[{"hash":"1159125485064879342","title":"Unknown","description":"The top GO terms span hormonal response, metabolism, DNA replication, RNA processing, iron-sulfur cluster assembly, neural guidance, and bone mineralization, with no clear common function tying them together. The sparse connectivity (1 edge, no triangles) supports the idea that this cluster does not represent a single coherent biological process, so a single, informative label cannot be assigned.","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071375","count":3},{"id":"GO:0071372","count":3},{"id":"GO:0019395","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0016226","count":2}]},{"hash":"597628337261001900","title":"Genome maintenance and transcription regulation","description":"The cluster centers on nuclear processes that preserve genome integrity and control gene expression: DNA replication and repair, chromatin/nucleosome dynamics, transcription initiation, splicing regulation, and ncRNA-mediated silencing; additional links to centrosome cycle and developmental gene expression align with cell division and embryonic morphogenesis.","confidence":"Medium","size":29,"edges":8,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0042766","count":2}]},{"hash":"263785025630541513","title":"DNA replication and SOS repair cluster","description":"This set is dominated by GO terms tied to DNA damage response and genome maintenance: SOS response, DNA recombination, DNA replication, and transcription-coupled nucleotide-excision repair, with sister chromatid biorientation also aligning to chromosomal maintenance. While a few terms (prespliceosome assembly, embryonic morphogenesis) are less connected, they appear as outliers, and do not override the central theme of replication and repair machinery. Overall, the cluster appears best characterized as DNA damage response and replication proteins.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0018144","count":2},{"id":"GO:0006260","count":2}]},{"hash":"21606669564352675","title":"Unknown","description":"The top GO terms span heart development, angiogenesis, visual perception, neural signaling, transcription, cell cycle, apoptosis, phosphorylation, and even plant ABA signaling, indicating a broad and heterogeneous set of functions with no clear common theme. Because of this mix and lack of a cohesive biological function tying the proteins together, a specific, representative label cannot be confidently assigned.","confidence":"","size":29,"edges":9,"triangles":4,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008218","count":5},{"id":"GO:0007507","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0001525","count":3}]},{"hash":"1324356713555377081","title":"Neural Development and Progenitor Proliferation","description":"This cluster combines neuronal development signals (hippocampus development, dendrite morphogenesis, excitatory synaptic activity) with cell-cycle and DNA replication processes, suggesting a cohesive role in neurodevelopment involving proliferating neural progenitors.","confidence":"Medium","size":29,"edges":61,"triangles":122,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":15},{"id":"GO:0060079","count":15},{"id":"GO:0006260","count":15},{"id":"GO:0048701","count":14},{"id":"GO:0031647","count":14}]},{"hash":"598453106114872332","title":"Chromatin remodeling and transcription regulation","description":"The cluster is dominated by GO terms for chromatin organization/remodeling, nucleosome assembly, and transcription by RNA polymerase II, indicating a cohesive role in chromatin dynamics that controls transcription and genome access. A subset of terms also points to DNA replication, suggesting coordinated chromatin changes during replication; together the terms imply a chromatin-centric regulatory module.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":2},{"id":"GO:0045899","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0034724","count":1}]},{"hash":"1364955086226476615","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006904","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2}]},{"hash":"932625442270100084","title":"Neural development and gene regulation","description":"The dominant GO terms point to neural development (forebrain development, neural tube closure) and transcriptional regulation, suggesting proteins in this cluster mainly function in neural development and gene expression control. Some terms related to stress responses and cell cycle are present but do not define a single cohesive module, making neural development the best representative theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1690171905811612864","title":"Glutamatergic Synapse Regulation and Learning","description":"The top GO terms converge on glutamatergic synapses and learning, including positive regulation of AMPA receptor activity, NMDA receptor clustering, and synaptic transmission, plus associative learning. A few developmental terms appear as outliers, but the core signal is neuronal synaptic signaling and plasticity.","confidence":"High","size":29,"edges":16,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090004","count":1},{"id":"GO:2000969","count":1},{"id":"GO:0008306","count":1},{"id":"GO:0007508","count":1},{"id":"GO:0035001","count":1}]},{"hash":"699938548430755644","title":"Diverse Metabolite and Lipid Transport","description":"The top GO terms point to transport of a range of molecules (heme, cysteine, thiamine, carbohydrates) and lipids (phospholipids, ceramide) as well as peroxisomal import, with a few metabolic terms tied to fatty acids. The 0 edges suggest annotation-based clustering rather than tight interaction networks. Overall, the shared theme is varied transport processes rather than a single pathway, hence this label. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0015886","count":1},{"id":"GO:0042760","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0043215","count":1}]},{"hash":"516437921940067664","title":"RNA processing and protein synthesis machinery","description":"Top terms cluster around RNA biology: transcription, mRNA splicing, ribosome biogenesis, and translation (cytoplasmic and general) with a note on translational fidelity. Some outlier terms exist (forebrain development, antibiotic response), but the dominant theme is RNA processing and protein synthesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0090116","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0030900","count":2}]},{"hash":"1548503892539194841","title":"DNA replication and mitotic chromosome regulation","description":"The majority of top GO terms cluster around DNA replication, cell-cycle transitions (G1/S, meiotic), and chromosome condensation/kinetochore localization, pointing to a core theme of nuclear division and chromatin regulation; peripheral terms (neural signaling, autophagy, insulin signaling) appear secondary. This justifies labeling the cluster with a DNA replication and mitotic chromosome regulation theme.","confidence":"Medium","size":28,"edges":9,"triangles":0,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0000082","count":6},{"id":"GO:0014044","count":5},{"id":"GO:0034501","count":5},{"id":"GO:0042220","count":5}]},{"hash":"93743190390631622","title":"Secretory pathway and cell cycle regulation","description":"This cluster combines strong signals for ER-to-Golgi and COPII vesicle trafficking (and Golgi-to-ER retrograde transport) with ubiquitin-proteasome\u2013dependent protein degradation tied to mitosis (APC-dependent) and mitotic cell cycle terms, plus development-related growth signals. The dominant theme appears to be coordination of the secretory pathway with cell-cycle\u2013related proteolysis during development, making \u201cSecretory pathway and cell cycle regulation\u201d a concise, representative label.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1175937653230916977","title":"Synaptic Vesicle Trafficking","description":"The top GO terms converge on intracellular vesicle transport and sorting, including neurotransmitter receptor transport and internalization, synaptic vesicle membrane organization, clathrin-coated vesicle loading, and ER-Golgi to Golgi-lysosome routes. These collectively point to vesicle trafficking processes at the synapse and endosome/lysosome pathways, with a few peripheral terms related to pigment or immune functions. Overall, the cluster appears driven by synaptic and endosomal vesicle trafficking.","confidence":"High","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098943","count":1},{"id":"GO:0032438","count":1},{"id":"GO:0061088","count":1},{"id":"GO:0090160","count":1},{"id":"GO:0035652","count":1}]},{"hash":"1847515158869248123","title":"Plant Growth Regulation and Chromatin Remodeling","description":"Top terms point to plant developmental regulation (seed growth, root meristem growth) and chromatin-related processes (heterochromatin formation, histone deacetylation), suggesting a theme around how plant growth is coordinated with chromatin state. Some generic terms (protein heterotrimerization, GTPase regulation) are present, but the combination of growth regulation and chromatin remodeling terms supports a cohesive, plant-focused cluster rather than unrelated functions.","confidence":"Medium","size":28,"edges":58,"triangles":5,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":2},{"id":"GO:0000186","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071230","count":2},{"id":"GO:1905778","count":2}]},{"hash":"156590269391049147","title":"Chromatin Remodeling and Stress-Responsive RNA Processing","description":"The enrichment centers on chromatin dynamics (chromatin remodeling, DNA topology, nucleosome mobilization) and stress responses (xenobiotic/menadione, stress granule localization), with concurrent RNA processing/ribosome biogenesis (5.8S rRNA maturation), implying coordinated gene regulation under stress.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0036245","count":2},{"id":"GO:0039707","count":1},{"id":"GO:0039547","count":1}]},{"hash":"1750051116013020314","title":"Mitotic regulation and RNA processing","description":"This cluster centers on mitosis-related processes (cell division, spindle orientation, cytokinesis-related septum activity) and genome maintenance, as well as gene expression control (DNA-templated transcription, mRNA splicing) and chromatin modification (histone methylation), plus DNA damage response and apoptosis. The convergence of cell cycle progression with transcription/splicing and chromatin regulation suggests a coherent module coordinating mitosis with gene expression and genome integrity. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0000920","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000132","count":2}]},{"hash":"1012478007917642605","title":"Vacuolar trafficking and ion homeostasis","description":"The top GO terms cluster around vacuolar processes (vacuole organization, vacuolar acidification, protein targeting to vacuole) and ion transport (proton transmembrane transport, proton motive force-driven ATP synthesis, sodium and copper ion homeostasis). This suggests a functional group involved in vacuole biogenesis/maintenance, membrane trafficking to the vacuole, and associated ion gradient energetics, with a minor note of actin-regulation terms that may relate to vacuolar dynamics. Overall, a cohesive theme of vacuolar function plus ion homeostasis fits best.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0015991","count":1}]},{"hash":"1295883095611765077","title":"Unknown","description":"The terms span viral process, plant hormone response, vacuolar acidification, cell wall biosynthesis, proton transport, growth, steroid receptor assembly, sex differentiation, interferon response, and prostate development, with no single clear function tying them together.","confidence":"","size":27,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0007035","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0015991","count":1}]},{"hash":"1546274159363669377","title":"Epithelial polarity and actin-driven migration","description":"The enrichment highlights actin filament bundle assembly and cell migration, plus establishment of epithelial cell polarity, supported by signaling terms such as regulation of JNK cascade, GTPase activity, and TGF-beta response. This points to a cohesive module of cytoskeletal remodeling and polarity signaling that drives cell movement; other terms like fat cell differentiation and grooming behavior appear less central to this cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0016477","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0045444","count":2}]},{"hash":"203424037927018086","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":33,"triangles":37,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0033129","count":4},{"id":"GO:0070935","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0006813","count":4}]},{"hash":"372252608020559120","title":"Telomere and chromatin DNA metabolism","description":"Based on the top GO terms, this cluster centers on nuclear DNA processes related to telomere biology and chromatin regulation, including subtelomeric heterochromatin formation, protection of telomeres from NHEJ, G-quadruplex DNA dynamics, and DNA-templated transcription. The presence of a few unrelated terms (dolichol metabolism, cell wall organization) suggests some noise or cross-annotation, but the core signal points to DNA metabolism at telomeres and chromatin-level control.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035390","count":2},{"id":"GO:0071919","count":2},{"id":"GO:0031848","count":2}]},{"hash":"1188545129889105810","title":"Diverse biosynthesis and methylation enzymes","description":"This cluster groups proteins involved in multiple biosynthetic pathways (hydrogen sulfide, cysteine, sterols, phosphatidylcholine, polyamines) and several methylation processes (peptidyl-arginine/lysine methylation, rRNA methylation), suggesting a collection of enzymes linked to general biosynthesis and post-translational or RNA modification activities rather than a single coherent pathway.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":2},{"id":"GO:0070814","count":2},{"id":"GO:0019344","count":2},{"id":"GO:0016126","count":1},{"id":"GO:0018364","count":1}]},{"hash":"1813888533252019","title":"Nuclear import and Golgi-ER trafficking","description":"This cluster centers on proteins involved in importing cargo into the nucleus and in retrograde Golgi-to-ER transport, reinforced by terms for protein transmembrane transport and regulatory steps of nuclear import. A couple of development-related terms are present but the dominant signal is intracellular trafficking and nuclear transport.","confidence":"Medium","size":27,"edges":209,"triangles":595,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":2},{"id":"GO:0071806","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0045740","count":2},{"id":"GO:0006606","count":1}]},{"hash":"1365528805481527453","title":"Glutamatergic synapse function and neural development","description":"GO terms point to synaptic signaling, especially glutamatergic transmission (AMPA receptor activity, NMDA receptor clustering, and associative learning) and neural development; while a few terms are broader developmental processes, the core theme is glutamatergic synapse organization and neural signaling.","confidence":"High","size":26,"edges":159,"triangles":278,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0090004","count":2},{"id":"GO:2000969","count":2},{"id":"GO:0008306","count":2},{"id":"GO:0007508","count":2},{"id":"GO:0035001","count":2}]},{"hash":"1612951762245308925","title":"Nutrient signaling and vesicle trafficking","description":"This group combines vesicle trafficking processes (intraciliary transport in cilium assembly; ER-Golgi transport) with metabolic and nutrient-sensing signals (TOR pathway activation; glucose/galactose metabolism; amino acid\u2013stimulated responses), pointing to a theme of coordinating trafficking with nutrient signaling and metabolic regulation, despite some peripheral terms like heat response or mushroom body development.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035735","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0034605","count":1},{"id":"GO:0032008","count":1},{"id":"GO:0000186","count":1}]},{"hash":"1409511763905080946","title":"ER-Golgi trafficking and cell growth","description":"The cluster prominently features vesicle transport between the ER and Golgi and COPII-coated vesicle budding, indicating a secretory pathway focus. It also includes ribosome biogenesis and cell proliferation/mitotic terms, suggesting a role in general cellular growth and development, with some terms pointing to a developmental context like brain development. Overall, a coherent theme around secretory trafficking coupled with growth during development.","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0000278","count":3}]},{"hash":"2221962428686298058","title":"Membrane transporters and xenobiotic response","description":"This cluster is dominated by transmembrane transport GO terms, including potassium ion, vitamin, nitrate assimilation, and xenobiotic/antibiotic transport, along with a notable \u201cresponse to xenobiotic stimulus\u201d term. The pattern points to a set of membrane transport proteins mediating uptake/export of ions and xenobiotics, with related responses to antibiotics. The presence of a few biosynthetic terms is secondary to the transport-centric signal, supporting a transporter-focused cluster with xenobiotic responsiveness.","confidence":"Medium","size":26,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":4},{"id":"GO:0042128","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0042891","count":3}]},{"hash":"1112456857403786279","title":"Bacterial cofactor biosynthesis and cell envelope formation","description":"The top GO terms cluster around biosynthesis of cofactors and pigments (biotin, protoporphyrinogen IX, menaquinone) and lipoteichoic acid biosynthesis, plus sporulation, which together point to metabolic and developmental pathways typical of Gram-positive bacteria. A few terms (mRNA splicing, RNAP II regulation) seem unrelated noise but do not alter the dominant theme. Confidence in this label is High.","confidence":"","size":26,"edges":17,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0045150","count":2}]},{"hash":"468562735752019948","title":"Developmental growth and mitosis with vesicle trafficking","description":"The terms center on growth and cell division (brain development, multicellular growth, mitotic cell cycle, mitotic spindle assembly, cell proliferation) and vesicle trafficking/cytoskeleton dynamics (retrograde Golgi-ER transport, COPII budding, actin depolymerization). This suggests a cohesive group of proteins coordinating development with cell cycle progression and secretory pathway function, justifying the label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0030042","count":3},{"id":"GO:0035264","count":3}]},{"hash":"1062085366020971228","title":"Sterol Biosynthesis and Lipid Metabolism","description":"Most prominent GO terms concern ergosterol biosynthetic process, cholesterol biosynthetic regulation, and fatty acid oxidation, pointing to lipid and sterol metabolism as the core theme. Other signals like IL-6 production and Hedgehog signaling are present but less central, so the lipid/sterol focus best represents the cluster.","confidence":"Medium","size":26,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071375","count":3},{"id":"GO:0071372","count":3},{"id":"GO:0019395","count":3},{"id":"GO:0043154","count":2},{"id":"GO:0006696","count":2}]},{"hash":"625696474846059965","title":"Neuronal synaptic vesicle trafficking","description":"The top terms center on vesicle exo-/endocytosis, endocytic recycling, and excitatory postsynaptic potential, indicating neuronal synaptic transmission and vesicle cycling; substantia nigra development further supports a brain-specific context, while other terms reflect broader cellular stress or pleiotropy rather than changing the core theme.","confidence":"High","size":26,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071872","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0032456","count":2}]},{"hash":"428116513047880965","title":"RNA processing and chromatin regulation","description":"The top GO terms emphasize chromatin state and RNA handling (chromatin remodeling; regulation of histone deacetylation; snoRNA localization; box C/D snoRNP assembly; negative regulation of transcription regulatory region DNA binding), suggesting a shared role in controlling gene expression at the chromatin and RNA-processing levels. Some terms related to insulin secretion and calcium signaling appear, but they are peripheral to the dominant theme of chromatin/RNA-based regulation. Therefore, a name focusing on RNA processing and chromatin regulation best represents this cluster.