation coupled with division.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1898801861307416358","title":"Protein quality control and ubiquitin regulation","description":"This cluster centers on chaperone-mediated assembly, regulation of proteolysis via ubiquitin-related mechanisms (positive regulation of ubiquitin-specific protease activity, SCF complex disassembly in response to cadmium stress), and inclusion body assembly, all pointing to protein homeostasis and degradation pathways. While some terms (DNA replication, viral genome replication) are less connected, the strongest cohesive theme is protein quality control and ubiquitin-mediated regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0051131","count":1},{"id":"GO:1903862","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0019079","count":1}]},{"hash":"170680134149854490","title":"Central Carbon Metabolism and Transcription","description":"The top GO terms point to core metabolic activities (pyruvate biosynthesis, oxaloacetate metabolism, D-serine biosynthesis) and metabolic signaling (cellular response to insulin stimulus), together with DNA-templated transcription and ribosome biogenesis. This pattern suggests a module where metabolism is linked to gene expression and growth. Some terms are obsolete, but the central theme appears to be metabolic regulation intertwined with transcriptional activity.","confidence":"Medium","size":15,"edges":32,"triangles":38,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042866","count":3},{"id":"GO:0032869","count":3},{"id":"GO:0019518","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006107","count":3}]},{"hash":"519446078771194523","title":"Ribosome Biogenesis and Translation","description":"The proteins are enriched for ribosome-related processes: ribosome biogenesis, translation, rRNA maturation, and rRNA base methylation, with additional signals for ribosomal large subunit export and biogenesis, pointing to a cohesive role in ribosome assembly and protein synthesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0070475","count":2},{"id":"GO:0007049","count":2}]},{"hash":"1469044889403901662","title":"Central Metabolism and Mitosis","description":"The cluster is enriched for core energy pathways (TCA cycle, glycolysis) alongside cell-cycle processes (mitotic cycle and spindle checkpoint) and redox/homeostasis functions, suggesting a link between metabolism and cell proliferation with oxidative stress regulation.","confidence":"Medium","size":15,"edges":23,"triangles":18,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0051301","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0000278","count":2}]},{"hash":"1819131219530000713","title":"Neural development and synaptic plasticity","description":"The cluster is dominated by neural-related GO terms: Schwann cell development, axonogenesis, dendritic spine morphogenesis, excitatory postsynaptic potential, and long-term potentiation, pointing to neural development and synaptic maturation. MAPK signaling terms (ERK and JNK cascades) further support a role in signaling that drives neural differentiation and synaptic plasticity. A couple of terms (angiogenesis, abscisic acid-activated signaling) are less core to neurons and may reflect broader pathway associations, but the primary theme across the cluster centers on neural development and synaptic signaling.","confidence":"Medium","size":15,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0014044","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0046330","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0001525","count":2}]},{"hash":"1141304977720329322","title":"Amino acid and vitamin biosynthesis","description":"This cluster centers on biosynthetic and metabolic processes, especially amino acid and vitamin biosynthesis (serine, valine, tyrosine, alanine), and related catabolic and lipid A biosynthesis terms. The presence of antibiotic biosynthetic process fits microbial secondary metabolism, while an outlier term like nervous system development may reflect cross-species annotations. Overall, the shared theme is metabolism and biosynthesis.","confidence":"Medium","size":15,"edges":22,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006564","count":3},{"id":"GO:0006574","count":3},{"id":"GO:0007399","count":2}]},{"hash":"15790741251633565","title":"Metabolism and RNA methylation","description":"Dominant themes are metabolic regulation and RNA methylation. The terms include redox homeostasis, starvation response, leucine catabolism, cAMP signaling, and cobalamin biosynthesis (metabolic processes), alongside RNA- and protein-methylation terms (tRNA/rRNA methylation, protein methylation). DNA replication and liver development appear as broader growth context signals but do not define a single cohesive pathway. Overall, the cluster centers on metabolism with methylation-related regulation of gene expression.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0006552","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0042594","count":2},{"id":"GO:0001889","count":2}]},{"hash":"1369390282359466715","title":"RNA processing and mitochondrial translation","description":"The cluster includes clear signals for RNA processing (alternative splicing, polyadenylation) together with translation-related processes (mitochondrial tRNA aminoacylation and general translation), suggesting a theme around RNA maturation and mitochondrial protein synthesis. Some terms like angiogenesis and sodium transport appear as noise and do not fit the core theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0001525","count":1}]},{"hash":"680991257457555762","title":"Developmental gene expression and cell cycle","description":"The top GO terms cluster around DNA-templated transcription, DNA replication, and mitotic cell cycle, together with several development-related terms such as forebrain development, neural tube closure, and multicellular organism development. This points to a shared theme of gene expression regulation and cell proliferation during development, with a few stress-related terms that may reflect context-specific regulation or incidental associations. Overall, the functions cohere around developmental transcriptional control and proliferation rather than a single, narrow process.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0006260","count":4}]},{"hash":"1383918413542365450","title":"Clathrin-mediated endocytosis and ubiquitination","description":"This cluster is characterized by GO terms for clathrin-dependent endocytosis, vesicle coating, and intracellular transport, with multiple entries for protein ubiquitination. While a few terms touch regulatory roles in cytokine production and chromatin assembly, the strongest shared theme is vesicle trafficking and protein turnover control, supported by endocytic processes and ubiquitination.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072583","count":2},{"id":"GO:0032691","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0032717","count":2},{"id":"GO:0016183","count":1}]},{"hash":"752975604653144028","title":"Phosphoinositide Signaling and Growth Factor Pathways","description":"These terms cluster around phosphatidylinositol-mediated signaling and growth factor\u2013related pathways, including PI signaling components, IGF receptor signaling, and regulation of phosphorylation. While a few terms touch on immune signaling or organ development, the dominant theme is membrane lipid signaling driving growth-related transduction. ","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046686","count":2},{"id":"GO:0032835","count":1},{"id":"GO:1902634","count":1},{"id":"GO:1900122","count":1},{"id":"GO:0048009","count":1}]},{"hash":"2219184185698385952","title":"Vacuolar acidification and proteolysis","description":"The top GO terms cluster around vacuolar function: proton-transporting V-type ATPase assembly, proton transmembrane transport, vacuolar acidification, and protein catabolic process in the vacuole, suggesting a shared role in acidifying the vacuole and degrading cargo. Iron-sulfur cluster maturation appears but is not central to the main theme; excretion and polyphosphate metabolism are ancillary terms.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097428","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0007588","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0043181","count":1}]},{"hash":"842635676430136882","title":"Unknown","description":"These proteins have GO terms spanning mitochondrial electron transport, copper ion homeostasis, vesicle targeting, neural and mesodermal development, signaling, and host\u2013pathogen interaction processes, with no clear single functional theme tying them together. Therefore, there isn\u2019t a coherent cluster function to label beyond Unknown.","confidence":"","size":15,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0048714","count":2},{"id":"GO:0021943","count":2}]},{"hash":"1030491084446681537","title":"p53-Mediated Stress Signaling and ER Response","description":"This cluster\u2019s terms converge on cellular stress responses and fate decisions, with items like mitotic G2 DNA damage checkpoint signaling, p53 mediator signaling, unfolded protein response, and protein ufmylation pointing to ER stress and DNA damage\u2013driven signaling pathways that influence apoptosis and nuclear localization. While gastrulation-related terms appear, the dominant shared theme is stress- and checkpoint-related signaling rather than a single specialized process, so the label reflects a cohesive but broad stress-response cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055113","count":1},{"id":"GO:0030262","count":1},{"id":"GO:0007095","count":1},{"id":"GO:0032088","count":1},{"id":"GO:0070586","count":1}]},{"hash":"1721913685600705142","title":"Post-transcriptional mRNA processing and export","description":"The cluster\u2019s GO terms highly emphasize post-transcriptional RNA processing\u2014alternative splicing via the spliceosome, regulation of mRNA splicing, mRNA export from the nucleus, and aspects of mRNA modification and stability\u2014pointing to a cohesive role in mRNA maturation and trafficking after transcription.","confidence":"High","size":14,"edges":71,"triangles":168,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000380","count":4},{"id":"GO:0048255","count":3},{"id":"GO:1900363","count":3},{"id":"GO:1905663","count":3},{"id":"GO:0048025","count":3}]},{"hash":"444589437707013307","title":"Golgi trafficking and protein folding","description":"The top GO terms emphasize Golgi-related processes (endosome-to-Golgi transport; regulation of Golgi organization) and protein processing (protein folding, ribosomal subunit export involvement in biogenesis). While there are some ancillary terms like xenobiotic response and ubiquinone biosynthesis, the strongest signal centers on Golgi trafficking and protein quality control, justifying this label.","confidence":"Medium","size":14,"edges":8,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0001300","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0006457","count":2}]},{"hash":"1764929643896175327","title":"Nuclear transcription, RNA processing, and chromatin remodeling","description":"This cluster centers on RNA Pol II transcription regulation (initiation, termination), RNA splicing dynamics, chromatin remodeling, transcription-coupled repair, and related nuclear processes, with additional support from nuclear mRNA surveillance and import. The dominant theme is nuclear gene expression regulation and genome maintenance.","confidence":"Medium","size":14,"edges":32,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006269","count":7},{"id":"GO:0071049","count":7},{"id":"GO:0017038","count":7},{"id":"GO:0045944","count":7}]},{"hash":"2284870406467677293","title":"DNA Replication and Repair with Cell Cycle","description":"The top GO terms cluster around DNA replication, DNA repair, and cell cycle processes (meiotic cell cycle, G1/S transition, DNA damage response, response to ionizing radiation), suggesting a nuclear maintenance/cell-cycle\u2013regulation theme. Development-related terms (multicellular organism development, heart development) indicate broader roles in development, though cholesterol biosynthesis and cocaine response appear as outliers. Overall, the core connection is DNA replication/repair and cell-cycle control with some developmental associations.