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":1},{"id":"GO:0031063","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0035774","count":1}]},{"hash":"253063816166710264","title":"ECM Remodeling and Morphogenesis","description":"This cluster is enriched for collagen catabolic process, basement membrane disassembly, bone resorption, and epithelial tube branching in lung morphogenesis, indicating extracellular matrix remodeling and developmental morphogenesis; it also includes proteolysis-related processes, supporting a theme of tissue restructuring.","confidence":"High","size":25,"edges":221,"triangles":967,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":9},{"id":"GO:0034769","count":9},{"id":"GO:0050790","count":9},{"id":"GO:2000179","count":9},{"id":"GO:0051603","count":9}]},{"hash":"1136590272828632820","title":"Nuclear transcription regulation and stress response","description":"Based on the top GO terms, the cluster centers on DNA-templated transcription and regulation of transcription by RNA polymerase II, with accompanying signals of cellular stress responses (oxidative and ER stress) and redox homeostasis, plus linked processes like protein repair, suggesting a group of nuclear transcription regulators coordinating stress-response pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0034599","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006662","count":2}]},{"hash":"1846536317927144165","title":"Ribosome biogenesis and translation","description":"The strongest signals are translation (GO:0006412) and 90S preribosome assembly (GO:0034463), pointing to ribosome production and protein synthesis. Additional RNA processing/transcription-related terms suggest coordination between ribosome biogenesis and RNA maturation. A few cell cycle terms may reflect proliferative contexts where ribosome activity is upregulated, butOverall, the cluster centers on ribosome assembly and translation, with peripheral transcription/RNA processing signals.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000082","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0097350","count":2}]},{"hash":"1214150043417460732","title":"Signaling and Stress Response Regulators","description":"The top GO terms cluster around regulation of kinase activity (positive regulation of protein serine/threonine kinase activity; autophosphorylation), GTPase activity, and cell cycle control (mitotic cell cycle), alongside cellular responses to stress ( xenobiotic stimulus and hypoxia). Additional terms for mRNA transport and modulation of insulin secretion imply broader regulatory roles in signaling, gene expression, and secretion. These collectively suggest a group of proteins that modulate signaling pathways and stress responses rather than a single cohesive pathway, justifying the label as signaling and stress response regulators. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0071456","count":2}]},{"hash":"2180646068546863833","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0051289","count":2},{"id":"GO:0006620","count":1},{"id":"GO:0051083","count":1},{"id":"GO:0035278","count":1}]},{"hash":"1372435313963301762","title":"Tissue Remodeling and Development","description":"The top GO terms cluster around tissue morphogenesis and remodeling: decidualization and epithelial tube branching indicate developmental tissue remodeling; collagen catabolic and bradykinin catabolic processes reflect extracellular matrix turnover; thyroid hormone response and neural precursor proliferation suggest broader developmental regulation. Taken together, the terms point to processes that shape tissues during development and remodeling rather than a single, narrow pathway.","confidence":"Medium","size":25,"edges":275,"triangles":1861,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0046697","count":11},{"id":"GO:0010813","count":11},{"id":"GO:0050790","count":11},{"id":"GO:0060441","count":11},{"id":"GO:0097067","count":11}]},{"hash":"2275182833006208135","title":"Unknown","description":"The top GO terms span diverse processes (mating-type regulation, neural development, foam cell differentiation) and chromatin-related events, with no single pathway linking them; plus there are no edges, so there is insufficient evidence for a cohesive function.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031496","count":1},{"id":"GO:0031452","count":1},{"id":"GO:0006990","count":1},{"id":"GO:0060358","count":1},{"id":"GO:0061412","count":1}]},{"hash":"566116149514668627","title":"Innate Immune Response and Phagocytosis","description":"These proteins show enrichment for innate immune response and phagocytosis (GO:0045087, GO:0006909), as well as related processes such as cell migration and apoptotic regulation, and signaling modulation (negative regulation of protein kinase activity). This pattern points to a cluster involved in immune cell\u2013mediated clearance and signaling, with possible links to tissue remodeling given bone development and proteoglycan biosynthesis terms. Overall, a cohesive theme centers on innate immunity and phagocytic activity, with ancillary remodeling signals.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071454","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0016477","count":2}]},{"hash":"278147810595197170","title":"Neuronal membrane trafficking and lipid metabolism","description":"This cluster centers on neuronal membrane dynamics (endocytosis, raft organization, depalmitoylation) and lipid-related processes (lipid catabolism, lysosomal acidification), with behavioral and neuron survival terms suggesting a broader neural function link. While individual GO terms are diverse, the common thread appears to be membrane trafficking and lipid regulation in neurons influencing neural signaling and behavior.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900244","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0002084","count":1},{"id":"GO:0032429","count":1},{"id":"GO:0007042","count":1}]},{"hash":"529630964158939869","title":"Unknown","description":"The cluster lists a mix of lipid catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine catabolism), redox/oxidation-reduction and detoxification terms, along with transcription and post-translational modification processes, and there are no connecting edges, suggesting no single cohesive pathway or theme tying all members together.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0006660","count":3},{"id":"GO:2000124","count":3}]},{"hash":"1859302818973932495","title":"DNA Replication and Repair","description":"This cluster centers on nucleic acid metabolism: DNA repair, DNA replication, and DNA biosynthesis are prominent, with RNA processing and stress-granule localization also represented. A few terms about lipopolysaccharide/G-CSF/T cell signaling appear, but they seem peripheral to the core DNA metabolism theme.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0051321","count":2}]},{"hash":"309459139275368521","title":"Muscle lineage differentiation and signaling","description":"The cluster\u2019s top GO terms center on muscle development and differentiation (myotube differentiation; axial mesoderm formation) and on signaling pathways important for tissue patterning and neuromuscular communication (ephrin receptor signaling; trans-synaptic signaling; osmosensory signaling). This combination suggests proteins functioning together in muscle lineage specification and related signaling cascades, with a few terms (apoptotic process, activated T cell proliferation) less tightly aligned and likely representing broader or pleiotropic roles.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0048013","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0043046","count":2}]},{"hash":"366324619401175851","title":"Chromatin Regulation and Transcription in Differentiation","description":"This cluster is enriched for chromatin-related terms (rDNA and subtelomeric heterochromatin formation, histone deacetylation) alongside transcription-related terms (DNA-templated transcription) and differentiation/ remodeling signals (cell differentiation, angiogenesis, muscle adaptation). The combination suggests a core theme of chromatin remodeling governing gene expression during development and tissue remodeling, with regulatory ties to signaling pathways like Rho and denervation responses. Overall, the label captures the dominant function with some related differentiation/tissue remodeling signals, giving it a Medium confidence.","confidence":"Medium","size":24,"edges":8,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0006351","count":3},{"id":"GO:1990414","count":3},{"id":"GO:0070933","count":3}]},{"hash":"2039637749387033456","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009048","count":3},{"id":"GO:0061158","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0045087","count":3}]},{"hash":"930804524708962460","title":"Neuro-muscular and cardiac development","description":"Based on the GO terms, the proteins cluster around developmental processes in the nervous system (axonogenesis, long-term potentiation, visual perception, Schwann cell development), muscle formation (myoblast fusion), and heart development, suggesting a cohesive theme of neuro-muscular-cardiac development. Some cross-species annotations (e.g., ABA signaling) may appear, but the dominant signal is developmental programs across neural, muscular, and cardiac lineages. ","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007121","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0009738","count":2}]},{"hash":"2133076663092507718","title":"Ubiquitin-Dependent Proteostasis and NF-kappaB Signaling","description":"GO terms center on ubiquitination and protein degradation (ubiquitin-dependent catabolic process, ERAD) and NF-kappaB pathway regulation (I-kappaB phosphorylation, NF-kappaB-inducing kinase). Supporting terms include mitochondrial import and iron response, suggesting a broader link to cellular stress responses. The cluster appears to group proteins involved in ubiquitin-mediated protein quality control and inflammatory signaling rather than a single specific process.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:0033151","count":1},{"id":"GO:0007250","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0046621","count":1}]},{"hash":"233324606481827115","title":"Hormone-responsive cell cycle and metabolism","description":"This cluster centers on GO terms tied to hormone signaling (cellular response to peptide hormone stimulus and follicle-stimulating hormone stimulus) alongside cell cycle transitions (G1/S, G1 to G0) and metabolic processes (fatty acid oxidation, nitrogen utilization) plus translation regulation. The combination suggests a theme where hormonal cues coordinate growth and proliferation with metabolic remodeling, with some broader developmental or stress-related terms appearing as ancillary signals. Overall, a cohesive interpretation is hormone-driven regulation of cell cycle and metabolism, though the mix of terms indicates some additional context-specific roles.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071375","count":2},{"id":"GO:0071372","count":2},{"id":"GO:0019395","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0019740","count":2}]},{"hash":"22418192716904896","title":"Cell Cycle and DNA Replication","description":"The cluster is dominated by GO terms for DNA replication, mitotic cell cycle, cell division, and DNA-templated transcription, pointing to proteins involved in genome duplication and proliferation. While other terms (developmental processes, innate immune response, response to cadmium) appear, they seem ancillary to the core theme of cell cycle machinery. Thus the label reflects the predominant function of the cluster as related to cell cycle and DNA replication, with some broader roles likely present. ","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006915","count":3}]},{"hash":"1967275759542061811","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":1},{"id":"GO:0042255","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0000461","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1610858747904528532","title":"ER membrane organization and trafficking","description":"This cluster highlights ER-related terms: endoplasmic reticulum inheritance, ER stress response, ER tubular network organization, and protein transport into membrane rafts, suggesting a theme of ER remodeling and trafficking of proteins through membranes. The other terms (RNA catabolic process, ribonucleotide excision repair, bitter taste, abscisic acid response) are diverse and weaker connections, indicating the overall linkage is limited. Without network connections (0 edges), the cluster appears functionally loose, supporting a low-confidence label.","confidence":"Low","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006401","count":1},{"id":"GO:1990516","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0048309","count":1},{"id":"GO:0009737","count":1}]},{"hash":"70579153808715688","title":"RNA methylation and ribosome biogenesis","description":"The top GO terms show multiple RNA and ribosome-related processes (tRNA methylation, rRNA methylation, peptidyl-glutamine methylation, and ribosomal small subunit export), indicating a common function in RNA modification and ribosome biogenesis. While other terms touch on vitamin biosynthesis and transport, the methylation and ribosome-related terms dominate, supporting this focused label.","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0070476","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0000056","count":3}]},{"hash":"1436066259155915376","title":"ER-Golgi Vesicle Transport and Localization","description":"This cluster centers on proteins involved in secretory pathway trafficking\u2014ER to Golgi and retrograde Golgi to ER transport, plus retention of proteins in the ER lumen and localization to the plasma membrane. These GO terms strongly suggest a shared role in vesicle trafficking within the early secretory route and membrane targeting, with other terms like transcription and oxidative stress likely representing broader cellular states or incidental associations. Overall, the core theme is ER-Golgi trafficking and membrane localization.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090004","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0071340","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0006621","count":1}]},{"hash":"1896380472036194338","title":"Negative regulation of cytokine signaling and immune responses","description":"These proteins appear to be enriched for terms that dampen signaling and immune activity, including negative regulation of IL-6 signaling, negative regulation of IL-8 production, and negative regulation of protein kinase activity via phosphorylation. The presence of receptor downregulation and immune response modulation supports a unifying theme of down-regulating signaling pathways and immune functions, even though a few terms touch on development or metabolic stress. Overall, the cluster centers on regulatory nodes that suppress signaling and immune outputs rather than promoting a specific pathway.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0036245","count":2},{"id":"GO:0036060","count":1}]},{"hash":"844706918220076278","title":"Ubiquitin-Dependent Protein Degradation (ERAD)","description":"The cluster is dominated by GO terms tied to ubiquitin-dependent protein catabolic processes, including the ERAD pathway and K48-linked ubiquitination, pointing to roles in targeting proteins for proteasomal degradation. Although a couple of terms (like Wnt receptor catabolic process and dosage compensation) appear, the core theme is ubiquitin-mediated protein turnover.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0090116","count":2},{"id":"GO:0060816","count":2}]},{"hash":"2104008570608231524","title":"Chromatin remodeling and transcription regulation","description":"The top terms are centered on chromatin dynamics: chromatin remodeling and nucleosome disassembly, with regulation of heterochromatin, suggesting these proteins mainly function in altering chromatin structure to modulate transcription. A few unrelated or deprecated terms (developmental/immune differentiation) appear incidental rather than defining the cluster. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0031496","count":1},{"id":"GO:0031452","count":1},{"id":"GO:0006990","count":1},{"id":"GO:0060358","count":1}]},{"hash":"1041186004451912390","title":"Proteolysis and ECM Remodeling","description":"The top GO terms cluster around proteolysis and peptide catabolism (proteolysis; collagen catabolic process; bradykinin and neuropeptide catabolic processes) and basement membrane disassembly, indicating extracellular matrix remodeling. While a few terms touch on development, the dominant theme is protein/ECM degradation and processing, suggesting a proteolytic remodeling function for this cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":1},{"id":"GO:0034769","count":1},{"id":"GO:0050790","count":1},{"id":"GO:2000179","count":1},{"id":"GO:0051603","count":1}]},{"hash":"2150662711992276432","title":"Unknown","description":"The top GO terms span hormone signaling (salicylic, jasmonic, abscisic acid), growth regulation (root meristem, seed growth), chromatin-related processes, and even viral processes, with several obsolete annotations. This diverse mix does not reveal a single, cohesive function for the cluster, so a precise label cannot be determined.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1905778","count":3},{"id":"GO:1903086","count":3},{"id":"GO:0080113","count":3},{"id":"GO:0035390","count":3},{"id":"GO:0010082","count":3}]},{"hash":"694645350125193019","title":"Unknown","description":"The top GO terms are highly diverse, including photosynthesis, metal transport (zinc and copper), multiple biosynthetic and catabolic processes, calcium homeostasis, and even a testosterone response. This mix suggests no single coherent function or theme for the cluster, making a precise label unreliable. ","confidence":"","size":22,"edges":10,"triangles":4,"max_degree":4,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0071577","count":3},{"id":"GO:0046380","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0019700","count":3}]},{"hash":"750525467348454585","title":"Cytoskeletal remodeling and cell migration","description":"The top GO terms cluster around cell movement and cytoskeletal regulation\u2014cell migration, podosome assembly, dendritic spine development regulation, and GTPase activity control\u2014along with calcium-dependent exocytosis and angiogenesis, all of which point to dynamic cytoskeletal remodeling guiding cellular movement and structural changes. Some terms (iron-sulfur cluster assembly, mitotic cell cycle) are less directly linked, but the dominant theme is cytoskeleton-driven motility and remodeling, supporting a label around cytoskeletal dynamics in migration. ","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0060999","count":3},{"id":"GO:0071803","count":3}]},{"hash":"1978033707360077902","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning immune differentiation, development, stress responses, and signaling regulation, with no single dominant function tying most proteins together. Because there is no cohesive theme, I can't assign a precise label beyond Unknown.","confidence":"","size":22,"edges":153,"triangles":484,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0045859","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0030225","count":1},{"id":"GO:1904515","count":1},{"id":"GO:0010963","count":1}]},{"hash":"292977945732557044","title":"Protein and RNA methylation","description":"The top GO terms cluster around various methylation processes, including peptidyl-glutamine, peptidyl-arginine dimethylation, peptidyl-lysine dimethylation, N-terminal glycine methylation, and rRNA methylation, which together point to a common theme of methylation-based modifications on proteins and RNA. Some lipid biosynthesis terms and immune-related responses appear, but the dominant theme is methylation-related modifications across substrates, suggesting a methylation-centered functional cluster.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":1},{"id":"GO:0016126","count":1},{"id":"GO:0018364","count":1},{"id":"GO:0019919","count":1},{"id":"GO:0031167","count":1}]},{"hash":"1046065855632814550","title":"Diverse substrate transport","description":"Most terms point to transport of diverse substrates across membranes (heme, long-chain fatty acids into peroxisomes, cysteine, thiamine, phospholipids, ceramide, carbohydrates, and even daunorubicin), suggesting a membrane-transport-focused cluster. The absence of network connections (edges/triangles) indicates these proteins may participate in varied transport roles rather than a single cohesive pathway, so a general membrane transport label is appropriate.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":1},{"id":"GO:0042760","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0043215","count":1},{"id":"GO:0042883","count":1}]},{"hash":"223063104922658171","title":"Unknown","description":"The top GO terms span very different processes (chromatin remodeling, regulation of mRNA stability, viral process, antibiotic response, hormone signaling, fungal defense, neural polarity) with little overlap and several obsolete terms. The sparse edge structure (2 edges, 0 triangles) suggests no coherent shared function among these proteins. Therefore the cluster cannot be assigned a specific biological theme, and is labeled Unknown with no confidence.","confidence":"","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0018189","count":2},{"id":"GO:0046677","count":2}]},{"hash":"811107908096135387","title":"Unknown","description":"The top GO terms include neural development (substantia nigra), skeletal muscle development, morphine response, miRNA processing regulation, meiotic and mitotic cell cycle related processes, ER-Golgi transport, and glycogen metabolism. These functions are very diverse and don\u2019t converge on a single clear biological theme for a concise label, so a specific, representative name isn\u2019t discernible.","confidence":"","size":21,"edges":157,"triangles":647,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043278","count":16},{"id":"GO:0021762","count":12},{"id":"GO:0048741","count":12},{"id":"GO:1903799","count":11},{"id":"GO:0051037","count":11}]},{"hash":"922277720703765795","title":"Mitotic cell cycle and ribosome biogenesis","description":"Dominant GO terms cluster around cell division (mitotic cell cycle, APC-dependent catabolic process, microtubule severing) and ribosome production (ribosome biogenesis, ribosomal large subunit biogenesis, maturation of SSU-rRNA). Chromatin organization also aligns with mitotic chromosome management. A few terms reference ER stress\u2013related apoptosis, but the core theme is growth and division machinery.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0031497","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0070059","count":3}]},{"hash":"1613317580232858135","title":"Development and cell cycle regulation","description":"The top GO terms point to broad developmental processes across tissues (lung, Schwann cells, skeletal muscle) together with key cell cycle events (G1/S transition, meiotic cycle) and related processes like kinetochore localization and neuronal signaling, suggesting a general theme of development intertwined with cell cycle control rather than a single tissue-specific function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0009742","count":2}]},{"hash":"2056758884100015889","title":"Plant Growth and Hormone Signaling","description":"The cluster shows a pattern of growth regulation terms (seed growth, root meristem growth) and defense hormone responses (salicylic, jasmonic, and abscisic acids), suggesting a cohesive role in plant development coupled with hormone signaling. Some terms are noise (obsolete or unrelated like subtelomeric heterochromatin formation and viral process), but the predominant theme points to growth regulation intertwined with hormone pathways.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1905778","count":1},{"id":"GO:1903086","count":1},{"id":"GO:0080113","count":1},{"id":"GO:0035390","count":1},{"id":"GO:0010082","count":1}]},{"hash":"196090327741153879","title":"Vesicle Trafficking and Secretion","description":"The dominant GO terms point to vesicle dynamics, including endocytosis, cytoplasm-to-vacuole targeting (a vesicular delivery pathway), and anterograde vesicle transport, with extracellular transport and IL-6 production further linking to secretion. Although a few terms reflect lipid biosynthesis and iron-sulfur cluster assembly, these processes support membrane trafficking and organelle function, reinforcing a vesicle trafficking/secretion theme for this cluster. ","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0009229","count":2},{"id":"GO:0048490","count":2},{"id":"GO:0006858","count":1}]},{"hash":"1198392080200197192","title":"Unknown","description":"The GO terms are highly diverse, spanning immune differentiation, neural and skin development, signaling, transport, and xenobiotic response, with no single dominant process or function tying the proteins together. This makes it hard to assign a cohesive, specific label beyond Unknown.","confidence":"","size":21,"edges":54,"triangles":18,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030225","count":3},{"id":"GO:1904515","count":3},{"id":"GO:0010963","count":3},{"id":"GO:0000755","count":3},{"id":"GO:0060789","count":3}]},{"hash":"2002954290489437274","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031081","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0090344","count":3},{"id":"GO:0030042","count":3},{"id":"GO:0030433","count":3}]},{"hash":"1419713531958915374","title":"Ribosome biogenesis and transcription machinery","description":"This cluster is strongly enriched for ribosome biogenesis and rRNA maturation (GO:0042254, GO:0000462), along with DNA replication (GO:0006260) and DNA-templated transcription (GO:0006351), indicating a core group of nucleic acid processing and ribosome assembly factors. Development-related terms (forebrain development, multicellular organism development) appear as broader, potential context-dependent roles but do not outweigh the nucleic acid processing signals.","confidence":"High","size":20,"edges":166,"triangles":764,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0032092","count":3},{"id":"GO:0000462","count":3}]},{"hash":"1644719957422711804","title":"Carbohydrate and Ion Transporters","description":"This cluster is driven by membrane transport of sugars and ions (fructose, arabinose, phosphate, nitrate, selenite) and related metabolites, pointing to a cohesive function as nutrient transporters; the metabolic GO terms (L-ascorbic acid metabolism) further support a transport-metabolism nexus.","confidence":"Medium","size":20,"edges":96,"triangles":175,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":5},{"id":"GO:1990539","count":4},{"id":"GO:0071332","count":4},{"id":"GO:0042128","count":4},{"id":"GO:1900754","count":4}]},{"hash":"2119780838217519863","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning development (forebrain, spinal cord, male gonad), intracellular transport (ER to Golgi), RNA processing (rRNA maturation), nutrient and growth factor responses, and DNA damage signaling, with an obsolete term also present. There is no single shared function or pathway linking these proteins, so a generic Unknown label is most appropriate.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":3},{"id":"GO:0000920","count":3},{"id":"GO:2001162","count":2},{"id":"GO:0072432","count":2},{"id":"GO:0071560","count":2}]},{"hash":"201170554835173127","title":"RNA processing and chromatin regulation","description":"This cluster centers on RNA processing steps (mRNA capping, tRNA wobble modification) and ribosome biogenesis, plus methylation activities affecting chromatin and transcription (histone and arginine methylation). While a few terms touch on metabolism and glucose response, the strongest signal is RNA processing coupled with chromatin-based transcription regulation, suggesting a gene-expression\u2013oriented cluster. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0016126","count":1},{"id":"GO:0019919","count":1},{"id":"GO:0046015","count":1},{"id":"GO:0006656","count":1}]},{"hash":"256328423654470731","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms cluster around ubiquitination and ubiquitin-dependent protein catabolism (protein ubiquitination, ubiquitin-dependent protein catabolic process, autoubiquitination) and related pathways like ubiquitin-dependent ERAD and peroxisome matrix import, which relies on ubiquitination. The presence of NF-kappaB signaling-related terms (I-kappaB phosphorylation, NF-kappaB-inducing kinase activity) and growth/regulation terms likely reflect ubiquitin-regulated signaling effects rather than a single distinct pathway. Overall, the dominant theme is ubiquitin-mediated protein modification and turnover.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0016558","count":4},{"id":"GO:0051865","count":4}]},{"hash":"359805522907773553","title":"Unknown","description":"The top GO terms are highly diverse (glycerol metabolism, guard cell morphogenesis, mushroom body development, TOR signaling, cilium transport, etc.), and the cluster has no edges or apparent unified function, making it hard to assign a cohesive biological theme.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006071","count":1},{"id":"GO:0010442","count":1},{"id":"GO:0030643","count":1},{"id":"GO:0034478","count":1},{"id":"GO:0032008","count":1}]},{"hash":"2008771668017747706","title":"DNA repair and oxidative stress response","description":"The cluster shows strong signals for base-excision repair and DNA recombination, indicating genome maintenance. It also includes redox-related terms (cell redox homeostasis and hydrogen peroxide response) and xenobiotic stimulus response, pointing to a coordinated response to cellular stress that couples DNA protection with redox balancing and detox signaling.","confidence":"Medium","size":20,"edges":19,"triangles":17,"max_degree":8,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006284","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0007568","count":3},{"id":"GO:2001153","count":2}]},{"hash":"2288464678215503685","title":"Phosphorylation and Translation Regulators","description":"The top terms cluster around regulation of phosphorylation and translation, including protein kinase activity regulation, protein phosphorylation, and cytoplasmic translation, suggesting a regulatory module that coordinates signaling with protein synthesis. Additional terms like endocytic recycling and membrane formation hint at broader cellular trafficking roles; while there are some tissue-specific terms (angiogenesis, cardiac contraction, memory), the dominant theme centers on control of signaling and protein production.","confidence":"Medium","size":19,"edges":10,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006468","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0032120","count":2}]},{"hash":"679954717442856917","title":"Cellular Redox Homeostasis and Antioxidant Detoxification","description":"Dominant redox signals (cellular redox homeostasis, oxidation-reduction, detoxification, removal of superoxide) define this cluster, suggesting a unified role in oxidative stress defense. Other terms like ECM organization or spermatogenesis appear but are peripheral.","confidence":"High","size":19,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0019430","count":3},{"id":"GO:2000648","count":2}]},{"hash":"2187453221621955666","title":"Motor Neuron Development and Axon Guidance","description":"This cluster is dominated by GO terms for neuronal development, cell morphogenesis, and specifically motor neuron axon guidance, indicating a neural development and axon-pathfinding theme. While a few terms relate to general nuclear processes (DNA replication, mRNA processing), the neural development signals are the strongest. So the label captures the primary function.","confidence":"High","size":19,"edges":94,"triangles":276,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":12},{"id":"GO:0048666","count":11},{"id":"GO:0000902","count":11},{"id":"GO:0032435","count":11},{"id":"GO:0006260","count":11}]},{"hash":"1228677774866707295","title":"DNA replication and transcription processing","description":"The cluster's terms center on nucleic acid metabolism and genome maintenance: many GO terms relate to DNA replication (GO:0006260, GO:0006268), DNA topological changes (GO:0006265), and DNA unwinding during replication, along with transcription termination by RNA Pol II (GO:0006369) and SOS response (GO:0009432). Additional terms point to RNA biogenesis (maturation of 5.8S rRNA; GO:0000466) and chromatin remodeling (GO:0042766). Some outliers like embryonic cranial skeleton morphogenesis or associative learning likely reflect annotation noise rather than a shared function. Overall, the cluster appears enriched for nucleic acid metabolism, genome maintenance, and transcription-related processes.","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":4},{"id":"GO:0048701","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0042766","count":3},{"id":"GO:0008306","count":3}]},{"hash":"21567618099951017","title":"Developmental gene regulation and mitotic control","description":"Based on the top GO terms, the proteins converge on controlling gene expression and cell division during development: DNA-templated transcription, mitotic cell cycle, and negative regulation of CDK activity point to transcriptional programs coupled to cell-cycle control. The presence of neural-development terms (forebrain development, neural tube closure) and multicellular organism development further supports a developmental theme. A few terms about metabolism and stress (glucose metabolic process, cellular response to cadmium) appear as background cellular context, but do not define the cluster as a metabolic module. Therefore the label reflects the central link between transcriptional regulation and mitosis in a developmental setting.","confidence":"Medium","size":19,"edges":17,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0045736","count":6},{"id":"GO:0034501","count":6},{"id":"GO:0006006","count":5}]},{"hash":"718683698084330628","title":"MAPK signaling and immune response","description":"The top GO terms highlight MAPK cascades (p38 and ERK) and DNA-templated transcription, with stimuli-responsive signals such as GM-CSF and PMA, pointing to a cluster of proteins involved in MAPK-driven signaling that leads to transcriptional changes and immune-related responses. While other terms like neutrophil clearance and axon regeneration appear, the shared MAPK axis provides the strongest, cohesive theme for this cluster.","confidence":"Medium","size":19,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0038066","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0097011","count":2},{"id":"GO:1904628","count":2}]},{"hash":"1934327548517184262","title":"Diverse Membrane Transporters (Sugars and Ions)","description":"The top GO terms are largely about transmembrane transport for various substrates, including arabinose, galactose, sialic acid, nitrate, nitrite, phosphate, and 4-hydroxyphenylacetate, suggesting a cluster of proteins involved in moving nutrients and ions across membranes. The ribosomal export term appears as an outlier, but the predominant theme is membrane transport activity across diverse substrates, justifying a transporter-focused label.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0042128","count":1},{"id":"GO:0042891","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0015751","count":1}]},{"hash":"2044493310879031714","title":"Neuronal development and synaptic regulation","description":"The top GO terms cluster around neural development (dendrite morphogenesis, striatum development) and synaptic signaling (negative regulation of excitatory postsynaptic potential), with a transcriptional program and protein interactions linking to neuronal function. Some nucleotide metabolism terms appear, but the dominant theme is neural development and synaptic modulation.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0048813","count":4},{"id":"GO:0006541","count":4},{"id":"GO:0019835","count":4},{"id":"GO:0021756","count":4}]},{"hash":"791887183803339808","title":"Unknown","description":"Top GO terms are highly diverse, spanning insulin secretion, retinal cone development, microtubule nucleation, Fc-epsilon receptor signaling, negative regulation of miRNA processing, regulation of heart contraction, fast/slow muscle fiber transitions, myosin II filament assembly, and polysaccharide catabolic processes. With no single dominant function linking these terms and only one protein per term, there is no coherent shared theme for the cluster. Therefore, Unknown with None confidence. ","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":1},{"id":"GO:0046549","count":1},{"id":"GO:0007020","count":1},{"id":"GO:0038095","count":1},{"id":"GO:1901841","count":1}]},{"hash":"1908202793073065887","title":"Golgi\u2013ER vesicle trafficking and endocytosis","description":"This cluster is enriched for GO terms centered on endocytosis and vesicle transport along the secretory pathway\u2014especially retrograde Golgi-to-ER and ER-to-Golgi transport, as well as related processes like Golgi inheritance and synaptic vesicle trafficking. While pigmentation and locomotion terms appear, the dominant pattern ties to intracellular vesicle movement and membrane trafficking within the Golgi-ER-endosome axis.