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051321","count":3},{"id":"GO:0006695","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006977","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1000940415296101594","title":"Calcium Homeostasis and Ion Transport","description":"The terms cluster around ion transport and calcium signaling, notably calcium import into the sarcoplasmic reticulum, intracellular calcium homeostasis, and maintenance of transmembrane electrochemical gradients, with supporting evidence from monoatomic and copper ion transport and membrane repolarization. While some terms reference metabolic pathways (P450 epoxygenase, stilbene catabolism) or hormone response (testosterone), the dominant theme centers on ions across membranes and calcium regulation.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":1},{"id":"GO:0010248","count":1},{"id":"GO:1990036","count":1},{"id":"GO:0006874","count":1},{"id":"GO:0033574","count":1}]},{"hash":"965745052585988032","title":"Multi-tissue differentiation and growth signaling","description":"Top GO terms indicate involvement in various signaling pathways (MAPK cascade, Rho signaling, VEGF receptor signaling) and differentiation processes across multiple tissues (myoblast and chondrocyte differentiation, dendritic cell proliferation, endothelial processes, and cardiac muscle proliferation). The inclusion of DNA replication and meiotic spindle checkpoint suggests roles tied to cell cycle control accompanying proliferation. Overall, the cluster appears to encompass proteins participating in broad developmental signaling and lineage specification across tissues rather than a single, cohesive function.","confidence":"Medium","size":14,"edges":13,"triangles":2,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0000196","count":9},{"id":"GO:0044565","count":9},{"id":"GO:0033316","count":9},{"id":"GO:0007266","count":9}]},{"hash":"1756864797009635824","title":"Plant development signaling and cell cycle control","description":"The top GO terms converge on plant growth and development: regulation of phosphorylation and CDK activity points to control of the cell cycle; protein export from the nucleus and kinetochore localization relate to cell division and nucleocytoplasmic transport; meristem identity maintenance and responses to growth factor\u2013like signaling (TGF-beta/BMP pathways) suggest developmental regulation. The photosystem stoichiometry adjustment term hints at integration with chloroplast function, typical of plant biology. Together, these terms imply a cluster of proteins involved in plant development signaling and cell cycle coordination, with ancillary roles in nuclear transport and organellar coordination.","confidence":"Medium","size":14,"edges":26,"triangles":23,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035970","count":8},{"id":"GO:0000173","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0034501","count":5},{"id":"GO:0045736","count":5}]},{"hash":"424890772499278079","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":49,"triangles":74,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0043547","count":7},{"id":"GO:0019236","count":7},{"id":"GO:0006547","count":6}]},{"hash":"1498420641591970242","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":11,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000480","count":3},{"id":"GO:0042273","count":3},{"id":"GO:1902626","count":3}]},{"hash":"1266805926404670412","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":31,"triangles":46,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0071033","count":2},{"id":"GO:0034476","count":2},{"id":"GO:0000973","count":2}]},{"hash":"1481123755624805792","title":"ER Protein Folding and ERAD","description":"The top GO terms center on endoplasmic reticulum\u2013related processes such as ubiquitin-dependent ERAD, ER protein folding, and post-translational targeting to membranes, which together suggest a theme of ER quality control and maturation. Some terms appear peripheral (viral process, DNA replication, mesoderm formation) or obsolete, indicating potential annotation noise, but the core signals point to ER-associated protein handling.","confidence":"Medium","size":13,"edges":13,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0016032","count":3},{"id":"GO:1902416","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0034975","count":2}]},{"hash":"152375053980732860","title":"Fungal cell wall biosynthesis","description":"Top GO terms point to fungal cell wall construction and glycoprotein components (cell wall organization, fungal-type cell wall biogenesis, cell wall mannoprotein biosynthetic, slime layer polysaccharide biosynthetic), suggesting the proteins operate in assembling and modifying the fungal cell envelope. Some noise terms (mRNA export, obsolete biosynthetic terms) are present, but the dominant signal supports a fungal cell wall biosynthesis theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0018279","count":2},{"id":"GO:0006535","count":1},{"id":"GO:0000032","count":1}]},{"hash":"886144752538637763","title":"Ribosome Biogenesis and Translational Regulation","description":"The cluster is enriched for GO terms on translation, ribosome biogenesis, cytoplasmic translation, and nuclear export of the large ribosomal subunit, indicating involvement in ribosome assembly and control of protein synthesis. Additional terms on mRNA decay and regulation of translation elongation reinforce the theme of translational regulation, suggesting these proteins function together in ribosome production and modulation of translation.","confidence":"High","size":13,"edges":14,"triangles":7,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0002181","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0000055","count":3}]},{"hash":"1342916250473772363","title":"Redox Homeostasis & Oxidative Stress Response","description":"Dominant redox theme: multiple GO terms point to oxidative stress response and redox homeostasis (cellular oxidant detoxification, cell redox homeostasis, cellular response to oxidative stress) and redox post-translational modification (protein deglutathionylation). A few terms appear incidental (nuclear transcription regulation, nucleotide biosynthesis) but do not define the core function. Therefore, a concise label capturing redox balance and stress response best describes the cluster.","confidence":"Medium","size":13,"edges":14,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":3},{"id":"GO:1903026","count":3},{"id":"GO:0045454","count":3},{"id":"GO:2000651","count":2}]},{"hash":"74079266047847033","title":"Unknown","description":"The 13 proteins show a mix of GO terms for core cellular processes (cell cycle, translation, transcription regulation) together with developmental terms (atrial septum development, prostate gland development, male sex differentiation) and a yeast-specific chromatin silencing term. There is no clear, single function or pathway tying these terms together, so a cohesive functional label cannot be assigned beyond Unknown.","confidence":"","size":13,"edges":11,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0003283","count":2}]},{"hash":"394229285728535089","title":"Unknown","description":"This cluster shows a mix of GO terms across development (multicellular organism development, skin development), sensory perception, signaling (TGF-beta response), and various cellular/metabolic processes (ribosome biogenesis, protein homooligomerization, detoxification). There isn\u2019t a single coherent function tying these terms together, suggesting the proteins do not share a clear common theme. ","confidence":"","size":13,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055119","count":2},{"id":"GO:0007608","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1938726246372033988","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0006369","count":2}]},{"hash":"1894087564867904737","title":"RNA processing and RNP biogenesis","description":"The terms cluster around RNA modification and processing (splicing, snRNA/pseudouridylation), assembly of ribonucleoprotein complexes (box H/ACA snoRNP, telomerase holoenzyme and its RNA localization/stabilization), as well as ribosome biogenesis and translation-related processes, indicating a theme of RNA-protein complex maturation and assembly.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000454","count":1},{"id":"GO:1905323","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0000493","count":1}]},{"hash":"498567087006326835","title":"RNA Methylation and Protein Modification","description":"This cluster is driven by both RNA modification (RNA guanine-N7 methylation; tRNA wobble uridine modification) and various protein modification processes (peptidyl-arginine hydroxylation; general methylation), with additional signals of cell growth and cell cycle context. The dominant theme suggests involvement in RNA and protein modification pathways that regulate gene expression and protein function, though a few terms (chlorophyll and antibiotic biosynthesis) may reflect broader enzyme families or cross-species annotations.","confidence":"Medium","size":13,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0001300","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0032259","count":2}]},{"hash":"1755145120777086852","title":"Unknown","description":"The GO terms span apoptosis, response to muramyl dipeptide, adipocyte differentiation, pain perception, synapse assembly, VEGF/hypoxia responses, kidney tubule development, and cell-matrix adhesion, with no single coherent function that unifies them. This diversity makes it hard to assign a specific label beyond Unknown.","confidence":"","size":13,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0032495","count":2},{"id":"GO:0090336","count":2},{"id":"GO:0019800","count":2},{"id":"GO:0019233","count":2}]},{"hash":"1851091643992884718","title":"N-terminal and polyamine acetylation","description":"The cluster is dominated by acetylation-related GO terms: N-terminal peptide/methionine acetylation and polyamine (putrescine, spermidine) acetylation, plus related N-acetyltransferase activity seen in melatonin biosynthesis. Some chromatin-related terms (subtelomeric heterochromatin formation, centromeric cohesion) may reflect regulation by acetylation of chromatin-associated proteins. Overall, this group appears to center on acetyltransferase activities across substrates.","confidence":"Medium","size":13,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":5},{"id":"GO:0017196","count":3},{"id":"GO:0006526","count":3},{"id":"GO:0061606","count":3},{"id":"GO:0045150","count":3}]},{"hash":"1498745334585837862","title":"Meiosis and Cell Cycle Regulation","description":"Top GO terms indicate a focus on meiosis (homologous chromosome pairing at meiosis, ascospore formation) and cell cycle control (G1/S transition). Transcriptional regulation terms (DNA-templated transcription, negative regulation of transcription by RNA Pol II) further support a theme of gene expression control during division and meiosis. Some metabolic terms appear but are likely incidental. Overall, the cluster seems to center on regulation of gene expression in meiosis and cell cycle progression.