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":3},{"id":"GO:0006623","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0048313","count":2}]},{"hash":"2055631147431805283","title":"Unknown","description":"The top terms span a wide and unrelated set of functions (tRNA aminoacylation, various signaling pathways, plant-specific responses, and miscellaneous processes) with no clear shared theme or cohesive pathway, and there are no edges among the proteins, suggesting no single responsible function for the cluster. Therefore a single, descriptive label cannot be assigned beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060548","count":1},{"id":"GO:0071277","count":1},{"id":"GO:0080148","count":1},{"id":"GO:0038128","count":1},{"id":"GO:0090332","count":1}]},{"hash":"1039110236575246540","title":"Neural and Eye Development","description":"This cluster is driven by terms tied to neural system formation and visual/brain development, including retina development, forebrain/brain development, and neural tube closure, suggesting a cohesive developmental program in neural and eye tissues. While there are some unrelated ribosomal RNA maturation terms, the dominant theme is neural/eye development, supporting a concise label focused on brain and retina formation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0030900","count":2}]},{"hash":"47953691995129436","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001162","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0032212","count":2}]},{"hash":"934371523839021696","title":"Unknown","description":"The top terms span ribosome quality control, apoptosis signaling, transcription regulation, metabolism, endosome size regulation, and synaptic transmission, with no single coherent function tying all proteins together. Therefore there is no clear shared theme to name the cluster; label is Unknown with None confidence.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990116","count":1},{"id":"GO:1902167","count":1},{"id":"GO:0072344","count":1},{"id":"GO:0018937","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1757691985244565251","title":"Ribosome biogenesis and translation","description":"Dominant GO terms center on translation and ribosome biogenesis, including cytoplasmic and mitochondrial translation, ribosomal subunit assembly, rRNA maturation, and translation termination. This pattern indicates a protein cluster focused on ribosome production and protein synthesis, with some related regulatory processes present.","confidence":"High","size":18,"edges":137,"triangles":666,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0042254","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0032543","count":2}]},{"hash":"749428211898063847","title":"ER Stress\u2013Driven RNA Modification and Translation","description":"This cluster centers on proteins involved in the unfolded protein response and ER stress-related translation control (GO terms for response to unfolded protein, positive regulation of translation initiation in response to ER stress) and RNA modification processes (pseudouridine synthesis of rRNA/tRNA). While there are accompanying terms related to DNA replication/chromatin assembly and meiosis that may reflect multifunctional proteins or annotation noise, the strongest pattern ties ER stress signaling to RNA modification and translation regulation.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0000455","count":1}]},{"hash":"1255468171221200077","title":"Plant Hormone Signaling and Growth Regulation","description":"This cluster centers on plant hormone responses (salicylic, jasmonic, and abscisic acids) and regulation of growth (seed and root meristem), with additional hints from chromatin-related processes (heterochromatin formation, histone deacetylation) and defense-related viral processes. This suggests a cohesive theme of how hormone signaling interfaces with growth regulation and chromatin-level gene control during plant development and defense. Confidence: Medium","confidence":"","size":18,"edges":23,"triangles":14,"max_degree":10,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1905778","count":4},{"id":"GO:1903086","count":4},{"id":"GO:0080113","count":4},{"id":"GO:0035390","count":4},{"id":"GO:0010082","count":4}]},{"hash":"1343643114423581156","title":"Developmental ECM remodeling and hair cell differentiation","description":"The top GO terms point to embryonic organ development, extracellular matrix organization, and hair cell differentiation, suggesting a developmental and tissue-remodeling role. While there are also core cellular processes (transcription, translation, DNA replication, and repair), the strongest signals cluster around development and ECM dynamics, including hair cell differentiation. This justifies a label centered on developmental extracellular matrix remodeling with a focus on sensory cell differentiation.","confidence":"Medium","size":18,"edges":67,"triangles":155,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030198","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0048568","count":3},{"id":"GO:0035315","count":3}]},{"hash":"1058371310407426521","title":"RNA splicing regulation in development","description":"This cluster is enriched for spliceosome and RNA processing activities (GO:0031047, GO:0000388, GO:0048026) and regulatory ncRNA-mediated gene silencing, pointing to a shared role in RNA maturation and gene expression control. The presence of embryonic development terms (mesoderm formation, cranial skeleton morphogenesis) suggests these RNA-processing proteins also function in developmental regulation. A DNA replication term is present but less central, and stress granule localization indicates involvement in RNA storage/translation control under stress.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":5},{"id":"GO:1903608","count":4},{"id":"GO:1990416","count":4},{"id":"GO:0031047","count":4}]},{"hash":"387456910701096045","title":"Glutamatergic synapse assembly and transmission","description":"The top GO terms cluster around glutamatergic neurotransmission and synapse organization, including AMPA receptor activity, NMDA receptor clustering, and synaptic transmission, with associative learning supporting a neural signaling theme. Developmental and adhesion terms may reflect pleiotropic roles but do not override the central synaptic function. ","confidence":"High","size":18,"edges":126,"triangles":467,"max_degree":16,"top_function":"wound healing","top_go_terms":[{"id":"GO:0090004","count":3},{"id":"GO:2000969","count":3},{"id":"GO:0008306","count":3},{"id":"GO:0007508","count":3},{"id":"GO:0035001","count":3}]},{"hash":"234013751098240333","title":"RNA transcription and ribosome biogenesis","description":"This cluster is dominated by GO terms for transcription by RNA polymerase I, II, and III, RNA-templated transcription, tRNA transcription by Pol III, transcription elongation and termination by Pol III, and ribosome biogenesis, pointing to nucleolar transcription and ribosome assembly as the core theme. Peripheral terms like retrograde ER-to-cytosol transport and development are present but do not redefine the main function.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006385","count":1},{"id":"GO:0006360","count":1}]},{"hash":"2153436859377792500","title":"Metabolic Biosynthesis and Catabolism","description":"This cluster centers on enzymes involved in various metabolism-related processes, including biosynthesis of biotin, menaquinone, and antibiotics, alongside catabolic pathways such as stilbene and phosphatidylserine degradation, plus participation in central metabolism like the TCA cycle. The mix of biosynthetic and catabolic GO terms suggests a module focused on small-molecule metabolism, with some links to growth-related processes (e.g., cell division). Overall, it reflects a metabolism-centric cluster with both construction and breakdown activities.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006099","count":3}]},{"hash":"460419826321621267","title":"Drosophila oocyte axis specification and mRNA localization","description":"The cluster is anchored by oocyte polarity signals, including oskar and bicoid mRNA localization and axis specification, indicating a Drosophila oocyte polarity module. Additional terms about ER-Golgi vesicle transport and regulation of receptor localization to synapse point to broader trafficking and receptor localization roles that complement polarity-related localization.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903743","count":1},{"id":"GO:0030722","count":1},{"id":"GO:1902684","count":1},{"id":"GO:0007120","count":1},{"id":"GO:2000311","count":1}]},{"hash":"2288079972005840256","title":"RNA Transcription and Ribosome Biogenesis","description":"This cluster is mainly enriched for GO terms related to RNA transcription by RNA polymerases I, II, and III, including transcription, transcription elongation, termination, and tRNA transcription, plus ribosome biogenesis. Together these terms point to proteins involved in fundamental nuclear gene expression and ribosome assembly processes. A few outlier terms like axonogenesis and meiosis II cytokinesis are included but do not define the core function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":1},{"id":"GO:0015914","count":1},{"id":"GO:0007111","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0006385","count":1}]},{"hash":"119292898246401635","title":"Sugar-nucleotide and polysaccharide biosynthesis","description":"This cluster centers on biosynthetic processes for nucleotide sugars (e.g., UDP-glucose, GDP-mannose, UDP-N-acetylglucosamine, dTDP-rhamnose) and various polysaccharides (glycogen, starch, extracellular polysaccharides, LPS core), suggesting a coherent function in sugar nucleotide production and polysaccharide assembly/cell wall biosynthesis.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006011","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0019252","count":1},{"id":"GO:0019305","count":1},{"id":"GO:0045226","count":1}]},{"hash":"1311749861479637108","title":"Stress-Responsive Translation and Ribosome Biogenesis","description":"The top GO terms center on translation and ribosome assembly (translation, ribosome biogenesis, formation of the translation preinitiation complex) and on regulation of translation initiation in response to stress (stress-related regulation of initiation, cellular response to amino acid starvation, ER stress). This suggests a cluster of proteins involved in protein synthesis machinery and its modulation under stress conditions.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0006413","count":2},{"id":"GO:0032057","count":1},{"id":"GO:1905098","count":1}]},{"hash":"1710472257441344505","title":"DNA replication and cell cycle","description":"The most represented GO terms are DNA replication, leading strand elongation, and cell division, indicating a core theme around genome duplication and cell cycle progression. Several other terms reference mitochondrial protein import and processing, ER polarization, and vesicle formation, which may reflect dual-localized proteins or broader housekeeping roles. Overall, the dominant signal points to DNA replication/cell cycle biology, with additional mitochondria-associated and protein handling functions.","confidence":"Medium","size":17,"edges":10,"triangles":3,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006272","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0045041","count":4},{"id":"GO:0030420","count":4}]},{"hash":"760930204793908612","title":"Ribosome Biogenesis and tRNA Processing","description":"This cluster is dominated by GO terms tied to the translation machinery and ribosome assembly: cytoplasmic translation, ribosomal small subunit biogenesis, threonyl-tRNA aminoacylation, and tRNA modification, suggesting a core function in ribosome biogenesis and protein synthesis. Other terms like iron transport or stress responses appear peripheral to this main theme, reinforcing the translation-centric interpretation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":1},{"id":"GO:0046685","count":1},{"id":"GO:0052046","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0002181","count":1}]},{"hash":"1366483381666443009","title":"Vacuolar trafficking and ion homeostasis","description":"This cluster centers on vacuole-related processes (vacuolar acidification, vacuole organization, protein targeting to vacuole) with supporting proton and ion transport terms, suggesting a cohesive role in vacuolar function and ion balance, despite a few outlier terms.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0015991","count":1}]},{"hash":"1664373769509246470","title":"Cytoskeletal Assembly in Muscle and Neuronal Development","description":"The top GO terms center on cytoskeletal processes: tubulin complex assembly, sarcomere organization, and skeletal muscle thin filament assembly, plus cell polarity and shape maintenance. Mitochondrial inheritance often relies on microtubule transport, while phagocytosis also depends on actin remodeling, linking these functions to cytoskeletal dynamics relevant to muscle structure and neuronal development (substantia nigra development). Overall, the cluster likely groups proteins involved in cytoskeletal organization that shape muscle and neural differentiation.","confidence":"Medium","size":17,"edges":109,"triangles":355,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":2},{"id":"GO:0010628","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0007021","count":2}]},{"hash":"2139048191682631121","title":"Gametogenesis-linked chromatin regulation","description":"The terms cluster around germ cell development processes (spermatogenesis, oogenesis, vitellogenesis, fertilization) and chromatin regulation/heterochromatin formation (subtelomeric and silent mating-type loci, histone methylation control), suggesting a set of proteins involved in coordinating chromatin state during gametogenesis. An outlier term (innate immune response) appears minor and unlikely to define the core function.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0031509","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0007296","count":1}]},{"hash":"1101811744564024913","title":"Redox homeostasis and transcription regulation","description":"Top GO signals emphasize redox processes and detoxification, coupled with transcriptional control by RNA polymerase II and DNA-templated transcription, indicating a cluster linked to redox-regulated transcription; a few metabolic and developmental terms appear less cohesive.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1069126425146086643","title":"Neural development and dendrite morphogenesis","description":"The top GO terms point to brain development and neuronal morphology, with references to hippocampus and substantia nigra development and dendrite morphogenesis, suggesting the cluster centers on neuronal development and dendritic growth. Other terms like cell cycle and innate immune response appear but are likely ancillary rather than the cluster's primary theme.","confidence":"High","size":17,"edges":12,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0032298","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0031647","count":3}]},{"hash":"1133019990244013418","title":"Endosome-to-lysosome transport and receptor cycling","description":"These terms cluster around vesicle trafficking and receptor recycling, including Golgi-to-lysosome transport, clathrin-coated vesicle cargo loading, and neurotransmitter receptor transport/internalization, plus melanosome organization which ties to lysosome-related organelles. A few terms pertain to nuclear processes (DNA replication regulation, meiosis, chromatin formation), likely annotation noise rather than core features of this cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098943","count":1},{"id":"GO:0006275","count":1},{"id":"GO:0032438","count":1},{"id":"GO:0060561","count":1},{"id":"GO:0051307","count":1}]},{"hash":"2053404842867371987","title":"General transcription initiation machinery","description":"This cluster is dominated by GO terms related to DNA-templated transcription and transcription initiation at both RNA polymerase II and III promoters, with related terms for promoter binding and start-site selection. The consistent theme across multiple initiation steps suggests these proteins function together as general transcription initiation machinery rather than a pathway-specific process.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070893","count":1},{"id":"GO:0050434","count":1},{"id":"GO:0006384","count":1},{"id":"GO:0006355","count":1}]},{"hash":"896460787959864010","title":"Synaptic signaling and plasticity regulation","description":"The GO terms cluster around neuronal synaptic function: AMPA receptor activity regulation, receptor localization to the synapse, and modulation of synaptic plasticity, with accompanying calcium signaling regulation and growth signals that influence synaptic strength, suggesting a coherent theme of synaptic signaling and plasticity rather than general metabolism. Some eye development term appears incidental rather than central.","confidence":"Medium","size":17,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0005981","count":2},{"id":"GO:0016242","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0000079","count":2},{"id":"GO:0050849","count":2}]},{"hash":"558289312896500859","title":"Dopaminergic neuron development and synaptic signaling","description":"These proteins show enrichment for neural development and presynaptic functions: axonogenesis, substantia nigra development, GPCR signaling, and regulation of synaptic vesicle exocytosis/endocytosis. While there are some immune and xenobiotic response terms present, the dominant theme aligns with neuronal development and synaptic communication, especially in dopaminergic contexts.","confidence":"Medium","size":17,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0007186","count":3},{"id":"GO:0042088","count":3}]},{"hash":"651162726692388411","title":"Diverse biosynthesis pathways","description":"The top GO terms cover a wide range of biosynthetic and metabolic processes, including retinoid and fatty acid synthesis, pigment and sporopollenin biosynthesis, sugar-nucleotide metabolism, and related catabolic steps, with no single dominant pathway. This points to a group of proteins involved in varied biosynthetic activities rather than one specific function, so a broad label like \"Diverse biosynthesis pathways\" is most representative.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002138","count":1},{"id":"GO:0030497","count":1},{"id":"GO:0009718","count":1},{"id":"GO:0080110","count":1},{"id":"GO:0019305","count":1}]},{"hash":"203957675997622111","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is dominated by GO terms related to ribosome maturation and ribosomal RNA processing (maturation of LSU- and 5.8S rRNA, and export of the large ribosomal subunit from the nucleus), with additional signals of broader RNA processing (mRNA splicing) and a general link to cell division. A few outlier terms (sperm binding, Ig isotype switching) likely reflect annotation noise rather than core function. Overall, the common theme tying these proteins together is involvement in ribosome assembly and RNA maturation processes.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1287768546688610543","title":"DNA Damage Repair and Translation Regulation","description":"This cluster mixes DNA repair and replication-related terms (nucleotide-excision repair, UV-C response, DNA-templated DNA replication) with translation-related terms (translation, regulation of translation, miRNA-mediated silencing by inhibition of translation, rRNA maturation). The common thread appears to be cellular stress responses that coordinate DNA repair with changes in protein synthesis, suggesting a function in stress-induced genome maintenance alongside translational control.","confidence":"Medium","size":16,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0042276","count":1},{"id":"GO:0006297","count":1},{"id":"GO:0071494","count":1},{"id":"GO:0006261","count":1}]},{"hash":"591074365892759657","title":"Ion transport and homeostasis","description":"The proteins co-cluster around transport and regulation of ions (potassium, sodium, protons) and related pH/volume control, as reflected by GO terms for intracellular potassium ion homeostasis, sodium/potassium transport across membranes, vacuolar acidification, and cell volume homeostasis. A cardiac conduction term and salt-stress response further support a unifying theme of membrane potential and ionic balance across tissues. This coherent pattern justifies labeling the cluster as ion transport and homeostasis.","confidence":"High","size":16,"edges":69,"triangles":109,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:1903281","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0086092","count":1}]},{"hash":"261263780936898318","title":"ESCRT/MVB Endosomal Trafficking and Exosomal Secretion","description":"Most top GO terms point to endosomal sorting and vesicle trafficking via the ESCRT/MVB pathway (multivesicular body assembly/sorting, endosome transport), exosomal secretion, and related processes, with several terms about viral budding regulated by ESCRT. A couple of terms (locomotory exploration behavior, glucose-repression of transcription) appear unrelated, likely noise. Overall, the cluster centers on vesicle trafficking and exosome biology.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035641","count":1},{"id":"GO:0000433","count":1},{"id":"GO:1903543","count":1},{"id":"GO:1904669","count":1},{"id":"GO:0010797","count":1}]},{"hash":"965591585086751224","title":"Ribosome biogenesis and rRNA maturation","description":"Enriched for ribosome biogenesis and rRNA processing terms (preribosome assembly, LSU rRNA maturation, ribosome biogenesis, cytoplasmic translation), supported by related chromatin remodeling and stress response terms, suggesting a core function in ribosome production with linked stress-related regulation.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0006289","count":2}]},{"hash":"1821458984903845023","title":"Endosomal Sorting and Vacuolar Transport","description":"The cluster shows strong enrichment for endocytosis and intracellular trafficking terms, including early endosome to Golgi, Golgi to endosome, multivesicular body sorting, and transport to vacuoles, pointing to a cohesive role in endosomal sorting and vacuolar delivery within the endomembrane system (with a few peripheral terms as noise).","confidence":"High","size":16,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0015032","count":1},{"id":"GO:0071985","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0009997","count":1}]},{"hash":"1724309180742649926","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":1},{"id":"GO:1904574","count":1},{"id":"GO:1903241","count":1},{"id":"GO:0048701","count":1},{"id":"GO:0006283","count":1}]},{"hash":"1021884894454694809","title":"Unknown","description":"The top GO terms span both developmental processes (embryonic cranial skeleton morphogenesis) and broad nuclear/stress-related functions (DNA replication, DNA topology changes, rRNA maturation, SOS and antibiotic responses, stress granule localization), with some terms being obsolete. There isn\u2019t a clear, single shared function linking all proteins in this cluster, so a concise, representative label cannot be determined beyond Unknown.","confidence":"","size":15,"edges":28,"triangles":20,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0009432","count":4},{"id":"GO:0046677","count":4},{"id":"GO:1903608","count":3}]},{"hash":"1410074626288474608","title":"Cell growth and translation machinery","description":"The top GO terms cluster around cell cycle and division (cell cycle, cell division, cell septum assembly) alongside translation-related processes (cytoplasmic translation, ribosomal subunit biogenesis, tRNA modification, threonyl-tRNA aminoacylation). Iron ion transport and homeostasis appear as supporting metabolic context. Together these suggest a theme of growth-related cellular activity, encompassing both division and protein synthesis, with iron metabolism as a peripheral but relevant factor.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0090529","count":1},{"id":"GO:0002181","count":1}]},{"hash":"449738309965217354","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0034475","count":4},{"id":"GO:0034476","count":4},{"id":"GO:0071042","count":4}]},{"hash":"1132069309947460397","title":"Neuronal vesicle trafficking and behavior","description":"The cluster\u2019s GO terms prominently point to neuronal processes involving vesicle endocytosis and membrane organization (e.g., positive regulation of synaptic vesicle endocytosis, pinocytosis, membrane raft organization) and to neuronal behaviors (adult locomotory behavior, grooming, associative learning). This suggests the proteins collectively participate in neuronal vesicle trafficking and regulation with links to neural function and behavior.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900244","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0002084","count":1},{"id":"GO:0032429","count":1},{"id":"GO:0007042","count":1}]},{"hash":"1500260696825293407","title":"Peptidyl and rRNA methylation","description":"A unifying theme in this cluster is methylation: multiple GO terms describe peptidyl methylations (arginine, lysine, N-terminal glycine) and rRNA methylation, suggesting involvement of methyltransferases or substrates of methylation. Additional terms about sterol/phosphatidylcholine biosynthesis imply lipid methylation links, while a few stress/immune response terms are present but secondary. Overall, the cluster centers on methylation-related processes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":1},{"id":"GO:0016126","count":1},{"id":"GO:0018364","count":1},{"id":"GO:0019919","count":1},{"id":"GO:0031167","count":1}]},{"hash":"742756649895205780","title":"Unknown","description":"The top GO terms cover diverse, largely unrelated processes (chromatin remodeling, transcription regulation under stress, development, immune differentiation) and many entries are obsolete, so there is no cohesive biological theme to name the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031496","count":1},{"id":"GO:0031452","count":1},{"id":"GO:0006990","count":1},{"id":"GO:0060358","count":1},{"id":"GO:0061412","count":1}]},{"hash":"1492184949958774534","title":"Immune regulation and lymphoid development","description":"This cluster is dominated by immune-related terms, including positive regulation of canonical NF-kappaB signaling and IL-17\u2013mediated signaling, as well as negative regulation of activated T cell proliferation and germinal center formation, and spleen development. Together they point to regulation of immune responses and lymphoid tissue development, with a minor outlier term (thiamine biosynthesis) likely representing annotation noise or secondary function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0090116","count":1},{"id":"GO:0050999","count":1},{"id":"GO:0048536","count":1},{"id":"GO:0007014","count":1}]},{"hash":"2203437645108099082","title":"Unknown","description":"The top GO terms are diverse: ubiquitin-related catabolic processes, muscle/sarcomere organization, germinal center formation, circadian rhythm regulation, plant glucosinolate catabolism, viral latency release, and other unrelated categories. There is no single shared function evident across the 15 proteins, and the network has no edges or cohesion to support a cohesive label; therefore Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031397","count":1},{"id":"GO:0072156","count":1},{"id":"GO:0002467","count":1},{"id":"GO:0019762","count":1},{"id":"GO:0045214","count":1}]},{"hash":"2252589391289091615","title":"Unknown","description":"The top GO terms are very heterogeneous (cilium assembly, brain development, ER-Golgi transport, rRNA maturation, stress responses), with no clear shared function tying the 15 proteins together, and the cluster shows no edges or triangles, suggesting no cohesive module. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":2},{"id":"GO:2001162","count":1},{"id":"GO:0072432","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0000466","count":1}]},{"hash":"432418366052187605","title":"Carbohydrate and secondary metabolite biosynthesis","description":"The GO terms point to a broad set of biosynthetic activities, including galactose and rhamnose sugar biosynthesis, GDP/UDP-sugar metabolism, SAM biosynthesis, and plant- or polymer-specific biosynthesis such as anthocyanin, sporopollenin, and PHB. This indicates a general theme of biosynthesis for carbohydrates and related metabolites rather than a single precise pathway, justifying a broad \u201cbiosynthesis\u201d label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019388","count":1},{"id":"GO:0009718","count":1},{"id":"GO:0080110","count":1},{"id":"GO:0010253","count":1},{"id":"GO:0019305","count":1}]},{"hash":"1306215742942815964","title":"Developmental cell cycle and DNA replication","description":"The cluster is dominated by GO terms tied to DNA replication, mitotic cell cycle, centrosome cycle, and telomere maintenance, indicating a core function in cell division and genome stability. Developmental processes such as embryonic cranial skeleton morphogenesis and angiogenesis point to a proliferative, tissue-development context where these cell-cycle regulators drive growth. A few terms like response to cocaine and excitatory postsynaptic potential may reflect broader neuronal-related annotations or cross-talk, but the common thread is cells proliferating and maintaining their genome during development.","confidence":"Medium","size":14,"edges":21,"triangles":13,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0048701","count":8},{"id":"GO:0001525","count":8},{"id":"GO:0007098","count":7},{"id":"GO:0010571","count":7}]},{"hash":"1593917019168519125","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to translation, ribosome biogenesis, and ribosomal subunit assembly, with multiple entries for translational fidelity regulation. This strongly suggests the proteins are involved in ribosome production and protein synthesis. Some unrelated terms may reflect annotation noise, but the core signal is clear.","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000027","count":3},{"id":"GO:0007338","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0042254","count":2}]},{"hash":"278606608583004775","title":"Endosomal sorting and autophagy","description":"The top GO terms cluster around vesicle trafficking and degradation: multivesicular body (MVB) sorting, ubiquitin-dependent protein catabolic process via MVB, and the Cvt pathway, all core to endosomal sorting and autophagy. Related terms like melanosome transport and pigment granule organization fit within vesicle transport processes, supporting a unifying theme despite some organism-specific development terms appearing. Overall, the strongest cohesive signal is endosomal sorting and autophagic pathways.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051877","count":1},{"id":"GO:0000433","count":1},{"id":"GO:1904669","count":1},{"id":"GO:0048749","count":1},{"id":"GO:0072116","count":1}]},{"hash":"1920898907667128066","title":"Ubiquitin-Dependent NF-\u03baB Signaling and Cell Death","description":"The proteins are enriched for ubiquitination-related processes (protein ubiquitination, ubiquitin-dependent catabolic process, K6-linked ubiquitination) and for NF-\u03baB pathway regulation (I-\u03baB phosphorylation, NF-\u03baB-inducing kinase activity) with links to apoptosis and necroptosis, suggesting a role in ubiquitin-mediated immune signaling and cell fate control; immune-related terms like V(D)J recombination and vitamin D response may reflect broader immune regulation context.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0033151","count":2},{"id":"GO:0007250","count":2}]},{"hash":"1113876669024788154","title":"Neuronal microtubule dynamics and spindle organization","description":"The GO terms cluster around microtubule-based processes, including plus- and minus-end dynamics, spindle assembly and orientation, centrosome separation, and nuclear migration along microtubules, indicating microtubule cytoskeleton regulation during cell division. The presence of cerebellar granular layer structural organization and neuron projection maintenance further ties these processes to neuronal structure and maintenance. This combination suggests a cohesive theme of microtubule-driven organization in neurons, spanning both structural maintenance and mitotic/spindle activities.","confidence":"High","size":14,"edges":50,"triangles":109,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0021685","count":10},{"id":"GO:1990942","count":10},{"id":"GO:0030473","count":10},{"id":"GO:0001560","count":10},{"id":"GO:1990535","count":10}]},{"hash":"1573824914415085708","title":"Mitotic Cell Cycle and Transcription Regulation","description":"The top GO terms cluster around cell division, mitotic cell cycle, chromosome condensation (histone H3-S10 phosphorylation), and DNA-templated transcription, with additional signals from Wnt signaling and protein processing/trafficking and a touch of stress responses, suggesting a coordinated focus on cell proliferation and transcriptional control.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0030968","count":2},{"id":"GO:0060070","count":2},{"id":"GO:0035494","count":2},{"id":"GO:0033197","count":1}]},{"hash":"1864298077249498039","title":"Ribosome Biogenesis and rRNA Maturation","description":"This cluster is driven by processes in ribosome assembly and RNA maturation: preribosome large subunit assembly, maturation of LSU and 5.8S rRNA, and rRNA base methylation, with supporting signals from translation and mRNA capping terms. A couple of virus-entry terms appear but do not shape the main function; the core signal points to ribosome production and RNA processing.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:1902626","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0097310","count":1},{"id":"GO:0006370","count":1}]},{"hash":"252422689583079614","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007099","count":2},{"id":"GO:0051298","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0046330","count":2}]},{"hash":"448969742896698319","title":"NF-kappaB/TNF signaling and apoptosis regulation","description":"The top GO terms are dominated by TNF-mediated signaling and NF-kappaB activation, including I-kappaB phosphorylation and ubiquitination, and they also encompass regulation of apoptosis. While a couple terms touch chromatin modification and V(D)J recombination, the shared theme centers on TNF/NF-kappaB signaling and cell survival/apoptotic control, suggesting this cluster reflects immune signaling and survival decisions. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":5},{"id":"GO:0090073","count":5},{"id":"GO:0033151","count":5},{"id":"GO:0033209","count":5},{"id":"GO:0007250","count":5}]},{"hash":"1680744244992235597","title":"Vacuolar amino acid transport","description":"The top GO terms point to transmembrane transport of various amino acids into and out of the vacuole (lysine, histidine, tyrosine, asparagine, proline, glutamate, serine, glutamine, etc.), with occasional regulatory terms. This suggests the proteins function as vacuolar amino acid transporters or regulators of amino acid movement across the vacuolar membrane. The consistency across multiple amino acid substrates supports a cohesive theme rather than unrelated functions.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0089707","count":2},{"id":"GO:0090513","count":2},{"id":"GO:0089708","count":2},{"id":"GO:0090514","count":2},{"id":"GO:0006867","count":2}]},{"hash":"1925771770238552950","title":"Unknown","description":"The terms span embryonic development, meiotic processes, transcription, and chromatin regulation with no single overlapping function, and there are no edges to connect them into a coherent theme. Given this heterogeneity, a meaningful, specific cluster name cannot be inferred beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008595","count":1},{"id":"GO:0006311","count":1},{"id":"GO:0060173","count":1},{"id":"GO:0045144","count":1},{"id":"GO:0006366","count":1}]},{"hash":"1863513166092625759","title":"ER-Golgi Trafficking and Stress Response","description":"This cluster is driven by terms related to endoplasmic reticulum processes and vesicle trafficking (ER to Golgi transport, SNARE complex disassembly) as well as cellular stress responses (ER stress, oxidative stress, apoptosis regulation). While a couple of terms (DNA replication, viral genome replication) are less cohesive with the trafficking/stress theme, the strongest shared signal centers on ER-Golgi trafficking and stress signaling, justifying a label focused on trafficking and stress response.","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0034976","count":2},{"id":"GO:0051301","count":2}]},{"hash":"319454870118989410","title":"Cell cycle and gene expression regulation","description":"This cluster centers on nuclear processes and growth control: DNA replication, DNA-templated transcription, mRNA processing, and regulation of apoptosis and cell proliferation, with some terms touching on developmental signaling and neuronal guidance. The common theme is coordination of gene expression and cell cycle progression, with a thread of signaling that can influence development and differentiation.","confidence":"High","size":13,"edges":19,"triangles":9,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0007100","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0043065","count":7},{"id":"GO:0016477","count":7}]},{"hash":"1269469932210113258","title":"Multisystem Developmental Signaling","description":"Top GO terms span mitotic cycle, angiogenesis, neural activity (excitatory postsynaptic potentials, visual perception), glial differentiation, myoblast fusion, and hormone signaling (insulin receptor, abscisic acid). This breadth points to a general developmental signaling theme rather than a specific pathway, suggesting the cluster captures broad signaling processes that guide development across multiple tissues and neural functions.","confidence":"Medium","size":13,"edges":52,"triangles":99,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0001525","count":6},{"id":"GO:0060079","count":6},{"id":"GO:0008286","count":6},{"id":"GO:0043065","count":6}]},{"hash":"537078624645146168","title":"Unknown","description":"The listed GO terms cover immune differentiation, signaling regulation, amino acid transport, fertilization-related cytogamy, mitochondrial depolarization, hair follicle placode formation, ER stress response, nuclear transport, neuromuscular balance, and brain development. The lack of a cohesive biological theme across these terms indicates no clear, common function tying the cluster together.","confidence":"","size":13,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030225","count":1},{"id":"GO:1904515","count":1},{"id":"GO:0010963","count":1},{"id":"GO:0000755","count":1},{"id":"GO:0051900","count":1}]},{"hash":"545616769497182035","title":"Chromatin Organization in Plants","description":"The GO terms predominantly point to chromatin structure and epigenetic regulation (nuclear speck organization, subtelomeric heterochromatin formation, histone deacetylation), with additional terms related to plant development (seed growth, root meristem growth) and defense signaling (salicylic and jasmonic acid responses). This suggests a cohesive theme of chromatin regulation in a plant context, potentially linking chromatin state to growth and stress responses.