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0022028","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0005979","count":2}]},{"hash":"1938304630687304865","title":"Photoreception and GPCR signaling","description":"The cluster shows two strong photoreception signals (detection of visible light; protein-chromophore linkage, though obsolete), suggesting a photoreceptor-related function. Additionally, terms like G protein-coupled acetylcholine receptor signaling and estrogen response indicate broader signaling roles. Because photoreception is a clear anchor but the rest is diverse, the label is plausible but not exclusive, yielding a Medium confidence. ","confidence":"Medium","size":13,"edges":10,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071318","count":3},{"id":"GO:0045429","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009584","count":2},{"id":"GO:0018298","count":2}]},{"hash":"87107062970162170","title":"Mitochondrial Energy Metabolism","description":"This cluster shows enrichment in mitochondrial transport and energy-related processes: transport of citrate, CoA, heme and thiosulfate; regulation of mitochondrial membrane potential; adaptive thermogenesis; fatty acid response; and insulin/IGF signaling responses. The combination of transporters and energy-regulation terms suggests proteins coordinating mitochondrial bioenergetics and metabolic signaling.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":5},{"id":"GO:1990845","count":4},{"id":"GO:0006843","count":4},{"id":"GO:1990314","count":4},{"id":"GO:0007565","count":4}]},{"hash":"2138271767735062621","title":"Autophagy and Protein Modification in Yeast","description":"This cluster\u2019s terms include macroautophagy and nucleophagy, alongside several protein post-translational modifications (sumoylation, urmylation, and lipidation). Additional terms touch on growth regulation, cell-cycle events, and tRNA modification, which are commonly connected to stress responses in yeast. The dominant theme appears to be autophagy-related protein processing and cellular stress response in a fungal context.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044805","count":2},{"id":"GO:0018192","count":2},{"id":"GO:2000220","count":2},{"id":"GO:0006501","count":2},{"id":"GO:0032447","count":2}]},{"hash":"1075986748771206049","title":"Cell stress signaling and apoptosis","description":"The cluster is enriched for stress- and signaling-related GO terms: cellular response to amino acid starvation, response to toxic substance, negative regulation of TORC1 signaling, MAPK cascade, protein phosphorylation, and apoptotic process. These collectively point to stress-activated signaling pathways that influence cell fate decisions. Some terms related to meiosis and broader signaling events suggest cross-talk with cell cycle and neural signaling networks, but the core theme remains stress-responsive signaling and apoptosis.","confidence":"Medium","size":12,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0034198","count":4},{"id":"GO:0009636","count":4},{"id":"GO:1904262","count":4},{"id":"GO:1903343","count":4},{"id":"GO:0035249","count":4}]},{"hash":"2199555996792911395","title":"Viral entry, replication, and release","description":"This cluster is dominated by GO terms describing key viral life-cycle steps: fusion of the viral membrane with the host, uncoating, host-mediated activation of viral genome replication, and viral release, suggesting a cohesive theme around virus entry and propagation. Some additional terms relate to host responses (leukocyte migration, UV-A response) that often accompany infection, while a couple of terms appear as noise or cross-annotation (e.g., sepal formation). ","confidence":"High","size":12,"edges":22,"triangles":22,"max_degree":6,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":5},{"id":"GO:0050714","count":4},{"id":"GO:0044829","count":4},{"id":"GO:0006457","count":4},{"id":"GO:0019064","count":4}]},{"hash":"1843822042469480383","title":"Chaperone-mediated folding and telomere localization","description":"The cluster shows strong representation of chaperone-related processes (protein stabilization, chaperone-mediated assembly, chaperone-dependent refolding) along with telomere biology signals (telomerase activity, telomerase RNA localization to Cajal bodies, localization to telomeres). While some developmental terms appear, the clearest common theme is protein quality control via chaperones connected to telomere maintenance/localization, consistent with a cohesive functional module. Medium","confidence":"","size":12,"edges":52,"triangles":115,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048741","count":6},{"id":"GO:0021762","count":6},{"id":"GO:0051973","count":4},{"id":"GO:0050821","count":4},{"id":"GO:0051131","count":4}]},{"hash":"1009560483510743638","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":2},{"id":"GO:0042351","count":2},{"id":"GO:0009244","count":2},{"id":"GO:0009699","count":2},{"id":"GO:0019673","count":2}]},{"hash":"1596812017302029913","title":"Translation Machinery","description":"This cluster's top GO terms are all translation-related (translation, translational initiation/termination, regulation), pointing to a cohesive protein-synthesis module; the single edge suggests tight functional linkage among translation factors or ribosomal components, while unrelated terms like retina development or antibiotic response likely reflect annotation noise.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006413","count":3},{"id":"GO:0006415","count":2},{"id":"GO:0006417","count":2},{"id":"GO:0046677","count":2}]},{"hash":"845914167075666781","title":"Endomembrane trafficking and protein localization","description":"The top GO terms cluster around intracellular vesicle transport within the endomembrane system (ER\u2013Golgi, endosome\u2013Golgi, endosome\u2013vacuole pathways) and regulation of protein localization to the plasma membrane, plus vacuolar targeting via the Cvt pathway. This points to a cohesive module of vesicle trafficking and membrane targeting. Developmental terms likely reflect broader roles of trafficking components rather than separate functions. ","confidence":"High","size":12,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0034498","count":3},{"id":"GO:1903078","count":3},{"id":"GO:0045022","count":3},{"id":"GO:0032258","count":3}]},{"hash":"2268257478853038075","title":"Proteostasis and Protein Assembly","description":"This cluster centers on chaperone-mediated protein complex assembly, ubiquitin-related regulation, and assembly/oligomerization of protein complexes, pointing to proteostasis and quality control of multi-protein assemblies. Additional terms reflect stress-responsive remodeling (cadmium/oxidative stress) and trafficking/assembly steps (ER\u2013Golgi transport, hexamerization). While there are a few replication-related terms, the strongest shared theme is maintenance and organization of protein folding, assembly, and turnover under stress.","confidence":"Medium","size":12,"edges":17,"triangles":6,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":2},{"id":"GO:1903862","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0019079","count":2}]},{"hash":"2227445161539936685","title":"Nuclear RNA Processing and Spliceosome Assembly","description":"The cluster centers on nuclear RNA maturation and splicing processes, with terms for spliceosomal and snRNP assembly, mRNA decapping in the nucleus, transcription termination, tRNA processing, and rRNA maturation, plus nuclear import. This pattern suggests a cohesive group of proteins involved in RNA processing and related nuclear functions, rather than a transport or cytoskeletal module.","confidence":"High","size":12,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:0051170","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0000290","count":1}]},{"hash":"296280175060674867","title":"Ubiquitin-ERAD Protein Quality Control","description":"This cluster centers on post-translational modification and turnover of proteins, highlighted by ubiquitination, sumoylation, deubiquitination, autoubiquitination, and protein deglycosylation, as well as ER-associated degradation and aggresome formation. The inclusion of GPCR internalization and neurotransmitter secretion regulation suggests broader membrane trafficking and signaling control linked to proteostasis, fitting a cohesive theme of cellular protein quality control under stress.","confidence":"High","size":12,"edges":43,"triangles":90,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0070842","count":5},{"id":"GO:1904049","count":4},{"id":"GO:1902236","count":4}]},{"hash":"1359299584845379221","title":"Ubiquitin-Mediated Proteolysis and Cell Cycle Control","description":"The cluster is dominated by ubiquitin-related processes: multiple ubiquitin linkages (K11, K48, K63, K6) and autoubiquitination, along with SCF-dependent proteasomal degradation. It also includes peroxisomal matrix import tied to ubiquitin signaling and regulation of canonical NF-kappaB signaling, plus mitotic cell cycle transitions (G2/M). This combination strongly points to a cohesive role in tagging proteins for degradation and coordinating cell cycle progression via ubiquitin pathways.","confidence":"High","size":12,"edges":34,"triangles":71,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":10},{"id":"GO:0070936","count":9},{"id":"GO:0051865","count":9},{"id":"GO:0016558","count":9},{"id":"GO:0085020","count":9}]},{"hash":"1332799853532772559","title":"Ribosome Biogenesis and ER-Golgi Trafficking","description":"The top GO terms point to two main themes: protein synthesis (translation and ribosome biogenesis) and secretory pathway processes (ER-to-Golgi vesicle transport, COPII vesicle coating regulation, and tubulin-related trafficking). Together these suggest a cluster centered on building ribosomes and handling protein trafficking through the secretory pathway, possibly with some neuron-development annotations reflecting broader expression. Confidence: Medium","confidence":"","size":12,"edges":13,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0021532","count":2},{"id":"GO:0021830","count":2}]},{"hash":"1342677215099876511","title":"Unknown","description":"The GO terms span highly diverse, seemingly unrelated biological processes (energy metabolism like ATP synthesis and ferredoxin metabolism; catabolic pathways like xanthine and phenylacetate; basic ion transport; and vascular development regulation such as VEGF signaling, endothelial differentiation, and vasculogenesis), plus lactation and nitrogen fixation. With only sparse, weak connections among terms and no clear shared function, there isn\u2019t a single coherent theme to name the cluster. Confidence: None","confidence":"","size":12,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":1},{"id":"GO:0009115","count":1},{"id":"GO:0007595","count":1},{"id":"GO:1900747","count":1},{"id":"GO:0009399","count":1}]},{"hash":"1183849610418514820","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0046050","count":1}]},{"hash":"67634176429127407","title":"mRNA processing and export regulation","description":"This cluster shows enrichment for post-transcriptional mRNA handling: stabilization, polyadenylation regulation, splicing via the spliceosome (both positive and negative regulation), export from the nucleus, and general mRNA modification. Together these terms point to a cohesive group of proteins involved in mRNA maturation and export rather than transcription or translation. ","confidence":"High","size":12,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":1},{"id":"GO:1900363","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0006406","count":1}]},{"hash":"1586806389533400157","title":"P-body\u2013driven mRNA decay and