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035063","count":1},{"id":"GO:1905778","count":1},{"id":"GO:0035092","count":1},{"id":"GO:1903086","count":1},{"id":"GO:0080113","count":1}]},{"hash":"386759597299466272","title":"Unknown","description":"The top GO terms are too diverse, spanning ubiquitin ligase regulation, SREBP signaling, translation initiation, RNA processing, DNA damage response, trafficking, and development, with no single cohesive function linking the cluster.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904668","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0001731","count":2},{"id":"GO:2001162","count":1},{"id":"GO:0072432","count":1}]},{"hash":"1422652611824880096","title":"Ribosome biogenesis and rRNA processing","description":"These proteins show a strong enrichment for ribosome biogenesis, preribosome assembly, rRNA maturation (LSU/SSU), and snoRNP assembly, all core nucleolar functions. While some terms relate to DNA replication, SOS response, and viral replication, the dominant, coherent theme is the production and maturation of ribosomes and associated RNA processing factors. Confidence: High","confidence":"","size":12,"edges":63,"triangles":191,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1902626","count":3}]},{"hash":"477909321030072619","title":"Synaptic vesicle trafficking and membrane delivery","description":"The proteins show enrichment for vesicle fusion and membrane localization processes, including presynaptic vesicle fusion, postsynaptic receptor insertion, and long-term potentiation, alongside related intracellular trafficking (Golgi-to-vacuole, Cvt pathway, and vacuole fusion). This points to a cohesive theme of vesicle transport and membrane protein delivery in synaptic contexts, with supporting general trafficking roles. ","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903078","count":2},{"id":"GO:1903575","count":2},{"id":"GO:0031629","count":2},{"id":"GO:0010811","count":2},{"id":"GO:0098967","count":2}]},{"hash":"2104279921857022280","title":"Unknown","description":"The terms include neural development (axonogenesis, Schwann cell development, long-term potentiation, visual perception, heart development) as well as plant signaling (abscisic acid-activated signaling) and bacterial/metabolic terms (menaquinone biosynthetic process, bioluminescence), with no single unifying function or pathway evident across the cluster. Therefore no coherent theme can be assigned.","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008218","count":4},{"id":"GO:0009234","count":3},{"id":"GO:0007121","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0009738","count":3}]},{"hash":"1737614835227718887","title":"Bacterial cell wall synthesis and division","description":"The top GO terms center on peptidoglycan biosynthesis/turnover, cell wall organization, capsule polysaccharide biosynthesis, and regulation of cell shape, along with cell cycle and cell division. This points to a cohesive function set focused on building and remodeling the bacterial cell envelope and coordinating growth/division. Some metabolism terms (one-carbon/folate pathways) appear secondary to growth needs but do not override the envelope-centric theme. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009254","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0045227","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0007049","count":1}]},{"hash":"1059065251213271143","title":"Unknown","description":"There are no shared GO terms, no edges or triangles, and a max degree of 0 among the 12 proteins, so a coherent functional theme cannot be inferred from the data provided.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2006201290922539218","title":"Unknown","description":"The terms span diverse processes across organisms (antibiotic and wybutosine biosynthesis, ERBB2 signaling, stomatal closure, dendrite extension, transcription regulation) with no clear common function or pathway linking the proteins, and the cluster has no edges to suggest cohesion. Therefore there is no coherent theme to name the cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0060548","count":1},{"id":"GO:0071277","count":1},{"id":"GO:0080148","count":1}]},{"hash":"486437721260161828","title":"Plant Growth Regulation and Hormone Response","description":"Most of the top GO terms relate to regulation of growth processes (seed growth, root meristem growth) and responses to key phytohormones (salicylic acid, jasmonic acid, abscisic acid). While a few terms appear obscure or obsolete, the recurring theme centers on controlling development via hormone signaling, with additional chromatin-related terms suggesting regulatory control mechanisms.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1905778","count":2},{"id":"GO:1903086","count":2},{"id":"GO:0080113","count":2},{"id":"GO:0035390","count":2},{"id":"GO:0010082","count":2}]},{"hash":"1006759309845569768","title":"Plant Transcription Regulation & Chromatin Remodeling","description":"The top GO terms strongly point to transcription control (DNA-templated transcription, negative regulation of transcription by RNA Pol II) and chromatin-associated processes (histone modification, nucleosome mobilization, histone deacetylation). Several plant-specific terms (seed coat development, trichome differentiation) further suggest a plant-context transcriptional regulation cluster, even though some terms are obsolete. Overall, the proteins appear to function in controlling gene expression via chromatin state.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0061085","count":1},{"id":"GO:2000653","count":1},{"id":"GO:0042766","count":1}]},{"hash":"81486958002645349","title":"Ribosome biogenesis and translation machinery","description":"The cluster centers on ribosome production and translation, with strong signals for cytoplasmic translation, ribosome biogenesis, and nucleolar transcription of rRNA and tRNA. While a few terms touch on RNA transcription and chromatin regulation, the predominant theme ties to ribosome assembly and protein synthesis.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0001172","count":1}]},{"hash":"1615038209715670522","title":"Cell Cycle and DNA Replication","description":"The most represented terms are mitotic cell cycle, DNA replication, and mitotic sister chromatid segregation, which together point to cell division as the cluster\u2019s core theme. Additional terms such as maturation of 5.8S rRNA and ER-to-Golgi transport appear but are less central to this theme, while forebrain development and multicellular organism development suggest broader developmental roles. Overall, the cluster seems best described as a cell-cycle/DNA-replication module with some peripheral processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000466","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1097931717571598989","title":"Epithelial adhesion and morphogenesis","description":"This cluster is dominated by terms such as hemidesmosome assembly, substrate adhesion-dependent cell spreading, and calcium-independent cell-matrix adhesion, plus epithelial apoptotic processes in palatal shelf morphogenesis, indicating a cohesive theme of epithelial cell adhesion and tissue morphogenesis. Some surrounding terms (zinc ion transport, sialic acid and LPS biosynthesis) may reflect secondary annotations or multifunctional proteins.","confidence":"High","size":11,"edges":49,"triangles":116,"max_degree":10,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0031581","count":4},{"id":"GO:0051968","count":4},{"id":"GO:0034446","count":4},{"id":"GO:0014909","count":4},{"id":"GO:0007161","count":4}]},{"hash":"1845640379426277128","title":"Neural and Craniofacial Development","description":"The top GO terms cluster around neural development (motor neuron axon guidance, visual learning) and craniofacial skeletal processes (embryonic cranial skeleton morphogenesis, regulation of bone mineralization), suggesting a shared role in shaping neural and facial skeletal structures. Several other terms reflect general cellular processes (DNA replication, mRNA processing, nuclear protein export) that may be common in development-associated proteins but do not override the stronger neural/skeletal theme.","confidence":"Medium","size":11,"edges":14,"triangles":13,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":7},{"id":"GO:0048701","count":5},{"id":"GO:0006260","count":5},{"id":"GO:1901196","count":4},{"id":"GO:0006397","count":4}]},{"hash":"790405783468948986","title":"Excitable-tissue signaling and secretion regulation","description":"The top terms span neural plasticity (long-term synaptic potentiation), calcium signaling (calcium channel activity), secretion (insulin release), muscle/heart function (fiber-type transitions, heart contraction), and cellular architecture (Golgi organization, microtubule nucleation), pointing to a broad role in signaling and secretory processes across excitable tissues like brain, heart, and muscle.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:1903358","count":2},{"id":"GO:0035774","count":2},{"id":"GO:0046549","count":2},{"id":"GO:0007020","count":2}]},{"hash":"413538266298726865","title":"Neurodevelopmental transcription and cell cycle regulation","description":"The proteins show strong ties to neural development (forebrain development, neural tube closure), plus core gene expression control (mRNA processing, DNA-templated transcription) and cell cycle activity (mitotic cell cycle, telomere maintenance). The presence of stress-related terms (ER-stress\u2013induced apoptosis, cadmium response) adds a stress-response dimension that complements development and proliferation roles, supporting a cohesive theme of neural development linked to transcriptional regulation and cell cycle control.","confidence":"Medium","size":11,"edges":9,"triangles":7,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006397","count":6},{"id":"GO:0032212","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0030900","count":6},{"id":"GO:0006351","count":6}]},{"hash":"788130658399695047","title":"Ubiquitin-Dependent Protein Degradation","description":"The Go terms show strong enrichment for ubiquitination and proteasomal/ERAD pathways (K48-linked ubiquitination, ubiquitin-dependent protein catabolic process, autoubiquitination, ERAD). Additional items touch on turnover of signaling components (Wnt receptor catabolic process) and broader protein quality control (negative regulation of organ growth and peroxisomal protein import), all of which tie to ubiquitin-mediated degradation and proteostasis. Thus the cluster is best described as ubiquitin-dependent protein degradation.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0060816","count":6},{"id":"GO:0030433","count":6},{"id":"GO:1900095","count":6}]},{"hash":"941677303464674557","title":"ER-Golgi trafficking and Wnt secretion","description":"The terms cluster around ER-to-Golgi transport and Golgi organization (COPI vesicle budding, ER exit regulation, Golgi ribbon formation) and secretion of Wnt proteins, pointing to a cohesive module of vesicle trafficking and secretion that also influences morphogen signaling; the developmental GO terms likely reflect broader organismal contexts but do not change the core trafficking theme.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035964","count":2},{"id":"GO:0032525","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0061357","count":2},{"id":"GO:0048042","count":2}]},{"hash":"2070199824824739506","title":"Metal ion transport across membranes","description":"This cluster is strongly characterized by GO terms for zinc, copper, and cadmium ion transmembrane transport, along with calcium ion homeostasis, indicating a cohesive theme of membrane transport and homeostasis of metal ions. While other terms related to carbohydrate and lipid biosynthesis appear, the dominant signal is metal ion transport across membranes, justifying the label.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0071577","count":3},{"id":"GO:0046380","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0019700","count":3},{"id":"GO:0097755","count":3}]},{"hash":"373073982158558310","title":"Genome maintenance and chromatin regulation","description":"This cluster includes terms tied to genome integrity and chromatin control, such as regulation of DNA-templated DNA replication initiation, replication fork protection, chromatin silencing at telomeres, and meiotic recombination nodules, as well as regulation of cell proliferation. These collectively point to a cohesive theme of genome maintenance and chromatin-level regulation during growth and division. A few outliers (root meristem growth, bacteriochlorophyll biosynthesis, ribosomal assembly) may reflect annotation noise or broader cellular context but do not overturn the core theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0030174","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0010082","count":1},{"id":"GO:0030163","count":1}]},{"hash":"1243464678188985990","title":"Developmental growth and cell-cycle regulation","description":"The cluster centers on core growth and division processes (DNA replication, centrosome duplication) and tied gene expression control (mRNA processing, translation regulation, proteasome-related regulation). The inclusion of embryonic skeleton morphogenesis and vascular development terms, plus response to epidermal growth factor and cell-matrix adhesion, suggests a broader theme of developmental growth, tissue morphogenesis, and signaling coordinating cell proliferation with differentiation. Overall, a cohesive label is developmentally linked growth and cell-cycle control.","confidence":"Medium","size":10,"edges":11,"triangles":5,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0048701","count":6},{"id":"GO:0007160","count":6},{"id":"GO:0060716","count":6},{"id":"GO:1901196","count":6}]},{"hash":"875594307299976493","title":"Embryonic Development and Vascular Differentiation","description":"The top GO terms center on developmental processes such as forebrain development and chorionic trophoblast differentiation, along with vascular formation through sprouting angiogenesis and lymphangiogenesis. Additional terms for apoptosis regulation and cell cycle control suggest broader regulatory roles during development. Together these indicate a cluster of proteins involved in embryonic tissue differentiation and vascular (blood/lymphatic) formation, with supporting transcriptional and mRNA stability regulation. Overall, a developmental and vascular differentiation theme is most plausible.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043276","count":2},{"id":"GO:0002040","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0060718","count":2}]},{"hash":"2258597006105915873","title":"Solute transport across the plasma membrane","description":"The cluster is dominated by GO terms related to transport of diverse solutes across the plasma membrane (fructose, arabinose, urate, selenite, hydroxyphenylacetate, etc.), with a few metabolic/regulatory terms as outliers. This suggests a cohesive theme around membrane uptake/transport of small molecules, despite some peripheral functions.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990539","count":1},{"id":"GO:0071332","count":1},{"id":"GO:0042128","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0060731","count":1}]},{"hash":"1845170748446449922","title":"Unknown","description":"The Top Terms are highly heterogeneous, including histone ubiquitination, cell-cycle transcription regulation, neural structure, ion channel regulation, RNA localization, plant hormone biosynthesis, mitotic checkpoint signaling, transcription elongation control, isotype switching, and integrin regulation. With only two edges and no clear unifying function across these terms, there is no coherent theme to label the cluster beyond Unknown.","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070535","count":2},{"id":"GO:0090282","count":1},{"id":"GO:0021685","count":1},{"id":"GO:1905150","count":1},{"id":"GO:0051237","count":1}]},{"hash":"176283103447933638","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":1},{"id":"GO:0006433","count":1},{"id":"GO:0006424","count":1},{"id":"GO:0006425","count":1}]},{"hash":"1616313814984892891","title":"Bacterial central carbon metabolism and biosynthesis","description":"The top GO terms point to core metabolic pathways: glycolysis, the glyoxylate cycle, and metabolism of TCA intermediates like malate and oxaloacetate, alongside NADH-related processes. There are also biosynthetic routes for serine and pyridoxine and a bacterial-specific process for lipopolysaccharide biosynthesis, with a note of regulation via cAMP response. Together these indicate a cluster of proteins involved in central carbon metabolism and associated biosynthetic pathways in bacteria.","confidence":"High","size":10,"edges":28,"triangles":42,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0051591","count":3},{"id":"GO:0009103","count":2},{"id":"GO:0006564","count":2}]},{"hash":"2100584882159233140","title":"Plant Growth, Hormone Signaling, and Chromatin Regulation","description":"The top GO terms point to regulatory roles in plants, including responses to major hormones (salicylic, jasmonic, and abscisic acids), regulation of seed and root growth, and chromatin-level control (heterochromatin formation and histone deacetylation). Although some terms are obsolete, the cluster appears to group proteins involved in coordinating development, stress signaling, and chromatin remodeling.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1905778","count":1},{"id":"GO:1903086","count":1},{"id":"GO:0080113","count":1},{"id":"GO:0035390","count":1},{"id":"GO:0010082","count":1}]},{"hash":"1394223857195042148","title":"Unknown","description":"The Top Terms are very heterogeneous, covering translation, germ-line masculinization, an obsolete MAPK/osmolarity pathway, photosystem adjustments, TGF-beta/SMAD signaling, protein dephosphorylation, nuclear export, and NF-kappaB regulation. There is no coherent unifying function or pathway linking these terms, and several entries are obsolete, so no clear theme emerges for this cluster.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0042006","count":1},{"id":"GO:0000173","count":1},{"id":"GO:0080005","count":1},{"id":"GO:0071560","count":1}]},{"hash":"1379025031007990808","title":"Nucleic acid repair and ribosome biogenesis","description":"This cluster prominently features DNA repair processes (base-excision and nucleotide-excision repair) and ribosome biogenesis, suggesting a growth- and genome-maintenance-related program. Additional terms like depyrimidination and nuclease-related activity support nucleic acid processing. While a couple of terms touch on cell division and a sugar-response, the dominant theme links nucleic acid maintenance with ribosome production.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006284","count":1},{"id":"GO:0045008","count":1}]},{"hash":"1412215621941646908","title":"Diverse membrane transporters","description":"The cluster\u2019s top GO terms center on transporting a wide range of substrates across membranes (heme, very long-chain fatty acids into peroxisomes, long-chain fatty acid import into peroxisomes, daunorubicin, cysteine, thiamine, phospholipids, ceramide, carbohydrates). This suggests a shared function in membrane transport rather than a single substrate class, with peroxisomal import and drug/export activities represented. Overall, the proteins appear to be diverse transport-related proteins rather than a single metabolic enzyme group.