silencing","description":"The GO terms cluster around deadenylation-dependent decapping and decay, P-body assembly, and miRNA-mediated post-transcriptional gene silencing, indicating a cohesive function in mRNA turnover and translational repression within processing bodies.","confidence":"High","size":12,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035195","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0061014","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0045944","count":1}]},{"hash":"513899281939265195","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000388","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006269","count":2}]},{"hash":"867222729267033115","title":"Unknown","description":"The top GO terms span telomere maintenance, virion attachment, protein kinase signaling, chaperone complex assembly, neuronal protection, proteasomal regulation, xenobiotic response, and otolith tethering, with no single cohesive biological function linking them all. Hence there isn\u2019t a clear, representative theme to name this cluster.","confidence":"","size":12,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007004","count":1},{"id":"GO:0051973","count":1},{"id":"GO:0019062","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0080117","count":1}]},{"hash":"2195951302808316742","title":"Unknown","description":"These proteins show a mix of nuclear functions (DNA binding regulation, DNA replication, transcriptional repression) and ER/secretory pathway processes (protein folding in ER, post-translational targeting to membrane, proline hydroxylation) plus oxidant detoxification. The GO terms do not converge on a single coherent function or pathway, so a concise, representative cluster name cannot be assigned beyond Unknown.","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043388","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0006260","count":1}]},{"hash":"856433368843055893","title":"Inositol/PI signaling and stress response","description":"The GO terms cluster around inositol and phosphatidylinositol biosynthesis, i.e., PI signaling, with ABA-activated signaling and salinity-related stress responses, suggesting a link to plant signaling under stress. Some other terms reflect broader metabolism or are peripheral, but the core theme is PI signaling coupled to stress response. ","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":2},{"id":"GO:0042538","count":1},{"id":"GO:0000103","count":1},{"id":"GO:0006661","count":1},{"id":"GO:0046855","count":1}]},{"hash":"1389518763169511205","title":"Immune Activation and Transcriptional Regulation","description":"The cluster shows enrichment for innate immune and inflammatory responses (innate immune response, inflammatory response, positive regulation of B cell proliferation) alongside transcription-related processes (DNA-templated transcription, RNA (guanine-N7)-methylation, negative regulation of gene expression), suggesting a group of proteins that modulate immune signaling and gene expression during immune activation and cell proliferation. Some terms (xylene catabolic process, obsolete regulation of cell aging) appear as noise rather than core functions.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0090344","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0045087","count":1}]},{"hash":"82639921012579733","title":"Oxidative Stress and Translation Initiation","description":"This cluster is driven by strong signals for oxidative stress response (cellular response to hydrogen peroxide) and redox homeostasis, alongside terms related to translation initiation and reinitiation (translation reinitiation, formation of translation preinitiation complex). Additional links to DNA repair, DNA recombination, and xenobiotic response point to a broader stress-adaptation module that couples genome maintenance and detoxification with regulation of protein synthesis. A few terms like neuron differentiation and aging are low in representation and likely peripheral.","confidence":"Medium","size":11,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":3},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006284","count":2}]},{"hash":"1461112144825010444","title":"Ubiquitination-Driven Endocytic Trafficking Regulation","description":"This cluster centers on ubiquitin-related processes (deubiquitination and autoubiquitination) and endocytic control (GPCR internalization, vesicle formation). Together, these GO terms point to a theme of ubiquitin-mediated regulation of membrane trafficking and related signaling pathways, with other terms reflecting broader signaling impacts via ubiquitin pathways.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":9},{"id":"GO:1904049","count":6},{"id":"GO:1902236","count":6},{"id":"GO:1903265","count":6},{"id":"GO:0051865","count":6}]},{"hash":"2111138792338209952","title":"Muscle development and skeletal morphogenesis signaling","description":"Dominant terms include myoblast differentiation involved in skeletal muscle regeneration, embryonic cranial skeleton morphogenesis, Rho signaling, and VEGF receptor signaling, indicating coordinated pathways for muscle formation, craniofacial skeletal development, and angiogenesis. Also present are DNA-templated transcription and DNA replication, suggesting transcriptional regulation and cell proliferation typical of developing tissues, and a MAPK cascade and spindle checkpoint signaling that support growth and division. Together, these terms point to a developmental program centered on muscle and skeletal morphogenesis with associated signaling networks.","confidence":"High","size":11,"edges":16,"triangles":6,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0048701","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0000196","count":8},{"id":"GO:0044565","count":8}]},{"hash":"2045486580336890033","title":"ER-Golgi to Plasma Membrane Vesicle Trafficking","description":"Most enriched terms describe vesicle transport along the secretory pathway (ER\u2192Golgi, Golgi\u2192plasma membrane, and retrograde Golgi\u2192ER) and general protein transport, with GTPase activity regulation supporting vesicle trafficking. Some terms seem incidental (e.g., hippocampus development), but the core signal is intracellular vesicle movement.","confidence":"High","size":11,"edges":11,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0043001","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0090316","count":3}]},{"hash":"990176765285526278","title":"Endomembrane trafficking to lysosome/vacuole","description":"This cluster is enriched for endosome-to-lysosome and Golgi-to-endosome transport, along with protein targeting to vacuole and exocytosis-related activities (vesicle docking, calcium-dependent exocytosis) and cytoskeletal involvement (tubulin assembly). The overarching pattern is intracellular vesicular transport and targeting to lysosome/vacuole compartments, with autophagy-related regulation supporting lysosomal function. High confidence that this label reflects the cluster\u2019s core function.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008333","count":4},{"id":"GO:0051291","count":4},{"id":"GO:0006895","count":4},{"id":"GO:0006623","count":4},{"id":"GO:0045956","count":4}]},{"hash":"99848353039920120","title":"Steroid and retinoid biosynthesis","description":"These proteins group around biosynthetic and metabolic processes for retinoids and steroid hormones (retinoic acid, retinol, glucocorticoids, testosterone), suggesting a cohesive theme of lipid hormone biosynthesis and retinoid signaling, with possible links to lung development. Some terms like antibiotic biosynthesis are present but not central to the core theme.","confidence":"High","size":11,"edges":12,"triangles":5,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030324","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0046677","count":7},{"id":"GO:0002138","count":7},{"id":"GO:0045150","count":7}]},{"hash":"490365652529003713","title":"Immune Signaling and Transcription Regulation","description":"The GO terms point to immune activation (cellular response to LPS, GM-CSF stimulus, T cell receptor signaling, innate immune response) alongside general transcription-related processes (DNA-templated transcription, DNA replication). This suggests a cluster of proteins involved in initiating immune signaling and regulating transcriptional programs, with auxiliary links to cell cycle and development terms.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0071222","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0097011","count":4},{"id":"GO:0045087","count":3}]},{"hash":"109626512885334994","title":"Neural tube and forebrain development","description":"The cluster is enriched with terms tied to neural tube closure, forebrain development, and dorsoventral neural patterning (including negative regulation of Hedgehog signaling), along with cell proliferation signals (DNA replication, mitotic cell cycle) and transcription. This combination points to a neurodevelopmental program involving neural tube formation and early brain development, with proliferative neural progenitors shaping the tissue. ","confidence":"High","size":11,"edges":12,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0001707","count":5},{"id":"GO:1901621","count":5},{"id":"GO:0071374","count":5},{"id":"GO:0001843","count":5}]},{"hash":"151603653454668569","title":"Developmental signaling and cytoskeleton remodeling","description":"These proteins cluster around signaling pathways that control development and morphogenesis, with emphasis on MAPK cascades, Rho signaling, and actin cytoskeleton dynamics (e.g., convergent extension, cytoskeleton reorganization). They also relate to differentiation and tissue-specific growth cues (myoblast differentiation, VEGF signaling, and modulation of muscle proliferation). The common theme is signaling networks coordinating cell fate decisions and cytoskeletal remodeling during development, though a few terms are more tissue-specific. Overall, a developmental signaling and cytoskeleton remodeling label fits well, with medium confidence due to some heterogeneity in the exact functions represented.","confidence":"Medium","size":11,"edges":11,"triangles":0,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0000196","count":4},{"id":"GO:0044565","count":4},{"id":"GO:0033316","count":4},{"id":"GO:0007266","count":4},{"id":"GO:0014835","count":4}]},{"hash":"2074029280634565946","title":"Midbrain dopaminergic neuron development","description":"Several top GO terms point to development and differentiation of midbrain dopaminergic neurons: substantia nigra development, neuron differentiation, and positive regulation of canonical Wnt signaling. Additional terms reflect calcium-channel\u2013mediated signaling and cell-cycle regulation typical of neuronal maturation in this lineage. While some terms are broader (e.g., response to ethanol), the strongest signals converge on midbrain dopaminergic neuron development and associated signaling pathways.","confidence":"High","size":11,"edges":10,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010950","count":3},{"id":"GO:0045471","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0051726","count":2}]},{"hash":"220315699713557786","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0039702","count":2},{"id":"GO:0019076","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0071031","count":1}]},{"hash":"811560792971504928","title":"Unknown","description":"The terms are scattered across many processes (cell division/proliferation; neuron and muscle differentiation; germ-line stem cell maintenance; transcriptional and translational regulation; DNA repair). With no shared function or pathway and no network connectivity, there is no coherent theme to label; thus Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0030182","count":1},{"id":"GO:1902416","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0008283","count":1}]},{"hash":"908195722992017912","title":"Ubiquitin-Proteasome Regulation in Stress and Immunity","description":"These terms cluster around ubiquitin-centric regulation of protein fate and genome maintenance, with robust signals for ubiquitin transferase activity, polyubiquitination, and proteasome-mediated quality control. The inclusion of chromatin organization and homologous recombination repair suggests links to DNA damage response and chromatin remodeling, while interferon-beta response and TRIF-dependent TLR signaling indicate an immune-stress dimension that is often modulated by ubiquitination. The ABA response reflects broader stress cross-talk. Together these points define a module of ubiquitin-regulated stress, immunity, and genome integrity.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0035458","count":10},{"id":"GO:0031497","count":10},{"id":"GO:0051443","count":10},{"id":"GO:0010994","count":10},{"id":"GO:0035666","count":10}]},{"hash":"946745913748691561","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":8,"triangles":0,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002635","count":5},{"id":"GO:0061470","count":5},{"id":"GO:0043029","count":5},{"id":"GO:0001782","count":5},{"id":"GO:0061158","count":5}]},{"hash":"379518559749826431","title":"Fungal sterol and sphingolipid metabolism","description":"The top GO terms cluster around lipid biosynthesis in fungi, notably ergosterol/sterol biosynthesis and sphingolipid metabolism (mannosyl-inositol phosphorylceramide) plus related unsaturated fatty acid biosynthesis. Some terms appear unrelated (myelin maintenance, sebaceous gland differentiation), likely cross-species annotations, but the core signal points to fungal lipid pathways. Confidence reflects a coherent lipid-focused theme with some noisy outliers.","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0000001","count":2}]},{"hash":"1996173606233705959","title":"Immune signaling and lymphocyte regulation","description":"Top GO terms indicate a core immune-function theme, including innate and adaptive immune activity (innate immune response, T cell proliferation, negative regulation of T-helper differentiation, RIG-I signaling) and ubiquitination processes (K48-linked and linear polyubiquitination) that frequently modulate immune signaling. The presence of V(D)J recombination hints at lymphocyte development. Although a couple of terms are less related (dosage compensation, transcription regulation), the dominant pattern is immune response regulation with ubiquitin-mediated control.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009048","count":1},{"id":"GO:0045087","count":1},{"id":"GO:1903886","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0097039","count":1}]},{"hash":"2048291230657762852","title":"Fungal cell cycle and DNA replication","description":"This cluster is dominated by GO terms for DNA replication and mitotic cell cycle (including G1/S and G2/M transitions) and a fungal mating-related term (karyogamy), pointing to core cell-cycle control in a fungal context. A minor signal for fungal beta-glucan wall biosynthesis suggests growth-related processes as well. A few terms about ER stress or hematopoietic differentiation appear less relevant; overall, the dominant theme is cell-cycle progression in fungi, with some accompanying cell-wall synthesis potential.","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0060316","count":2}]},{"hash":"177813002574635035","title":"Unknown","description":"The GO terms are highly diverse, including translation, copper transport, lipid and amino acid biosynthesis, LPS biosynthesis, calcium homeostasis, hormone response, and more. The cluster has minimal connectivity and no single coherent function linking these terms, so there isn\u2019t a reliable label beyond Unknown.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0070126","count":1},{"id":"GO:0006825","count":1},{"id":"GO:0006114","count":1},{"id":"GO:0009244","count":1}]},{"hash":"578260894676716258","title":"Fungal cell growth and cell-wall biosynthesis","description":"Top GO terms point to fungal-specific processes such as beta-glucan cell-wall biosynthesis and karyogamy (fungal mating), alongside general essential cellular functions like translation and DNA replication. This pattern suggests a cluster of proteins involved in fungal growth and cell-wall assembly, with some broad cellular machinery components. Overall, this label captures the most distinctive and coherent theme among the enriched terms, though some annotations are cross-species or broad. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0016226","count":3},{"id":"GO:1902037","count":2},{"id":"GO:0070880","count":2},{"id":"GO:1903382","count":2}]},{"hash":"2140165541910367765","title":"Fungal mating and cytokinesis during sporulation","description":"The top GO terms point to mating- and sporulation-related processes (karyogamy, ascospore wall assembly) along with cytoskeletal and cytokinesis machinery (actin patches, contractile ring assembly) and membrane trafficking regulation (endocytosis). Chromatin dynamics terms appear but include obsolete annotations, yet the overall theme supports a fungal reproductive program involving nucleus fusion, spore development, and cytoskeletal-driven cell division. Some terms seem unrelated (muscle/neuronal development) and likely represent annotation noise. ","confidence":"Medium","size":9,"edges":29,"triangles":43,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":4},{"id":"GO:0030476","count":3},{"id":"GO:0030100","count":3},{"id":"GO:0000147","count":3},{"id":"GO:0048741","count":3}]},{"hash":"2176312808595336778","title":"mRNA splicing and processing regulation","description":"The proteins cluster around regulation of mRNA maturation and fate: positive and negative control of mRNA splicing via the spliceosome, ncRNA-mediated gene silencing, and downstream mRNA export, stabilization, and poly(A) tail regulation, indicating a cohesive module governing RNA processing and stability.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048255","count":1},{"id":"GO:1900363","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1618748990756323769","title":"Chaperone-assisted folding and ubiquitin regulation","description":"The dominant GO terms center on chaperone-mediated protein folding/refolding and assembly, plus regulation of ubiquitin-related processes (including deubiquitinase activity and SCF complex dynamics), all pointing to protein quality control and proteostasis. Additional terms relate to ER-Golgi trafficking and stress-related inclusion body formation, reinforcing a proteostasis/quality-control theme rather than a specific replication function. Confidence: Medium","confidence":"","size":9,"edges":7,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0070389","count":5},{"id":"GO:0051131","count":4},{"id":"GO:1903862","count":4},{"id":"GO:0006888","count":4}]},{"hash":"392194915606623665","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to ribosome assembly and translation, including ribosomal large subunit export from the nucleus, ribosome biogenesis, and multiple translation steps (initiation/elongation/termination), indicating a cohesive role in ribosome production and protein synthesis. Some auxiliary terms (mRNA decay, stress/antibiotic response) are secondary associations but do not override the main theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000055","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":3},{"id":"GO:1901001","count":2},{"id":"GO:0046677","count":2}]},{"hash":"100921205751608213","title":"Membrane Transport and Cofactor Biosynthesis","description":"The cluster shows clear enrichment for membrane-associated transport terms (proton and sodium ion transmembrane transport), plus multiple cofactor and vitamin biosynthesis processes (thiamine, biotin, molybdenum cofactor). While RNA methylation terms are present, the dominant theme appears to be transport together with biosynthetic pathways for essential cofactors, suggesting proteins involved in both transport and cofactor metabolism. Confidence: Medium","confidence":"","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015992","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0070475","count":1},{"id":"GO:0018339","count":1},{"id":"GO:0006777","count":1}]},{"hash":"1026900758155331438","title":"GPCR signaling and cytoskeletal remodeling in neurons","description":"The cluster is enriched for GPCR signaling and modulation of neuronal excitability (negative regulation of excitatory postsynaptic potential), along with multiple terms related to cytoskeletal dynamics (lamellipodium assembly, actin cytoskeleton reorganization) and junctional remodeling (tight junction assembly). There are also hints of broader signaling and stress-response roles (ER stress\u2013related apoptosis regulation, spindle orientation checkpoints), suggesting a suite of related processes centered on signaling-driven cytoskeletal changes and neuronal function rather than a single, narrowly defined function. Therefore, the label GPCR signaling and cytoskeletal remodeling in neurons best captures the common theme, with moderate confidence due to some heterogeneity.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0007186","count":2},{"id":"GO:0043497","count":1},{"id":"GO:1902236","count":1},{"id":"GO:0031578","count":1}]},{"hash":"1515591724982463225","title":"Mitochondrial Electron Transport & Oxidative Phosphorylation","description":"This cluster is dominated by GO terms for mitochondrial electron transport and oxidative phosphorylation, including proton translocation and aerobic respiration, indicating a cohesive role in energy production and ATP synthesis. A few terms refer to photosynthetic ETC, which are related to energy transduction in another system, but the core functional theme is mitochondrial respiration.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0006123","count":1},{"id":"GO:0009767","count":1},{"id":"GO:0006119","count":1}]},{"hash":"444619543625652059","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":11,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0000349","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000480","count":1}]},{"hash":"1473756733235953850","title":"Post-transcriptional mRNA processing and translation initiation","description":"The terms span splicing, export, stabilization, modification, and translation initiation/reinitiation, indicating a coherent group of proteins involved in post-transcriptional RNA processing and regulation of translation.","confidence":"High","size":9,"edges":20,"triangles":22,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":7},{"id":"GO:0002188","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0048255","count":4}]},{"hash":"758214182749902601","title":"Epigenetic Regulation of Development","description":"This cluster combines tissue development terms (hippocampus, cerebellar cortex, myotube) with epigenetic processes (DNA methylation, antisense RNA transcription, response to histone deacetylase inhibitors), pointing to a theme of development modulated by epigenetic regulation; a few terms are peripheral, so confidence is Medium.