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":1},{"id":"GO:0042760","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0043215","count":1},{"id":"GO:0042883","count":1}]},{"hash":"1650577462350088616","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1904574","count":2},{"id":"GO:1903241","count":2},{"id":"GO:0048701","count":2}]},{"hash":"1226893851744252626","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3},{"id":"GO:1902626","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":2}]},{"hash":"294957959346321763","title":"Unknown","description":"The listed GO terms are highly diverse, spanning chromatin regulation, seed and root development, responses to multiple plant hormones (SA, JA, ABA), and viral processes, with no clear unifying function or pathway tying the proteins together. Hence no cohesive label can be confidently assigned.","confidence":"","size":9,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1905778","count":1},{"id":"GO:1903086","count":1},{"id":"GO:0080113","count":1},{"id":"GO:0035390","count":1},{"id":"GO:0010082","count":1}]},{"hash":"1087794486169290624","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0035750","count":1},{"id":"GO:0019634","count":1},{"id":"GO:0016188","count":1}]},{"hash":"749155823065331696","title":"TGF-\u03b2/SMAD and NF-kappaB Signaling Regulation","description":"The cluster is dominated by terms related to modulation of TGF-\u03b2 signaling (TGF-\u03b2 receptor signaling, SMAD-related regulation, cellular response to TGF-\u03b2) and negative regulation of NF-kappaB signaling, with supporting terms about SMAD complex assembly and related phosphorylation control. While a few terms are peripheral (e.g., vacuole fusion, photosystem-related terms), the core pattern points to regulation of growth factor\u2013driven signaling pathways. ","confidence":"Medium","size":9,"edges":11,"triangles":6,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0042006","count":6},{"id":"GO:0000173","count":6},{"id":"GO:0080005","count":6},{"id":"GO:0071560","count":6}]},{"hash":"1763304474406512757","title":"Nuclear DNA replication and transcription machinery","description":"This cluster is enriched for core nuclear processes: DNA replication, DNA-templated transcription, and mRNA processing. These terms indicate the proteins collectively participate in genome expression and maintenance. While there are a few signaling terms (JNK cascade, TORC1 regulation), they are less representative of the main theme, which centers on nuclear gene expression and replication machinery.","confidence":"Medium","size":8,"edges":11,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":3},{"id":"GO:1901196","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0008045","count":2}]},{"hash":"1857998116618611779","title":"Ribosome biogenesis and translation; cell division","description":"The cluster is dominated by translation- and ribosome-related terms (translation, cytoplasmic translation, ribosome biogenesis, ribosomal small subunit biogenesis) with supporting signals for cell cycle and septum assembly, indicating a set of proteins involved in ribosome production and coordination with cell division.","confidence":"Medium","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0006400","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0090529","count":2}]},{"hash":"1771520238651249391","title":"Meiotic Chromosome Cohesion and Segregation","description":"This cluster centers on meiotic cell cycle processes, including meiotic sister chromatid cohesion, spindle elongation, and both meiotic and mitotic chromatid separation, indicating a module devoted to chromosome segregation during meiosis. Regulatory activities such as regulation of catalytic activity and serine dephosphorylation supplement this as a coordinated meiotic control program, with additional notes on protein complex assembly and protein turnover. Overall, the terms point to meiotic chromosome cohesion and segregation plus its regulation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0050790","count":2},{"id":"GO:1903538","count":2},{"id":"GO:0042176","count":2}]},{"hash":"1925738163461164794","title":"Cell Cycle and Genome Maintenance","description":"The cluster's top GO terms cluster around core nuclear processes: mitotic cell cycle, DNA replication, DNA repair, and transcription, with apoptosis also represented. While a few terms (e.g., cerebral cortex development, sperm capacitation) seem less connected and may reflect annotation noise, the dominant themes point to cell division and genome integrity. This justifies a label focused on cell cycle progression and genome maintenance.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0045793","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1594225032826480351","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":24,"triangles":38,"max_degree":7,"top_function":"autophagy","top_go_terms":[{"id":"GO:0006541","count":6},{"id":"GO:0006508","count":4},{"id":"GO:0044210","count":3},{"id":"GO:0019240","count":3},{"id":"GO:0071548","count":3}]},{"hash":"934736181881409200","title":"Retroviral genome replication and latency","description":"The top terms point to core retroviral lifecycle steps: DNA replication, RNA-templated DNA biosynthetic process (reverse transcription), proviral latency establishment, and viral release from the host cell. While a few other terms (protein folding, lipid droplets, UV response) appear ancillary, the dominant signal is retroviral replication and latency, justifying this label.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0009611","count":2},{"id":"GO:0034389","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0006457","count":1}]},{"hash":"812620146574810701","title":"Unknown","description":"The top terms span immune signaling (Fc-epsilon receptor, TRIF-dependent TLR signaling, interferon-beta response), stress and kinase signaling (JNK cascade), as well as genome maintenance and chromatin processes (nucleotide-excision repair, chromatin organization, spindle checkpoint regulation) with no clear, single functional theme tying them together. This dispersion suggests no cohesive cluster function to name beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038095","count":1},{"id":"GO:0070911","count":1},{"id":"GO:0051443","count":1},{"id":"GO:0030466","count":1},{"id":"GO:1901487","count":1}]},{"hash":"96701729818045239","title":"Stress-Responsive Signaling and Autophagy Regulation","description":"The cluster prominently features terms tied to cellular stress signaling and growth control, including the JNK cascade, negative regulation of TORC1 signaling, and negative regulation of macroautophagy, suggesting a shared role in modulating stress responses and autophagy. Additional terms span broader cellular processes (mRNA processing, neuronal and immune functions), which may reflect multifunctionality of the proteins but do not outweigh the core stress-growth signaling theme. Therefore, this name best captures the central, coherent theme of the set.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901196","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0008045","count":2},{"id":"GO:0051973","count":2},{"id":"GO:0030500","count":2}]},{"hash":"1385905969859502199","title":"Dendritic Spine Morphogenesis and Actin Remodeling","description":"The top GO terms cluster around neuronal morphology and actin cytoskeleton dynamics: regulation and positive regulation of dendritic spine morphogenesis and development; Rac protein signal transduction; lamellipodium and ruffle assembly; hippocampus development. These indicate proteins coordinating actin remodeling and membrane protrusions to shape dendritic spines in neurons, with supporting roles from trafficking and TORC2 signaling. Overall, the cluster captures neuronal spine formation driven by actin dynamics.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0061001","count":4},{"id":"GO:0016601","count":4},{"id":"GO:0021766","count":4},{"id":"GO:0060999","count":4},{"id":"GO:0097178","count":4}]},{"hash":"550506895842429596","title":"Meiosis-associated microtubule organization and chromosome pairing","description":"The terms cluster around cytoskeletal organization of microtubules/tubulin and meiosis-specific chromosome events (homologous pairing, chiasma assembly), with supportive roles for protein folding and cytoplasmic quality control, implying coordinated cytoskeletal dynamics and proteostasis during meiosis. ","confidence":"Medium","size":8,"edges":25,"triangles":41,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043622","count":2},{"id":"GO:0051131","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0071629","count":2}]},{"hash":"433799276996151283","title":"Retinoid and androgen metabolism","description":"The cluster is dominated by GO terms for retinol/retinal metabolism and androgen metabolic processes (e.g., retinol/retinal metabolic processes and testosterone biosynthetic process), suggesting a shared theme around metabolism of vitamin A derivatives and steroid hormones. Some other terms are present (e.g., JAK-STAT signaling regulation, urine volume regulation) but are less representative of the core function. ","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0042574","count":2}]},{"hash":"1122715112342691841","title":"Diverse Transmembrane Transporters","description":"The GO terms show transport across membranes for nitrate, nitrite, phosphates, sugars (arabinose, galactose), sialic acid, potassium, and related substrates, indicating a cluster of membrane transporter proteins with broad substrate specificity. This common theme is transmembrane transport rather than a single substrate or pathway, justifying the name.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":1},{"id":"GO:0042891","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0035435","count":1}]},{"hash":"398872249240561440","title":"Plant chromatin organization and heterochromatin maintenance","description":"The prominent GO terms map to nucleosome assembly and heterochromatin formation (including subtelomeric regions), indicating epigenetic regulation of chromatin state in plants; a few growth/hormone-response terms are peripheral.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":3},{"id":"GO:0000183","count":3},{"id":"GO:1905778","count":2},{"id":"GO:1903086","count":2},{"id":"GO:0080113","count":2}]},{"hash":"372036478353704627","title":"Unknown","description":"The GO terms associated with this cluster are highly heterogeneous, including thiamine and biotin biosynthesis, actin filament severing, manganese ion response, innate immune signaling (MyD88-dependent TLR pathway), and detection of bacterial lipoproteptide, among others, with no single dominant biological theme or shared pathway. With only single-term representations and no clear cohesion, this cluster cannot be reliably labeled with a specific function. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":1},{"id":"GO:0009102","count":1},{"id":"GO:0051188","count":1},{"id":"GO:0051014","count":1},{"id":"GO:0071287","count":1}]},{"hash":"711847494162886475","title":"Unknown","description":"There are no GO terms or network connections to define a shared function for this cluster, making it impossible to assign a specific label. The ReCIPE note offers little functional insight, suggesting these proteins may be uncharacterized. Therefore, the cluster is best described as Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1916388789095284155","title":"Ubiquitin-Proteasome Proteostasis","description":"Top GO terms cluster around ubiquitin-dependent protein catabolism and quality control in the cytoplasm (cytoplasm protein quality control by the ubiquitin-proteasome system, ribosome-associated ubiquitin-dependent degradation), including histone H2A ubiquitination, the N-end rule pathway, TOR signaling regulation, and RISC complex assembly. This points to a cohesive proteostasis network governed by ubiquitination and proteasomal degradation, with links to translation regulation and signaling.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033522","count":2},{"id":"GO:1901718","count":2},{"id":"GO:1990116","count":2},{"id":"GO:0001967","count":2},{"id":"GO:0071596","count":2}]},{"hash":"674365296047267872","title":"Lipoprotein remodeling and lipid metabolism","description":"The GO terms point to lipid handling and transport processes, especially remodeling of HDL and VLDL particles, along with phospholipid biosynthesis/catabolism, lipid storage, and cholesterol homeostasis, indicating a cohesive theme around lipid metabolism and lipoprotein remodeling.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0034375","count":2},{"id":"GO:0006656","count":2},{"id":"GO:0046338","count":2},{"id":"GO:0034372","count":2}]},{"hash":"40495140892730400","title":"Unknown","description":"The listed GO terms cover a wide range of unrelated processes (histone methylation, DNA damage checkpoint signaling, TGF-beta response, rRNA maturation, various developmental programs, ER-Golgi transport, metal response, and spindle checkpoint control). With no evident common function or pathway linking these terms and no edges indicating a shared interaction, there isn\u2019t a coherent theme to label the cluster beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001162","count":1},{"id":"GO:0072432","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0030900","count":1}]},{"hash":"1465009781093476809","title":"Unknown","description":"The GO terms for this cluster are highly disparate (cocaine response, mRNA processing, axon guidance, visual learning, bone mineralization, TORC1/JNK signaling, autophagy), with several obsolete terms and no clear shared function or interaction evidence. Because there is no coherent overarching theme linking these proteins, a meaningful label cannot be assigned beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:1901196","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0008045","count":2},{"id":"GO:0051973","count":2}]},{"hash":"1983259892165199890","title":"Nuclear RNA Processing and Chromatin Regulation","description":"This cluster centers on terms such as termination of RNA pol II transcription, spliceosomal snRNP assembly, deadenylation-dependent mRNA decapping, histone mRNA metabolism, and chromatin organization, indicating a shared function in nuclear RNA processing and chromatin control. Some outlier terms (metabolic processes) may reflect multifunctional proteins, but the core signal supports a nuclear processing/chromatin theme. ","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042426","count":2},{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0030574","count":1}]},{"hash":"280031263766769939","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006363","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0031440","count":1},{"id":"GO:0042790","count":1},{"id":"GO:0031564","count":1}]},{"hash":"1157217823993317481","title":"Ribosome Biogenesis and Translation","description":"This cluster is enriched for GO terms related to ribosome production and protein synthesis (cytosolic ribosome assembly, ribosomal large subunit biogenesis, rRNA processing, translation, cytoplasmic translation). These core processes suggest the proteins mainly participate in assembling ribosomes and translating mRNA. The other terms (centrosome duplication, macroautophagy, cerebral cortex development, sperm capacitation) may reflect broader cellular growth, turnover, or tissue-specific contexts but are not central to the core ribosome-assembly/translation theme.","confidence":"Medium","size":7,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051298","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0042256","count":1}]},{"hash":"934893065515351363","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0009395","count":1},{"id":"GO:0030420","count":1},{"id":"GO:1903999","count":1},{"id":"GO:0034414","count":1}]},{"hash":"1299621624531157204","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0071166","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0000244","count":1}]},{"hash":"1882853021447880097","title":"Unknown","description":"The top GO terms are highly diverse, including germ-line masculinization, an obsolete osmosensory MAPK cascade, photosystem adjustment, and multiple signaling/transport processes (TGF-beta/SMAD, NF-kappaB, nuclear export). This mix lacks a coherent single biological function or pathway across the 7 proteins, making it unclear how these proteins share a common role. Therefore I label this cluster Unknown with no confidence in a representative function.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042006","count":2},{"id":"GO:0000173","count":2},{"id":"GO:0080005","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0035970","count":2}]},{"hash":"15924352109548457","title":"Plant growth regulation and hormone response","description":"This cluster centers on GO terms related to growth control (seed growth, root meristem regulation) and responses to key plant hormones (salicylic, jasmonic, and abscisic acids), suggesting a cohesive theme of growth regulation intertwined with stress signaling. Some terms about chromatin modification and viral processes hint at broader transcriptional regulation under stress, but the dominant pattern is growth and hormone response. Overall, the label reflects the primary functions represented in the cluster.","confidence":"Medium","size":7,"edges":8,"triangles":1,"max_degree":4,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1905778","count":4},{"id":"GO:1903086","count":4},{"id":"GO:0080113","count":4},{"id":"GO:0035390","count":4},{"id":"GO:0010082","count":4}]},{"hash":"1149924240427971881","title":"Zinc Ion Transport and Homeostasis","description":"The top terms cluster around zinc ion transmembrane transport, zinc ion homeostasis, detoxification of zinc ions, and related metal ion transport, suggesting the proteins function together to regulate zinc flux and intracellular zinc buffering/detoxification.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071577","count":2},{"id":"GO:0055072","count":2},{"id":"GO:0071584","count":2},{"id":"GO:0006877","count":2},{"id":"GO:0032119","count":2}]},{"hash":"1233013099867237031","title":"Cytokine regulation and leukocyte chemotaxis","description":"The GO terms cluster around immune signaling and leukocyte behavior, including regulation of cytokine production (IL-1, IL-8), monocyte chemotaxis, and neutrophil apoptosis, plus a note on exocytosis regulation. While there are a few endocrine-related terms (prolactin secretion, estrous cycle), the dominant theme is immune modulation and leukocyte trafficking, justifying this label as representative of the cluster.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000733","count":3},{"id":"GO:0045920","count":2},{"id":"GO:0033031","count":2},{"id":"GO:0044849","count":2},{"id":"GO:2000483","count":2}]},{"hash":"1158594981997248208","title":"RNA processing and splicing machinery","description":"The proteins show strong enrichment for spliceosome assembly, mRNA splicing via spliceosome, transcription termination, mRNA decapping/decay, and rRNA/tRNA maturation, indicating a cohesive RNA metabolism module; ABA response may reflect plant-specific regulation but does not change the core function.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":4},{"id":"GO:0000387","count":4},{"id":"GO:0006369","count":4},{"id":"GO:0000290","count":4},{"id":"GO:0008334","count":4}]},{"hash":"681766767145028145","title":"Unknown","description":"There are no GO terms or connections to define a shared function for this cluster: the Top Terms are empty, there are no edges or triangles, and the ReCIPE note lacks functional context. Without a unifying theme, the cluster cannot be confidently labeled beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2090249556583192554","title":"Unknown","description":"No GO terms are provided for this cluster, so there is no clear shared function or process to name it after; with only network metrics and six proteins, the label Unknown is safest.