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045857","count":1},{"id":"GO:1903699","count":1},{"id":"GO:0035984","count":1},{"id":"GO:0033082","count":1},{"id":"GO:0045128","count":1}]},{"hash":"191708491296187762","title":"Membrane Sugar and Ion Transport","description":"GO terms point to transmembrane transport of sugars (fructose, glucose, galactose), ions (potassium), and other substrates, along with an osmotic stress response. This suggests a cohesive cluster of membrane transport proteins handling sugar and ion uptake under osmotic conditions.","confidence":"High","size":9,"edges":12,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":2},{"id":"GO:0015706","count":2},{"id":"GO:1990539","count":2},{"id":"GO:0071332","count":2},{"id":"GO:0044381","count":2}]},{"hash":"1677764672947923296","title":"Proteostasis via Ubiquitin-Proteasome Pathway","description":"Most of the enriched terms center on ubiquitination/deubiquitination and proteasome function (protein turnover). The antigen presentation term points to proteasome-generated peptides for MHC I, reinforcing a proteostasis/antigen-processing theme. Confidence: High","confidence":"","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0061418","count":5},{"id":"GO:0051436","count":5},{"id":"GO:0010950","count":5},{"id":"GO:0080129","count":5},{"id":"GO:0016579","count":5}]},{"hash":"1212808521565469601","title":"Endomembrane trafficking and endocytic recycling","description":"This cluster centers on vesicle transport within the secretory and endocytic pathways: Golgi to endosome, endosome to lysosome, endocytic recycling, and ER-to-Golgi transport are represented, indicating a coherent endomembrane trafficking module. The inclusion of a neurotrophin receptor signaling term suggests a neuronal context, but the dominant signal is vesicle movement and recycling. The low connectivity supports a focused trafficking-related cluster rather than broad signaling.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902953","count":2},{"id":"GO:1900452","count":1},{"id":"GO:0006895","count":1},{"id":"GO:1902955","count":1},{"id":"GO:1902960","count":1}]},{"hash":"212138629324315066","title":"Translation and translational quality control","description":"This cluster is dominated by cytoplasmic translation, translation, prolyl-tRNA aminoacylation, and regulation of translational fidelity, pointing to a core role in protein synthesis and its quality control. Additional terms touch on proteostasis and ER-associated transport, which are connected to processing newly made proteins.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006433","count":1},{"id":"GO:0006450","count":1}]},{"hash":"1489353838965625183","title":"Ribosome Biogenesis and Cell Growth","description":"Terms center on ribosome biogenesis, ribosomal subunit export, and tRNA modification, with accompanying signals for cell cycle and septum assembly, implying growth and division; other terms reflect stress regulation and iron metabolism that frame this context.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000055","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0007049","count":2},{"id":"GO:1903833","count":2}]},{"hash":"1893861482825414648","title":"Bacterial Metabolic Biosynthesis","description":"These GO terms span multiple metabolic and biosynthetic processes across microbes, including fatty acid metabolism (long-chain and medium-chain), acetyl-CoA and pyruvate-derived biosynthesis, lipoteichoic acid production (Gram-positive cell wall component), siderophore biosynthesis (iron acquisition), and even bioluminescence. The common thread is broad bacterial metabolism and biosynthesis rather than a single pathway, so the label captures the overall theme.","confidence":"Medium","size":8,"edges":14,"triangles":12,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019427","count":4},{"id":"GO:0008218","count":4},{"id":"GO:0070395","count":4},{"id":"GO:0001676","count":4},{"id":"GO:0008206","count":4}]},{"hash":"1209917534839178092","title":"Angiogenesis and vascular remodeling","description":"This cluster is dominated by GO terms related to blood vessel formation and vascular signaling, including angiogenesis, VEGF receptor signaling, and endothelial cell migration, along with Rho/MAPK pathways and muscle regeneration signals, suggesting a vascular development/regeneration program. Some terms (e.g., meiotic spindle checkpoint, dendritic cell proliferation) appear less directly connected and may reflect broader signaling cross-talk or noise.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046827","count":6},{"id":"GO:0001525","count":5},{"id":"GO:0043536","count":5},{"id":"GO:0000196","count":4},{"id":"GO:0044565","count":4}]},{"hash":"269600962727246725","title":"Post-transcriptional mRNA processing and stability","description":"This cluster is dominated by GO terms related to post-transcriptional control of mRNA, including stability, export from the nucleus, splicing regulation, and polyadenylation/modification, with a minor signal of GTPase activity regulation that may reflect broader RNA processing control under stress.","confidence":"Medium","size":8,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0048255","count":1},{"id":"GO:1900363","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1440826956666654585","title":"Neural and glial development with translational regulation","description":"The cluster shows enrichment for neural/glial development terms (oligodendrocyte development, regulation of presynapse assembly) and for translational control components (positive regulation of eIF4F complex assembly, negative regulation of translational initiation), suggesting a theme around neural development tied to protein synthesis control; broader developmental terms appear but do not overwhelm the core pattern.","confidence":"Low","size":8,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001541","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0002176","count":1},{"id":"GO:2000507","count":1}]},{"hash":"1548093066726279380","title":"Neuro-muscular development and angiogenesis","description":"This cluster is dominated by terms related to developmental processes in neural and muscular systems (axonogenesis, myoblast fusion, long-term synaptic potentiation, visual perception) and also includes angiogenesis and general development. Together these suggest coordinated growth and differentiation of neural, muscular, and vascular tissues, with a minor outlier term (abscisic acid signaling) that is plant-specific. Overall, the label captures the main theme of developmental neural-muscular-vascular growth.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0014850","count":2}]},{"hash":"686189140559956152","title":"Chromatin dynamics and cell cycle control","description":"This cluster is driven by GO terms related to DNA replication-dependent chromatin assembly and meiotic chromosome condensation, as well as negative regulation of mitotic cell cycle, suggesting a core theme of chromatin dynamics and cell-cycle regulation. While a few terms touch on signaling and cytoskeleton (e.g., GTPase activity, actin organization) and some entries are obsolete, the predominant signal centers on chromatin and cell division processes.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0032471","count":1},{"id":"GO:0045976","count":1},{"id":"GO:0000188","count":1}]},{"hash":"922150710268500257","title":"RNA Modification and Transcription Regulation","description":"Explanation: Dominant signals are RNA and protein modification (tRNA wobble uridine modification, RNA guanine-N7 methylation, peptidyl-arginine hydroxylation) and transcription regulation (negative regulation of RNA polymerase II). Some terms reference biosynthetic or stress-response processes that seem peripheral, but the core theme centers on modification-driven control of gene expression.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030961","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1024371372948457073","title":"ER Protein Folding and Redox Homeostasis","description":"Based on the prominent ER-related terms (protein folding in ER, protein retention in ER lumen, and protein maturation by folding) together with redox homeostasis and cellular oxidant detoxification, the cluster seems to group proteins involved in ER-assisted folding and quality control that rely on redox processes. Some immune-related terms appear only weakly (NF-kappaB regulation, NK cell cytotoxicity) and may reflect broader signaling annotations, but do not redefine the core ER-folding theme.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0043388","count":2},{"id":"GO:0022417","count":2},{"id":"GO:0098869","count":2}]},{"hash":"578559808824007682","title":"Neuronal development and synaptic signaling","description":"The cluster is dominated by GO terms tied to nervous system development, hippocampus development, excitatory synaptic activity, and calcium-dependent exocytosis, with ERK signaling and actin cytoskeleton remodeling supporting neurite outgrowth and synaptic function. A few terms (mitotic cell cycle, beta selection) are less related, but the overall theme points to neuronal development and synaptic regulation.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0060079","count":4},{"id":"GO:0031532","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0021766","count":3}]},{"hash":"1728459745514629668","title":"Neural migration and axon guidance","description":"The prominent GO terms center on neuronal migration (tangential migration from SVZ to the olfactory bulb) and ROBO signaling (axon guidance), suggesting a neural development and guidance theme; other terms indicate related cell movement and developmental signaling, but the migration/axon guidance motif is strongest.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0022028","count":4},{"id":"GO:0090051","count":4},{"id":"GO:0045197","count":3},{"id":"GO:0043931","count":3},{"id":"GO:0071260","count":3}]},{"hash":"1806542120637973424","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0000494","count":1},{"id":"GO:1990258","count":1},{"id":"GO:0048254","count":1}]},{"hash":"1435756688177235567","title":"Chromosome maintenance and cell cycle control","description":"This cluster is enriched for DNA replication, DNA repair, meiotic and mitotic cell cycle terms, telomere capping, and kinetochore localization, pointing to chromosome maintenance and regulation of cell division; peripheral terms like Schwann cell development or response to cocaine are less central.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0051321","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0006281","count":3}]},{"hash":"1021494844536253165","title":"RNA Transcription and Processing","description":"The top GO terms are dominated by transcription-related processes across RNA polymerases I, II, and III, including tRNA processing, RNA-templated transcription, rRNA transcription, and transcription initiation/termination activities. Although a few terms touch on unrelated processes, the core signal points to RNA transcription and processing as the cluster\u2019s shared function.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:2000676","count":1},{"id":"GO:1990737","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0097394","count":1}]},{"hash":"1625606756300909155","title":"DNA Replication and Cell Cycle","description":"This cluster's top GO terms center on DNA replication primer synthesis, DNA-templated transcription, cell division, and mitotic cell cycle, indicating a core nuclear/genomic maintenance role. While a few terms reference peroxisome import or ER-associated degradation (likely noise or outdated terms), the strongest signal is genome replication and cell cycle control.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006269","count":1},{"id":"GO:0030420","count":1}]},{"hash":"1351350053912464738","title":"Chromatin organization and transcription regulation","description":"The GO terms here converge on chromatin structure maintenance (nucleosome assembly, heterochromatin formation, pericentric heterochromatin formation, chromatin organization) and transcription-related processes (DNA-templated transcription, transcription elongation by RNA polymerase II), with links to DNA replication and repair. This suggests a cluster of proteins involved in regulating chromatin state that modulates transcription and genome maintenance.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1041411425478220639","title":"Bacterial Competence and DNA Repair under Antibiotic Stress","description":"This cluster centers on DNA uptake competence, DNA replication and transcription regulation, and nucleotide-excision repair, with concurrent signals of antibiotic response and protein folding stress. The combination suggests a bacterial DNA maintenance/uptake program activated under antibiotic pressure; a few older or less relevant GO terms may reflect annotation noise but do not override the core theme.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0030420","count":2},{"id":"GO:0071712","count":2}]},{"hash":"896190608688779688","title":"Transcriptional and Signaling Regulation","description":"The cluster mixes DNA-templated transcription with multiple signaling pathways (MAPK, Rho, insulin receptor) and various regulatory processes (differentiation, glycogen regulation, proteasomal control, and even behavioral responses). The common thread appears to be regulation of cellular function via transcriptional control and signaling cascades, rather than a single concrete pathway, so this name captures the broad regulatory theme. ","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000196","count":1},{"id":"GO:0044565","count":1},{"id":"GO:2000465","count":1},{"id":"GO:0033316","count":1}]},{"hash":"2005445783747302423","title":"DNA Damage Response and Apoptosis","description":"The cluster\u2019s GO terms center on DNA repair, DNA-templated transcription, and explicit p53-mediated intrinsic apoptotic signaling, plus the apoptotic process, indicating a coherent theme where DNA damage triggers programmed cell death. Additional nucleotide catabolic and epigenetic regulation terms support a stress-response context, reinforcing the label. Confidence: High","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2000757","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0009154","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006154","count":1}]},{"hash":"1245037261463796290","title":"Unknown","description":"The top GO terms are heterogeneous: nitrite and formate transport, cardiac jelly and atrioventricular canal development, and RNA polymerase II preinitiation complex assembly. There is no single cohesive function linking these proteins, so a unifying label cannot be confidently assigned.","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":1},{"id":"GO:0015724","count":1},{"id":"GO:1905072","count":1},{"id":"GO:0036302","count":1},{"id":"GO:0051123","count":1}]},{"hash":"267034490465961355","title":"ER-Golgi Vesicle Trafficking","description":"This cluster is best described by terms centered on the secretory pathway, especially movement between the ER and Golgi and vesicle-mediated transport (intracellular transport, ER-to-Golgi transport, and clathrin-coated vesicle cargo loading). The globoside biosynthetic process also aligns with Golgi-associated glycosphingolipid synthesis, reinforcing a vesicle-trafficking/golgi-associated role. A few outlier terms (meiotic chromosome condensation, heterochromatin formation, and NK T cell differentiation) are unlikely to define the core function for these proteins, suggesting annotation noise or moonlighting roles, but the dominant signal supports ER-Golgi vesicle trafficking. Confidence: Medium","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0001576","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0030466","count":1}]},{"hash":"231334792205934272","title":"Nuclear gene expression and genome maintenance","description":"This cluster is dominated by GO terms pointing to DNA-templated transcription and other DNA/RNA processing activities (e.g., DNA strand renaturation, nonfunctional rRNA decay), with some signals of protein folding/unfolding and proteostasis. Although several terms are obsolete, the common thread appears to be nuclear gene expression and genome maintenance processes, including transcription and RNA quality control, alongside basic protein homeostasis in the nucleus.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030420","count":2},{"id":"GO:0071712","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0035072","count":2}]},{"hash":"75464608378156048","title":"Virus-Host Interaction and Viral Life Cycle","description":"Several GO terms strongly point to viral processes, including fusion of the virus membrane with the host plasma membrane, uncoating of the virus, and viral release from the host cell, as well as host-mediated activation of viral genome replication. These indicate a cluster centered on virus entry, replication, and exit in the context of host interaction. A few terms reflect general cellular processes or host responses (spliceosomal assembly, protein folding, leukocyte migration, UV-A response) that are less defining for the cluster\u2019s core theme. Overall, the label captures the dominant viral life cycle and host interaction signals, with medium confidence.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0050714","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0006457","count":1}]},{"hash":"798040261000322475","title":"Actin Cytoskeleton Remodeling During Division","description":"This cluster centers on actin-related processes (postsynaptic actin cytoskeleton organization; actin cortical patch assembly) and cell division activities (meiotic chromosome movement toward spindle pole; mitotic cytokinesis), with supporting terms on endocytosis regulation and calcium signaling, suggesting a cohesive theme of cytoskeleton remodeling linked to division and surface dynamics.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051592","count":1},{"id":"GO:0030476","count":1},{"id":"GO:0043981","count":1},{"id":"GO:0016344","count":1},{"id":"GO:0030100","count":1}]},{"hash":"1507002583418120182","title":"DNA Replication and Repair","description":"The dominant GO terms point to genome maintenance: DNA replication, DNA repair, DNA-templated transcription, and the SOS response, indicating proteins involved in replication fidelity and DNA damage response. Some terms are outdated or peripheral (e.g., viral latency, fertility), but the core theme remains DNA maintenance and transcription regulation in response to DNA damage.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":2},{"id":"GO:0006281","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0000746","count":1}]},{"hash":"123912463900191457","title":"Nuclear mRNA Processing and Export","description":"The GO terms cluster around core nuclear mRNA maturation activities\u2014stabilization, export, spliceosome-regulated splicing (both positive and negative), polyadenylation-related regulation, and RNA modification. Together they point to a cohesive role in processing and preparing mRNA for export, rather than downstream translation. A stray term about viral translation is incidental. ","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":1},{"id":"GO:1900363","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0006406","count":1}]},{"hash":"1654202422805346944","title":"Spindle assembly and nuclear migration","description":"This cluster\u2019s top GO terms cluster around microtubule- and spindle-centered processes, including karyogamy, nuclear migration, spindle midzone assembly, and kinetochores-microtubule attachments, suggesting roles in chromosome segregation and nuclear movement during cell division. Some terms (chloroplast movement, cerebellar structure, Rap signaling) appear more peripheral, but the dominant signal supports a spindle/mitotic nexus. ","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":6},{"id":"GO:0000915","count":6},{"id":"GO:0033624","count":6},{"id":"GO:0030951","count":6},{"id":"GO:0051255","count":6}]},{"hash":"619570171310094115","title":"Nucleotide Metabolism and RNA Editing","description":"This cluster is dominated by GO terms tied to nucleotide metabolism and RNA processing, including cytosine/cytidine/deoxycytidine metabolism, uridine biosynthesis, UMP salvage, and tRNA wobble adenosine editing, with riboflavin biosynthesis suggesting related cofactor metabolism. Together these point to nucleotide turnover and RNA modification as the shared theme, supporting a label focused on nucleotide metabolism and RNA processing.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019858","count":2},{"id":"GO:0009972","count":1},{"id":"GO:0002100","count":1},{"id":"GO:0009231","count":1},{"id":"GO:0006217","count":1}]},{"hash":"272445411181347058","title":"Nucleotide metabolism and DNA repair","description":"The top GO terms cluster around nucleotide biosynthesis and salvage (AMP salvage, CDP, ADP, ITP, NAD+/NAD+ related, CoA biosynthesis) and a DNA repair process, suggesting a group of proteins involved in nucleotide metabolism and genome maintenance. Some terms like brain development and viral process appear only once and are likely incidental noise. This combination points to a core function in nucleotide metabolism with a repair-related role.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0044209","count":2},{"id":"GO:0016032","count":1},{"id":"GO:0046705","count":1},{"id":"GO:0007420","count":1}]},{"hash":"482506485758116291","title":"Mitochondrial energy metabolism and insulin signaling","description":"The GO terms cluster around mitochondrial function (citrate and CoA transport, membrane potential and permeability regulation, adaptive thermogenesis) and metabolic signaling (insulin/IGF, fatty acid response), with a nod to pregnancy-related metabolism. This points to a group of proteins involved in mitochondrial energy production and metabolic regulation under insulin signaling.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990845","count":3},{"id":"GO:0006843","count":3},{"id":"GO:1990314","count":3},{"id":"GO:0007565","count":3},{"id":"GO:0015709","count":3}]},{"hash":"417925206134766514","title":"Unknown","description":"The GO terms for this cluster are highly diverse, covering protein catabolic and glycolytic/sugar metabolism processes, amino acid biosynthesis, respiratory and immune-related responses, DNA damage signaling regulation, and even cardiac-apoptosis and cobalt response terms. There is no clear, cohesive functional theme linking all six proteins into a single biological process, so a precise, representative label cannot be assigned.","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030163","count":1},{"id":"GO:0007585","count":1},{"id":"GO:0006000","count":1},{"id":"GO:0045730","count":1},{"id":"GO:1902153","count":1}]},{"hash":"1835463254189473365","title":"mRNA Processing and Export Regulation","description":"The cluster centers on mRNA processing and export, with terms for stabilization, polyadenylation regulation, splicing via the spliceosome, mRNA export, and RNA modification, indicating a cohesive role in post-transcriptional maturation and nucleocytoplasmic transport; the presence of a viral translation term is an outlier.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:1900363","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1195205965816912837","title":"Ribosome Biogenesis and Cell Cycle","description":"This cluster is dominated by GO terms for ribosome production and maturation (ribosome biogenesis; ribosomal large subunit export from nucleus; tRNA modification) and for cell proliferation (cell division; cell cycle). A few terms touch on spermatid development and organism growth, but the strongest signal ties to ribosome assembly and progression through the cell cycle, so the label aptly captures the core function of the cluster.