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"1049140316413551736","title":"Large-subunit ribosome biogenesis and rRNA maturation","description":"Primarily characterized by GO terms for ribosome assembly, large subunit biogenesis, preribosome maturation, and LSU-rRNA processing, indicating a core function in assembling and maturing the large ribosomal subunit. Contextual terms such as DNA replication initiation and SOS response appear ancillary rather than defining the cluster.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0042255","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0018144","count":2}]},{"hash":"1636728345639459085","title":"Neural development and axon growth signaling","description":"This cluster shows strong signals for neural development and axon dynamics, including axon regeneration and extension, integrin-mediated signaling, and substrate adhesion\u2013dependent spreading, which together point to neuronal connectivity and guidance during development. Embryonic cranial skeleton morphogenesis and associative learning further support neural-related roles, while DNA-templated transcription and DNA replication suggest general gene expression activity shared across the proteins. Overall, the dominant theme is neural development with axon growth mechanisms.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":2},{"id":"GO:0008306","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0048680","count":2}]},{"hash":"885257660931707751","title":"Unknown","description":"The GO terms are diverse (mRNA processing, motor neuron axon guidance, learning, signaling regulation, bone mineralization, immune processes) and include obsolete entries, giving no clear shared function across the proteins; thus a single interpretable label cannot be inferred.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901196","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0008045","count":2},{"id":"GO:0051973","count":2},{"id":"GO:0030500","count":2}]},{"hash":"745609037357784864","title":"Unknown","description":"There is no clear shared function tying these GO terms together: the terms span histone modification, DNA damage response, TGF-beta signaling, rRNA processing, multiple developmental programs, vesicle transport, metal ion response, and spindle checkpoint regulation, with no edges connecting the proteins. This makes it impossible to assign a cohesive, specific cluster label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001162","count":1},{"id":"GO:0072432","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0030900","count":1}]},{"hash":"1030079634701673476","title":"Innate Immune Signaling and Chromatin Regulation","description":"Based on the frequent GO terms, the cluster centers on innate immune signaling pathways (Fc-epsilon receptor signaling, TRIF-dependent TLR signaling, interferon-beta response, and JNK cascade) with supporting roles for ubiquitin-mediated regulation. The presence of chromatin organization/heterochromatin formation terms suggests a link to transcriptional regulation in response to signaling. Overall, the functions point to immune signal transduction with associated chromatin regulation.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0038095","count":6},{"id":"GO:0070911","count":6},{"id":"GO:0051443","count":6},{"id":"GO:0030466","count":6},{"id":"GO:1901487","count":6}]},{"hash":"166844624726414341","title":"Mitochondrial import and chaperone activity","description":"The cluster\u2019s top terms point to mitochondrial intermembrane space protein import (GO:0045041) and chaperone-related processes (GO:0051131, GO:0048291), plus a link to oxidative stress regulation (GO:1903427). Together these suggest a theme of mitochondrial proteostasis and protein folding/assembly rather than a single, cohesive immune or signaling function. Other terms appear unrelated and are likely noise. Confidence in this thematic label is moderate.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":3},{"id":"GO:0007339","count":3},{"id":"GO:0048291","count":3},{"id":"GO:0051085","count":3},{"id":"GO:1903427","count":3}]},{"hash":"108569254468633728","title":"Mitotic/meiotic cell-cycle regulation and chromatin dynamics","description":"The top GO terms point to control of chromosome segregation and cell-cycle checkpoints (attachment of kinetochore-bound microtubules, meiotic recombination checkpoint signaling, regulation of transcription in meiosis) and chromatin binding regulation, with additional signals from miRNA processing and NFAT signaling. These together suggest a cluster focused on coordinating cell-cycle progression, chromosome dynamics, and associated regulatory pathways, with some ancillary roles in transport and stress response. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1903799","count":5},{"id":"GO:0051037","count":5},{"id":"GO:0005981","count":5},{"id":"GO:0014883","count":5},{"id":"GO:0072462","count":5}]},{"hash":"1929020647722832344","title":"Unknown","description":"Top GO terms include immune signaling pathways (Fc-epsilon receptor signaling, TRIF-dependent TLR signaling, cellular response to interferon-beta, JNK cascade) alongside nuclear processes (chromatin organization, heterochromatin formation, nucleotide-excision repair, ubiquitin transferase activity, spindle checkpoint). The combination spans both cytoplasmic signaling and nuclear regulation with no clear single function linking all members, so I cannot assign a cohesive label.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0038095","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0051443","count":5},{"id":"GO:0030466","count":5},{"id":"GO:1901487","count":5}]},{"hash":"1949192192155151295","title":"Unknown","description":"The top GO terms show a wide mix across metabolism (fatty acid oxidation), hormone response, DNA replication, mRNA processing, axon guidance, bone mineralization, and visual learning, with a couple of obsolete terms. There isn\u2019t a clear, single pathway or function tying these proteins together, and the small cluster size with modest connectivity supports an Unknown label rather than a coherent theme.","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019395","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0071372","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1901196","count":2}]},{"hash":"1617101530227452396","title":"Spindle assembly and neuronal microtubule organization","description":"The GO terms cluster around microtubule dynamics crucial for spindle formation and chromosome movement (centrosome separation, spindle midzone assembly, plus/minus end dynamics) and neuron structure maintenance (cerebellar granular layer organization, neuron projection maintenance), indicating a shared theme of microtubule-based organization in dividing cells and neurons.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021685","count":1},{"id":"GO:1990942","count":1},{"id":"GO:0030473","count":1},{"id":"GO:0001560","count":1},{"id":"GO:1990535","count":1}]},{"hash":"271488134979114898","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904574","count":2},{"id":"GO:1903241","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0017038","count":2}]},{"hash":"1948193855263115376","title":"Sugar Metabolism and Glycolysis","description":"The top GO terms are dominated by carbohydrate catabolic and glycolytic processes (e.g., D-allose catabolic, glucose-6-phosphate metabolic, glycolytic process) with multiple sugar-related pathways (N-acetylglucosamine/neuraminate/mannosamine). This points to a cluster of proteins involved in carbohydrate metabolism and energy production, despite a few outlier terms likely due to annotation noise.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019316","count":1},{"id":"GO:0009254","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0051156","count":1},{"id":"GO:0006096","count":1}]},{"hash":"1460289564168611346","title":"tRNA aminoacylation and translation machinery","description":"This cluster is driven by GO terms for translation and multiple tRNA aminoacylation activities (prolyl-, glutamyl-, glutaminyl-tRNA), plus rRNA maturation related to ribosome biogenesis, suggesting a ribosome-associated translation module. A few other metabolic terms appear but are not central to the core theme.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":1},{"id":"GO:0006433","count":1},{"id":"GO:0006424","count":1},{"id":"GO:0006425","count":1}]},{"hash":"1992609826649161608","title":"DNA Replication and Repair Machinery","description":"The dominant GO terms describe mitotic cell cycle, DNA-templated transcription, DNA replication, and DNA repair, pointing to nuclear DNA processing machinery active during replication and genome maintenance. Minor terms relate to general RNA processing and other functions but don't redefine the core theme. Therefore this cluster best represents proteins involved in DNA replication and repair/maintenance during cell cycle.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0006260","count":4},{"id":"GO:1901196","count":2}]},{"hash":"550663978391620259","title":"Heat stress response and mitochondrial dynamics","description":"The cluster\u2019s top GO terms cluster around heat/unfolded protein response and stress (GO:0006986, GO:0009408), with additional terms tied to mitochondria distribution/inheritance and autophagy (GO:0014873, GO:0048312, GO:0000001, GO:0048312). This points to a theme of cellular stress response coupled with mitochondrial quality control and organelle dynamics, rather than a single narrowly defined function.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0009408","count":2},{"id":"GO:1903423","count":1},{"id":"GO:0016236","count":1},{"id":"GO:0033572","count":1}]},{"hash":"1629769672096834278","title":"Regulation of Developmental Signaling","description":"This cluster combines GO terms tied to regulatory signaling pathways (glucocorticoid signaling; auxin polar transport; cytokinin signaling) with developmental processes (root meristem growth, skeletal muscle and lung development), plus aspects of cellular organization and polarity that support developmental contexts. The shared theme is regulation of signaling in developmental programs, though the terms span multiple kingdoms, so the fit is moderate.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042921","count":1},{"id":"GO:0048642","count":1},{"id":"GO:0060430","count":1},{"id":"GO:0080037","count":1},{"id":"GO:1905793","count":1}]},{"hash":"1745660476448166122","title":"Unknown","description":"The GO terms associated with this cluster are highly diverse, spanning cell cycle regulation, transcription by RNA polymerase III, photoreceptor organization, histone methylation, mitochondrial distribution, metal response, and various developmental processes. There is no single coherent theme or shared biological function linking these proteins, making a specific, intuitive cluster label not justifiable.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046944","count":1},{"id":"GO:0007346","count":1},{"id":"GO:0001041","count":1},{"id":"GO:0035845","count":1},{"id":"GO:2001162","count":1}]},{"hash":"1742417746169054577","title":"Endomembrane trafficking and Golgi-lysosome transport","description":"The top GO terms cluster around endomembrane system organization, endosomal transport and vesicle fusion, and Golgi-to-lysosome transport, with related signals in pinocytosis and PI5P metabolism, plus regulatory signaling pathways (TLR3/4, TGF-beta). This suggests a cohesive role in vesicular trafficking within the endomembrane network, especially between the Golgi and lysosome, with potential modulation of receptor signaling.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":1},{"id":"GO:0090160","count":1},{"id":"GO:0007179","count":1},{"id":"GO:0034145","count":1},{"id":"GO:0016197","count":1}]},{"hash":"1985773278690304290","title":"Chromatin regulation and DNA damage response","description":"The strongest shared signal among the terms is chromatin-related: histone H3-K79 methylation, chromatin organization, and cellular responses tied to the G1 DNA damage checkpoint. These point to epigenetic control of gene expression and genome maintenance. Other terms (development, ER-Golgi transport, rRNA processing) are present but don\u2019t align as tightly with the main theme, suggesting either broader roles or annotation noise, while the chromatin/DNA damage signals remain the core driver of this cluster.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001162","count":1},{"id":"GO:0072432","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0030900","count":1}]},{"hash":"337815383860886808","title":"Mitochondrial import and chaperone folding","description":"The top GO terms cluster around mitochondrial intermembrane space protein import and chaperone-assisted folding/assembly, with supporting signals of ROS regulation, suggesting a theme of mitochondrial protein maturation and quality control via chaperones. Some terms are unrelated or obsolete, likely annotation noise, but the central pattern supports a mitochondrial import/folding focus.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":3},{"id":"GO:0007339","count":3},{"id":"GO:0048291","count":3},{"id":"GO:0051085","count":3},{"id":"GO:1903427","count":3}]},{"hash":"1101117868654942916","title":"Stress-Responsive Translation and Protein Stability","description":"Based on the GO terms, the cluster centers on core protein synthesis functions (translation and ribosomal small subunit assembly) and proteostasis (protein stabilization, negative regulation of ubiquitin-dependent degradation) under cellular stress. Elements related to actinomycin D response and p53-mediated signaling further link translation with cell-cycle regulation during stress, supporting a cohesive theme of coordinated translation and protein homeostasis under stress conditions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0071157","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0072717","count":1},{"id":"GO:0032986","count":1}]},{"hash":"787978917155825759","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009090","count":1},{"id":"GO:0044210","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0046939","count":1},{"id":"GO:0009089","count":1}]},{"hash":"1890130130731295522","title":"DNA Repair and Recombination","description":"The top GO terms primarily relate to DNA replication, repair, and recombination, including resolution of recombination intermediates, DNA repair, and mitotic cell cycle checkpoint regulation. This points to proteins involved in genome maintenance and chromosomal stability, with additional notes of responses to DNA-damaging agents (cisplatin, ionizing radiation).","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071140","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0090267","count":2}]},{"hash":"335836962720826939","title":"Microtubule Dynamics in Division and Neurons","description":"The GO terms cluster around microtubule-based processes, including spindle assembly and orientation, centrosome separation, and plus/minus-end microtubule dynamics, plus neuronal structural maintenance such as cerebellar granular layer organization and neuron projection upkeep. This suggests a shared theme of microtubule-driven organization in both cell division and neuronal structure, making the label representative.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021685","count":3},{"id":"GO:1990942","count":3},{"id":"GO:0030473","count":3},{"id":"GO:0001560","count":3},{"id":"GO:1990535","count":3}]},{"hash":"126359254200228795","title":"Innate Immune Signaling","description":"Based on the top GO terms, the proteins are enriched for pathways typical of innate immunity, including Fc-epsilon receptor signaling, TRIF-dependent Toll-like receptor signaling, and interferon-beta response, with downstream JNK cascade involvement. While there are some chromatin and DNA repair-related terms, the strongest shared theme is immune signal transduction and related stress responses, suggesting a cluster of proteins involved in innate immune signaling and downstream signaling cascades.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0038095","count":3},{"id":"GO:0070911","count":3},{"id":"GO:0051443","count":3},{"id":"GO:0030466","count":3},{"id":"GO:1901487","count":3}]},{"hash":"822445782439964744","title":"Phosphorylation-regulated signaling cluster","description":"This cluster centers on terms about regulating signaling pathways and phosphorylation states: negative regulation of kinase activity, dephosphorylation, PI3K/AKT signaling, focal adhesion and VEGF signaling, plus cell cycle regulation and neuronal signaling terms (circadian rhythm, postsynaptic density, habituation). The starch catabolic process seems like an outlier, but the prevailing theme is control of signaling networks through phosphorylation and related regulatory processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071850","count":2},{"id":"GO:0044387","count":2},{"id":"GO:0005983","count":2},{"id":"GO:0007623","count":2},{"id":"GO:0051898","count":2}]},{"hash":"650362146428517402","title":"Unknown","description":"The GO terms are diverse, including nitrogen metabolism (nitrate assimilation, nitric oxide biosynthesis), lipid and sterol biosynthesis (unsaturated fatty acid biosynthesis, ergosterol metabolism, glycosphingolipid metabolism), nucleotide/nucleoside catabolism (NAD salvage, uridine catabolic process), and tissue/neuronal roles (sebaceous gland differentiation, CNS myelin maintenance). There is no single cohesive function linking all terms, so a specific label isn\u2019t justified. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":1},{"id":"GO:0006809","count":1},{"id":"GO:0001949","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0000001","count":1}]},{"hash":"1768008845526843074","title":"Mitochondrial genome maintenance and dynamics","description":"The top GO terms cluster around mitochondrial functions: regulation of mitochondrial DNA replication, mitochondrial inheritance, membrane potential, and stress-induced mitochondrial fusion, suggesting a shared role in maintaining mitochondrial genome and mitochondrial dynamics. Other terms like SREBP signaling and extracellular matrix disassembly appear less central, potentially reflecting ancillary pathways or annotation overlap; overall, the mitochondrial maintenance/dynamics theme best explains the set.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090297","count":2},{"id":"GO:0001302","count":2},{"id":"GO:1990046","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0007588","count":2}]},{"hash":"1120559604693450026","title":"Unknown","description":"No GO terms or functional signals are provided for this cluster, so there is no clear common function to label; answer is Unknown.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"425996664024177505","title":"Ion transport and membrane potential regulation","description":"This cluster is dominated by GO terms related to intracellular potassium homeostasis, regulation and stabilization of membrane potential, and transmembrane transport of ions (K+, Na+, H+), including cardiac-related membrane repolarization and conduction. The common thread is ion transport that underlies membrane excitability, with a few peripheral terms on mechanosensation. Confidence is high that this name captures the main function of the cluster.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:0060075","count":1},{"id":"GO:0030322","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0071805","count":1}]}]