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0000747","count":1}]},{"hash":"623882264454498461","title":"Post-transcriptional mRNA processing and export regulation","description":"The cluster centers on mRNA metabolism processes: stabilization, splicing regulation via the spliceosome (both positive and negative), polyadenylation regulation, mRNA tail shortening, mRNA modification, and export from the nucleus. These together point to coordinated post-transcriptional control of mRNA fate rather than transcriptional events or translation. ","confidence":"High","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048255","count":3},{"id":"GO:1900363","count":3},{"id":"GO:1905663","count":3},{"id":"GO:0048025","count":3},{"id":"GO:0006406","count":3}]},{"hash":"1924424029185143151","title":"Development and Morphogenesis","description":"This cluster shows GO terms tied to developmental and morphogenetic processes across species (ascospore formation, lung and mesoderm development, EMT, cell budding, meiosis), plus supporting terms like cell adhesion and cell cycle transitions, suggesting a general link to development and tissue formation rather than a single pathway.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030437","count":4},{"id":"GO:0030324","count":4},{"id":"GO:0007114","count":4},{"id":"GO:0001837","count":4},{"id":"GO:0010780","count":4}]},{"hash":"1936667767554527082","title":"DNA Replication and Transcription Regulation","description":"The GO terms cluster around DNA-templated processes: DNA strand elongation during replication, DNA-templated transcription, and regulation of DNA replication initiation, indicating a shared role in nucleic acid synthesis and transcription control. Some terms (e.g., competence for transformation, proliferation regulation) are more context-specific or peripheral, and a couple are obsolete or related to protein folding, likely reflecting annotation noise. Overall, the set points to proteins involved in DNA replication and transcription regulation.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006271","count":1},{"id":"GO:0042127","count":1},{"id":"GO:0030420","count":1},{"id":"GO:0071712","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1132336468519834439","title":"Chromatin regulation and differentiation","description":"The cluster\u2019s terms largely center on chromatin-level transcriptional control (negative regulation of RNA polymerase II transcription, histone methylation, heterochromatin formation) and developmental differentiation (osteoblast, muscle, pro-B cell differentiation, multicellular growth). Immune-response terms are present but less cohesive; overall the common theme is regulation of gene expression via chromatin state during development.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0051572","count":1},{"id":"GO:0019731","count":1},{"id":"GO:0001649","count":1},{"id":"GO:0000183","count":1}]},{"hash":"653909517905188811","title":"Calcium Transport and Homeostasis","description":"This cluster shows multiple GO terms centered on calcium handling, including calcium ion transport into the sarcoplasmic reticulum, calcium ion transport from cytosol to the endoplasmic reticulum, and intracellular calcium ion homeostasis, suggesting a core theme of calcium signaling. Other terms present (copper transport, testosterone response, various metabolic processes) are less cohesive, but the recurrent calcium-related terms provide the strongest signal for this label.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":1},{"id":"GO:1990036","count":1},{"id":"GO:0006874","count":1},{"id":"GO:0033574","count":1},{"id":"GO:0006564","count":1}]},{"hash":"1159108370474927153","title":"Cell Cycle Regulation and Signaling","description":"The top GO terms cluster around DNA replication, meiotic spindle assembly checkpoint signaling, and MAPK/Rho signaling, which together indicate cell-cycle regulation and central signaling circuits. Some terms also touch on differentiation and growth (myoblast differentiation, VEGF signaling, dendritic cell proliferation), suggesting broader proliferation cues, but the dominant theme remains cell-cycle\u2013related processes. Therefore, this label captures the core connection among the terms while acknowledging broader signaling roles.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000196","count":2},{"id":"GO:0044565","count":2},{"id":"GO:0033316","count":2},{"id":"GO:0007266","count":2}]},{"hash":"2036203589432413595","title":"Developmental and neural differentiation","description":"The top GO terms cluster around forebrain development, multicellular organism development, and skeletal system development, with additional terms linked to neural plasticity, suggesting a shared theme of developmental programs and neural maturation. Some other terms (e.g., obsolete aging, hypoxia response) appear incidental, but the core signal points to developmental and neural differentiation processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0001501","count":2}]},{"hash":"1543880120368082094","title":"Cytoskeleton remodeling and Ras signaling","description":"The terms cluster around cytoskeletal dynamics, including tubulin assembly/folding and actin cytoskeleton organization with actin filament severing, suggesting a core role in cytoskeletal remodeling. The presence of GTPase and Ras-related regulation (positive regulation of GTPase activity, Ras protein signal transduction) ties signaling to cytoskeletal changes. Maintenance of Golgi location also fits with vesicle trafficking dependent on microtubule and actin networks, reinforcing a cytoskeleton-centric functional module.","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0045761","count":1},{"id":"GO:0007265","count":1},{"id":"GO:0051684","count":1}]},{"hash":"1051752090131592157","title":"Unknown","description":"There are no GO terms to connect the five proteins, so no shared function is identifiable; this cluster cannot be confidently labeled.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"52156082356643549","title":"Ribosome biogenesis and translation","description":"Predominant GO terms reflect ribosome assembly/biogenesis, cytoplasmic translation, and SRP-dependent cotranslational targeting to membranes, plus rRNA processing steps. A single \u201cresponse to antibiotic\u201d term appears incidental. Overall, the cluster centers on ribosome production and protein synthesis.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000448","count":1},{"id":"GO:0042255","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006614","count":1}]},{"hash":"1423666765668431827","title":"ER folding and ER-Golgi trafficking","description":"The top GO terms point to protein folding in the endoplasmic reticulum, chaperone-mediated protein complex assembly, and ER-to-Golgi vesicle transport, suggesting core roles in ER quality control and trafficking to the Golgi. Other terms (oxidative phosphorylation regulation, DNA replication, viral genome replication) are less central to the cluster, so the label focuses on the ER folding/trafficking theme. ","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:1903862","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0051131","count":1}]},{"hash":"821443806167226540","title":"Nucleolar RNA Processing and Ribosome Biogenesis","description":"These proteins are annotated with rRNA and snRNA pseudouridine synthesis and with ribosome biogenesis, suggesting roles in RNA modification and ribosome assembly in the nucleus. The telomerase-related terms hint at broader nuclear RNP trafficking, but the dominant theme is RNA processing and ribosome biogenesis in the nucleolus. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007004","count":1},{"id":"GO:0031118","count":1},{"id":"GO:0000469","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0031120","count":1}]},{"hash":"821480749188985743","title":"Peroxisomal Fatty Acid and Amino Acid Catabolism","description":"Based on the top GO terms, the cluster is enriched for peroxisome- and glyoxysome-associated catabolic processes: ketone body catabolic process, propionyl-CoA biosynthetic process, L-isoleucine catabolic process, and glyoxysome organization. Aromatic compound degradation and antibiotic biosynthesis plus response to starvation support a metabolism- and stress-focused gene set. While terms like liver development and cholesterol transport are present, the central pattern points to peroxisomal lipid and amino acid catabolism as the core function of the proteins in this cluster.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046952","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0042594","count":2},{"id":"GO:1902860","count":2},{"id":"GO:0001889","count":2}]},{"hash":"325865323298058452","title":"Nuclear RNP biogenesis and RNA processing","description":"These GO terms cluster around nuclear RNA metabolism and RNP assembly: import into the nucleus, spliceosomal/snRNP and tRNA/rRNA processing, mRNA decapping, and transcription termination by RNA Pol II. This suggests a coherent theme of nuclear RNP biogenesis and processing. A couple of terms (pericentric heterochromatin formation and hair cycle) are broader/non-specific but may reflect ancillary nuclear roles.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0000387","count":3},{"id":"GO:0000290","count":3},{"id":"GO:0006369","count":3}]},{"hash":"2247735713820491916","title":"Purine nucleotide metabolism","description":"The Top Terms are dominated by nucleotide metabolism and related phosphorylation and salvage processes (CDP biosynthesis, ADP biosynthesis, AMP salvage, nucleoside monophosphate phosphorylation, purine ribonucleotide interconversion, ITP metabolic process). This points to enzymes involved in purine nucleotide biosynthesis and salvage as the core function of the cluster. The presence of brain and liver development terms is sporadic and likely reflects broader or contextual annotations rather than a shared function, so they do not override the primary nucleotide metabolism signal. Confidence reflects a solid link to purine nucleotide processing, with minor ambiguity from developmental terms.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046705","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0046939","count":2},{"id":"GO:0006172","count":2}]},{"hash":"281217662093654237","title":"Nuclear mRNA Maturation and Export","description":"The GO terms cluster around nuclear post-transcriptional mRNA processing: stabilization, splicing regulation via spliceosome, polyadenylation regulation, mRNA modification, and export from the nucleus. Together these indicate a cohesive theme of mRNA maturation and trafficking rather than translation or degradation, justifying a label focused on nuclear mRNA processing and export.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:1900363","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1524722954953875784","title":"Mitochondrial dynamics and processing","description":"Based on the GO terms, the cluster centers on mitochondrial functions: stress-induced mitochondrial fusion, cardiolipin metabolism, mitochondrial protein processing, and mitochondrial calcium transport, suggesting a cohesive theme around mitochondrial dynamics and processing, with the adhesion-related terms likely incidental.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000049","count":1},{"id":"GO:1900210","count":1},{"id":"GO:1990046","count":1},{"id":"GO:0034982","count":1},{"id":"GO:0060355","count":1}]},{"hash":"393230271924312164","title":"Proton Transmembrane Transport","description":"This cluster is dominated by the GO term proton transmembrane transport (2 annotations), suggesting the proteins share membrane transport activity. The other terms are scattered and supported by single proteins, indicating diverse roles beyond transport. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":2},{"id":"GO:0032471","count":1},{"id":"GO:0045976","count":1},{"id":"GO:0000188","count":1},{"id":"GO:0043547","count":1}]}]